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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2162209
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160379.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160998.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2162265
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Expression, purification and characterization of human glutamate dehydrogenase (GDH) allosteric regulatory mutations
Cloning and molecular analysis of the human citrate synthase gene
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Potential role of protein kinase B in insulin-induced glucose transport, glycogen synthesis, and protein synthesis
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The molecular mechanisms that control thrombopoiesis
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Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency
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A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena
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Novel 5 alpha-steroid reductase (SRD5A3, type-3) is overexpressed in hormone-refractory prostate cancer
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Cellular circadian pacemaking and the role of cytosolic rhythms
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This event has been computationally inferred from an event that has been demonstrated in another species. The inference is based on the homology mapping in Ensembl Compara. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation. More details and caveats of the event inference in Reactome. For details on the Ensembl Compara system see also: Gene orthology/paralogy prediction method.
The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68419
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The E3 ubiquitin ligase TRIM21 negatively regulates the innate immune response to intracellular double-stranded DNA
IP3 receptor/Ca2+ channel: from discovery to new signaling concepts
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192655.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_193044.3
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Molecular determinants of regulated exocytosis
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
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Enzyme-substrate intermediate formation at lysine 329 of human deoxyhypusine synthase
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Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_244939.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_217427.2
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SRD5A3-CDG: a patient with a novel mutation
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Identification and characterization of a novel inositol polyphosphate 5-phosphatase
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The molecular dissection of Fc gamma receptor mediated phagocytosis
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_231725.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_151106.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_222451.2
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_236266.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_193043.3
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Mutations in orthologous genes in human spondyloepimetaphyseal dysplasia and the brachymorphic mouse
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Architecture of the human origin recognition complex.
Role of second messengers in netrin-1 signaling
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Mutations in a gene encoding a novel protein tyrosine phosphatase cause progressive myoclonus epilepsy
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IDH2 dimer (name copied from entity in Homo sapiens)
Citrate Synthase Holoenzyme (name copied from entity in Homo sapiens)
NNT dimer (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E1 complex (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E2 trimer (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111745
lactate dehydrogenase AB3 complex (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3495.2
MPC1:MPC2 (name copied from entity in Homo sapiens)
Human MSH2 (hMSH2) protein controls ATP processing by hMSH2-hMSH6
pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
Role of LAT2/NTAL/LAB on calcium mobilization
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_235596.1
BLNK mediates Syk-dependent Btk activation
Conformational transition associated with E1-E2 interaction in small ubiquitin-like modifications
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15596.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_237680.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596949
lactate dehydrogenase A4 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A3B complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A2B2 complex (name copied from entity in Homo sapiens)
GCH1 decamer (name copied from entity in Homo sapiens)
Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis.
GCH1 dimer (name copied from entity in Homo sapiens)
The SUMO-specific protease SENP5 is required for cell division
p-S1177-eNOS:CaM:HSP90:p-AKT1:BH4 (name copied from entity in Homo sapiens)
p-S1177-eNOS:CaM:HSP90:p-AKT1:BH2 (name copied from entity in Homo sapiens)
A three-dimensional working model of the multienzyme complex of aminoacyl-tRNA synthetases based on electron microscopic placements of tRNA and proteins
p-S1177-eNOS:CaM:HSP90:p-AKT1 (name copied from entity in Homo sapiens)
p-S1177-eNOS dimer (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_203689.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68424
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596662
dihydroorotate dehydrogenase holoenzyme (name copied from entity in Homo sapiens)
Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ
adenylosuccinate synthetase holoenzyme (name copied from entity in Homo sapiens)
AMPD1 tetramer (name copied from entity in Homo sapiens)
AMPD2 tetramer (name copied from entity in Homo sapiens)
AMPD3 tetramer (name copied from entity in Homo sapiens)
ADAL:Zn (name copied from entity in Homo sapiens)
HGPRT homotetramer (name copied from entity in Homo sapiens)
CAD hexamer (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3288.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68422
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2531.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3748.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113499
adenylosuccinate synthetase holoenzyme dimer (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593254
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Subcellular localization and regulation of coenzyme A synthase
adenylosuccinate synthetase like 1 holoenzyme (name copied from entity in Homo sapiens)
Proximal signaling events in Fc epsilon RI-mediated mast cell activation
J. Allergy Clin. Immunol. 119:544-52; quiz 553-4
adenylosuccinate synthetase like 1 holoenzyme dimer (name copied from entity in Homo sapiens)
Comparison of messenger RNA distribution for 60 proteins in fat cells vs the nonfat cells of human omental adipose tissue
Targeting purine and pyrimidine metabolism in human apicomplexan parasites
alpha-ketoglutarate dehydrogenase E1 holoenzyme (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E2 holoenzyme (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase complex (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E1 homodimer (name copied from entity in Homo sapiens)
IMP (inosine monophosphate) dehydrogenase 1 tetramer (name copied from entity in Homo sapiens)
Succinyl-CoA synthetase heterodimer (ADP-forming) (name copied from entity in Homo sapiens)
adenylosuccinate lyase tetramer (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_206437.2
2-Hydroxy-1,2,3-propanetricarboxylic acid
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_217227.2
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PCYT1A dimer (name copied from entity in Homo sapiens)
PCYT1B dimer (name copied from entity in Homo sapiens)
Cellular signalling mechanisms of neural cell adhesion molecules
LPIN3:Mg2+ (name copied from entity in Homo sapiens)
CEPT1:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
PISD:Pyruvoyl (name copied from entity in Homo sapiens)
Distinct nucleotide binding/hydrolysis properties and molar ratio of MutSalpha and MutSbeta determine their differential mismatch binding activities
LPIN2:Mg2+ (name copied from entity in Homo sapiens)
LPIN1:Mg2+ (name copied from entity in Homo sapiens)
The role of mast cells in allergic inflammation
ADP/ATP translocase 1 homodimer (name copied from entity in Homo sapiens)
eNOS:CaM:HSP90:p-AKT1 (name copied from entity in Homo sapiens)
eNOS:CaM:HSP90 (name copied from entity in Homo sapiens)
Active Calmodulin (name copied from entity in Homo sapiens)
palmitoylated, myristoylated eNOS dimer (name copied from entity in Homo sapiens)
HPGDS dimer (name copied from entity in Homo sapiens)
LTA4H:Zn2+ (name copied from entity in Homo sapiens)
SPTLC1:SPTLC3 (name copied from entity in Homo sapiens)
SPTLC1:SPTLC2 (name copied from entity in Homo sapiens)
PIP4K2A:PIP4K2A (name copied from entity in Homo sapiens)
PIP4K2A:PIP4K2B (name copied from entity in Homo sapiens)
Receptor-mediated endocytosis of cobalamin (vitamin B12)
ARF1/3:GTP:PI4KB (name copied from entity in Homo sapiens)
PIP4K2B:PIP4K2B (name copied from entity in Homo sapiens)
ACSL1 (name copied from entity in Homo sapiens)
Members of the human glyceraldehyde-3-phosphate dehydrogenase-related gene family map to dispersed chromosomal locations.
Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase.
Lecithin: cholesterol acyltransferase: effects of substrate composition upon enzyme activity
Nucleocytoplasmic shuttling modulates activity and ubiquitination-dependent turnover of SUMO-specific protease 2
ARF1:GTP (name copied from entity in Homo sapiens)
CDIPT:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
CDS1:Mg2+ (name copied from entity in Homo sapiens)
CHPT1:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_248889.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596935
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_249423.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_256993.1
mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons
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Complex III releases superoxide to both sides of the inner mitochondrial membrane
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Human peroxiredoxin 5 is a peroxynitrite reductase
Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding.
Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113533
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116583.1
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Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_229745.1
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Molecular cloning of a novel member of the eukaryotic polypeptide chain-releasing factors (eRF). Its identification as eRF3 interacting with eRF1.
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The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone
Human aquaporin adipose (AQPap) gene. Genomic structure, promoter analysis and functional mutation
Roles of C-terminal processing, and involvement in transacylation reaction of human group IVC phospholipase A2 (cPLA2gamma)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15572.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_174167.3
XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
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Uninterrupted MCM2-7 function required for DNA replication fork progression.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_254969.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3508.3
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Genetic defects of folate and cobalamin metabolism
Association of the human SUMO-1 protease SENP2 with the nuclear pore
Src-family kinases in B-cell development and signaling
Phosphoglucomutase 1: a gene with two promoters and a duplicated first exon
Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathway, causing early-onset fatal hypertrophic cardiomyopathy
Molecular cloning of a human cDNA encoding a trifunctional enzyme of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase in de Novo pyrimidine synthesis
Facilitated folding of actins and tubulins occurs via a nucleotide-dependent interaction between cytoplasmic chaperonin and distinctive folding intermediates
BLNK: a central linker protein in B cell activation
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Aquaporins in the hepatobiliary tract. Which, where and what they do in health and disease
Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16119.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17466.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110291
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Conversion of palmitic acid to very long chain fatty acyl-CoAs
Synthesis of very long-chain fatty acyl-CoAs
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Expression of SRPR (SRP Receptor subunit alpha)
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Biotransformation of Aflatoxin B1 and Its Relationship with the Differential Toxicological Response to Aflatoxin in Commercial Poultry Species,
Aflatoxins - Biochemistry and Molecular Biology (Book)
Pol II mediated transcription of microRNA genes
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15595.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23357.1
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Expression of SRPRB (SRP Receptor subunit beta)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5428.1
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Neuregulin-1 only induces trans-phosphorylation between ErbB receptor heterodimer partners
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_248133.1
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The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
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Multiple forms of an inositol polyphosphate 5-phosphatase form signaling complexes with Shc and Grb2
Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
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Structural relationships and the classification of aminoacyl-tRNA synthetases
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Triggering and augmentation mechanisms, granule pools, and biphasic insulin secretion
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Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria
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Cloning, sequencing, and expression of cDNA for human beta-galactosidase
Biochem. Biophys. Res. Commun. 157:238-44
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(S)-3-Hydroxyisobutyryl-CoA [ChEBI:28259]
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Reverse transcriptase motifs in the catalytic subunit of telomerase
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Identification, purification, and partial characterization of a novel Mr 28,000 integral membrane protein from erythrocytes and renal tubules
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Identification of holocarboxylase synthetase (HCS) proteins in human placenta
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A novel PtdIns3P and PtdIns(3,5)P2 phosphatase with an inactivating variant in centronuclear myopathy
Structure/function studies of human beta-cell glucokinase. Enzymatic properties of a sequence polymorphism, mutations associated with diabetes, and other site-directed mutants.
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The spectrum of latent tuberculosis: rethinking the biology and intervention strategies
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Molecular basis of signaling specificity of insulin and IGF receptors: neglected corners and recent advances
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Mismatch Repair proteins are recruited to replicating DNA through interaction with Proliferating Cell Nuclear Antigen (PCNA)
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GPI7 is the second partner of PIG-F and involved in modification of glycosylphosphatidylinositol
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Identification and characterization of a novel human phosphatidylinositol 4-kinase
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ALAS1 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
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The presence and release of alpha 2-antiplasmin from human platelets
HMBS:DIPY (name copied from entity in Homo sapiens)
8xALAD:Pb2+:Zn2+ (name copied from entity in Homo sapiens)
8x(ALAD:Zn2+) (name copied from entity in Homo sapiens)
ALAS2 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
GSS (name copied from entity in Homo sapiens)
2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
2xCPO (name copied from entity in Homo sapiens)
2xUROD (name copied from entity in Homo sapiens)
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Phosphate incorporation during glycogen synthesis and Lafora disease
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Biosynthesis of delta-aminolevulinic acid and the regulation of heme formation by immature erythroid cells in man
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Many cuts to ruin: a comprehensive update of caspase substrates
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Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type
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Protein folding: versatility of the cytosolic chaperonin TRiC/CCT
Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors
Response to elevated platelet cytosolic Ca2+
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Glucose-sensing mechanisms in pancreatic beta-cells
Philos Trans R Soc Lond B Biol Sci 360:2211-25
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1-chloro-2,4-dinitrobenzene [ChEBI:34718]
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Isolation and characterization of a full-length expressible cDNA for human hypoxanthine phosphoribosyl transferase
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Genomic basis of mucopolysaccharidosis type IIID (MIM 252940) revealed by sequencing of GNS encoding N-acetylglucosamine-6-sulfatase
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Redox function of tetrahydrobiopterin and effect of L-arginine on oxygen binding in endothelial nitric oxide synthase
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Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me)
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Expression, characterization, and tissue distribution of a new cellular selenium-dependent glutathione peroxidase, GSHPx-GI
The role of phosphatidylinositol 3-kinase in neural cell adhesion molecule-mediated neuronal differentiation and survival
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ChEBI:60125 N-epsilon-(1-(1-carboxy)ethyl)lysine
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Aquaporin expression in normal human kidney and in renal disease
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Argonaute proteins: mediators of RNA silencing
Deletion of steroid 5 alpha-reductase 2 gene in male pseudohermaphroditism
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SMG1:SMG8:SMG9 Complex (name copied from entity in Homo sapiens)
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Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction (name copied from entity in Homo sapiens)
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Exon Junction:UPF2:UPF3 Complex (name copied from entity in Homo sapiens)
Core Exon Junction Complex (Core EJC) (name copied from entity in Homo sapiens)
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Magoh-Y14 complex (name copied from entity in Homo sapiens)
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GDP bound eRF3 (name copied from entity in Homo sapiens)
mRNA Complex with a Premature Termination Codon Preceding an Exon Junction (name copied from entity in Homo sapiens)
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Cap Binding Complex (CBC) (name copied from entity in Homo sapiens)
80S ribosome (name copied from entity in Homo sapiens)
SMG1:Phosphorylated UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
SMG1:UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings
Mucopolysaccharidosis type I: current knowledge on its pathophysiological mechanisms
Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).
SPO11 Dimer (name copied from entity in Homo sapiens)
NLR functions beyond pathogen recognition
Lsm1-7 Complex (name copied from entity in Homo sapiens)
Deadenylated mRNA:Lsm1-7 Complex (name copied from entity in Homo sapiens)
SPO11:double stand break (name copied from entity in Homo sapiens)
pPLCgamma:PIP2 (name copied from entity in Homo sapiens)
HuR with phosphoserine221 and phosphoserine318:mRNA Complex (name copied from entity in Homo sapiens)
HuR with Unknown Phosphorylation: mRNA Complex (name copied from entity in Homo sapiens)
Decapped mRNA:LSM1-7 Complex (name copied from entity in Homo sapiens)
HuR with phosphoserine221 and phosphoserine158:mRNA Complex (name copied from entity in Homo sapiens)
RNA primer-DNA primer:G-strand extended telomere:PCNA (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
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DNA polymerase epsilon:G-strand extended telomere end (name copied from entity in Homo sapiens)
RNA primer:G-strand extended telomere end:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
RNA primer-DNA primer:G-strand extended telomere (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end (name copied from entity in Homo sapiens)
PCNA homotrimer (name copied from entity in Homo sapiens)
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RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
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RNA primer-DNA primer:origin duplex:PCNA (name copied from entity in Homo sapiens)
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DNA polymerase alpha:primase:DNA polymerase alpha:G-strand extended telomere end (name copied from entity in Homo sapiens)
Mechanism of metal activation of human hematopoietic prostaglandin D synthase
RFC Heteropentamer:RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
RFC Heteropentamer (name copied from entity in Homo sapiens)
Mcm4,6,7 complex (name copied from entity in Homo sapiens)
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Characterization of two novel subunits of the alpha-class glutathione S-transferases of human liver
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ubiquitinated Cdc6 (name copied from entity in Homo sapiens)
Peroxisome proliferator activated receptors and lipoprotein metabolism
Mcm2-7 complex (name copied from entity in Homo sapiens)
26S proteasome (name copied from entity in Homo sapiens)
CDK (name copied from entity in Homo sapiens)
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ubiquitinated Orc1 (name copied from entity in Homo sapiens)
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RNA primer-DNA primer:origin duplex with DNA damage (name copied from entity in Homo sapiens)
DNA polymerase epsilon (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase:DNA polymerase alpha:origin complex (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
RNA primer:origin duplex:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
eIF2:GTP (name copied from entity in Homo sapiens)
ternary complex (name copied from entity in Homo sapiens)
phospho-L13a associated wth the 3' UTR GAIT element of ceruloplasmin mRNA within the translation initiation complex (name copied from entity in Homo sapiens)
EIF2S1:EIF2S2:EIF2S3 (name copied from entity in Homo sapiens)
DNA polymerase epsilon:origin complex (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase (name copied from entity in Homo sapiens)
Fibroblast Growth Factor Receptor (FGFR) signaling
43S complex (name copied from entity in Homo sapiens)
40S ribosomal complex (name copied from entity in Homo sapiens)
eIF4F (name copied from entity in Homo sapiens)
eIF4A subunits complex (name copied from entity in Homo sapiens)
eIF3 subunits complex (name copied from entity in Homo sapiens)
43S: Ceruloplasmin mRNA:eIF4F:eIF4B:eIF4H:PABP (name copied from entity in Homo sapiens)
60s ribosomal complex lacking L13a subunit (name copied from entity in Homo sapiens)
ATP activates a reactive oxygen species-dependent oxidative stress response and secretion of proinflammatory cytokines in macrophages
60S ribosomal complex (name copied from entity in Homo sapiens)
Kinesins:microtubule (name copied from entity in Homo sapiens)
Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion
Regulation of Ins(3,4,5,6)P(4) signaling by a reversible kinase/phosphatase
The distribution and function of phosphatidylserine in cellular membranes
KIF18A dimer (name copied from entity in Homo sapiens)
Kinesin-14 (name copied from entity in Homo sapiens)
14-3-3zeta dimer (name copied from entity in Homo sapiens)
The PI-3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3
14-3-3-zeta:Raf1 (name copied from entity in Homo sapiens)
F-actin capping protein (name copied from entity in Homo sapiens)
Kinesin-5 homotetramer (name copied from entity in Homo sapiens)
DSIF complex (name copied from entity in Homo sapiens)
HMGB1/HMGB2- bound chromatin (name copied from entity in Homo sapiens)
Activated cGMP-dependent protein kinase (PKGs) (name copied from entity in Homo sapiens)
FACT complex (name copied from entity in Homo sapiens)
Enzymatic, metabolic and secretory patterns in human islets of type 2 (non-insulin-dependent) diabetic patients
InsP3-mediated intracellular calcium signalling is altered by expression of synaptojanin-1
Mitochondrial localization of human PANK2 and hypotheses of secondary iron accumulation in pantothenate kinase-associated neurodegeneration
Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization.
FDX1L (reduced) (name copied from entity in Homo sapiens)
FDXR:FADH2 (name copied from entity in Homo sapiens)
FDX1L (oxidized) (name copied from entity in Homo sapiens)
AKR7L dimer (name copied from entity in Homo sapiens)
FDXR:FAD (name copied from entity in Homo sapiens)
AKR7A2 dimer (name copied from entity in Homo sapiens)
AKR7A3 dimer (name copied from entity in Homo sapiens)
2xHPGDS (name copied from entity in Homo sapiens)
Regulation of Geminin and Cdt1 expression by E2F transcription factors
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Molecular mechanisms involved in the regulation of the endothelial nitric oxide synthase
Am J Physiol Regul Integr Comp Physiol 284:R1-12
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
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Structure and sequence of the human sulphamidase gene
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Immunoglobulin G-mediated phagocytosis activates a calcium-independent, phosphatidylethanolamine-specific phospholipase
Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2.
Binding of MET-TRNAf and GTP to homogeneous initiation factor MP.
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Immunoreceptor DAP12 bearing a tyrosine-based activation motif is involved in activating NK cells
AHCY:NAD+ (name copied from entity in Homo sapiens)
4x(AHCY:NAD+) (name copied from entity in Homo sapiens)
MAT I homotetramer (name copied from entity in Homo sapiens)
MAT III homodimer (name copied from entity in Homo sapiens)
MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
OTC trimer (name copied from entity in Homo sapiens)
branched-chain alpha-ketoacid dehydrogenase E1 complex (name copied from entity in Homo sapiens)
Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding
ARG2 trimer (name copied from entity in Homo sapiens)
ARG1 trimer (name copied from entity in Homo sapiens)
ATP-dependent interaction of human mismatch repair proteins and dual role of PCNA in mismatch repair
Insulin signalling and the regulation of glucose and lipid metabolism
Functional properties and genomics of glucose transporters
CTPS2 tetramer (name copied from entity in Homo sapiens)
CTPS tetramer (name copied from entity in Homo sapiens)
ribonucleotide reductase M1 polypeptide dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) variant (name copied from entity in Homo sapiens)
ribonucleotide reductase M2 polypeptide dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) dimer (name copied from entity in Homo sapiens)
deoxythymidylate kinase (thymidylate kinase) holoenzyme (name copied from entity in Homo sapiens)
TS dimer (name copied from entity in Homo sapiens)
Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases
PYCR1 decamer (name copied from entity in Homo sapiens)
OAT hexamer (name copied from entity in Homo sapiens)
ITPA dimer (name copied from entity in Homo sapiens)
NME4 hexamer (name copied from entity in Homo sapiens)
ER-mediated phagocytosis: a new membrane for new functions
branched-chain alpha-ketoacid dehydrogenase complex (name copied from entity in Homo sapiens)
GLUD1 hexamer (name copied from entity in Homo sapiens)
ASNS dimer (name copied from entity in Homo sapiens)
nucleoside diphosphate kinase 1A:5B heterohexamer (name copied from entity in Homo sapiens)
2xTXNRD1:2xFAD (name copied from entity in Homo sapiens)
2xGSR-2:2xFAD (name copied from entity in Homo sapiens)
Primary structure of human triosephosphate isomerase
Characterization of the human mitochondrial methionyl-tRNA synthetase
Purification and properties of uroporphyrinogen I synthase from human erythrocytes. Identification of stable enzyme-substrate intermediates.
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Is the mammalian serine palmitoyltransferase a high-molecular-mass complex?
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Maple syrup urine disease (branched-chain ketoaciduria)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1971-2005
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
Mechanism of porphobilinogen synthase. Requirement of Zn2+ for enzyme activity.
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Organic acidemias due to defects in lysine oxidation: 2-ketoadipic acidemia and glutaric acidemia
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2195-2204
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Mammalian G proteins and their cell type specific functions
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The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci
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Overexpression of a mammalian ethanolamine-specific kinase accelerates the CDP-ethanolamine pathway
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Genetics of mammalian meiosis: regulation, dynamics and impact on fertility
Phagosomes are competent organelles for antigen cross-presentation
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ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells
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Requirement of TRPC channels in netrin-1-induced chemotropic turning of nerve growth cones
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Epidermal Growth Factor Receptor (EGFR) signaling
Defective MMAB causes methylmalonic aciduria type cblB
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Endonucleolytic function of MutLalpha in human mismatch repair
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Requirement of the DEAD-Box protein ded1p for messenger RNA translation.
Control of translation and mRNA degradation by miRNAs and siRNAs
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Hemostasis and Thrombosis: Basic Principles and Clinical Practice
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Phosphoinositides in cell regulation and membrane dynamics
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Human and murine glycerol kinase: influence of exon 18 alternative splicing on function
Identification and characterization of an enzyme involved in the elongation of n-6 and n-3 polyunsaturated fatty acids
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Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
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Isolation and characterization of the human pyruvate kinase M gene
5,10-methylenetetrahydrofolate polyglutamate
5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1
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Platelet activation, signaling and aggregation
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The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2.
Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1
Cloning and expression of a human kinesin heavy chain gene: interaction of the COOH-terminal domain with cytoplasmic microtubules in transfected CV-1 cells
Conversion of alpha-linolenic acid to eicosapentaenoic, docosapentaenoic and docosahexaenoic acids in young women
Human spermidine synthase gene: structure and chromosomal localization
Eicosapentaenoic and docosapentaenoic acids are the principal products of alpha-linolenic acid metabolism in young men*
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Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain
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Identification and characterization of novel spliced variants of neuregulin 4 in prostate cancer
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3201.3
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_253661.1
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Formation of molecular species of mitochondrial cardiolipin. 1. A novel transacylation mechanism to shuttle fatty acids between sn-1 and sn-2 positions of multiple phospholipid species
Von Willebrand factor: looking back and looking forward
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Structure of the human MutSalpha DNA lesion recognition complex
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Generation of second messenger molecules
The PTEN-regulating microRNA miR-26a is amplified in high-grade glioma and facilitates gliomagenesis in vivo
Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: insights into substrate recognition, tRNA binding, and angiogenesis activity
Novel variants in human Aquaporin-4 reduce cellular water permeability
The porphobilinogen synthase catalyzed reaction mechanism
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Production of phosphatidylinositol 5-phosphate by the phosphoinositide 3-phosphatase myotubularin in mammalian cells
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Effects of cyclic GMP on smooth muscle relaxation
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Retinoids for treatment of retinal diseases
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Mechanisms, regulation and consequences of protein SUMOylation
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A general map of iron metabolism and tissue-specific subnetworks
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Kinesin-5 regulates the growth of the axon by acting as a brake on its microtubule array
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192692.3
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Acid-sensing ion channels (ASICs): pharmacology and implication in pain
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Purification and characterization of human Syk produced using a baculovirus expression system
[A NEW DYSOSTOSIS WITH URINARY ELIMINATION OF CHONDROITIN SULFATE B]
Antigen processing and presentation: TAPping into ABC transporters
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379743
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23144.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15833.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_77273.4
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The isolation and characterisation of a platelet-specific beta-globulin (beta-thromboglobulin) and the detection of antiurokinase and antiplasmin released from thrombin-aggregated washed human platelets
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Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
Inborn errors of ketogenesis and ketone body utilization
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Molecular cloning and expression of human hepatocyte growth factor
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_174140.3
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Beta-arrestin-mediated activation of MAPK by inverse agonists reveals distinct active conformations for G protein-coupled receptors
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Low affinity Ca2+-binding sites of calcineurin B mediate conformational changes in calcineurin A
Wnt/Ca2+ signaling pathway: a brief overview
Acta Biochim. Biophys. Sin. (Shanghai) 43:745-56
Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_253924.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111524.1
XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
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Synthesis and interconversion of nucleotide di- and triphosphates
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15975.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111624.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379776
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595896
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379771
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1236918
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595084
Identification of a human mitochondrial ABC transporter, the functional orthologue of yeast Atm1p
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15877.1
Enzymes of the human erythrocyte. IV. Phosphoglucose isomerase, purification and properties.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124109.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2213226
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_233669.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_125085.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595073
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597050
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15779.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192688.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379768
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597046
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192694.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230422.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595105
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15914.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597051
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379742
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192713.3
SLC11 family of H+-coupled metal-ion transporters NRAMP1 and DMT1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595125
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379758
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379766
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15638.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595123
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595122
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
Selective vitamin B12 malabsorption and proteinuria in young people. A syndrome
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2965.2
Vertebrates have conserved capping protein alpha isoforms with specific expression patterns
Molecular machinations of the MHC-I peptide loading complex
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595314
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595082
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595820
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17479.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_227839.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597045
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192695.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595042
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15991.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379739
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29506
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2616.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_206140.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595044
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29702
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_259176.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379725
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597035
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595075
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595712
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_231520.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_254048.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597033
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_249357.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597034
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595080
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_236584.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595077
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595078
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15645.1
VEGFs and receptors involved in angiogenesis versus lymphangiogenesis
Switching of origins to a post-replicative state
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379778
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595710
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16086.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595709
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595067
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24806.1
Phase III randomized trial of cisplatin plus placebo compared with cisplatin plus cetuximab in metastatic/recurrent head and neck cancer: an Eastern Cooperative Oncology Group study
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241671.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=938699
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24449.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879473
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230225.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379748
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16123.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595096
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879484
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24248.2
acetaminophen glutathione conjugate [ChEBI:32639]
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596266
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_204238.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596269
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_209418.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597084
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191581.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596761
Anomalous megakaryocytopoiesis in mice with mutations in the c-Myb gene
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595706
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595704
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1250243
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_245223.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595708
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595903
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76566.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596865
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=428981
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20410.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596250
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_205539.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20105.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=428980
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3333.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=140356
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_193013.3
Purification and partial characterization of aldehyde dehydrogenase from human erythrocytes.
The unfolded protein response: a pathway that links insulin demand with beta-cell failure and diabetes
Defective platelet activation in G alpha(q)-deficient mice
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COPI-coated ER-to-Golgi transport complexes segregate from COPII in close proximity to ER exit sites
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596464
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2395973
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148079.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595713
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_219530.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595714
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_205071.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597112
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596466
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596467
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_193014.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597113
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596465
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160853.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3134845
DNA primase from KB cells. Characterization of a primase activity tightly associated with immunoaffinity-purified DNA polymerase-alpha.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5822.2
Biological & physiological aspects of action of insulin-like growth factor peptide family
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Holocarboxylase synthetase: correlation of protein localisation with biological function
Purification and characterization of a novel alpha-class glutathione transferase from human liver
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593794
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593817
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594377
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593926
Platelets in thrombotic and non-thrombotic disorders.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3734.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593777
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83925
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593758
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3820.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593791
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29382
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_242783.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594270
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593805
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593806
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593803
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594267
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594269
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593912
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594268
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596723
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593756
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_204804.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593738
Purine ribonucleoside monophosphate biosynthesis
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_251054.1
Bestrophin and TMEM16-Ca(2+) activated Cl(-) channels with different functions
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The second messenger system of mouse epidermis. IV. Cyclic AMP and cyclic GMP phosphodiesterase.
Platelet C1- inhibitor. A secreted alpha-granule protein.
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Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
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Cloning and identification of amino acid residues of human phospholipase C delta 1 essential for catalysis
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Purification and properties of human cytosolic folylpoly-gamma-glutamate synthetase and organization, localization, and differential splicing of its gene
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Isolation and characterization of human nuclear and cytosolic multisynthetase complexes and the intracellular distribution of p43/EMAPII
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Mitochondrial release of AIF and EndoG requires caspase activation downstream of Bax/Bak-mediated permeabilization.
Association of B cell antigen receptor with protein tyrosine kinase Lyn
DHFR/MSH3 amplification in methotrexate-resistant cells alters the hMutSalpha/hMutSbeta ratio and reduces the efficiency of base-base mismatch repair
Proc. Natl. Acad. Sci. U.S.A. 94:10144-9
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
The formation of citric and alpha-ketoglutaric acids in the mammalian body
Regulation of the cyclin E gene by transcription factor E2F1
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Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
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Cloning of DGAT2, a second mammalian diacylglycerol acyltransferase, and related family members
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Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
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HER4-mediated biological and biochemical properties in NIH 3T3 cells. Evidence for HER1-HER4 heterodimers
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Heterotrimeric G protein activation by G-protein-coupled receptors
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Aldo-keto reductases and bioactivation/detoxication
Annu. Rev. Pharmacol. Toxicol. 47:263-92
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Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site
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Adenylate kinases in man: evidence for a third locus
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Core protein machinery for mammalian phosphatidylinositol 3,5-bisphosphate synthesis and turnover that regulates the progression of endosomal transport. Novel Sac phosphatase joins the ArPIKfyve-PIKfyve complex
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Cloning and identification of a new member of water channel (AQP10) as an aquaglyceroporin
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Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation
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Back in the water: the return of the inositol phosphates
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Homo sapiens dullard protein phosphatase shows a preference for the insulin-dependent phosphorylation site of lipin1
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The human EPRS locus (formerly the QARS locus): a gene encoding a class I and a class II aminoacyl-tRNA synthetase
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Execution of nonsense-mediated mRNA decay: what defines a substrate?
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Role of gastrin peptides in carcinogenesis
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Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties.
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Role of leptin in the pancreatic ?-cell: effects and signaling pathways
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Human GMP synthetase. Protein purification, cloning, and functional expression of cDNA
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29496
Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases
In vitro characterization of enzymatic properties and inhibition of the p53R2 subunit of human ribonucleotide reductase
From hematopoietic stem cells to platelets
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Identification and partial purification of PAPS translocase
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=200493
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_202750.2
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GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_252012.1
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Cloning, sequencing and expression of a cDNA encoding mammalian valyl-tRNA synthetase
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Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins
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Regulation and dysregulation of aquaporins in water balance disorders
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16024.2
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15767.1
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Role of two residues proximal to the active site of Ubc9 in substrate recognition by the Ubc9.SUMO-1 thiolester complex
Truncated mutants of human thioredoxin reductase 1 do not exhibit glutathione reductase activity
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192035.3
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192014.3
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Sulfotransferase catalyzing sulfation of heterocyclic amines
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_247130.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_257822.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_232892.1
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The role of aminoacyl-tRNA synthetases in genetic diseases
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Cloning of a water channel homolog expressed in brain meningeal cells and kidney collecting duct that functions as a stilbene-sensitive glycerol transporter
Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
Purification and some properties of inorganic pyrophosphatase from human erythrocytes
The mucopolysaccharidoses: a success of molecular medicine
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Receptor-to-effector signaling through G proteins: roles for beta gamma dimers as well as alpha subunits
GRB2: a pivotal protein in signal transduction
A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.
GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination
Functional properties of a Drosophila homolog of the E2F1 gene
Note: the coordinates are copied over from Homo sapiens.
Sentrin-specific protease 5 ecNumber3.4.22.68/ecNumber
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Sentrin-specific protease 2 ecNumber3.4.22.68/ecNumber
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595793
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25925.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=947592
Similar idiotypic specificity for the membrane IgD and IgM of human B lymphocytes
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Sentrin-specific protease 1 ecNumber3.4.22.68/ecNumber
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26149.2
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596641
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596334
Probable ATP-dependent RNA helicase DDX11
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241718.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_152181.1
Pnpla3/Adiponutrin deficiency in mice does not contribute to fatty liver disease or metabolic syndrome
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_205842.2
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Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent
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Phagosomal maturation (early endosomal stage)
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The cDNA and protein sequences of human lactate dehydrogenase B
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UDP-N-acetylhexosamine pyrophosphorylase
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
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Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
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Enzymatic hydration of leukotriene A4. Purification and characterization of a novel epoxide hydrolase from human erythrocytes
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Mannose-1-phosphate guanyltransferase beta
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UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
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UDP-N-acetylglucosamine transferase subunit ALG14 homolog
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DNA polymerase delta, an essential enzyme for DNA transactions.
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High-resolution x-ray structure of human aquaporin 5
N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
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Biochemical characterization of human GMP synthetase
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Eukaryotic tranlation initiation factor 5A2
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Eukaryotic translation initiation factor 5A-1
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Eukaryotic translation initiation factor 5A
Separation of the two enzymatic phases in active sulfate synthesis
Role of the vascular endothelial growth factor pathway in tumor growth and angiogenesis
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Cellular regulation of endothelial nitric oxide synthase
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Raf and akt mediate distinct aspects of sensory axon growth
ATF6 activated by proteolysis binds in the presence of NF-Y (CBF) directly to the cis-acting element responsible for the mammalian unfolded protein response
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Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide
DNA mismatch repair and mutation avoidance pathways
Fine-tuning of GPCR activity by receptor-interacting proteins
Species-specific detection of the antiviral small-molecule compound CMA by STING
E2F-dependent accumulation of hEmi1 regulates S phase entry by inhibiting APC(Cdh1)
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Glucagon and regulation of glucose metabolism
Am J Physiol Endocrinol Metab 284:E671-8
MicroRNAs: biogenesis, function and applications
Expression, purification, and characterization of human acetyl-CoA carboxylase 2
The cellular response to neuregulins is governed by complex interactions of the erbB receptor family
Stimulation of phosphatidylglycerolphosphate phosphatase activity by unsaturated fatty acids in rat heart
DCT1 (NRAMP2) mediates divalent iron uptake across the apical membrane of enterocytes
NRAMP1 transports divalent metal ions across phagosomal membranes of macrophages
HMIT co-transports myo-inositol with a proton
Cloning, sequencing, expression, and Gq-independent activation of phospholipase C-beta 2
Human chromokinesin KIF4A functions in chromosome condensation and segregation
alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP
glucokinase [nucleoplasm] => glucokinase [cytosol]
ABC7, mABC1 and mABC2 mediate heme transport
MTABC3 transports porphyrin into mitochondria
Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I
Testis-specific Y-encoded-like protein 2
WD repeat domain phosphoinositide-interacting protein 1
Synthesis of pyrophosphates in the cytosol
DNA double-strand breaks: signaling, repair and the cancer connection.
Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates
ArfGAP1 dynamics and its role in COPI coat assembly on Golgi membranes of living cells
Fcgamma receptors: old friends and new family members
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Leukotriene A4 hydrolase in human leukocytes. Purification and properties
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SRP-dependent cotranslational protein targeting to membrane
Nuclear organization of DNA replication initiation proteins in mammalian cells.
Homologous DNA pairing by human recombination factors Rad51 and Rad54
Crystal structure of human uroporphyrinogen decarboxylase
A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes
When do Lasses (longevity assurance genes) become CerS (ceramide synthases)?: Insights into the regulation of ceramide synthesis
Mechanism of selectivity in aquaporins and aquaglyceroporins
Morquio's syndrome: deficiency of a chondroitin sulfate N-acetylhexosamine sulfate sulfatase
A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor
Association of licensing factors with the pre-replicative complex
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Innate immune activation through Nalp3 inflammasome sensing of asbestos and silica
Advanced glycosylation endproduct receptor signaling
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Peroxisome proliferator-activated receptors: nuclear control of metabolism
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Complete amino acid sequence of the neurone-specific gamma isozyme of enolase (NSE) from human brain and comparison with the non-neuronal alpha form (NNE)
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Oncogenic signaling from the hematopoietic growth factor receptors c-Kit and Flt3
Cloning of a human cDNA for CTP-phosphoethanolamine cytidylyltransferase by complementation in vivo of a yeast mutant
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Cancer-derived mutations in the regulatory subunit p85alpha of phosphoinositide 3-kinase function through the catalytic subunit p110alpha
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di-retinoid-pyridinium-ethanolamine [ChEBI:71980]
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Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
Immunohistochemical localisation of thrombospondin in human megakaryocytes and platelets
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Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine
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Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages
Specific protein domains mediate cooperative assembly of HuR oligomers on AU-rich mRNA-destabilizing sequences
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Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
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Isolation of two cDNAs encoding functional human cytoplasmic cysteinyl-tRNA synthetase
Molecular basis for methionine synthase reductase deficiency in patients belonging to the cblE complementation group of disorders in folate/cobalamin metabolism
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PCNA function in the activation and strand direction of MutL? endonuclease in mismatch repair
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[Receptors for cholecystokinin and gastrin]
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Removal of licensing factors from origins
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Mutations in phosphoinositide metabolizing enzymes and human disease
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Enzymatic phosphorylation of nucleoside diphosphates
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Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin
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Upf1 senses 3'UTR length to potentiate mRNA decay
Cloning of the sulphamidase gene and identification of mutations in Sanfilippo A syndrome
Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors
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Platelet alpha2-macroglobulin and alpha1-antitrypsin
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Nramp2 expression is associated with pH-dependent iron uptake across the apical membrane of human intestinal Caco-2 cells
ZnT-2, a mammalian protein that confers resistance to zinc by facilitating vesicular sequestration
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Stem cell factor and its receptor c-Kit as targets for inflammatory diseases
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Regulation of small GTPases at epithelial cell-cell junctions
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AU-rich elements and associated factors: are there unifying principles?
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The joining of ribosomal subunits in eukaryotes requires eIF5B.
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Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase
Superoxide dismutase [Mn], mitochondrial ecNumber1.15.1.1/ecNumber
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Fatty acid elongases in mammals: their regulation and roles in metabolism
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Platelet factor 4 and adenosine diphosphate release during human platelet aggregation
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Inorganic pyrophosphatase 2, mitochondrial
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The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision
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Threonine 308 phosphorylated form of Akt translocates to the nucleus of PC12 cells under nerve growth factor stimulation and associates with the nuclear matrix protein nucleolin
Peroxiredoxin-2 ecNumber1.11.1.15/ecNumber
Cold Spring Harb Perspect Biol 4:a007864
Peroxiredoxin-5, mitochondrial ecNumber1.11.1.15/ecNumber
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Peroxiredoxin-1 ecNumber1.11.1.15/ecNumber
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Formation of a pool of free 40S subunits
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Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase
Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli
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The genetics of mammalian circadian order and disorder: implications for physiology and disease
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Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
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Signal transduction via the stem cell factor receptor/c-Kit
Mechanism underlying replication protein a stimulation of DNA ligase I
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AKT phosphorylates targets in the cytosol
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The solute carrier 26 family of proteins in epithelial ion transport
Identification and characterization of a novel inositol hexakisphosphate kinase
The role of mismatched nucleotides in activating the hMSH2-hMSH6 molecular switch
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U5 small nuclear ribonucleoprotein 200 kDa helicase
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116 kDa U5 small nuclear ribonucleoprotein component (U5 snRNP- specific protein, 116 kDa) (U5-116 kDa)
116 kDa U5 small nuclear ribonucleoprotein component
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High mobility group-like nuclear protein 2 homolog 1
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Spliceosomal U5 snRNP-specific 15 kDa protein
Thioredoxin-like U5 snRNP protein U5-15kD
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Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
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Multisynthetase complex auxiliary component p43
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The roles of anabolic and catabolic reactions in the synthesis and recycling of polyunsaturated fatty acids
Prostaglandins Leukot Essent Fatty Acids 67:79-83
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Signaling mechanisms utilized by antigen receptors and integrins: common intermediates, different outcomes?
Translational silencing of ceruloplasmin requires the essential elements of mRNA circularization: poly(A) tail, poly(A)-binding protein, and eukaryotic translation initiation factor 4G
Human geranylgeranyl diphosphate synthase: isolation of the cDNA, chromosomal mapping and tissue expression
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Processing of Capped Intron-Containing Pre-mRNA
Identification and characterization of a mammalian mitochondrial ATP-binding cassette membrane protein
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Functionally defective high-density lipoprotein: a new therapeutic target at the crossroads of dyslipidemia, inflammation, and atherosclerosis
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Functional expression and characterisation of a new human phosphatidylinositol 4-kinase PI4K230
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Mutations in ATP2C1, encoding a calcium pump, cause Hailey-Hailey disease
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Formation of tubulin folding intermediates by CCT/TriC
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DNA double strand break repair, chromosome synapsis and transcriptional silencing in meiosis
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Mechanisms of digestion and absorption of dietary vitamin A
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Identification of autophosphorylation sites of HER2/neu
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PERK in the life and death of the pancreatic beta-cell
SnapShot: motor proteins in spindle assembly
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CHIP28 water channels are localized in constitutively water-permeable segments of the nephron
The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats
Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase.
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Phosphoinositide phosphatases in cell biology and disease
The proteasome and MHC class I antigen processing
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Immunoglobulin E receptor signaling and asthma
ATP bound to the origin recognition complex is important for preRC formation.
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STING specifies IRF3 phosphorylation by TBK1 in the cytosolic DNA signaling pathway
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Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases
Fcgamma receptor signaling in phagocytes
Regulation of the insulin gene by glucose and fatty acids
The PDGF family: four gene products form five dimeric isoforms
Activation of ErbB4 by the bifunctional epidermal growth factor family hormone epiregulin is regulated by ErbB2
Interaction between citrate synthase and malate dehydrogenase. Substrate channeling of oxaloacetate
The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA.
Raf-1 kinase possesses distinct binding domains for phosphatidylserine and phosphatidic acid. Phosphatidic acid regulates the translocation of Raf-1 in 12-O-tetradecanoylphorbol-13-acetate-stimulated Madin-Darby canine kidney cells
Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation
Mutations of phosphorylation sites in lamin A that prevent nuclear lamina disassembly in mitosis
Origin, Recognition, Signaling and Repair of DNA Double-Strand Breaks in Mammalian Cells
Damage Surveillance and Repair (Keith Caldecott, editor)1-40
TC II deficiency: avoidance of false-negative molecular genetics by RNA-based investigations
Multiple splice variants of the human calcium-independent phospholipase A2 and their effect on enzyme activity
Regulators of neurite outgrowth: role of cell adhesion molecules
Three tRNA binding sites in rabbit liver ribosomes and role of the intrinsic ATPase in 80S ribosomes from higher eukaryotes
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The role of transient receptor potential cation channels in Ca2+ signaling
Cold Spring Harb Perspect Biol 2:a003962
Transformation and Stat activation by derivatives of FGFR1, FGFR3, and FGFR4
Tubulin subunits exist in an activated conformational state generated and maintained by protein cofactors
Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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Metabolism of amino acids and derivatives
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Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
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Aflatoxin B1-induced hepatocellular carcinoma in developing countries: Geographical distribution, mechanism of action and prevention
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Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
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Protein kinase C and a calcium-independent phospholipase are required for IgG-mediated phagocytosis by Mono-Mac-6 cells
Failure of blood-island formation and vasculogenesis in Flk-1-deficient mice
Splicing factor 3B subunit 1 (Spliceosome associated protein 155) (SAP 155) (SF3b155) (Pre-mRNA splicing factor SF3b 155 kDa subunit)
Pre-mRNA splicing factor SF3b 155 kDa subunit
Splicing factor 3B subunit 4 (Spliceosome associated protein 49) (SAP 49) (SF3b50) (Pre-mRNA splicing factor SF3b 49 kDa subunit)
Pre-mRNA splicing factor SF3b 49 kDa subunit
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Pre-mRNA splicing factor SF3b 10 kDa subunit
Pre-mRNA splicing factor SF3b 145 kDa subunit
Splicing factor 3B subunit 2 (Spliceosome associated protein 145) (SAP 145) (SF3b150) (Pre-mRNA splicing factor SF3b 145 kDa subunit)
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Pre-mRNA splicing factor SF3b 130 kDa subunit
Splicing factor 3B subunit 3 (Spliceosome associated protein 130) (SAP 130) (SF3b130) (Pre-mRNA splicing factor SF3b 130 kDa subunit)
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Splicing factor, arginine/serine-rich 1 (pre-mRNA splicing factor SF2, P33 subunit) (Alternative splicing factor ASF-1)
pre-mRNA splicing factor SF2, P33 subunit
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Hypothetical protein CGI-110 (Protein HSPC175)
U6 snRNA-associated Sm-like protein LSm2
Small nuclear ribonuclear protein D homolog
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RNA Pol II (unphosphorylated) largest subunit
DNA-directed RNA polymerase II largest subunit
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Small nuclear ribonucleoprotein associated proteins B and B'
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20 kDa nuclear cap binding protein (NCBP 20 kDa subunit) (CBP20) (NCBP interacting protein 1) (NIP1)
Both human ferredoxins 1 and 2 and ferredoxin reductase are important for iron-sulfur cluster biogenesis
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The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.
Expression, purification, and characterization of human and rat acetyl coenzyme A carboxylase (ACC) isozymes
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Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase
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Adenosine deaminase-like protein 1 (ADAL1): characterization and substrate specificity in the hydrolysis of N(6)- or O(6)-substituted purine or 2-aminopurine nucleoside monophosphates
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Maintaining copper homeostasis: regulation of copper-trafficking proteins in response to copper deficiency or overload
Identification and functional characterization of adipose-specific phospholipase A2 (AdPLA)
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Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity
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Molybdenum cofactors, enzymes and pathways
Function and biogenesis of iron-sulphur proteins
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Deoxyhypusine hydroxylase is a Fe(II)-dependent, HEAT-repeat enzyme. Identification of amino acid residues critical for Fe(II) binding and catalysis [corrected].
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Structural basis for activation of calcineurin by calmodulin
Specific features of glycogen metabolism in the liver
Megakaryocyte development and platelet production
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Perifosine, a novel alkylphospholipid, inhibits protein kinase B activation
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26S proteasome non-ATPase regulatory subunit 7
Multicatalytic endopeptidase complex subunit C8
Activator of multicatalytic protease subunit 3
Multicatalytic endopeptidase complex subunit C2
Multicatalytic endopeptidase complex subunit C3
Characterization of human exonuclease 1 in complex with mismatch repair proteins, subcellular localization and association with PCNA
NMD: multitasking between mRNA surveillance and modulation of gene expression
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Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors.
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Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors.
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Multicatalytic endopeptidase complex subunit C9
Activator of multicatalytic protease subunit 2
Activator of multicatalytic protease subunit 1
Interferon gamma up-regulated I-5111 protein
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26S proteasome non-ATPase regulatory subunit 12
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Multicatalytic endopeptidase complex zeta chain
26S proteasome non-ATPase regulatory subunit 9
Multicatalytic endopeptidase complex subunit C13
Proteasome subunit beta type 8 precursor
26S proteasome non-ATPase regulatory subunit 8
Multicatalytic endopeptidase complex delta chain
Proteasome subunit beta type 6 precursor
Multicatalytic endopeptidase complex epsilon chain
Proteasome subunit beta type 5 precursor
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DNA polymerase epsilon, catalytic subunit A
Identification of the global transcriptomic response of the hypothalamic arcuate nucleus to fasting and leptin
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Cloning and functional expression of human aquaporin8 cDNA and analysis of its gene
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Serine 228 is essential for catalytic activities of 85-kDa cytosolic phospholipase A2
DNA polymerase alpha holoenzyme-associated protein P1
Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes.
Characterization of human UMP/CMP kinase and its phosphorylation of D- and L-form deoxycytidine analogue monophosphates.
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Cell division protein kinase 2 (EC 2.7.1.-)(p33 protein kinase)(CDK2)
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Phospholipid synthesis in a membrane fraction associated with mitochondria
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Expression of the SNT-1/FRS2 phosphotyrosine binding domain inhibits activation of MAP kinase and PI3-kinase pathways and antiestrogen resistant growth induced by FGF-1 in human breast carcinoma cells
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Vesicular tubular clusters between the ER and Golgi mediate concentration of soluble secretory proteins by exclusion from COPI-coated vesicles
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Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36)
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Leptin-cytokine crosstalk in breast cancer
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Multicatalytic endopeptidase complex subunit MECl-1
Proteasome subunit beta type 10 precursor
Multicatalytic endopeptidase complex iota chain
26S proteasome non-ATPase regulatory subunit 11
26S proteasome non-ATPase regulatory subunit 13
26S proteasome non-ATPase regulatory subunit 1
Multicatalytic endopeptidase complex beta chain
Proteasome subunit beta type 4 precursor
Probable 26S protease regulatory subunit 8
Proteasome regulatory particle subunit p44S10
26S proteasome non-ATPase regulatory subunit 6
Multicatalytic endopeptidase complex chain 7
Proteasome subunit beta type 9 precursor
26S proteasome non-ATPase regulatory subunit 4
26S proteasome non-ATPase regulatory subunit 3
Tumor necrosis factor type 1 receptor associated protein 2
26S proteasome non-ATPase regulatory subunit 2
Chaperonins: The hunt for the Group II mechanism
Multicatalytic endopeptidase complex subunit C5
Multicatalytic endopeptidase complex subunit C7-I
The ratio between tetrahydrobiopterin and oxidized tetrahydrobiopterin analogues controls superoxide release from endothelial nitric oxide synthase: an EPR spin trapping study
Molecular cloning of human Syk. A B cell protein-tyrosine kinase associated with the surface immunoglobulin M-B cell receptor complex
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Structure of human holocarboxylase synthetase gene and mutation spectrum of holocarboxylase synthetase deficiency
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Nitric oxide, tetrahydrobiopterin, oxidative stress, and endothelial dysfunction in hypertension
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U6 snRNA-associated Sm-like protein LSm5
U6 snRNA-associated Sm-like protein LSm3
U6 snRNA-associated Sm-like protein LSm4
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U6 snRNA-associated Sm-like protein LSm7
U6 snRNA-associated Sm-like protein LSm6
Biological characterization of various forms of elongation factor 1 from rabbit reticulocytes
Signal transduction during Fc receptor-mediated phagocytosis
Mutational analysis in longest known survivor of mucopolysaccharidosis type VII
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Elongation factor Tu, a GTPase triggered by codon recognition on the ribosome: mechanism and GTP consumption
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GLUT2 in pancreatic and extra-pancreatic gluco-detection (review)
The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review)
Intracellular mechanisms of antigen cross presentation in dendritic cells
Specificity, promiscuity and localization of ARF protein interactions with NCS-1 and phosphatidylinositol-4 kinase-III beta
Cross-presentation of soluble exogenous antigens (endosomes)
'GTP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
Alteration of decreased plasma NO metabolites and platelet NO synthase activity by paroxetine in depressed patients
ChREBP activates metabolic gene expression
NLRs join TLRs as innate sensors of pathogens
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
The mitochondrial ADP/ATP carrier: structural, physiological and
Regulation of nitric oxide-sensitive guanylyl cyclase
Glycosaminoglycan storage disorders: a review
The crystal structure of yeast thiamin pyrophosphokinase
Targeting the oncogene and kinome chaperone CDC37
Identification, characterization, and crystal structure of the Omega class glutathione transferases
Genetic analysis of chromosome pairing, recombination, and cell cycle control during first meiotic prophase in mammals
CD28/CTLA-4 and CD80/CD86 families: signaling and function
Remodelling of high density lipoproteins by plasma factors
Internalization of the epidermal growth factor receptor: role in signalling
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Identification and characterization of human cDNAs specific to BCS1, PET112, SCO1, COX15, and COX11, five genes involved in the formation and function of the mitochondrial respiratory chain
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G proteins and opioid receptor-mediated signalling
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17419.1
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Metabolism of highly unsaturated n-3 and n-6 fatty acids
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Molecular Mechanisms of Phagocytosis (Book): 97-116
MHC class I endosomal and lysosomal trafficking coincides with exogenous antigen loading in dendritic cells
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Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain
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Cloning of a new aquaporin (AQP10) abundantly expressed in duodenum and jejunum
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Prolactin and ErbB4/HER4 signaling interact via Janus kinase 2 to induce mammary epithelial cell gene expression differentiation
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The amino acid sequence of cytosolic aspartate aminotransferase from human liver
The E3 ligase Aip4/Itch ubiquitinates and targets ErbB-4 for degradation
Human pancreatic islets express mRNA species encoding two distinct catalytically active isoforms of group VI phospholipase A2 (iPLA2) that arise from an exon-skipping mechanism of alternative splicing of the transcript from the iPLA2 gene on chromosome 22q13.1
Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis
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Differences in regulatory properties between human and rat glucokinase regulatory protein
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Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains
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IMMPORT:Bioinformatics for the future of immunology
Functional characterization of human aquaporin 9 as a facilitative glycerol carrier
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Assembly and export of MHC class I peptide ligands
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Chromosomal localization of the gene for human glucosamine-6-sulphatase to 12q14
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High-throughput mass spectrometry screening for inhibitors of phosphatidylserine decarboxylase
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Identification and characterization of human ethanolaminephosphotransferase1
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Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae.
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Male pseudohermaphroditism resulting from a novel mutation in the human steroid 5 alpha-reductase type 2 gene (SRD5A2)
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Chemokine-mediated interaction of hematopoietic progenitors with the bone marrow vascular niche is required for thrombopoiesis
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Molecular cloning of cDNAs from human kidney coding for two alternatively spliced products of the cardiac Ca2+-ATPase gene
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benzo[a]pyrene diol epoxide I [ChEBI:30614]
(+/-)-Benzo(a)pyrene-7,8-diol-9,10-epoxide, anti-
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SUMOylation and deSUMOylation at a glance
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Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics
Expert Opin Drug Metab Toxicol 2:895-921
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Eukaryotic peptide chain release factor subunit 1
Leptin receptor signaling: pathways to leptin resistance
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DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladenine DNA glycosylase) (N-methylpurine- DNA glycosirase)
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Coatomer:Arf1-GTP:GAP Lattice (name copied from entity in Homo sapiens)
N-glycosylase/DNA lyase (Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP lyase))
DNA-(apurinic or apyrimidinic site) lyase
Coatomer:GAP Lattice (name copied from entity in Homo sapiens)
Coatomer:ARFGAP1 lattice (name copied from entity in Homo sapiens)
Coatomer:Arf1-GDP:GAP Lattice (name copied from entity in Homo sapiens)
Endonuclease III-like protein 1 (EC 4.2.99.18)
The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes.
Activity and genomic organization of human glucose transporter 9 (GLUT9), a novel member of the family of sugar-transport facilitators predominantly expressed in brain and leucocytes
Cloning of a human cDNA encoding a novel enzyme involved in the elongation of long-chain polyunsaturated fatty acids
DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (XAP4) (RPB5)
DNA-directed RNA polymerase II 23 kDa polypeptide
DNA-directed RNA polymerase II 19 kDa polypeptide
DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-repair protein complementing XP-F cell
DNA-repair protein complementing XP-F cell (Xeroderma pigmentosum group F complementing protein) (DNA excision repair protein ERCC-4)
Xeroderma pigmentosum group F complementing protein
DNA repair protein RAD51 homolog 1 (hRAD51) (HsRAD51)
The complete amino acid sequence of human skeletal-muscle fructose-bisphosphate aldolase
DNA-directed RNA polymerase II 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPB14.4)
DNA-directed RNA polymerase II 14.4 kDa polypeptide
DNA-directed RNA polymerase II 14.5 kDa polypeptide
The in vitro replication of DNA containing the SV40 origin.
DNA-directed RNA polymerase II 13.3 kDa polypeptide
DNA-directed RNA polymerase II 33 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6)
Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs
Atg9a controls dsDNA-driven dynamic translocation of STING and the innate immune response
Proc. Natl. Acad. Sci. U.S.A. 106:20842-6
Mismatch repair endonuclease PMS2 ecNumber3.1.-.-/ecNumber
Oligosaccharyl transferase 48 kDa subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189411
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Probable ATP-dependent RNA helicase DDX41
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Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
Quantitating protein synthesis, degradation, and endogenous antigen processing
Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function
Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform
Serine/threonine protein phosphatase 2B catalytic subunit, alpha isoform
Protein phosphatase 3 regulatory subunit B alpha isoform 1
Protein phosphatase 2B regulatory subunit 1
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Involvement of ACSL in local synthesis of neutral lipids in cytoplasmic lipid droplets in human hepatocyte HuH7
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MHC molecules and microbial antigen processing in phagosomes
Calcineurin, testis-specific catalytic subunit
Calmodulin-dependent calcineurin A subunit, gamma isoform
Serine/threonine protein phosphatase 2B catalytic subunit, gamma isoform
Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
eukaryotic translation initiation factor 5
Translation initiation factor eIF-2B gamma subunit
eIF-2B GDP-GTP exchange factor, gamma subunit
translation initiation factor 2B gamma subunit
eIF-2B GDP-GTP exchange factor, epsilon subunit
Translation initiation factor eIF-2B epsilon subunit
translation initiation factor 2B epsilon subunit
Protein transport protein Sec61 subunit alpha isoform 1
mRNA with premature termination codon not preceding exon junction
Double-strand DNA containing a 3-methyladenine
Double-strand DNA containing an ethenoadenine
Double-strand DNA containing a hypoxanthine
Remodeling of cardiolipin by phospholipid transacylation
mRNA with premature termination codon preceding exon junction
Double-strand DNA containing a cytosine glycol
Double-strand DNA containing an adenine opposite to an 8-oxo guanine
Double-strand DNA containing an 8-oxo guanine opposite to a cytosine
Double-strand DNA containing a formamidopyrimidine
DNA containing an apurinic/apyrimidinic (AP) site
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Mitochondrial ATP-binding cassette proteins
translation initiation factor 2B delta subunit
eIF-2B GDP-GTP exchange factor, delta subunit
Translation initiation factor eIF-2B delta subunit
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translation initiation factor 2B beta subunit
eIF-2B GDP-GTP exchange factor, beta subunit
Translation initiation factor eIF-2B beta subunit
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translation initiation factor 2B alpha subunit
Translation initiation factor eIF-2B alpha subunit
eIF-2B GDP-GTP exchange factor, alpha subunit
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T-complex protein 1 subunit alpha (TCP-1-alpha)
Human glyceraldehyde 3-phosphate dehydrogenase-2 gene is expressed specifically in spermatogenic cells.
mRNA Transcript Targeted by HuR Phosphorylated on Ser221 and Ser318
mRNA Transcript Targeted by HuR with Unknown Phosphorylation
mRNA Transcript Targeted by HuR Phosphorylated on Ser158 and Ser318.
mature mRNA (eukaryotic, capped and deadenylated)
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MutLalpha and proliferating cell nuclear antigen share binding sites on MutSbeta
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160577.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=432659
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2466848
T-complex protein 1 subunit gamma (TCP-1-gamma)
T-complex protein 1 subunit epsilon (TCP-1-epsilon)
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T-complex protein 1 subunit zeta (TCP-1-zeta)
microtubule (name copied from entity in Homo sapiens)
The kinesin-8 motor Kif18A suppresses kinetochore movements to control mitotic chromosome alignment
T-complex protein 1 subunit delta (TCP-1-delta)
RNA primer:origin duplex with DNA damage
T-complex protein 1 subunit beta (TCP-1-beta)
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T-complex protein 1 subunit eta (TCP-1-eta)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_193023.3
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The tyrosine kinase network regulating mast cell activation
hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci
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WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus
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The role of adipokines in beta-cell failure of type 2 diabetes
COPII (Coat Protein 2) Mediated Vesicle Transport
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nascent polypeptide with signal sequence
Genetic disorders of vitamin B12 metabolism: eight complementation groups--eight genes
RNA-binding protein in RNP (ribonucleoprotein) complexes
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K48-polyubiquitinated partially digested Ag
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Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes
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DNA containing IDL greater than 1 base and single strand incision
damaged DNA substrate:nascent mRNA hybrid
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repaired DNA template:nascent mRNA hybrid
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damaged DNA substrate:nascent mRNA hybrid with dual incisions
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DNA containing 1-2 base mismatch and single-strand incision
DNA containing single strand nick (5' phosphate, 3' hydroxyl)
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Identification of a mammalian long chain fatty acyl elongase regulated by sterol regulatory element-binding proteins
Unifying concepts in CD28, ICOS and CTLA4 co-receptor signalling
Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
Double-strand DNA containing a thymine glycol
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Double-strand DNA containing a dihydrouracil
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Heteroduplex DNA with D-loop structure with extended pairing between invading strand and complementary heteroduplex strand and containing newly synthesized ends
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The NLRP3 inflammasome: a sensor of immune danger signals
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Molecular basis of hereditary fructose intolerance: mutations and polymorphisms in the human aldolase B gene
Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
Alg14 recruits Alg13 to the cytoplasmic face of the endoplasmic reticulum to form a novel bipartite UDP-N-acetylglucosamine transferase required for the second step of N-linked glycosylation
Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control
LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor
A protein cofactor of lecithin:cholesterol acyltransferase
Na+/Ca2+-K+ exchangers (NCKX): functional properties and physiological roles
A revised picture of the E2F transcriptional network and RB function.
A "slow" homotetrameric kinesin-related motor protein purified from Drosophila embryos
A novel arachidonic acid-selective cytosolic PLA2 contains a Ca(2+)-dependent translocation domain with homology to PKC and GAP
Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
Cytoplasmic chaperonin containing TCP-1: structural and functional characterization
Multimerin is found in the alpha-granules of resting platelets and is synthesized by a megakaryocytic cell line
The biosynthesis of delta-9,12,15,18-tetracosatetraenoic and of delta-6,9,12,15,18-tetracosapentaenoic acids by rat testes
Identification of a mammalian H(+)-myo-inositol symporter expressed predominantly in the brain
Inhibiting glycogen synthesis prevents lafora disease in a mouse model
Characterization of human and murine PMP20 peroxisomal proteins that exhibit antioxidant activity in vitro
A novel diacylglycerol acyltransferase (DGAT2) is decreased in human psoriatic skin and increased in diabetic mice
Zinc efflux and compartmentalization by the SLC30 family
The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination
Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria
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Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
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Ins and outs of cellular cobalamin transport
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N (epsilon)-(carboxymethyl)lysine protein adduct is a major immunological epitope in proteins modified with advanced glycation end products of the Maillard reaction
Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII
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An updated overview on Wnt signaling pathways: a prelude for more
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Identification of the gene responsible for the cblA complementation group of vitamin B12-responsive methylmalonic acidemia based on analysis of prokaryotic gene arrangements
Proc. Natl. Acad. Sci. U.S.A. 99:15554-9
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Ligand discrimination in signaling through an ErbB4 receptor homodimer
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The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
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Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
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Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair.
ER-mediated phagocytosis: myth or reality?
Insights into Lafora disease: malin is an E3 ubiquitin ligase that ubiquitinates and promotes the degradation of laforin
Proc. Natl. Acad. Sci. U.S.A. 102:8501-6
L1 and NCAM adhesion molecules as signaling coreceptors in neuronal migration and process outgrowth
Vascular endothelial growth factor family of ligands and receptors: review
Cloning of a human type II phosphatidylinositol 4-kinase reveals a novel lipid kinase family
Regulation of telomerase by telomeric proteins
A critical review of the origin and control of adrenal androgens
Baillieres Clin Obstet Gynaecol 11:229-48
The molecular mechanics of eukaryotic translation
Reconstitution of two recombinant LSm protein complexes reveals aspects of their architecture, assembly, and function
Iron-sulfur proteins in health and disease
The human ATP-binding cassette (ABC) transporter superfamily
Pyrimidine pathways in health and disease
Isozymes of glyceraldehyde-3-phosphate dehydrogenase in man and other mammals.
The control of glycogen metabolism in the liver
Central leptin receptor action and resistance in obesity
AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors
Recognition and association of DNA glycosylase with site containing an affected pyrimidine
alpha-linolenic (omega3) and linoleic (omega6) acid metabolism
Glucokinase and molecular aspects of liver glycogen metabolism
Tumor necrosis factor-alpha-converting enzyme is required for cleavage of erbB4/HER4
Nuclear import of hepatic glucokinase depends upon glucokinase regulatory protein, whereas export is due to a nuclear export signal sequence in glucokinase
Quantitative and dynamic assessment of the contribution of the ER to phagosome formation
The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
Molecular tinkering of G protein-coupled receptors: an evolutionary success
Targeting the phosphoinositide 3-kinase pathway in cancer
Orchestrating nuclear envelope disassembly and reassembly during mitosis
Insulin degradation: progress and potential.
Ribosomal scanning and start codon recognition
Identification of the nuclear factor HMG2 as an activator for DFF nuclease activity
Molecular enzymology of carnitine transfer and transport
The expanding role of mitochondria in apoptosis.
Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site
Aquaporin-11: a channel protein lacking apparent transport function expressed in brain
PIG-B, a membrane protein of the endoplasmic reticulum with a large lumenal domain, is involved in transferring the third mannose of the GPI anchor
Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism
Nicotinamide N-methyltransferase knockdown protects against diet-induced obesity
Aquaporins in the kidney: from molecules to medicine
The human calcium-independent phospholipase A2 gene multiple enzymes with distinct properties from a single gene
The human AQP4 gene: definition of the locus encoding two water channel polypeptides in brain
Identification of heme as the ligand for the orphan nuclear receptors REV-ERBalpha and REV-ERBbeta
Pyruvate metabolism and Citric Acid (TCA) cycle
Group VIB Ca2+-independent phospholipase A2gamma promotes cellular membrane hydrolysis and prostaglandin production in a manner distinct from other intracellular phospholipases A2
cyclic purine dinucleotide [ChEBI:47037]
Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes.
A protein interaction framework for human mRNA degradation
Crystal structure of the kinesin motor domain reveals a structural similarity to myosin
Mechanisms of leptin action and leptin resistance
Crystal structure of the motor domain of the kinesin-related motor ncd
A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily
Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues
SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases
CATERPILLERs, pyrin and hereditary immunological disorders
A novel bifunctional phospholipase c that is regulated by Galpha 12 and stimulates the Ras/mitogen-activated protein kinase pathway
Regulation of a novel human phospholipase C, PLCepsilon, through membrane targeting by Ras
Human GTP cyclohydrolase I: only one out of three cDNA isoforms gives rise to the active enzyme
Protein kinase C alpha-dependent phosphorylation of the mRNA-stabilizing factor HuR: implications for posttranscriptional regulation of cyclooxygenase-2
Expression of the HsOrc1 gene, a human ORC1 homolog, is regulated by cell proliferation via the E2F transcription factor
Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate
The role for endoplasmic reticulum stress in diabetes mellitus
Signaling through PI3Kgamma: a common platform for leukocyte, platelet and cardiovascular stress sensing
Heregulin-dependent delay in mitotic progression requires HER4 and BRCA1
Thioredoxin-interacting protein links oxidative stress to inflammasome activation
Clinical findings and biochemical and molecular analysis of four patients with holocarboxylase synthetase deficiency
Genetic disorders of carnitine metabolism and their nutritional management.
Transcript-selective translational silencing by gamma interferon is directed by a novel structural element in the ceruloplasmin mRNA 3' untranslated region
Insulin vesicle release: walk, kiss, pause ... then run
From molecular action to physiological outputs: peroxisome proliferator-activated receptors are nuclear receptors at the crossroads of key cellular functions
Molecular cloning and expression of a novel human aquaporin from adipose tissue with glycerol permeability
Smooth muscle contraction and relaxation
Molecular cloning and identification of 3'-phosphoadenosine 5'-phosphosulfate transporter
Synergy between Ca2+ and protein kinase C is the major factor in determining the level of secretion from human platelets
Myotubularin phosphatases: policing 3-phosphoinositides
Human skeletal-muscle aldolase: N-terminal sequence analysis of CNBr- and o-iodosobenzoic acid-cleavage fragments
Hypophosphorylation of residue Y1045 leads to defective downregulation of EGFRvIII
T cell growth factor receptors. Quantitation, specificity, and biological relevance
1D-myo-Inositol 1,3,4-trisphosphate [ChEBI:810]
Conservation of the human telomere sequence (TTAGGG)n among vertebrates
NODs: intracellular proteins involved in inflammation and apoptosis
Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells
The FGF family: biology, pathophysiology and therapy
An atomic-level mechanism for activation of the kinesin molecular motors
Presentation of antigens by MHC class II molecules: getting the most out of them
Overview of retinoid metabolism and function
Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1
VEGF receptor signalling - in control of vascular function
System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties
Neuronal TRP channels: thermometers, pathfinders and life-savers
Endosomal proteolysis of internalized proteins.
Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
The rate of bulk flow from the endoplasmic reticulum to the cell surface
Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms
Physiological functions of the pentose phosphate pathway
Neurotrophin signal transduction in the nervous system
Compartmentalization of aquaporins in the human intestine
ChEBI:18278 N-acetyl-D-glucosaminyldiphosphodolichol
Cold Spring Harb Perspect Biol 5:a012633
Long G tails at both ends of human chromosomes suggest a C strand degradation mechanism for telomere shortening
In the kidney water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surface and AQP3 and AQP4 on their basolateral surface to transport water across the epithelium. The permeability of the epithelium is regulated by vasopressin, which activates the phosphorylation and subsequent translocation of AQP2 from intracellular vesicles to the plasma membrane.
Aquaporin-7 (AQP7) passively transports glycerol and water across the plasma membrane according to the osmotic gradient. AQP7 is expressed in adipocytes under the direct control of the PPARG and RXRA nuclear receptors. Expression of AQP7 correlates with release of glycerol from adipocytes. AQP7 is seen to translocate from the nuclear periphery to the plasma membrane during adrenaline-stimulated lipolysis. In rat AQP7 also transports urea.
Aquaporins (AQP's) are six-pass transmembrane proteins that form channels in membranes. Each monomer contains a central channel formed in part by two asparagine-proline-alanine motifs (NPA boxes) that confer selectivity for water and/or solutes. The monomers assemble into tetramers. Most aquaporins (i.e. AQP0/MIP, AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10) passively transport water into and out of cells according to the osmotic gradient across the membrane. Four aquaporins (the aquaglyceroporins AQP3, AQP7, AQP9, AQP10) conduct glycerol, three aquaporins (AQP7, AQP9, AQP10) conduct urea, and one aquaporin (AQP6) conducts anions, especially nitrate. AQP8 also conducts ammonia in addition to water. AQP11 and AQP12, classified as group III aquaporins, were identified as a result of the genome sequencing project and are characterized by having variations in the first NPA box when compared to more traditional aquaporins. Additionally, a conserved cysteine residue is present about 9 amino acids downstream from the second NPA box and this cysteine is considered indicative of group III aquaporins. Purified AQP11 incorporated into liposomes showed water transport. Knockout mice lacking AQP11 had fatal cyst formation in the proximal tubule of the kidney. Exogenously expressed AQP12 showed intracellular localization. AQP12 is expressed exclusively in pancreatic acinar cells. Aquaporins are important in fluid and solute transport in various tissues. In adipocytes, glycerol generated by triglyceride hydrolysis is exported by AQP7 and is imported by liver cells via AQP9. AQP1 plays a role in forming cerebrospinal fluid and AQP1, AQP4, and AQP9 appear to be important in maintaining fluid balance in the brain. AQP0, AQP1, AQP3, AQP4, AQP8, AQP9, and AQP11 play roles in the physiology of the hepatobiliary tract. In the kidney, water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surfaces and AQP3 and AQP4 on their basolateral surfaces to transport water across the epithelium. The permeability of the epithelium is regulated by vasopressin, which activates a signaling cascade leading to the phosphorylation of AQP2 and its translocation from intracellular vesicles to the apical membrane of collecting duct cells. Here, three views of aquaporin-mediated transport have been annotated: a generic view of transport mediated by the various families of aquaporins independent of tissue type, a view of the role of specific aquaporins in maintenance of renal water balance, and a view of the role of specific aquaporins in glycerol transport from adipocytes to the liver.
Aquaporin-3 (AQP3) passively transports water and glycerol across the plasma membrane according to the osmotic gradient. AQP3 is expressed in airway epithelia, secretory glands, skin, the collecting ducts of the kidney, and the basolateral surface of intestinal epithelium..
The function of V-type proton pumping ATPases is basically the same as that of F-type ATPases, except that V-ATPases cannot synthesize ATP from the proton motive force, the reverse reaction of pumping. When pumping, ATP hydrolysis drives a 120 degree rotation of the rotor which leads to movement of three protons into the phagosome (Adachi et al. 2007).
Aquaporin-9 (AQP9) passively transports water, glycerol, urea, and some other small neutral solutes across the plasma membrane according to the osmotic gradient. AQP9 is expressed in the sinusoidal plasma membrane in the liver facing the portal vein where it is believed to be responsible for glycerol uptake as part of gluconeogenesis. AQP9 is also expressed in glia, neurons, and peripheral leukocytes.
Triglycerides stored in adipocytes are hydrolyzed to yield fatty acids and glycerol. The glycerol is passively transported out of the adipocyte and into the bloodstream by Aquaporin-7 (AQP7) located in the plasma membrane of adipocytes. Glycerol in the bloodstream is passively transported into liver cells by AQP9 located in the plasma membrane of hepatocytes. Once inside the liver cell the glycerol is a substrate for gluconeogenesis.
Endocytosis of iron loaded transferrin/receptor complex leads, after acidification of the endosome, to the separation of iron and its diffusion out of the vesicle. The endosome is not fused with a lysosome but recycles its content back to the cell surface where soon transferrin dissociates from its receptor (Dautry-Varsat, 1986).
microRNA Biogenesis and Function : An overview
Intracellular pools of Ca2+ serve as the source for inositol 1,4,5-trisphosphate (IP3) -induced alterations in cytoplasmic free Ca2+. In most human cells Ca2+ is stored in the lumen of the sarco/endoplastic reticulum by ATPases known as SERCAs (ATP2As). In platelets, ATP2As transport Ca2+ into the platelet dense tubular network. ATP2As are P-type ATPases, similar to the plasma membrane Na+ and Ca+-ATPases. Humans have three genes for SERCA pumps; ATP2A1-3. Studies on ATP2A1 suggest that it binds two Ca2+ ions from the cytoplasm and is subsequently phosphorylated at Asp351 before translocating Ca2+ into the SR lumen. There is a counter transport of two or possibly three protons ensuring partial charge balancing.
The transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell via the main path (by transferrin endocytosis), its goal is not the (still elusive) chelated iron pool in the cytosol nor the lysosomes but the mitochondria, where heme is synthesized and iron-sulfur clusters are assembled (Kurz et al,2008, Hower et al 2009, Richardson et al 2010).
Accumulation of calcium into the Golgi apparatus is mediated by sarco(endo)plasmic reticulum calcium-ATPases (SERCAs) and by secretory pathway calcium-ATPases (SPCAs). There are two human genes which encode SPCAs; ATP2C1 and ATP2C2 which encode magnesium-dependent calcium-transporting ATPase type 2C members 1 and 2 (ATP2C1 and 2) respectively (Sudbrak et al, 2000; Vanoevelen et al, 2005). Defects in ATP2C1 are the cause of Hailey-Hailey disease (HHD), an autosomal dominant disease characterized by persistent blisters and erosions of the skin (Hu et al, 2000).
Diverse mutations in the aldolase B gene that underlie the prevalence of hereditary fructose intolerance
The plasma membrane contains a broad range of lipids making up the bilayer. Aminophospholipids such as phosphatidylserine (PS) and phosphatidylethanolamine (PE) are distributed in this bilayer and their arrangement is mediated by the P-type ATPases type IV family (Paulusma and Oude Elferink, 2005).
The plasma membrane contains a broad range of lipids making up the bilayer. Aminophospholipids (APLs) such as phosphatidylserine (PS) and phosphatidylethanolamine (PE) are distributed in this bilayer and their arrangement is mediated by the P-type ATPases type IV family (Paulusma and Oude Elferink, 2005).
The P-type ATPases (E1-E2 ATPases) are a large group of evolutionarily related ion pumps that are found in bacteria, archaea and eukaryotes. They are referred to as P-type ATPases because they catalyze auto-phosphorylation of a key conserved aspartate residue within the pump. They all appear to interconvert between at least two different conformations, E1 and E2. Most members of this transporter family pump a large variety of cations (Kuhlbrandt W, 2004).
The sperm-specific Na+/H+ exchanger SLC9C1 (aka sodium/hydrogen exchanger 10, NHE10) is localized to the flagellar membrane and is involved in pH regulation of spermatozoa required for sperm motility and fertility. The activity of human SLC9C1 is inferred from experiments using mouse Slc9c1 (Wang et al. 2003).
Ion channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et al. 2012, Deval et al. 2010) and the transient receptor potential channels (TRPCs) (Takahashi et al. 2012, Numata et al. 2011 in "TRP Channels" Zhu, MX editor, CRC Press, 2011, Ramsey et al. 2006, Montell 2005). Many channels are sensitive to changes in calcium (Ca2+) levels, both inside and outside the cell. Examples are protein tweety homologs 2 and 3 (TTYH2, 3) (Suzuki 2006), bestrophins 1-4 (BEST1-4) (Sun et al. 2002, Tsunenari et al. 2003, Kunzelmann et al. 2009, Hartzell et al. 2008) and ryanodine receptor tetramers (RYRs) (Beard et al. 2009).
The murine pantothenate kinase (Pank1) gene encodes two differentially regulated pantothenate kinase isozymes
Ion channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore for the flow of ions. There are different types of ion channels. P-type ATPases undergo conformational changes to translocate ions. Ligand-gated ion channels operate like a gate, opened or closed by a chemical signal. Voltage-gated ion channels are activated by changes in electrical potential difference at the membrane (Purves, 2001; Kuhlbrandt, 2004).
Structure, function and evolution of the signal recognition particle
Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
Molecular cloning and expression of ribosome releasing factor
Alveolar macrophages normally develop their phagosome along the endolysosomal pathway. However, after having internalized Mtb, this development is arrested at an early stage and only includes acidification, nitric oxide and superoxide production, as well as the use of a few other proteins that can be gained from other endosomes which still can interact with the phagosome (Flannagan et al. 2009).
Inactive Raf-1 is associated in the cytoplasm with 14-3-3. 14-3-3 binds to Raf-1 via the Ser259 phosphorylation site (S1). This interaction stabilises the inactive conformation of Raf-1 in which the Ras-binding Cysteine-rich domain (CRD) is obscured. The Raf-1 molecule contains an additional p21ras-binding domain (RBD), a second serine phosphorylation site at S621 (S2) and two tyrosine phosphorylation sites (at 340, Y1 and 341, Y2).
This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events.
Activated epidermal growth factor receptors (EGFR) can stimulate phosphatidylinositol (PI) turnover. Activated EGFR can activate phospholipase C-gamma1 (PLC-gamma1, i.e. PLCG1) which hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 is instrumental in the release of calcium from intracellular stores and DAG is involved in protein kinase C activation.
Upon increase in calcium concentration, calmodulin (CaM) is activated by binding to four calcium ions.
Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin).
Infection by Mycobacterium tuberculosis (Mtb) is soon countered by the host's immune system, the organism is however almost never eradicated; ten per cent of infections will develop into "open tuberculosis", while the other ninety per cent become "latent", a state that can persist for decades until loss of immune control. A third of the world's population is estimated to harbour latent tuberculosis. Latent infection involves the bacterium being internalized by macrophages where it stops and counters the innate immune answer (Russell 2011, Russell et al. 2010). When a status-quo is reached, Mtb enters a non-replicating persistent state (Barry et al. 2009, Boshoff & Barry 2005).
Inositol 1,4,5-triphosphate (IP3) is a second messenger produced by phospholipase C (PLC) metabolism of phosphoinositol 4,5-bisphosphate (PIP2) (Canossa et al. 2001).
Specific role for cathepsin S in the generation of antigenic peptides in vivo
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Organic cation/anion/zwitterion transport
Cathepsin S required for normal MHC class II peptide loading and germinal center development
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GRB2 can bind EGFR directly or through another SH2-containing protein, SHC1. This association leads to RAS activation.
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Autophosphorylated EGFR tyrosine residues are docking sites for many downstream effectors in EGFR signaling. The adaptor protein GRB2 binds to phosphotyrosine residues in the C-tail of EGFR through its SH2 domain. GRB2 is constitutively associated with SOS, a guanine nucleotide exchange factor of RAS. GRB2 binding to phosphorylated EGFR results in the recruitment of SOS to the plasma membrane where it comes in proximity to RAS. This mechanism has been seen to be the model for RAS activation.
The MAP kinase cascade describes a sequence of phosphorylation events involving serine/threonine-specific protein kinases. Used by various signal transduction pathways, this cascade constitutes a common 'module' in the transmission of an extracellular signal into the nucleus.
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Phosphorylated RAF is activated by Ras binding and stabilised in its active form by transient disassociation and reassociation of 14-3-3, as well as further phosphorylation.
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Signaling by AKT is one of the key outcomes of receptor tyrosine kinase (RTK) activation. AKT is activated by the cellular second messenger PIP3, a phospholipid that is generated by PI3K. In ustimulated cells, PI3K class IA enzymes reside in the cytosol as inactive heterodimers composed of p85 regulatory subunit and p110 catalytic subunit. In this complex, p85 stabilizes p110 while inhibiting its catalytic activity. Upon binding of extracellular ligands to RTKs, receptors dimerize and undergo autophosphorylation. The regulatory subunit of PI3K, p85, is recruited to phosphorylated cytosolic RTK domains either directly or indirectly, through adaptor proteins, leading to a conformational change in the PI3K IA heterodimer that relieves inhibition of the p110 catalytic subunit. Activated PI3K IA phosphorylates PIP2, converting it to PIP3; this reaction is negatively regulated by PTEN phosphatase. PIP3 recruits AKT to the plasma membrane, allowing TORC2 to phosphorylate a conserved serine residue of AKT. Phosphorylation of this serine induces a conformation change in AKT, exposing a conserved threonine residue that is then phosphorylated by PDPK1 (PDK1). Phosphorylation of both the threonine and the serine residue is required to fully activate AKT. The active AKT then dissociates from PIP3 and phosphorylates a number of cytosolic and nuclear proteins that play important roles in cell survival and metabolism. For a recent review of AKT signaling, please refer to Manning and Cantley, 2007.
GAB1 is recruited to the activated EGFR indirectly, through GRB2. GAB1 acts as an adaptor protein that enables formation of an active PIK3, through recruitment of PIK3 regulatory subunit PIK3R1 (also known as PI3Kp85), which subsequently recruits PIK3 catalytic subunit PIK3CA (also known as PI3Kp110). PIK3, in complex with EGFR, GRB2 and GAB1, catalyzes phosphorylation of PIP2 and its conversion to PIP3, which leads to the activation of the AKT signaling.
PIP3 generated by PI3K recruits AKT (also known as protein kinase B) to the membrane, through its PH (pleckstrin-homology) domains. The binding of PIP3 to the PH domain of AKT is the rate-limiting step in AKT activation (Scheid et al. 2002). In mammals there are three AKT isoforms (AKT1-3) encoded by three separate genes. The three isoforms share a high degree of amino acid identity and have indistinguishable substrate specificity in vitro. However, isoform-preferred substrates in vivo cannot be ruled out. The relative expression of the three isoforms differs in different mammalian tissues: AKT1 is the predominant isoform in the majority of tissues, AKT2 is the predominant isoform in insulin-responsive tissues, and AKT3 is the predominant isoform in brain and testes. All 3 isoforms are expressed in human and mouse platelets (Yin et al. 2008; O'Brien et al. 2008). Note: all data in the pathway refer to AKT1, which is the most studied.
GSK3 (glycogen synthase kinase-3) participates in the Wnt signaling pathway. It is implicated in the hormonal control of several regulatory proteins including glycogen synthase, and the transcription factors MYB and JUN. GSK3 phosphorylates JUN at sites proximal to its DNA-binding domain, thereby reducing its affinity for DNA. GSK3 is inhibited when phosphorylated by AKT1.
Following activation, AKT can phosphorylate an array of target proteins in the cytoplasm, many of which are involved in cell survival control. Phosphorylation of TSC2 feeds positively to the TOR kinase, which, in turn, contributes to AKT activation (positive feedback loop).
Activation of the FGF receptor underlies neurite outgrowth stimulated by L1, N-CAM, and N-cadherin
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AKT, phosphorylated at threonine (AKT1 308; AKT2 309; AKT3 305) and serine (AKT1 473; AKT2 474; AKT3 472) translocates to the nucleus, reaching a maximum after 15 min and returning to a basal level after 45 min of NGF stimulation. Control of the amount of nuclear AKT is achieved through the action of the phosphatase PP2A.
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Signaling by EGFR is frequently activated in cancer through either genomic amplification of the EGFR locus, resulting in over-expression of the wild-type protein, or through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein. Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009). In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006). Both EGFR kinase domain mutants and EGFRvIII mutant need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008). Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007). While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007). EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1045, a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006). Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010). Recombinant monoclonal antibody Cetuximab acts as an antagonist of EGFR ligand binding, and is approved for the treatment of tumors that over-express wild-type EGFR receptor (Cunningham et al. 2004, Li et al. 2005, Burtness et al. 2005).
Benzoquinoid ansamycins (geldanamycin, herbimycin, and geldanamycin derivatives 17-AAG, 17-DMAG and IPI-504) are antitumor antibiotics that inactivate HSP90 by binding to its substrate-binding pocket.
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The FRS family of scaffolding adaptor proteins has two members, FRS2alpha and FRS2beta (also known as FRS3 or SNT-2). Activation of FGFR tyrosine kinase allows FRS2 proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase SHP2. Subsequently, SHP2 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2alpha acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
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The pathway "Signaling by EGFR in Cancer" shows "Signaling by constitutively active EGFR" in parallel with "Signaling by EGFR". This allows users to compare signaling by constitutively active EGFR cancer mutants with the wild-type EGFR protein. Red lines emphasize cancer related events and physical entities, while wild-type entities and events are shaded. Please refer to "Signaling by constitutively active EGFR" and "Signaling by EGFR" for detailed pathway summations.
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The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1045 in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. For a recent review of EGFR signaling, please refer to Avraham and Yarden, 2011.
Class II phosphoinositide 3-kinases are downstream targets of activated polypeptide growth factor receptors
The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development. Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events. This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins. The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site. In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
The pathway 'Signaling by FGFR in disease' shows 'Signaling by FGFR mutants' in parallel with the wild-type pathway 'Signaling by FGFR', allowing users to compare disease and normal events. FGFR mutants and events associated with germline diseases and cancer are highlighted in red. The wild-type pathway is shaded in the background. For detailed pathway summations, please see 'Signaling by FGFR mutants' and 'Signaling by FGFR'.
The ability of human lactate dehydrogenase to catalyze the reaction of phenylalanine with NADH + H+ to form phenyllactate and NAD+ is inferred from the properties of bovine heart lactate dehydrogenase (Meister 1951). As these studies were carried out only on the one bovine isoform, the reaction is inferred only for the corresponding human isoform. The reaction rate measured for bovine LDHB acting on phenylpyruvate is approximately 2% of its rate on pyruvate, but could yield appreciable amounts of phenyllactate under conditions of high phenylpyruvate concentration.
Phenylalanine hydroxylase (PAH) catalyzes the conversion of phenylalanine to tyrosine. In the absence of functional PAH, phenylalanine accumulates to high levels in the blood (Mitchell and Scriver 2010) and is converted to phenylpyruvate and phenyllactate (Clemens et al. 1990; Langenbeck et al. 1992). The extent of these conversions is modulated by genetic factors distinct from PAH, as siblings with the identical PAH defect can produce different amounts of them (Treacy et al. 1996). Both L-amino acid oxidase (Boulland et al. 2004) and Kynurenine--oxoglutarate transaminase 3 (Han et al. 2004) can catalyze the conversion of phenylalanine to phenylpyruvate and lactate dehydrogenase can catalyze the conversion of the latter molecule to phenyllactate (Meister 1951). Elevated levels of phenylalanine, phenylpyruvate, and phenyllactate are all thought to contribute to the symptoms of phenylketonuria. One possible target is the metabolism of kynurenine.
Mucopolysaccharidosis type I (MPS I, Hurler syndrome, Hurler's disease, gargoylism, Scheie, Hirler-Scheie syndrome; MIM:607014, 607015 and 607016) is an autosomal recessive genetic disorder where there is a deficiency of alpha-L iduronidase (IDUA, MIM:252800), a glycosidase that removes non-reducing terminal alpha-L-iduronide residues during the lysosomal degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate (McKusick 1959). In 1992, Scott and colleagues were able to clone and purify the gene that encodes this enzyme, IDUA, demonstrating that it spans approximately 19 kb and contains 14 exons (Scott et al. 1992). Hurler syndrome is named after a German paediatrician Gertrud Hurler (1919, no reference available). The result is build up of heparan sulfate and dermatan sulfate in the body and increased urinary excretion of these GAGs. Symptoms and signs include hepatosplenomegaly, dwarfism, unique facial features, corneal clouding, retinopathy, progressive mental retardation appears during childhood and early death can occur due to organ damage (Campos & Monaga 2012). MPS I is divided into three subtypes, ranging from severe to mild phenotypes; Mucopolysaccharidosis type IH (MPSIH, Hurler syndrome, MIM:607014), mucopolysaccharidosis type IH/S (MPSIH/S, HurlerScheie syndrome, MIM: 607015) and mucopolysaccharidosis type IS (MPSIS, Scheie syndrome, MIM: 607016) respectively (McKusick 1972).
Mucopolysaccharidosis II (MPS II, Hunter syndrome, MIM:309900) is an X-linked, recessive genetic disorder which therefore primarily affects males. MPS II was first described in 1917, by Major Charles Hunter (Hunter 1917) and is caused by a deficiency (or absence) of iduronate-2-sulfatase (IDS, MIM:300823), which would normally hydrolyse the 2-sulfate groups of the L-iduronate 2-sulfate units of dermatan sulfate, heparan sulfate and heparin. Without IDS, these GAGs accumulate in the body and are excessively excreted in urine. Although the disease was known since the early 1970s, being the first MPS to be defined clinically in humans, it wasn't until the 1990s that IDS was cloned. It is now known to be localized to Xq28 (Wilson et al. 1991) and contain 9 exons (Flomen et al. 1993) spanning approximately 24 kb (Wilson et al. 1993). Build up can occur in the liver and spleen as well as in the walls and valves of the heart (reduced hepatic and cardiac function, liver/spleen hepatosplenomegaly), airways (leading to obstructive airway disease), all major joints and bones (joint stiffness and skeletal deformities) and in brain (severe mental retardation). The rate of progression and degree of severity of the disorder can be different for each person with MPS II. Severe forms of the disorder can result in death in childhood whereas those with a "milder" form can expect to live to their 20's or 30's. Some patients even survive into their fifth and sixth decades of life (Wraith et al. 2008, Beck 2011).
PAPS (3'-phosphoadenosine-5'-phosphosulfate), which functions as a sulfate donor in the cell, is synthesized from sulfate and two molecules of ATP in a two-step process (Robbins & Lipmann 1958) catalyzed in vertebrates by a bifunctional enzyme (Venkatachalam et al. 1998). PAPS synthesis takes place in the cytosol, and it is either consumed there in the sulfonation of a variety of hormones and xenobiotics, or it is transported to the Golgi apparatus and consumed in the synthesis of proteoglycans like chondroitin sulfate. Two isoforms of the human bifunctional enzyme are known, mutations in one of which are associated with defects in proteoglycan biosynthesis (Girard et al. 1998, ul Haque et al. 1998).
Glycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)) and a uronic acid (glucuronate or iduronate). They can be heavily sulfated. GAGs are located primarily in the extracellular matrix (ECM) and on cell membranes, acting as a lubricating fluid for joints and as part of signalling processes. They have structural roles in connective tissue, cartilage, bone and blood vessels (Esko et al. 2009). GAGs are degraded in the lysosome as part of their natural turnover. Defects in the lysosomal enzymes responsible for the metabolism of membrane-associated GAGs lead to lysosomal storage diseases called mucopolysaccharidoses (MPS). MPSs are characterised by the accumulation of GAGs in lysosomes resulting in chronic, progressively debilitating disorders that in many instances lead to severe psychomotor retardation and premature death (Cantz & Gehler 1976, Clarke 2008). The biosynthesis and breakdown of the main GAGs (hyaluronate, keratan sulfate, chondroitin sulfate, dermatan sulfate and heparan sulfate) is described here.
Computational insights into the role of glutathione in oxidative stress
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). MPS IIIB (Mucopolysaccharidosis type IIIB, MPS IIIB, Sanfilippo syndrome type B; MIM:252920) is an autosomal recessive genetic disorder due to loss of function of alpha-N-acetylglucosaminidase (NAGLU; MIM:609701), involved in the hydrolysis of terminal non-reducing N-acetylglucosamine residues in heparan sulfate (HS) The gene encoding NAGLU was cloned in 1996 by Zhao and colleagues. It contains 6 exons and spans 8.3 kb on chromosome 17q21 (Zhao et al. 1996). MPSIIIB is characterized by severe CNS retardation but only mild somatic disease and death usually occurs in the second or third decade of life (Zhao et al. 1996, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). MPS IIIB shows extensive molecular heterogeneity (Schmidtchen et al. 1998).
Mucopolysaccharidosis III (MPS III, Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A, MIM:252900) is a rare, autosomal recessive lysosomal storage disease characterised by severe CNS degeneration in early childhood leading to death between 10 and 20 years of age. A deficiency of the enzyme N-sulphoglucosamine sulphohydrolase (SGSH, MIM:605270), which normally hydrolyses the sulfate group from the terminal N-sulphoglucosamine residue of heparan sulfate (HS), leads to the build-up of HS in cells and tissues and its presence in urine (van de Kamp et al. 1981, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). The gene encoding N-sulfoglucosamine sulfohydrolase, SGSH, was cloned in 1995 (Scott et al.1995) and, later, shown to contain 8 exons spanning approximately 11 kb (Karageorgos et al. 1996).
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome D, MIM:252940) is an autosomal recessive genetic disorder due to the loss of N-acetyl-D-glucosamine 6-sulfatase (GNS; MIM:607664), that hydrolyses the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of the glycosaminoglycans (GAGs) heparan sulfate and keratan sulfate. GNS is localized to chromosome 12q14 and has 14 exons spanning 46 kb (Robertson et al. 1988, Mok et al. 2003). Loss of enzyme activity leads to lysosomal accumulation and urinary excretion of heparan sulfate and N-acetylglucosamine 6-sulfate residues (Mok et al. 2003). Keratan sulphate does not accumulate in MPS IIID, as beta-linked N-acetyl-D-glucosamine 6-sulphate can be cleaved by beta-hexosaminidase A (Kresse et al. 1980). This disorder is characterized by progressive mental deterioration but only moderate physical abnormalities and death duing the second or third decade of life, presenting a phenotype similar to MPSIIIA (Jones et al. 1997, de Ruijter et al. 2011).
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). Mucopolysaccharidosis type IIIC (MPS IIIC, Sanfilippo syndrome C; MIM:252930) is an autosomal recessive genetic disorder due to the loss of heparan alpha-glucosaminide N-acetyltransferase (HGSNAT; MIM:610453) that normally acetylates the non-reducing terminal alpha-glucosamine residue of heparan sulfate. The molecular defects underlying MPS IIIC remained unknown for almost three decades due to the low tissue content and instability of HGSNAT. But, during the last decade, the gene was cloned in parallel by two different groups and shown to contain 18 exons and span approximately 62Kb (Fan et al. 2006, Hrebicek et al. 2006). Loss of HGSNAT results in build up of this glycosaminglycan (GAG) in cells and tissues and is characterized by severe central nervous system degeneration but only with mild somatic disease and death occurs typically during the second or third decade of life (Kresse et al. 1978, Klein et al. 1978, Feldhammer et al. 2009, de Ruijter et al. 2011).
Agmatine: biological role and therapeutic potentials in morphine analgesia and dependence
Acyl-coenzyme A synthetases in metabolic control
Structure-function relationships in dihydrolipoamide acyltransferases.
Functional impairment of lens aquaporin in two families with dominantly inherited cataracts
Lipin is required for efficient breakdown of the nuclear envelope in Caenorhabditis elegans
Inactivation of the C. elegans lipin homolog leads to ER disorganization and to defects in the breakdown and reassembly of the nuclear envelope
beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
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The eukaryotic polypeptide chain releasing factor (eRF3/GSPT) carrying the translation termination signal to the 3'-Poly(A) tail of mRNA. Direct association of erf3/GSPT with polyadenylate-binding protein.
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Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine
Identification and characterization of a selective radioligand for ELOVL6
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The human gene ABCB6 encodes a mitochondrial half-type ATP-binding cassette (ABC) protein MTABC3 which is uniquely located on the outer mitochondrial membrane and is functional as a homodimer (Krishnamurthy et al. 2006). It plays a crucial role in heme synthesis by mediating porphyrin uptake into mitochondria (Mitsuhashi et al. 2000, Krishnamurthy et al. 2006).
Mitochondrial ABC transporters are thought to play a key role in iron metabolism and heme biosynthesis. All mitochondrial ABC transporters described to date are of the half-transporter type and would probably function as dimers (Ramjeesingh et al. 2003) but their dimerization partners have not yet been identified. ABC7 is the functional human orthologue of yeast Atm1p (Csere et al. 1998), is predicted to dimerize in the same way as Atm1p (Chloupková et al. 2004) and is probably involved in iron homeostasis. Defects in ABCB7 are the cause of X-linked sideroblastic anemia with ataxia (ASAT) [MIM:301310] (Allikmets et al. 1999). Human genes ABCB8 and ABCB10 encode mABC1 and mABC2 respectively (Hogue et al. 1999, Zhang et al 2000 respectively). They would be expected to dimerize, as demonstrated for mABC2 (Graf et al. 2004). Both are believed to have similar functionality to ABC7 although this has not been demonstrated yet.
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The appended C-domain of human methionyl-tRNA synthetase has a tRNA-sequestering function
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Teleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively inorganic cations and anions across membranes : SLC4 plays a pivotal role in mediating Na+ - and/or Cl- -dependent transport of basic anions [e.g. HCO3-, (CO3)2-] in various tissues and cell types (in addition to pH regulation, specific members of this family also contribute to vectorial trans-epithelial base transport in several organ systems including the kidney, pancreas, and eye) (Pushkin A and Kurtz I, 2006); SLC8 is a group of Na+/Ca2+ exchangers (SLC8A1 is involved in cardiac contractility) (Quednau BD et al, 2004); SLC24 is a group of Na+/Ca2+ or Na+/K+ exchangers (Altimimi HF and Schnetkamp PP, 2007); SLC9 comprises Na+/H+ exchanger proteins involved in the electroneutral exchange of sodium ion and protons (Orlowski J and Grinstein S, 2004); SLC12 functions as Na+, K+ and Cl- ion electroneutral symporters (Hebert SC et al, 2004); SLC26 is the trans-epithelial multifunctional anion (e.g. sulfate, oxalate, HCO-, Cl-) exchanger family, important in cartilage development, production of thyroid hormone, sound amplification in the cochlea etc (Sindic A et al, 2007; Dorwart MR et al, 2008; Ashmore J, 2008). SLC34 is an important Type II Na+/(HPO4)2- symporter (Forster IC et al, 2006; Virkki LV et al, 2007); SLC20 was originally identified as a viral receptor, and functions as a Type III Na+/(H2PO4)- symporter (Collins JF et al, 2004; Virkki LV et al, 2007). Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
Cytosolic glucokinase and the three isoforms of hexokinase catalyze the irreversible reaction of glucose and ATP to form glucose 6 phosphate and ADP. In the body glucokinase is found only in hepatocytes and pancreatic beta cells. Glucokinase and the hexokinase enzymes differ in that glucokinase has a higher Km than the hexokinases and is less readily inhibited by the reaction product. As a result, glucokinase should be inactive in the fasting state when glucose concentrations are low but in the fed state should have an activity proportional to glucose concentration. These features are thought to enable efficient glucose uptake and retention in the liver, and to function as a sensor of glucose concentration coupled to insulin release in pancreatic beta cells (Thorens 2001). Glucokinase mutations are associated with MODY2, a heritable early onset form of type II diabetes (Tanizawa et al. 1991; Takeda et al. 1993). Three human hexokinase enzymes have been characterized, HK1 (Aleshin et al. 1998), HK2 (Lehto et al. 1995), and HK3 (Rijksen at al. 1982).
Free glucokinase (GCK1) leaves the nucleus via the nuclear pore. While the GCK1 protein contains a nuclear export sequence motif, the molecular details of the GCK1 export process remain to be worked out (Shiota et al. 1999).
The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition
Mammalian ABC transporters are usually found on the plasma membrane and on organelles such as the ER and peroxisome but a small number are also located on the mitochondria. Here they are thought to play roles in heme biosynthesis and iron-sulphur cluster synthesis (Burke & Ardehali 2007).
Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
Differential recruitment of DNA Ligase I and III to DNA repair sites
The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
There are two transporters of this type; The genes SLC20A1 and SLC20A2 encode for PiT1 (phosphate transporter 1) and PiT2 respectively. They both have a broad tissue distribution and may play a general housekeeping role in phosphate transport such as absorbing phosphate from interstitial fluid and in extracellular matrix and cartilage calcification as well as in vascular calcification. These proteins were originally described as retroviral receptors for the gibbin ape leukemia virus receptor 1 (GLVR1, now called PiT1) (O'Hara B et al, 1990) and GLVR2 (now called PiT2) (van Zeijl M et al, 1994). However, they were found to possess Na+-coupled phosphate cotransporter function (Fernandes I et al, 1999). The transport is electrogenic with a stoichiometry of 2:1 (Na+:Pi).
Phosphorus is an essential element that is critical for structural and metabolic roles in all living organisms. Cells obtain phosphorus in the form of negatively-charged inorganic phosphate (Pi). Two SLC families transport phosphate in mammals; SLC34 (Murer H et al, 2004) and SLC20 (Collins JF et al, 2004). Both are secondary-active, Na+-coupled transporter systems which use the inward Na+ gradient (from the Na+-K+-ATPase) to drive phosphate influx into cells (Virkki LV et al, 2007).
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Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism
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Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy
The human gene SLC30A2 encodes zinc transporter ZnT2. Its function is inferred from experiments using rat Znt2 (Palmiter RD et al, 1996).
The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC11A2 encodes the divalent cation transporter DCT1 (NRAMP2, Natural resistance-associated macrophage protein 2). NRAMP2 resides on the apical membrane of enterocytes and mediates the uptake of ferrous iron into these cells (Tandy S et al, 2000). DCT1 can also accept a broad range of transition metal ions.
Natural resistance-associated macrophage proteins (NRAMPs) regulates macrophage activation for antimicrobial activity against intracellular pathogens. They do this by mediating metal ion transport across macrophage membranes and the subsequent use of these ions in the control of free radical formation. The human gene SLC11A1 encodes NRAMP1 (Kishi F, 2004; Kishi F and Nobumoto M, 1995) which can utilize the protonmotive force to mediate divalent iron (Fe2+), zinc (Zn2+) and manganese (Mn2+) influx to or efflux from phagosomes.
Myo-Inositol is a neutral cyclic polyol, abundant in mammalian tissues. It plays important roles; it is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and as key regulators of many cell functions. It can also serve as a compatible osmolyte during volume regulation in many tissues where cells are exposed to hyperosmotic conditions. Three members of the glucose transporter families are inositol transporters. Two (SMIT1 and SMIT2) couple myo-inositol transport with two Na+ ions. Unlike SMIT1, SMIT2 also transports D-chiro_inositol. The third transporter (HMIT), couples myo-inositol transport with a proton.
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Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction (Joost and Thorens 2001). Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs. Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
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Glucokinase (GCK1) is negatively regulated by glucokinase regulatory protein (GKRP), which reversibly binds the enzyme to form an inactive complex. Binding is stimulated by fructose 6-phosphate and sorbitol 6-phosphate (hence high concentrations of these molecules tend to reduce GCK1 activity) and inhibited by fructose 1-phosphate (hence a high concentration of this molecule tends to increase GCK1 activity). Once formed, the complex is translocated to the nucleus. In the presence of high glucose concentrations, the nuclear GCK1:GKRP complex dissociates, freeing GCK1 to return to the cytosol. The free GKRP is thought also to return to the cytosol under these conditions, but this return has not been confirmed experimentally. Possible physiological roles for this sequestration process are to decrease futile cycling between glucose and glucose 6 phosphate in hepatocytes under low-glucose conditions, and to decrease the lag between a rise in intracellular glucose levels and the onset of glucose phosphorylation in both hepatocytes and pancreatic beta cells (Brocklehurst et al. 2004; Shiota et al. 1999).
Molecular characterization of cytosolic phospholipase A2-beta
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SLC2A13 encodes a H+/myo-inositol co-transporter, HMIT (Uldry M et al, 2001) which is abundantly expressed in the brain. A proton is co-transported with myo-inositol uptake into cells. No glucose transport function has been detected to date.
Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is the main energy source used by cells to make energy. Im mammals, blood glucose levels are tightly controlled and glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost HG and Thorens B, 2001).
Class III facilitative transporters consist of five members; GLUT6, 8, 10, 12 and HMIT (a H+/myo-inositol transporter). They possess a characteristic glycosylation site on loop 9 (found in loop 1 of classes I and II transporters). Four class III facilitative transporters can transport glucose. SLC2A6 encodes GLUT6, expressed mainly in brain, spleen and leucocytes (Doege H et al, 2000a). In literature, this protein is incorrectly described as GLUT9. SLC2A8 encodes GLUT8 and is expressed in brain, testis and adipose tissue (Doege H et al, 2000b). SLC2A10 (located in the Type 2 diabetes-linked region of human chromosome 20q12-13.1) encodes GLUT10, a transporter with high affinity for glucose (McVie-Wylie AJ et al, 2001) . GLUT10 is highly expressed in liver and pancreas but is present in most tissues in lower levels. Defects in SLC2A10 are the cause of arterial tortuosity syndrome (ATS), an autosomal recessive disorder characterized by tortuosity and elongation of major arteries, often resulting in death at a young age (Coucke PJ et al, 2006). SLC2A12 encodes GLUT12, which is highly expressed in skeletal muscle, heart and prostate, with lower levels in brain, placenta and kidney. It was originally cloned from the human breast cancer cell line MCF-7 (Rogers S et al, 2002).
Hexoses, notably fructose, glucose, and galactose, generated in the lumen of the small intestine by breakdown of dietary carbohydrate are taken up by enterocytes lining the microvilli of the small intestine and released from them into the blood. Uptake into enterocytes is mediated by two transporters localized on the lumenal surfaces of the cells, SGLT1 (glucose and galactose, together with sodium ions) and GLUT5 (fructose). GLUT2, localized on the basolateral surfaces of enterocytes, mediates the release of these hexoses into the blood (Wright et al. 2004). GLUT2 may also play a role in hexose uptake from the gut lumen into enterocytes when the lumenal content of monosaccharides is very high (e.g., Kellet and Brot-Laroche, 2005) and GLUT5 mediates fructose uptake from the blood into cells of the body, notably hepatocytes. Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction. Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs. Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
Mucopolysaccharidosis type III (Sanfilippo Syndrome): emerging treatment strategies
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Mucopolysaccharidosis Type II (Hunter Syndrome): clinical picture and treatment
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DNA mismatch repair efficiency and fidelity are elevated during DNA synthesis in human cells
Glutathione metabolism and its selective modification
Hexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse across cellular membranes, and require transporter proteins for entry into and exit out of cells. Four gene families encode hexose transporter proteins (He et al, 2009). SLC2 family contains 14 genes and encode facilitative glucose transporters (GLUTs) (Uldry M and Thorens B, 2004). SLC5 family contains 12 genes and encode Na+/glucose symporters (Wright EM and Turk E, 2004). SLC37 family contains 4 members and encode sugar-phosphate/phosphate exchangers (Bartoloni L and Antonarakis SE, 2004). SLC45 family has 4 members and encode putative sugar/H+ symporters.
The SLC22 gene family of solute carriers function as organic cation transporters (OCTs), cation/zwitterion transporters (OCTNs) and organic anion transporters (OATs). The SLC22 family belongs to the major facilitator superfamily and comprises uniporters, symporters and antiporters.Most of this family are polyspecific transporters. Since many of these transporters are expressed in the liver, kidney and intestine, they play an important role in drug absorption and excretion. Substrates include xenobiotics, drugs, and endogenous amine compounds (Koepsell H and Endou H, 2004).
The human gene SLC33A1 encodes acetyl-CoA transporter AT1 (Kanamori A et al, 1997).Acetyl-CoA is transported to the lumen of the Golgi apparatus, where it serves as the substrate of acetyltransferases that modify the sialyl residues of gangliosides and glycoproteins. Defects in SLC33A1 are the cause of spastic paraplegia autosomal dominant type 42 (SPG42) which is a neurodegenerative disorder (Lin P et al, 2008).
Six SLC gene families encode proteins which mediate transport of metals. The families are SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41 (He L et al, 2009; Bressler JP et al, 2007).
Zinc is an essential element for all organisms because it serves as a catalytic or structural cofactor for many different proteins. Cellular zinc homoeostasis is co-ordinated through Zn2+-specific transporters which are members of two distinct gene families. Members of the SLC39 gene family (ZRTL-like import proteins1-14, ZIP1-14) are responsible for Zn2+ import into the cytoplasm, either across the plasma membrane or out of intracellular organelles. In contrast, members of the SLC30 gene family (zinc transporters 1-10, ZnT1-10) export Zn2+ from the cytoplasm, either across the plasma membrane into the extracellular space or into intracellular organelles (Murakami M and Hirano T, 2008; Devirgiliis C et al, 2007; Eide DJ, 2006).
The organic cation transporters comprise three SLC22 members, OCT1-3. They can transport a wide range of organic cations including weak bases. All transport by OCTs is electrogenic, sodium-independent and bidirectional. Two further organic cation transporters mediate transport of ergothioneine and carnitine (Koepsell H and Endou H, 2004).
The human gene SLC22A18 encodes organic cation transporter-like protein 2 (ORCTL2). It is expressed to high levels in kidney, liver and colon. ORCTL2 can transport chloroquine and quinidine with the antiport of protons (Reece M et al, 1998). Defects in SLC22A18 may play a role in tumorigenesis (Schwienbacher C et al, 1998).
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The human gene SLC30A3 encodes zinc transporter ZnT3. Through experiments on the mouse homologue Znt3, it is thought this transporter is expressed mainly in brain and testis and mediated the accumulation of zinc into synaptic vesicles (Palmiter et al, 1996).
PTEN1 is frequently mutated in primary endometrial carcinomas
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The human SLC30 gene family of solute carriers is thought to participate in the homeostasis of zinc ions and facilitate zinc transport into specialized compartments of the cell such as endosomes, golgi network and synaptic vesicles. There are 10 members of this family, named ZnT1-10. ZnT4, ZnT9 and ZnT10 have no function determined as of yet (Palmiter RD and Huang L, 2004).
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The human SLC30A8 gene encodes the zinc transporter ZnT8 which is specifically expressed in pancreatic beta cells (Chimienti et al. 2005). Zinc is required for zinc-insulin crystallization within secretory vesicles of these cells. After glucose stimulation, large amounts of zinc are secreted locally in the extracellular matrix together with insulin. It has been suggested that this co-secreted zinc plays a role in islet cell paracrine and/or autocrine communication (Chimienti F et al, 2006). Loss of function mutations in SLC30A8 are strongly protective against type 2 diabetes, suggesting SLC20A8 inhibition as a therapeutic target in T2D prevention. (Flannick et al. 2014).
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1D-myo-inositol 1,3,4,5-tetrakisphosphate
Aquaporin-9 (AQP9) and AQP10 are 6-pass transmembrane proteins that passively transport urea across the plasma membrane through a pore in each subunit of a homotetramer.
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1D-myo-inositol 1,3,4,6-tetrakisphosphate
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
myo-inositol 1,3,4,5,6-pentakisphosphate
Association of alternative complement pathway components with human blood platelets: secretion and localization of factor D and beta 1H Globulin
Aquaporin-3 (AQP3), AQP7, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport glycerol across the plasma membrane through a pore in each subunit of a homotetramer.
Identification and characterization of a major liver lysophosphatidylcholine acyltransferase
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Aquaporin-0 (AQP0, also known as MIP), AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport water across the plasma membrane according to the concentration gradient. Each molecule contains a water channel and subunits assemble into homotetramers. In principle water can move in either direction through an aquaporin, however in vivo flow may occur in only one direction. Conductance of water by AQP0 and AQP11 are low relative to other aquaporins.
Proteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of the substrates across the membrane, against their electrochemical gradient. Channels at the open state can transfer the substrates (ions or water) down their electrochemical gradient, at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate âeither against or following their concentration gradient, at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. According to the Human Genome Organization (HUGO) Gene Nomenclature Committee, all human transporters can be grouped into the solute-carrier (SLC) superfamily. Currently, there are 55 SLC families in the superfamily, with a total of at least 362 putatively functional protein-coding genes (Hediger et al, 2004; He et al., 2009). At least 20-25% amino-acid sequence identity is shared by members belonging to the same SLC family. No homology is shared between different SLC families. While the HUGO nomenclature system by definition only includes human genes, the nomenclature system has been informally extended to include rodent species through the use of lower cases letters (e.g., Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene). And it's worthwhile to mention that pumps, channels and aquporins are not included in SLC superfamily.
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This pathway groups the processes mediated by SLC transporters, by which vitamins and cofactors, as well as nucleosides, nucleotides, nucleobases, and related molecules cross lipid bilayer membranes.
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phosphatidylinositol 1,3,4,5-tetrakisphosphate
Nucleotide sugars are used as sugar donors by glycosyltransferases to create the sugar chains for glycoconjugates such as glycoproteins, polysaccharides and glycolipids. Glycosyltransferases reside mainly in the lumen of the Golgi apparatus and endoplasmic reticulum (ER) whereas nucleotide sugars are synthesized in the cytosol. The human solute carrier family SLC35 encode nucleotide sugar transporters (NSTs) which can mediate the antiport of nucleotide sugars in exchange for the corresponding nucleoside monophosphates (eg. UMP for UDP-sugars). Owing to their function, NSTs are primarily located on Golgi and ER membranes (He L et al, 2009; Handford M et al, 2006; Ishida N and Kawakita M, 2004).
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The human gene SLC35C1 encodes the GDP-fucose transporter FUCT1. It resides on the Golgi membrane and mediates the transport of UDP-fucose into the Golgi lumen. Defects in SLC35C1 causes the congenital disorder of glycosylation type 2C, also known as leukocyte adhesion deficiency type II (LAD2) (Lubke T et al, 2001).
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The human gene SLC35B2 encodes the adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPST1) (Ozeran et al. 1996, Kamiyama et al. 2003). In human tissues, PAPST1 is highly expressed in the placenta and pancreas and present at lower levels in the colon and heart. The human gene SLC35B3 encodes a human PAPS transporter gene that is closely related to PAPST1. Called PAPST2, it is predominantly expressed in the colon (Kamiyama et al. 2006).
Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
Haplotype analysis suggests that the two predominant mutations in Japanese patients with holocarboxylase synthetase deficiency are founder mutations
1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration
Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner
S-adenosylmethionine: nothing goes to waste
Nitric oxide and peroxynitrite in health and disease
Hexosamine biosynthetic pathway mutations cause neuromuscular transmission defect
Release of apoptotic factors from the mitochondria
Biochemical properties of human pantothenate kinase 2 isoforms and mutations linked to pantothenate kinase-associated neurodegeneration
Phosphoglycerate mutase isozyme marker for tissue differentiation in man
Clustering of mutations in the biotin-binding region of holocarboxylase synthetase in biotin-responsive multiple carboxylase deficiency
Processive synthesis on the lagging strand
Occurrence of surface IgM, IgD, and free light chains of human lymphocytes
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
ChEBI:18348 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
Molecular basis of phenotypic variation in patients with argininemia
N,N'-Diacetylchitobiosyldiphosphodolichol [ChEBI:7069]
Protease-activated receptors in hemostasis, thrombosis and vascular biology
6-(L-erythro-1,2-Dihydroxypropyl 3-triphosphate)-7,8-dihydropterin
7,8-dihydroneopterin 3'-triphosphate [ChEBI:18372]
2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate
S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
GPVI and integrin alphaIIb beta3 signaling in platelets
Metabolism of alpha-linolenic acid in humans
Prostaglandins Leukot Essent Fatty Acids 75:161-8
Trk receptors: roles in neuronal signal transduction
Identification of galectin-3 as a high-affinity binding protein for advanced glycation end products (AGE): a new member of the AGE-receptor complex
The type 4 subfamily of P-type ATPases, putative aminophospholipid translocases with a role in human disease
Function of eukaryotic initiation factor 5 in the formation of an 80 S ribosomal polypeptide chain initiation complex.
Purification and subunit structure studies of human placental threonyl-tRNA synthetase
The oxidation of pyruvate in pigeon breast muscle
Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response
A refined structure of human aquaporin-1
Mechanisms of caspase-1 activation by P2X7 receptor-mediated K+ release
Characterization of protein synthesis factors from rabbit reticulocytes
latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant.
Elongation factor 1 beta of artemia: localization of functional sites and homology to elongation factor 1 delta
Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation.
The role of calcium signaling in phagocytosis
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
Natural resistance-associated macrophage protein 1
Solute carrier family 2, facilitated glucose transporter member 10
Solute carrier family 2, facilitated glucose transporter member 12
Natural resistance-associated macrophage protein 2
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates
RNA polymerase III transcribes human microRNAs
Role of multiple phosphorylation sites in the COOH-terminal tail of aquaporin-2 for water transport: evidence against channel gating
XTRPC1-dependent chemotropic guidance of neuronal growth cones
Factors involved in megakaryocyte development and platelet production
Insulin degradation: mechanisms, products, and significance.
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Sarco/endoplasmic reticulum Ca2+ ATPases (SERCAs)
Sarcoplasmic/endoplasmic reticulum calcium ATPase 3
Biosynthesis of A2E, implicated in retinal degradation
Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Sarco/endoplasmic reticulum Ca2+ ATPases
pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response
Metabolism of water-soluble vitamins and cofactors
Phosphoinositide-metabolizing enzymes at the interface between membrane traffic and cell signalling
Adenosine 3'-phospho 5'-phosphosulfate transporter 1
Adenosine 3'-phospho 5'-phosphosulfate transporter 2
Altered aquaporin 9 expression and localization in human hepatocellular carcinoma
Organic cation transporter-like protein 2
Structural basis of hereditary coproporphyria
9Z,12Z,15Z,18Z-Tetracosatetraenoyl-CoA (TTA-CoA)
pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I
(S)-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid
ZnT-3, a putative transporter of zinc into synaptic vesicles
7Z,10Z,13Z,16Z,19Z-docosapentaenoyl-CoA (DPA-CoA)
9Z,12Z,15Z,18Z,21Z-tetracosapentaenoyl-CoA (TPA-CoA)
Performing in vitro sumoylation reactions using recombinant enzymes
7Z,10Z,13Z,16Z-docosatetraenoyl-CoA (DTA-CoA)
Cell signaling by receptor tyrosine kinases
8Z,11Z,14Z,17Z-Eicosatetraenoyl-CoA (ETA-CoA)
1-phosphatidyl-1D-myo-inositol 4-phosphates
1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
1-phosphatidyl-1D-myo-inositol 3-phosphate
Interleukin 2 high-affinity receptor expression requires two distinct binding proteins
1-phosphatidyl-1D-myo-inositol 4-phosphate
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate
Transition state model and mechanism of nucleophilic aromatic substitution reactions catalyzed by human glutathione S-transferase M1a-1a
1-phosphatidyl-1D-myo-inositol 5-phosphate
Molecular components of the mammalian circadian clock
The NRAMP family of metal-ion transporters
1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
Type II phosphoinositide 5-phosphatases have unique sensitivities towards fatty acid composition and head group phosphorylation
Role of Stargardt-3 macular dystrophy protein (ELOVL4) in the biosynthesis of very long chain fatty acids
Assignment of the gene for human arylsulfatase B, ARSB, to chromosome region 5p11----5qter
long-chain fatty acid anion [ChEBI:57560]
Structure of Rev-erbalpha bound to N-CoR reveals a unique mechanism of nuclear receptor-co-repressor interaction
Removal of DNA patch containing abasic residue
Immunolocalization of AQP9 in liver, epididymis, testis, spleen, and brain
SUMO protease SENP1 induces isomerization of the scissile peptide bond
Myotubularin lipid phosphatase binds the hVPS15/hVPS34 lipid kinase complex on endosomes
Temporal and spatial regulation of the phosphatidate phosphatases lipin 1 and 2
Formation of the ternary complex, and subsequently, the 43S complex
Molecular identification of mammalian phosphopentomutase and glucose-1,6-bisphosphate synthase, two members of the alpha-D-phosphohexomutase family
(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12R,14Z)-12-hydroxy-5,8,10,14-eicosatetraenoic acid
12(R)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
12(R)-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12R,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
12(S)-hydroxy-5,8,14(Z),10(E)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
12(S)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12S,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
(12S)-12-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
Signal transduction induced by opioids in immune cells: a review
Partial amino acid sequence of the glutamate dehydrogenase of human liver and a revision of the sequence of the bovine enzyme
Cathepsins B and D are dispensable for major histocompatibility complex class II-mediated antigen presentation
Synaptojanin 2, a novel Rac1 effector that regulates clathrin-mediated endocytosis
Chaperonin-mediated folding of vertebrate actin-related protein and gamma-tubulin
Control of cross-over by single-strand DNA resection.
Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3
Reconstitution of the B cell antigen receptor signaling components in COS cells
Fibroblast growth factor receptors: lessons from the genes
Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
Probable phospholipid-transporting ATPase IG
The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37)
Probable phospholipid-transporting ATPases
Probable phospholipid-transporting ATPase IA
Calcium-transporting ATPase type 2C member 1
Calcium-transporting ATPase type 2C member 2
Lysosomal cathepsin B plays an important role in antigen processing, while cathepsin D is involved in degradation of the invariant chain inovalbumin-immunized mice
Intracellular signaling by the neural cell adhesion molecule
Direct role of ChREBP.Mlx in regulating hepatic glucose-responsive genes.
Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
Beta glucuronidase deficiency: report of clinical, radiologic, and biochemical features of a new mucopolysaccharidosis
Mast cell signaling: the role of protein tyrosine kinase Syk, its activation and screening methods for new pathway participants
Purified human erythrocyte pyrroline-5-carboxylate reductase. Preferential oxidation of NADPH.
A lipid-anchored Grb2-binding protein that links FGF-receptor activation to the Ras/MAPK signaling pathway
A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD
AU-rich elements and the control of gene expression through regulated mRNA stability
Human plasma epidermal growth factor/beta-urogastrone is associated with blood platelets
Synthesis of PIPs at the plasma membrane
The nonsense-mediated decay RNA surveillance pathway
Mechanisms of COPII vesicle formation and protein sorting
AQP10 tetramer (name copied from entity in Homo sapiens)
Aquaporins that transport water across the plasma membrane.
AQP0 (MIP), AQP1, p-AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10, AQP11
Aquaporin-0, Aquaporin-1, Phospho-Aquaporin-2, Aquaporin-3, Aquaporin-4, Aquaporin-5, Aquaporin-7, Aquaporin-8, Aquaporin-9, Aquaporin-10, Aquaporin-11
AQP3 tetramer (name copied from entity in Homo sapiens)
AQP7 tetramer (name copied from entity in Homo sapiens)
AQP9 tetramer (name copied from entity in Homo sapiens)
MTABC3 dimer (name copied from entity in Homo sapiens)
ABC7 dimer (name copied from entity in Homo sapiens)
The human kinesin Kif18A is a motile microtubule depolymerase essential for chromosome congression
The Src, Syk, and Tec family kinases: distinct types of molecular switches
Molecular cloning of AMP deaminase isoform L. Sequence and bacterial expression of human AMPD2 cDNA
Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
1-Hydroxypropane-1,2,3-tricarboxylic acid
Identification of cell cycle-regulated phosphorylation sites on nuclear lamin C
In vitro disassembly of the nuclear lamina and M phase-specific phosphorylation of lamins by cdc2 kinase
Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
Mathematical and computational models of oxidative and nitrosative stress
(S)-alpha-amino-beta-phenylpropionic acid
RNA Polymerase II Pre-transcription Events
Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity.
Mitochondrial iron-sulfur cluster biogenesis
RasGRP links T-cell receptor signaling to Ras
Identification of natural resistance-associated macrophage protein in peripheral blood lymphocytes
Identification of distinct classes and functional domains of Wnts through expression of wild-type and chimeric proteins in Xenopus embryos
Cloning, sequencing, purification, and Gq-dependent activation of phospholipase C-beta 3
Regulation of Endoplasmic Reticulum Stress-induced Cell Death by ATF4 in Neuroectodermal Tumor Cells
Biotinidase deficiency: "if you have to have an inherited metabolic disease, this is the one to have"
Purification from placenta, amino acid sequence, structure comparisons and cDNA cloning of human glutaredoxin
Specificity of the deoxyhypusine hydroxylase-eukaryotic translation initiation factor (eIF5A) interaction: identification of amino acid residues of the enzyme required for binding of its substrate, deoxyhypusine-containing eIF5A
Messenger RNA decay in mammalian cells: the exonuclease perspective
2'-Deoxyinosine 5'-phosphate [ChEBI:28806]
Cloning, expression and characterization of the pig liver GDP-mannose pyrophosphorylase. Evidence that GDP-mannose and GDP-Glc pyrophosphorylases are different proteins
The protein deficient in Lowe syndrome is a phosphatidylinositol-4,5-bisphosphate 5-phosphatase
Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.
STING is a direct innate immune sensor of cyclic di-GMP
Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
WW domain-containing proteins, WWOX and YAP, compete for interaction with ErbB-4 and modulate its transcriptional function
ATPase switches controlling DNA replication initiation.
Transport of vitamins, nucleosides, and related molecules
NaPO(4) cotransport type III (PiT1) expression in human embryonic kidney cells and regulation by PTH
Emerging roles for E2F: beyond the G1/S transition and DNA replication.
Access of soluble antigens to the endoplasmic reticulum can explain cross-presentation by dendritic cells
Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products
Aminoacyl tRNA synthetases and their connections to disease
Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways
A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis
Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat
Mechanism of biotin responsiveness in biotin-responsive multiple carboxylase deficiency
Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
Signal transduction by VEGF receptors in regulation of angiogenesis and lymphangiogenesis
Mechanisms of disease: molecular and metabolic mechanisms of insulin resistance and beta-cell failure in type 2 diabetes
Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
Tyrosine-phosphorylated forms of Ig beta, CD22, TCR zeta and HOSS are major ligands for tandem SH2 domains of Syk
Glycoprotein folding, quality control and ER-associated degradation
Acquired and inherited disorders of cobalamin and folate in children
Neurotrophin-regulated signalling pathways
Philos Trans R Soc Lond B Biol Sci 361:1545-64
Porphyrin accumulation in mitochondria is mediated by 2-oxoglutarate carrier
Novel aspects of tetramer assembly and N-terminal domain structure and function are revealed by recombinant expression of human AMP deaminase isoforms
Mismatch repair deficiency associated with overexpression of the MSH3 gene
Proc. Natl. Acad. Sci. U.S.A. 95:8568-73
Purification, molecular cloning, and sequencing of phospholipase C-beta 4
EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length
The 40-kDa subunit of DNA fragmentation factor induces DNA fragmentation and chromatin condensation during apoptosis
Pathways of DNA double-strand break repair during the mammalian cell cycle.
Properties and functions of diacylglycerol kinases
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
Purification of the serine palmitoyltransferase complex responsible for sphingoid base synthesis by using affinity peptide chromatography techniques
CDC6 association with the ORC:origin complex
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
Human cytosolic asparaginyl-tRNA synthetase: cDNA sequence, functional expression in Escherichia coli and characterization as human autoantigen
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Mutations and polymorphisms in GUSB gene in mucopolysaccharidosis VII (Sly Syndrome)
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The prosthetic group of crystalline d-glyceraldehyde-3-phosphate dehydrogenase
The reaction between the superoxide anion radical and cytochrome c
Endogenous synthesis of coenzyme Q in eukaryotes
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Kinetic evaluation of human cloned coproporphyrinogen oxidase using a ring isomer of the natural substrate
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
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The vitelliform macular dystrophy protein defines a new family of chloride channels
Proc. Natl. Acad. Sci. U.S.A. 99:4008-13
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Apical GLUT2: a major pathway of intestinal sugar absorption
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Benzo(a)pyrene-7,8-diol-glutathione conjugate
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Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
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Endoplasmic reticulum (ER) chaperone regulation and survival of cells compensating for deficiency in the ER stress response kinase, PERK
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Evidence that the head of kinesin is sufficient for force generation and motility in vitro
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Hyperhomocysteinemia due to methionine synthase deficiency, cblG: structure of the MTR gene, genotype diversity, and recognition of a common mutation, P1173L
Proximal events in Wnt signal transduction
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Mismatch recognition and DNA-dependent stimulation of the ATPase activity of hMutSalpha is abolished by a single mutation in the hMSH6 subunit
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Principles of bioactive lipid signalling: lessons from sphingolipids
Coregulation of estrogen receptor by ERBB4/HER4 establishes a growth-promoting autocrine signal in breast tumor cells
The TREM receptor family and signal integration
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Membrane lipids: where they are and how they behave
Membrane recognition by phospholipid-binding domains
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Atomic structure of GTP cyclohydrolase I
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The secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is made up of distinct organelles, including the endoplasmic reticulum (ER), Golgi complex, plasma membrane, and tubulovesicular transport intermediates. These organelles mediate intracellular membrane transport between themselves and the cell surface. Membrane traffic within this system flows along highly organized directional routes. Secretory cargo is synthesized and assembled in the ER and then transported to the Golgi complex for further processing and maturation. Upon arrival at the trans Golgi network (TGN), the cargo is sorted and packaged into post-Golgi carriers that move through the cytoplasm to fuse with the cell surface. This directional membrane flow is balanced by retrieval pathways that bring membrane and selected proteins back to the compartment of origin.
Secretory transport depends on membrane-bounded carriers to move protein and lipid between intracellular compartments. The COPI coat has a central role in this process, creating a sorting domain on the membrane into which cargo proteins, destined to return to the endoplasmic reticulum (ER), concentrate. The membrane domain deforms into a coated bud, pinches off the membrane as a coated carrier, and then uncoats. Successful operation of the COPI coat system is necessary for selective retrieval of protein and lipid components back to the ER.
The anterograde membrane flow from the ER to the Golgi is compensated for by a retrograde pathway. This pathway's functions include the recycling of membrane and proteins to the ER.
Ultimately the hydrolysis of Arf1-bound GTP, induced by the recruited ArfGAP, allows the inactive Arf1-GDP to diffuse away from the membrane, initiating disassembly of the lattice from the vesicle (Lippincott-Schwartz and Liu 2006).
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Together, the complex of coatomer, Arf1, and ArfGAP assembles into a lattice that concentrates cargo proteins and deforms the membrane. Eventually this membrane pocket forms into a bud that pinches off the membrane, and is released into the cytoplasm (Lippincott-Schwartz and Liu 2006).
All of the key components and regulators of the COPI coat (GBF1, Arf1, ArfGAP1 and coatomer) cycle on and off the Golgi membrane. This cycle is required for vesicle formation, but is uncoupled from the actual vesicle release. Continuous membrane binding and release of these molecules enables the COPI lattice to be dynamically modulated. Once the vesicle is released from the Golgi apparatus, this lattice is completely disassociated from the vesicle.
The hydrolysis of Arf1-bound GTP is induced by the recruited ArfGAP.
Inactive Arf1-GDP then diffuses away from the membrane, initiating the disassembly of the lattice.
Peroxiredoxin 1 (PRDX1), PRDX2, and PRDX5 in the cytosol reduce hydrogen peroxide (H2O2) with thioredoxin yielding oxidized thioredoxin and water (Yamashita et al. 1999, Lee et al. 2007, Nagy et al. 2011).
Peroxiredoxin 5 (PRDX5) very efficiently reduces peroxynitrite using thioredoxin to yield nitrite (NO2-), water, and oxidized thioredoxin (Dubuisson et al. 2004). The N-terminal cysteine (Cys 47) of PRDX5 attacks the O-O peroxide bond of peroxynitrite.
Reactive oxygen species such as superoxide (O2.-), peroxides (ROOR), singlet oxygen, peroxynitrite (ONOO-), and hydroxyl radical (OH.) are generated by cellular processes such as respiration (reviewed in Murphy 2009, Brand 2010) and redox enzymes and are required for signaling yet they are damaging due to their high reactivity (reviewed in Imlay 2008, Buettner 2011, Kavdia 2011, Birben et al. 2012, Ray et al. 2012). Aerobic cells have defenses that detoxify reactive oxygen species by converting them to less reactive products. Superoxide dismutases convert superoxide to hydrogen peroxide and oxygen (reviewed in Fukai and Ushio-Fukai 2011). Catalase and peroxidases then convert hydrogen peroxide to water. Humans contain 3 superoxide dismutases: SOD1 is located in the cytosol and mitochondrial intermembrane space, SOD2 is located in the mitochondrial matrix, and SOD3 is located in the extracellular region. Superoxide, a negative ion, is unable to easily cross membranes and tends to remain in the compartment where it was produced. Hydrogen peroxide, one of the products of superoxide dismutase, is able to diffuse across membranes and pass through aquaporin channels. In most cells the primary source of hydrogen peroxide is mitochondria and, once in the cytosol, hydrogen peroxide serves as a signaling molecule to regulate redox-sensitive proteins such as transcription factors, kinases, phosphatases, ion channels, and others (reviewed in Veal and Day 2011, Ray et al. 2012). Hydrogen peroxide is decomposed to water by catalase, decomposed to water plus oxidized thioredoxin by peroxiredoxins, and decomposed to water plus oxidized glutathione by glutathione peroxidases (Presnell et al. 2013).
Cells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissues to modulate molecular processes in response to such external stresses is essential to the maintenance of tissue homeostasis (Kultz 2005).
In models of COPI coat assembly and disassembly, after GBF1 activates Arf1 on membranes, the active form of Arf1 recruits coatomer complexes from the cytoplasm.
Once both coatomer and the active form of Arf1 have been recruited to the Golgi membrane surface, ArfGAP joins the complex.
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Glutathione-S-transferase P1 is a critical regulator of Cdk5 kinase activity
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Telomeres shorten during ageing of human fibroblasts
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Transcriptional regulation by calcium, calcineurin, and NFAT
Rad51 recombinase and recombination mediators.
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Defective MMACHC causes methylmalonic aciduria and homocystinuria type cblC
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Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay
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Two novel rat liver membrane proteins that bind advanced glycosylation endproducts: relationship to macrophage receptor for glucose-modified proteins
Renal physiology of SLC26 anion exchangers
Human alanyl-tRNA synthetase: conservation in evolution of catalytic core and microhelix recognition
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Human Mcm proteins at a replication origin during the G1 to S phase transition.
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The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs
Frequent deletions at Xq28 indicate genetic heterogeneity in Hunter syndrome
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Sequence of the human iduronate 2-sulfatase (IDS) gene
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isovaleryl-CoA, a-methylbutyryl-CoA, isobutyryl-CoA
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Precise binding of single-stranded DNA termini by human RAD52 protein.
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Human frataxin is an allosteric switch that activates the Fe-S cluster biosynthetic complex
The canonical retinoid cycle in rods (twilight vision)
A natural ErbB4 isoform that does not activate phosphoinositide 3-kinase mediates proliferation but not survival or chemotaxis
Which DNA polymerases are used for DNA-repair in eukaryotes?
a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
Functions and regulatory mechanisms of Gq-signaling pathways
Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization
Identification of mammalian microRNA host genes and transcription units
The role of Akt in the signaling pathway of the glycoprotein Ib-IX induced platelet activation
Histidine-rich glycoprotein is present in human platelets and is released following thrombin stimulation
Characterization of phospholipase D activity in bovine photoreceptor membranes
Regulation of mammalian liver methionine adenosyltransferase
Cellular glutathione peroxidase as a predominant scavenger of hydroperoxyeicosatetraenoic acids in rabbit alveolar macrophages
A novel cardiolipin-remodeling pathway revealed by a gene encoding an endoplasmic reticulum-associated acyl-CoA:lysocardiolipin acyltransferase (ALCAT1) in mouse
Identification, cloning, expression, and purification of three novel human calcium-independent phospholipase A2 family members possessing triacylglycerol lipase and acylglycerol transacylase activities
Elongation factor 1 beta gamma from Artemia. Purification and properties of its subunits.
Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription
Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis.
Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent
CD28-mediated co-stimulation: a quantitative support for TCR signalling
Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors
Cloning and characterization of a mammalian fatty acyl-CoA elongase as a lipogenic enzyme regulated by SREBPs
BRCA2-dependent and independent formation of RAD51 nuclear foci.
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Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
2-Phospho-D-glycerate <=> 3-Phospho-D-glycerate
malate [mitochondrial matrix] + alpha-ketoglutarate [cytosol] <=> malate [cytosol] + alpha-ketoglutarate [mitochondrial matrix]
Exchange of malate and alpha-ketoglutarate (2-oxoglutarate) across the inner mitochondrial membrane
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT1]
Separate SCF(CDC4) recognition elements target Cdc6 for proteolysis in S phase and mitosis.
Glyceraldehyde 3 phosphate, NAD+, and orthophosphate react to form 1,3 bisphosphoglycerate and NADH + H+
D-glyceraldehyde 3-phosphate + orthophosphate + NAD+ <=> 1,3-bisphospho-D-glycerate + NADH + H+
1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases
phosphoenolpyruvate + ADP => pyruvate + ATP
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT2]
3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
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Inositol polyphosphates: a new frontier for regulating gene expression
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Release of platelet fibronectin (cold-insoluble globulin) from alpha granules induced by thrombin or collagen; lack of requirement for plasma fibronectin in ADP-induced platelet aggregation
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D-fructose 1-phosphate <=> D-glyceraldehyde + dihydroxyacetone phosphate
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
Mast cell signal transduction from the high-affinity IgE receptor
1,3-bisphospho-D-glycerate + NADH + H+ <=> D-glyceraldehyde 3-phosphate + Orthophosphate + NAD+
D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate <=> D-fructose 1,6-bisphosphate
D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
alpha-D-Glucose 6-phosphate <=> D-Glucose 1-phosphate
D-Glucose 1-phosphate <=> alpha-D-Glucose 6-phosphate
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Intraphagosomal pH is lowered to 5 by V-ATPase
P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane
P-type ATPase type IV subfamily transporters may mediate phospholipid transfer
Aminophospholipids are transported from in the internal to the external side of the plasma membrane
P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane
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Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes
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Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.
dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
AKT1 E17K mutant translocates to the nucleus
AKT inhibitors block AKT membrane recruitment
Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
D-fructose 1,6-bisphosphate <=> dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate
phenylpyruvate + NADH + H+ => phenyllactate + NAD+
guanylyl-(3'->5')-3'-guanylic acid, cyclic 3'->5'''-nucleotide
cyclic-bis(3',5')diguanylic acid
cyclic-bis(3'->5') dimeric GMP
bis-(3'-5')-cyclic dimeric guanosine monophosphate
Guanosine 3',5'-cyclic monophosphate
bis(3',5')-cyclic diguanylic acid
HSP90 is inactivated by binding to benzaquinoid ansamycins
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ZnT3 transports zinc into synaptic vesicles
ZnT2 facilitates zinc vesicular sequestration
SLC35B2,3 transport cytosolic PAPS to Golgi lumen
Human thymidylate kinase. Purification, characterization, and kinetic behavior of the thymidylate kinase derived from chronic myelocytic leukemia
AT1 transports acetyl-CoA into the Golgi lumen
ORCTL2 mediates the transport of chloroquine and quinidine with efflux of protons
ZnT8 transports zinc into the secretory vesicles of pancreatic beta cells specifically
SLC30A8 transports Zn2+ from cytosol to secretory granule
Aquaporins passively transport glycerol into cells
Aquaporins passively transport water out of cells
Aquaporins passively transport water into cells
SLC35C1 mediates the transport of UDP-fucose into the Golgi lumen
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Dynamics of transitional endoplasmic reticulum sites in vertebrate cells
Mycobacterium tuberculosis and the intimate discourse of a chronic infection
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Aquaporins passively transport glycerol out of cells
Aquaporins passively transport urea out of cells
Aquaporins passively transport urea into cells
Aquaporin-7 passively transports glycerol out of cell
Aquaporin-3 passively transports water out of cell
Acidification of Tf:TfR1 containing endosome
Aquaporin-9 passively transports glycerol into cell
Sequestration of Ca2+ to intracellular stores
ATP2A1-3 transport cytosolic Ca2+ to ER lumen
ATP2A1-3 transport cytosolic Ca2+ to dense tubular network lumen
Sequestration of Ca2+ to dense tubular network lumen
Calcium is sequestered to the golgi by secretory pathway calcium-ATPases (SPCAs)
ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen
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Isolation and characterization of mutations in the human holocarboxylase synthetase cDNA
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c-Kit--a hematopoietic cell essential receptor tyrosine kinase
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mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
ditrans, polycis-polyprenol pyrophosphate
mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
guanosine 5'-(3-(alpha-D-mannopyranosyl) dihydrogen diphosphate)
Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Phosphoinositides as regulators of membrane trafficking in health and disease
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Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
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The structure and function of G-protein-coupled receptors
The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
From structure to disease: the evolving tale of aquaporin biology
Signal transduction by immunoglobulin is mediated through Ig alpha and Ig beta
Mechanisms of glycerophospholipid homeostasis in mammalian cells
The transport of pyruvate in rat liver mitochondria
Sanfilippo syndrome type C: deficiency of acetyl-CoA:alpha-glucosaminide N-acetyltransferase in skin fibroblasts
Dissecting and manipulating the pathway for glycosylphosphatidylinositol-anchor biosynthesis
Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture
Expression of CD83 is regulated by HuR via a novel cis-active coding region RNA element
Purification and characterization of membrane-bound phospholipase C specific for phosphoinositides from human platelets
Phosphoinositide phosphatases in a network of signalling reactions
G-strand Chromosome end with two additional single strand repeats - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTATTAGGGTTA - 3' (in human)
A novel SH2-containing phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase (SHIP2) is constitutively tyrosine phosphorylated and associated with src homologous and collagen gene (SHC) in chronic myelogenous leukemia progenitor cells
A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans
Aquaporin-1, nothing but a water channel
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation
(S)-alpha-Amino-1H-imidazole-4-propionic acid
Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F.
Differential expression of aquaporin 7 in adipose tissue of lean and obese high fat consumers
Purification of human platelet-derived growth factor
The role of a group III AQP, AQP11 in intracellular organelle homeostasis
Mechanism of tyrosine phosphorylation and activation of phospholipase C-gamma 1. Tyrosine 783 phosphorylation is not sufficient for lipase activation
TRP channels: sensors and transducers of gasotransmitter signals
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
A novel calcium-independent phospholipase A2, cPLA2-gamma, that is prenylated and contains homology to cPLA2
Nucleotide-promoted release of hMutSalpha from heteroduplex DNA is consistent with an ATP-dependent translocation mechanism
Aquaporins: translating bench research to human disease
Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin B(12)
Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA.
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Glycosylation-induced conformational modification positively regulates receptor-receptor association: a study with an aberrant epidermal growth factor receptor (EGFRvIII/DeltaEGFR) expressed in cancer cells
Intracellular transport and kinesin superfamily proteins, KIFs: structure, function, and dynamics
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
Purification, sequencing, and molecular identification of a mammalian PP-InsP5 kinase that is activated when cells are exposed to hyperosmotic stress
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Calcium signalling: past, present and future
Rich tapestry of G protein-coupled receptor signaling and regulatory mechanisms
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate [ChEBI:62919]
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate
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Gastrin-CREB signalling pathway via PKC and MAPK
A three-step purification of manganese superoxide dismutase from human liver on both large and small scales
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Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
An isoform of hPANK2, deficient in pantothenate kinase-associated neurodegeneration, localizes to mitochondria
BMAL1:CLOCK,NPAS2 activates circadian gene expression
Human mismatch repair: reconstitution of a nick-directed bidirectional reaction
Kit- and Fc epsilonRI-induced differential phosphorylation of the transmembrane adaptor molecule NTAL/LAB/LAT2 allows flexibility in its scaffolding function in mast cells
Association of Fyn and Lyn with the proline-rich domain of glycoprotein VI regulates intracellular signaling
Elevation of cellular NAD levels by nicotinic acid and involvement of nicotinic acid phosphoribosyltransferase in human cells
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
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Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study
Human hexokinase II gene: exon-intron organization, mutation screening in NIDDM, and its relationship to muscle hexokinase activity
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Expression of human thymidylate synthase in Escherichia coli
Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins
7,8-dihydro-7-hydroxy-8S-glutathionylbenzo[a]pyrene [ChEBI:34479]
Resolution of AP sites via the multiple-nucleotide patch replacement pathway
Protein kinase C alpha activates RAF-1 by direct phosphorylation
Phospholipid meets all-trans-retinal: the making of RPE bisretinoids
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Critical role for the docking-protein FRS2 alpha in FGF receptor-mediated signal transduction pathways
Enzymatic characterization of the individual mammalian primase subunits reveals a biphasic mechanism for initiation of DNA replication.
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The primary structure of mitochondrial aspartate aminotransferase from human heart
Specificity of the myotubularin family of phosphatidylinositol-3-phosphatase is determined by the PH/GRAM domain
hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA
Phospholipases and phagocytosis: the role of phospholipid-derived second messengers in phagocytosis
The nucleoside diphosphate kinase D (NM23-H4) binds the inner mitochondrial membrane with high affinity to cardiolipin and couples nucleotide transfer with respiration
The sulfur-containing amino acids: an overview
Localization of platelet osteonectin at the internal face of the alpha-granule membranes in platelets and megakaryocytes
Advances in the understanding of cobalamin assimilation and metabolism
Signalling via integrins: implications for cell survival and anticancer strategies
Receptor-mediated endocytosis: the intracellular journey of transferrin and its receptor
Intracellular calcium release from human platelets: different messengers for multiple stores
NUDT16 and ITPA play a dual protective role in maintaining chromosome stability and cell growth by eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals
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Overexpression of the normal phosphoribosylpyrophosphate synthetase 1 isoform undelies catalytic superactivity of human phosphoribosylpyrophosphate synthetase
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LMBRD1 transports lysosomal Cbl to cytosol
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pantothenate + ATP => phosphopanthothenate + ADP
Pantothenate is phosphorylated [PANK1;3;4]
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Phosphorylation of dephospho-CoA to produce CoA
COASY transfers an adenylyl group from ATP to PPANT
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Phosphopantothenoylcysteine is decarboxylated
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Condensation of phosphopantothenate with cysteine
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addition of diphosphate (PP) to ribose 5-phosphate to form 5'-Phospho-alpha-D-ribose 1-diphosphate (PRPP)
D-ribose 5-phosphate + ATP => 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + adenosine 5'-monophosphate
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
xylulose 5-phosphate <=> D-ribulose 5-phosphate
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D-ribulose 5-phosphate <=> xylulose 5-phosphate
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D-glyceraldehyde 3-phosphate + sedoheptulose 7-phosphate<=> xylulose 5-phosphate+ribose 5-phosphate
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ribose 5-phosphate + xylulose 5-phosphate <=> sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate
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D-glyceraldehyde 3-phosphate + D-fructose 6-phosphate <=> xylulose 5-phosphate + D-erythrose 4-phosphate
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xylulose 5-phosphate + D-erythrose 4-phosphate <=> D-glyceraldehyde 3-phosphate + D-fructose 6-phosphate
ribose 5-phosphate <=> D-ribulose 5-phosphate
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D-ribulose 5-phosphate <=> ribose 5-phosphate
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Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues suggesting a site-specific role in the inflammatory response
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A phosphoribosyl group is added to nicotinate to form nicotinate mononucleotide (NaMN)
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NFS1 transfers sulfur from cysteine onto MOCS3
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5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine
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PI(4,5)P2 is hydrolysed to I(1,4,5)P3 and DAG by cytosolic PLC[2] at the plasma membrane
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Defective HLCS does not biotinylate apo-CBXs
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Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
The helicase DDX41 recognizes the bacterial secondary messengers cyclic di-GMP and cyclic di-AMP to activate a type I interferon immune response
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Conversion of cytosolic THF to THF-polyglutamate
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Tetrahydrofolate polyglutamate (THF polyglutamate) + serine <=> 5,10-methyleneTHF polyglutamate + glycine
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Conversion of mitochondrial THF to THF-polyglutamate
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Oxidative stress and antioxidant defense
Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis
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Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
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Epidermal growth factor receptor: elements of intracellular communication
Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer curvature
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Epidermal growth factor receptors with tyrosine kinase domain mutations exhibit reduced Cbl association, poor ubiquitylation, and down-regulation but are efficiently internalized
Interaction network of human aminoacyl-tRNA synthetases and subunits of elongation factor 1 complex
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Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1
Mucopolysaccharidosis IV A: molecular cloning of the human N-acetylgalactosamine-6-sulfatase gene (GALNS) and analysis of the 5'-flanking region
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Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
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1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62923]
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The visual cycle of the cone photoreceptors of the retina
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Non-vesicular lipid transport by lipid-transfer proteins and beyond
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Fate of linoleic, arachidonic, and docosa-7,10,13,16-tetraenoic acids in rat testicles
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Structural and mechanistic aspects of flavoproteins: electron transfer through the nitric oxide synthase flavoprotein domain
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Integrated signalling pathways for mast-cell activation
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Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation
Localization and identification of Ca2+ATPases in highly purified human platelet plasma and intracellular membranes. Evidence that the monoclonal antibody PL/IM 430 recognizes the SERCA 3 Ca2+ATPase in human platelets
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The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)
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Mechanisms involved in the intestinal digestion and absorption of dietary vitamin A
Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases
Birth Defects Res. C Embryo Today 90:243-56
The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications
Neuronal phosphoproteins. Mediators of signal transduction
Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants
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Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease G
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History of the events leading to the formulation of the apoptosis concept
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Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4.
A novel protein tyrosine phosphatase gene is mutated in progressive myoclonus epilepsy of the Lafora type (EPM2)
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Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
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Differential processing of human and rat E1 alpha precursors of the branched-chain alpha-keto acid dehydrogenase complex caused by an N-terminal proline in the rat sequence
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Hereditary juvenile cobalamin deficiency caused by mutations in the intrinsic factor gene
Proc. Natl. Acad. Sci. U.S.A. 102:4130-3
NGF signalling via TRKA from the plasma membrane
PTG depletion removes Lafora bodies and rescues the fatal epilepsy of Lafora disease
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SLC4 base (HCO3 -, CO3 2-) transporters: classification, function, structure, genetic diseases, and knockout models
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Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency
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Metal transporters in intestine and brain: their involvement in metal-associated neurotoxicities
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Expression and characterization of human mitochondrial ferredoxin reductase in Escherichia coli
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Isolation of a human cDNA for heme A:farnesyltransferase by functional complementation of a yeast cox10 mutant
Phosphoglycerate mutase BB isoenzyme deficiency in a patient with non-spherocytic anemia: familial and metabolic studies
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The control of mammalian DNA replication: a brief history of space and timing.
GPD1L links redox state to cardiac excitability by PKC-dependent phosphorylation of the sodium channel SCN5A
Am J Physiol Heart Circ Physiol 297:H1446-52
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Role of the Zn(2+) motif of E1 in SUMO adenylation
Hot-spot mutations in p110alpha of phosphatidylinositol 3-kinase (pI3K): differential interactions with the regulatory subunit p85 and with RAS
The Bcl2 family: regulators of the cellular life-or-death switch
Catalytic pathway of manganese superoxide dismutase by direct observation of superoxide
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Kinetics and equilibria of pyrimidine nucleoside monophosphate kinase from human erythrocytes
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Allelism, non-allelism, and genetic compounds among the mucopolysaccharidoses
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Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa
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SUMO-specific proteases: a twist in the tail
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
Import of palmitoyl-CoA into the mitochondrial matrix
Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association
Cloning of human agmatinase. An alternate path for polyamine synthesis induced in liver by hepatitis B virus
Am J Physiol Gastrointest Liver Physiol 282:G375-81
Inositol hexakisphosphate kinase products contain diphosphate and triphosphate groups
Negative regulation of mast cell signaling and function by the adaptor LAB/NTAL
Superoxide dismutases: role in redox signaling, vascular function, and diseases
Human mitochondrial pyrophosphatase: cDNA cloning and analysis of the gene in patients with mtDNA depletion syndromes
Positive and negative regulation of FcepsilonRI-mediated signaling by the adaptor protein LAB/NTAL
Rad52 and Ku bind to different DNA structures produced early in double-strand break repair.
Analysis and update of the human solute carrier (SLC) gene superfamily
Involvement of the ERK signaling cascade in protein kinase C-mediated cell cycle arrest in intestinal epithelial cells
First-in-man clinical trial of the oral pan-AKT inhibitor MK-2206 in patients with advanced solid tumors
PIP kinase Igamma is the major PI(4,5)P(2) synthesizing enzyme at the synapse
Amino acid synthesis and interconversion (transamination)
Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
Mitochondrial metabolic states regulate nitric oxide and hydrogen peroxide diffusion to the cytosol
PTEN loss in the continuum of common cancers, rare syndromes and mouse models
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Mammalian ABC transporters in health and disease
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Identification of nuclear beta II protein kinase C as a mitotic lamin kinase
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Synthesis of substrates in N-glycan biosythesis
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Membrane-bound enzymes of cholesterol synthesis from lanosterol
Familial deficiency of glutathione reductase in human blood cells
Cytosolic sulfonation of small molecules
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A novel B lymphocyte-associated adaptor protein, Bam32, regulates antigen receptor signaling downstream of phosphatidylinositol 3-kinase
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Molecular identity and cellular distribution of advanced glycation endproduct receptors: relationship of p60 to OST-48 and p90 to 80K-H membrane proteins
Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
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Ca2+-activated ATPase in microsomes from human liver
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Asparaginyl endopeptidase: case history of a class II MHC compartment protease
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STIM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1
A cytoplasmic chaperonin that catalyzes beta-actin folding
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Mechanisms of MHC class I-restricted antigen processing and cross-presentation
Lysosomes in iron metabolism, ageing and apoptosis
Cross-presentation: underlying mechanisms and role in immune surveillance
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Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family
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The SLC20 family of proteins: dual functions as sodium-phosphate cotransporters and viral receptors
Molecular physiology and pathology of the nucleotide sugar transporter family (SLC35)
Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer
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Stoichiometric and reversible phosphorylation of a 46-kDa protein in human platelets in response to cGMP- and cAMP-elevating vasodilators
Assembly of the human origin recognition complex.
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Human cataract lens membrane at subnanometer resolution
Antigen processing and presentation by the class I major histocompatibility complex
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Purification of superoxide dismutases from human placenta using immunoadsorbent columns
Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis
Catalytic cycle of human glutathione reductase near 1 A resolution
Endoplasmic reticulum stress induction of insulin-like growth factor-binding protein-1 involves ATF4
Obesity, leptin, and Alzheimer's disease
Pannexin-1 mediates large pore formation and interleukin-1beta release by the ATP-gated P2X7 receptor
Targeting death and decoy receptors of the tumour-necrosis factor superfamily
MutSbeta exceeds MutSalpha in dinucleotide loop repair
Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113593
The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase
Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
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hMutSbeta, a heterodimer of hMSH2 and hMSH3, binds to insertion/deletion loops in DNA
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Discovery of a lysophospholipid acyltransferase family essential for membrane asymmetry and diversity
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation
Expression of isoforms of the human receptor tyrosine kinase c-kit in leukemic cell lines and acute myeloid leukemia
Crystallization and properties of human liver ornithine aminotransferase
Receptor specificity of the fibroblast growth factor family. The complete mammalian FGF family.
Superoxide dismutase in redox biology: the roles of superoxide and hydrogen peroxide
Cleavage of 3-methyladenine by MPG glycosylase
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
hNTH1 glycosylase mediated recognition and binding of dihydrouracil
hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
hNTH1 glycosylase mediated recognition and binding of thymine glycol
Cleavage of ethenoadenine by MPG glycosylase
Cleavage of hypoxanthine by MPG glycosylase
Cleavage of 8-oxo guanine by hOGG1 glycosylase
High mobility group proteins stimulate DNA cleavage by apoptotic endonuclease DFF40/CAD due to HMG-box interactions with DNA
(5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate [ChEBI:246]
Cleavage of formamidopyrimidine by hOGG1 glycosylase
Cleavage 8-oxo guanine by MYH glycosylase
hOGG1 glycosylase mediated recognition and binding of a formamidopyrimidine
MYH glycosylase mediated recognition and binding of an adenine opposite to an 8-oxo guanine
hOGG1 glycosylase mediated recognition and binding of an 8-oxo guanine opposite to a cytosine
MPG glycosylase mediated recognition and binding of ethenoadenine
MPG glycosylase mediated recognition and binding of hypoxanthine
Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
MPG glycosylase mediated recognition and binding of 3-methyladenine
Cytosolic sensors of pathogen-associated DNA
SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
Cetuximab monotherapy and cetuximab plus irinotecan in irinotecan-refractory metastatic colorectal cancer
Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7
5' to 3' exoribonuclease hydrolyzes decapped mRNA
Ligation of newly synthesized repair patch to incised DNA in TC-NER
Resumption of transcription after TC-NER
MSH2:MSH6 binds 1 base mismatch or 1-2 base insertion/deletion loop
MutSalpha binds mismatch or 1-2 base insertion/deletion loop
MSH2:MSH6 recruits MLH1:PMS2 to mismatch and interacts with PCNA
MutSalpha binds ATP and recruits MutLalpha to mismatch
MLH1:PMS2 makes single strand incision near 1-2 base mismatch
EXO1 interacts with MSH2:MSH6 (MutSalpha) and MLH1:PMS2 (MutLalpha)
DNA ligase I ligates single stranded nick in double stranded DNA
MLH1:PMS2 makes single strand incision near insertion/deletion loop of 2 bases or more
EXO1 interacts with MSH2:MSH3 (MutSbeta) and MLH1:PMS2 (MutLalpha)
Structural and biochemical properties of cloned and expressed human and rat steroid 5 alpha-reductases
Mechanistic insights into the superoxide-cytochrome c reaction by lysine surface scanning
Ligand-regulated association of ErbB-4 to the transcriptional co-activator YAP65 controls transcription at the nuclear level
Cleavage of cytosine glycol by hNTH1 glycosylase
Cleavage of dihydrouracil by hNTH1 glycosylase
Association of RAD51 with the resected ends of the DNA double-strand break
Ligation of DNA and formation of Holliday structures following repair synthesis
Cleavage of formamidopyrimidine by hNTH1 glycosylase
Formation of active Pol II complex with lesioned DNA template
The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids
RNA Pol II is blocked by the lesion leading to reduced transcription
Formation of ERCC1-XPF heterodimeric complex
Ligation of newly synthesized repair patch to incised DNA in GG-NER
Cleavage of thymine glycol by hNTH1 glycosylase
Phosphoinositides in constitutive membrane traffic
Detection of damage during initiation of DNA synthesis in S-phase
DNA polymerase epsilon binds at the origin
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin
The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin
DNA polymerase alpha:primase binds at the origin
1D-myo-Inositol 1,4-bisphosphate [ChEBI:812]
Nerve growth factor signaling, neuroprotection, and neural repair
Dissociation of L13a from the 60s ribosomal subunit
Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
Kinesins move along microtubules consuming ATP
F-actin capping protein is a heterodimer
Release of 78 kDa glucose-regulated protein
Release of (inferred) platelet cytosolic components
The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway
Novel molecular defects of the delta-aminolevulinate dehydratase gene in a patient with inherited acute hepatic porphyria
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere
Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere
RFC binding displaces Pol Alpha on the C-strand of the telomere
SPO11 hydrolyzes DNA forming double-strand breaks
RFC dissociates after sliding clamp formation on the C-strand of the telomere
1D-myo-Inositol 1,3,4,5-tetrakisphosphate [ChEBI:808]
D-myo-Inositol 1,3,4,5-tetrakisphosphate
Mouse, but not Human STING, Binds and Signals in Response to the Vascular Disrupting Agent 5,6-Dimethylxanthenone-4-Acetic Acid
RFC dissociates after sliding clamp formation
1,2-diacyl-glycerol 3-phosphate + H2O => 1,2-diacyl-glycerol + orthophosphate
LPIN catalyzes conversion of phosphatidic acid to diacylglycerol
The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere
Mcm4,6,7 trimer forms and associates with the replication fork
Rearrangement and mobilization of Mcm2-7
Ubiquitinated Cdc6 is degraded by the proteasome
Loading of PCNA - Sliding Clamp Formation
Ubiquitinated Orc1 is degraded by the proteasome
Phosphorylated Orc1 is ubiquitinated while still associated with chromatin
Phosphorylated Cdc6 is exported from the nucleus
ChEBI:16723 4-methylthio-2-oxobutanoate (1-)
Clinical issues and frequent questions about biotinidase deficiency
Human Rad51 protein can form homologous joints in the absence of net strand exchange.
(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylate [ChEBI:151]
Post-translational modification: synthesis of GPI-anchored proteins
Human peroxiredoxin 1 and 2 are not duplicate proteins: the unique presence of CYS83 in Prx1 underscores the structural and functional differences between Prx1 and Prx2
acylglucosaminylphosphatidylinositol [ChEBI:52572]
The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria
Multiple phosphoinositide 3-kinase-dependent steps in activation of protein kinase B
The autosomal recessively inherited progressive myoclonus epilepsies and their genes
N-retinylidene-N-retinylphosphatidylethanolamine [ChEBI:52592]
Stimulator of IFN gene is critical for induction of IFN-beta during Chlamydia muridarum infection
Physiology and pathophysiology of vascular signaling controlled by guanosine 3',5'-cyclic monophosphate-dependent protein kinase [corrected]
Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
Mechanisms and functions of DNA mismatch repair
The renal plumbing system: aquaporin water channels
The Drosophila tweety family: molecular candidates for large-conductance Ca2+-activated Cl- channels
The solution structure of the guanine nucleotide exchange domain of human elongation factor 1beta reveals a striking resemblance to that of EF-Ts from Escherichia coli
Prog Nucleic Acid Res Mol Biol 42:259-287
Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
The Drosophila claret segregation protein is a minus-end directed motor molecule
Cross-talk between the allosteric effector-binding sites in mouse ribonucleotide reductase
Lsm1-7-Pat1 complex: A link between 3' and 5'-ends in mRNA decay?
Mammalian Orc1 protein is selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle.
Compartmentation of hexokinase in human blood cells. Characterization of soluble and particulate enzymes.
Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
Actin cytoskeletal dynamics in smooth muscle: a new paradigm for the regulation of smooth muscle contraction
Antigen processing and presentation in human muscle: cathepsin S is critical for MHC class II expression and upregulated in inflammatory myopathies
RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease
New regulatory mechanisms of TGF-beta receptor function
Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase delta.
Expression, purification and kinetic properties of human recombinant phospholipase C delta 3
Localization and trafficking of aquaporin 2 in the kidney
G protein betagamma subunits: central mediators of G protein-coupled receptor signaling
A structural change in the kinesin motor protein that drives motility
Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology and structure similarity to the theta class enzyme
The secretory pathway Ca2+/Mn2+-ATPase 2 is a Golgi-localized pump with high affinity for Ca2+ ions
Assembly of the RAD51-ssDNA nucleoprotein complex
Phosphorylation inhibits guanine nucleotide exchange on eukaryotic initiation factor 2.
The NOD: a signaling module that regulates apoptosis and host defense against pathogens
Oncogenic role and therapeutic target of leptin signaling in breast cancer and cancer stem cells
Chapter 155: Inherited Disorders of Folate and Cobalamin Transport and Metabolism
The Online Metabolic and Molecular Bases of Inherited Disease (Book)
Desaturation and chain elongation of n - 3 and n - 6 polyunsaturated fatty acids in the human CaCo-2 cell line
beta-hydroxy-trimethyllysine => gamma-butyrobetaine aldehyde + glycine
Putrescine + dc-Adenosyl methionine => Spermidine + 5'-methylthioadenosine
SAM is sythesized from methionine's reaction with ATP
Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay
carbamoyl phosphate + ornithine => citrulline + orthophosphate
arginine + H2O => ornithine + urea [ARG2]
arginine + H2O => ornithine + urea [ARG1]
Conversion of coproporphyrinogen III to protoporphyrinogen IX
Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
Ferrous iron is inserted into protoporphyrin IX to form heme
Structure and sequence of the human alpha-L-iduronidase gene
Two molecules of ALA condense to form porphobilinogen (PBG)
ALAD octamer associates with Pb++, forming a catalytically inactive complex
Succinyl CoA and glycine condense to form 5-aminolevulinate (ALA)
ALAS condenses SUCC-CoA and Gly to form dALA
Association of HMGB1/HMGB2 with chromatin
Integrating signals from RTKs to ERK/MAPK
Release of Cytochrome c from mitochondria
abacavir monophosphate + H2O => carbovir monophosphate + cyclopropylamine
Deamination of abacavir monophosphate to form carbovir monophosphate
gamma-glutamylcysteine combines with glycine to form glutathione
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
GST dimers conjugate GSH with cytosolic substrates
Glutathione conjugation of cytosolic substrates
Proteoglycans and Sulfated Glycosaminoglycans
CDC6 protein is synthesized under the control of E2F transcription factors
Characteristics of human types 1, 2 and 3 17 beta-hydroxysteroid dehydrogenase activities: oxidation/reduction and inhibition
Transcriptional activation of Acetyl-CoA carboxylase by ChREBP:MLX
Transcriptional activation of pyruvate kinase gene by ChREBP:MLX
Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex.
NEUROD1- and PDX1-dependent synthesis of glucokinase (GCK) protein
Release of platelet cytosolic components
Exocytosis of platelet alpha granule contents
DAG kinase produces phosphatidic acid from DAG
Wnt-5a/Ca2+-induced NFAT activity is counteracted by Wnt-5a/Yes-Cdc42-casein kinase 1alpha signaling in human mammary epithelial cells
threonine + tRNA(Thr) + ATP => Thr-tRNA(Thr) + AMP + pyrophosphate
tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
valine + tRNA(Val) + ATP => Val-tRNA(Val) + AMP + pyrophosphate
pyrophosphate + H2O => 2 orthophosphate [mitochondrial]
SOD2 catalyzes 2H+ + 2O2.- => O2 + H2O2 (mitochondrial matrix)
Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons
methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
Distribution of aquaporin water channels AQP1 and AQP5 in the ductal system of the human pancreas
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
glutamine + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
Signaling by distinct classes of phosphoinositide 3-kinases
glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
histidine + tRNA(His) + ATP => His-tRNA(His) + AMP + pyrophosphate
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
alanine + tRNA(Ala) + ATP => Ala-tRNA(Ala) + AMP + pyrophosphate
asparagine + tRNA(Asn) + ATP => Asn-tRNA(Asn) + AMP + pyrophosphate
pyrophosphate + H2O => 2 orthophosphate [cytosolic]
tyrosine + tRNA(Tyr) + ATP =>Tyr-tRNA(Tyr) + AMP + pyrophosphate
Receptor for advanced glycation end products (RAGE) regulates sepsis but not the adaptive immune response
Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
isoleucine + tRNA(Ile) + ATP => Ile-tRNA(Ile) + AMP + pyrophosphate
The way Wnt works: Components and mechanism
glutamine + tRNA(Gln) + ATP => Gln-tRNA(Gln) + AMP + pyrophosphate
cysteine + tRNA(Cys) + ATP => Cys-tRNA(Cys) + AMP + pyrophosphate
Phospholipase C-gamma as a signal-transducing element
arginine + tRNA(Arg) + ATP => Arg-tRNA(Arg) + AMP + pyrophosphate
The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)
ATAC spliceosome mediated Lariat formation,5' splice site cleavage
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
Molecular cloning of two new human paralogs of 85-kDa cytosolic phospholipase A2
Transfer of SUMO1 from E1 to UBE2I (UBC9)
Transfer of SUMO3 from E1 to UBE2I (UBC9)
Transfer of SUMO2 from E1 to UBE2I (UBC9)
Downstream signaling events of B Cell Receptor (BCR)
Cloning and expression of a human choline/ethanolaminephosphotransferase: synthesis of phosphatidylcholine and phosphatidylethanolamine
Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Genetic heterogeneity and clinical variability in the Sanfilippo syndrome (types A, B, and C)
Aquaporins in complex tissues. II. Subcellular distribution in respiratory and glandular tissues of rat
Addition of the second N-acetyl-glucosamine to the N-glycan precursor
Addition of N-acetyl-D-glucosamine to Dolichyl phosphate
Regulation of endothelium-derived nitric oxide production by the protein kinase Akt
Activation of nitric oxide synthase in endothelial cells by Akt-dependent phosphorylation
Cargo, Sec31p:Sec13p, and v-SNARE recruitment
Mannose 6-phosphate isomerizes to Mannose 1-phosphate
Mannose-1-phosphate converted to GDP-Mannose
Sequence of the human erythrocyte phosphoglycerate mutase by microsequencer and mass spectrometry
GlcNAc1P is dephosphorylated to UDP-N-acetyl-glucosamine
Aquaporins in complex tissues. I. Developmental patterns in respiratory and glandular tissues of rat
ATP-binding cassette sub-family B member 6, mitochondrial
ATP-binding cassette sub-family B member 7, mitochondrial
Sodium-dependent phosphate transporter 2
Novel mutations in COX15 in a long surviving Leigh syndrome patient with cytochrome c oxidase deficiency
Sodium-dependent phosphate transporter 1
DHDDS elongates E,E-FPP with (n)IPPP to form pPPP
Mechanisms of human DNA repair: an update.
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
GFPT1,2 transfer an amino group from L-Gln to F6P to form GlcN6P
mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate
glucosaminyl-PI + fatty acyl-CoA -> glucosaminyl-acyl-PI + CoA-SH
N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate
Exchange of ADP for ATP in CCT/TriC:actin complex
EIF5A + spermidine <=> EIF5A(Dhp) + 1,3-diaminopropane
EIF5A(Dhp) + 1,3-diaminopropane <=> EIF5A + spermidine
The 7 TM G-protein-coupled receptor target family
Human geranylgeranyl diphosphate synthase. cDNA cloning and expression.
Hydrolysis of ATP and release of tubulin folding intermediate from CCT/TriC
Dual role of the tyrosine activation motif of the Ig-alpha protein during signal transduction via the B cell antigen receptor
ADP is exchanged for ATP in the (ADP:CCT/TriC):tubulin complex
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
Regeneration of eEF1A:GTP by eEF1B activity
Translocation of ribosome by 3 bases in the 3' direction
Peptide transfer from P-site tRNA to the A-site tRNA
Role of glutathione peroxidase and hexose monophosphate shunt in the platelet lipoxygenase pathway
Formation of eIF2:GDP:eIF2B intermediate
The 60S subunit joins the translation initiation complex
The SRP receptor binds the SRP:nascent peptide:ribosome complex
Synthesis of nascent polypeptide containing signal sequence
eEF1A:GTP:aminoacyl tRNA ternary complex formation.
Aminoacyl-tRNA binds to the ribosome at the A-site
Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
Nitric Oxide as a Unique Bioactive Signaling Messenger in Physiology and Pathophysiology
Molecular basis of GM1 gangliosidosis and Morquio disease, type B. Structure-function studies of lysosomal beta-galactosidase and the non-lysosomal beta-galactosidase-like protein
(5Z,8Z,10E,14Z)-(12S)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoate [ChEBI:250]
Formation of the 43S pre-initiation complex
(5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium salt
The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks
Initiating DNA synthesis: from recruiting to activating the MCM complex.
Structure and properties of a human non-pancreatic phospholipase A2
ChEBI:16618 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Cloning and expression of a human placenta inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase
Human arginase II: crystal structure and physiological role in male and female sexual arousal
Conserved initiator proteins in eukaryotes.
The known unknowns of antigen processing and presentation
xanthosine 5'-monophosphate [ChEBI:15652]
Synthesis of 12-eicosatetraenoic acid derivatives
Structural basis for featuring of steroid isomerase activity in alpha class glutathione transferases
Glycogen metabolism and glycolytic enzymes
Understanding RAGE, the receptor for advanced glycation end products
Constitutive and inducible expression and regulation of vascular endothelial growth factor
5-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoate [ChEBI:2061]
Defective LMBRD1 causes methylmalonic aciduria and homocystinuria type cblF
STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling
Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha.
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
Mechanism of the exchanges catalysed by the oxoglutarate translocator of rat-heart mitochondria. Kinetics of the external-product inhibition
Phosphoinositide 3-kinase in T cell activation and survival
Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway
Defective AMN causes hereditary megaloblastic anemia 1
Biology, structure and mechanism of P-type ATPases
'cAMP [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Ac-CoA [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'D-Fructose 1,6-bisphosphate [cytosol]' positively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'ATP [nucleoplasm]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Mg2+ [cytosol]' is required for 'A phosphoribosyl group is added to nicotinate to form nicotinate mononucleotide (NaMN)'
'CIT [cytosol]' positively regulates 'acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate'
'BH4 [cytosol]' negatively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'L-Phe [cytosol]' positively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
Mitochondrial association of a plus end-directed microtubule motor expressed during mitosis in Drosophila
OMMBID Chapter 71: Glycogen Storage Diseases
Insulin effects increased synthesis of Xylulose-5-Phosphate
Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.
The role of EF-hand domains and C2 domain in regulation of enzymatic activity of phospholipase Czeta
Molecular cloning, cDNA sequence, and bacterial expression of human glutamine:fructose-6-phosphate amidotransferase
Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes
Nuclear localization of human DNA mismatch repair protein exonuclease 1 (hEXO1)
Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing
Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
The canonical Notch signaling pathway: unfolding the activation mechanism
CDK-mediated phosphorylation and removal of Cdc6
Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)
Cloning and recombinant expression of phospholipase A2 present in rheumatoid arthritic synovial fluid
Aspartate 155 of human transketolase is essential for thiamine diphosphate-magnesium binding, and cofactor binding is required for dimer formation
Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry
A novel molecular mechanism to explain biotin-unresponsive holocarboxylase synthetase deficiency
The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutS?
Diabetes-associated sustained activation of the transcription factor nuclear factor-kappaB
Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young
Tandem phosphorylation of serine 221 and 318 by PKC{delta} coordinates mRNA binding and nucleo-cytoplasmic shuttling of HuR
Sanfilippo disease type D: deficiency of N-acetylglucosamine-6-sulfate sulfatase required for heparan sulfate degradation
Insights into lysosomal cobalamin trafficking: lessons learned from cblF disease
Mammalian nuclei become licensed for DNA replication during late telophase.
Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1489-1520
Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system.
Identification of protein kinase C (PKC) phosphorylation sites on human lamin B. Potential role of PKC in nuclear lamina structural dynamics
Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
The Enzymes, 2nd ed (Boyer PD, Lardy H, Myrback K, editors) 6:75-83
The toxicology of aflatoxins as a basis for public health decisions
The mechanism of regulation of hexokinase: new insights from the crystal structure of recombinant human brain hexokinase complexed with glucose and glucose-6-phosphate
Proteasomal clevage of exogenous antigen
NCAM-induced intracellular signaling revisited
14-3-3 is not essential for Raf-1 function: identification of Raf-1 proteins that are biologically activated in a 14-3-3- and Ras-independent manner
Production of AA by iPLA2 upon FCGR activation
Purification and properties of two DNA ligases from human placenta
Translocation of CaN:CaM:NFAT to nucleus
Autophosphorylation and activation of MEKK1
Release of 40S and 60S subunits from the 80S ribosome
translocation of NFATC1:CaN:CaM to nucleus
Inactive catalytic PP2B is activated by the binding of calmodulin
Met-tRNAi binds to eIF2:GTP to form the ternary complex
The cyclin-dependent kinase Cdc28p regulates distinct modes of Cdc6p proteolysis during the budding yeast cell cycle.
Amplification and kinetics of the activation steps in phototransduction
RAGE mediates a novel proinflammatory axis: a central cell surface receptor for S100/calgranulin polypeptides
The Ras branch of small GTPases: Ras family members don't fall far from the tree
LSm proteins form heptameric rings that bind to RNA via repeating motifs
Molecular genetics of mucopolysaccharidosis type IIIA and IIIB: Diagnostic, clinical, and biological implications
Human platelet-derived mitogens. II. Subcellular localization of insulinlike growth factor I to the alpha-granule and release in response to thrombin.
Expression of human asparagine synthetase in Escherichia coli
5-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by PPIP5K1/2 in the cytosol
IP6 is phosphorylated to 1-PP-IP5 by PPIP5K1/2 in the cytosol
Glc6P is isomerised to I3P by ISYNA1 in the cytosol
I(1,4,5)P3 is dephosphorylated to I(1,4)P2 by INPP5(4) in the cytosol
An overview of sphingolipid metabolism: from synthesis to breakdown
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL3]
arachidonate + CoASH + ATP => arachidonoyl-CoA + AMP + pyrophosphate + H2O [ACSL4]
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL5]
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL6]
cholesterol + phosphatidylcholine (lecithin) => cholesterol ester + 2-lysophosphatidylcholine (lysolecithin)
acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate
Formation of Malonyl-CoA from Acetyl-CoA (liver)
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL1]
Conversion of palmitic acid to palmitoyl-CoA
A theory of marginotomy. The incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon.
Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication.
Differential activation of recombinant human acetyl-CoA carboxylases 1 and 2 by citrate
I(1,3,4,6)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
I(1,4,5,6)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
I(1,4,5)P3 is phosphorylated to I(1,3,4,5)P4 by IPMK in the nucleus
Distinct flippases translocate glycerophospholipids and oligosaccharide diphosphate dolichols across the endoplasmic reticulum
I(1,3,4,5)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
PI(4,5)P2 is hydrolysed to I(1,4,5)P3 and DAG by tethered PLC[1] at the plasma membrane
I(1,3,4,5)P4 is dephosphorylated to I(1,3,4)P3 by INPP5[3]/ITPK1 in the cytosol
1,2-diacyl-glycerol + acyl-CoA => triacylglycerol + CoASH [DGAT1]
Conversion of Diacylglycerol to Triacylglycerol [DGAT1]
Conversion of Phosphatidic Acid to Diacylglycerol
Formation of Malonyl-CoA from Acetyl-CoA (muscle)
Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
Addition of isopentenyl pyrophosphate to DMAPP
Another isopentenyl pyrophosphate is added to geranyl pyrophosphate
Reduction of androstenedione to testosterone
Testosterone is converted to 5-alpha-dihydroxytestosterone
Bone morphogenetic protein receptors and signal transduction
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL3]
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL2]
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL1]
Nucleotide-sugar transporters: structure, function and roles in vivo
Cytokines and chemokines in autoimmune disease: an overview
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL6]
arachidoyl-CoA + malonyl-CoA => 3-oxobehenoyl-CoA + CO2 + CoASH [ELOVL7]
lignoceroyl-CoA + malonyl-CoA => 3-oxocerotoyl-CoA + CO2 + CoASH [ELOVL4]
arachidonoyl-CoA + malonyl-CoA => 3-oxo-(7,10,13,16)-docosatetraenoyl-CoA + CO2 + CoASH [ELOVL5]
Conversion of Dihydroxyacetone Phosphate to Glycerol -3- phosphate
Conversion of Glycerol to Glycerol-3-phosphate
3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + NADPH + H+ => 3-hydroxyoctadecanoyl-CoA + NADP+
trans-octadec-2-enoyl-CoA + NADPH + H+ => stearoyl-CoA + NADP+
Peroxisome proliferator-activated receptor alpha target genes
Interleukin-2 receptor signaling in regulatory T cell development and homeostasis
Mutations in HYAL1, a member of a tandemly distributed multigene family encoding disparate hyaluronidase activities, cause a newly described lysosomal disorder, mucopolysaccharidosis IX
Proc. Natl. Acad. Sci. U.S.A. 96:6296-300
N-Acetyl-D-glucosamine 1-phosphate [ChEBI:7125]
Regulation of enterocyte apoptosis by acyl-CoA synthetase 5 splicing
Evolution of leptin structure and function
Characterization of type II phosphatidylinositol 4-kinase isoforms reveals association of the enzymes with endosomal vesicular compartments
(R)-4'-Phosphopantothenoyl-L-cysteine [ChEBI:328]
Nicotinate D-ribonucleotide [ChEBI:7561]
The human sugar-phosphate/phosphate exchanger family SLC37
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595302
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595915
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595209
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593336
3-Hydroxy-N6,N6,N6-trimethyl-L-lysine [ChEBI:15786]
N-Acetyl-D-glucosamine 6-phosphate [ChEBI:7127]
Water channel expression in human ADPKD kidneys
Defective GIF causes intrinsic factor deficiency
DNA chain length dependence of formation and dynamics of hMutSalpha.hMutLalpha.heteroduplex complexes
PIK3R1 (p85?) is somatically mutated at high frequency in primary endometrial cancer
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch
ChEBI:16500 1-phosphatidyl-1D-myo-inositol 5-phosphate
[Exchange between extra- and intramitochondrial adenine nucleotides]
phosphatidylinositol 1,4,5-trisphosphate
1-phosphatidyl-1D-myo-inositol 4,5- bisphosphate
Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways
Crystalline D-glyceraldehyde-3-phosphate dehydrogenase from rabbit muscle
Identification of the expressed form of human cytosolic phospholipase A2beta (cPLA2beta): cPLA2beta3 is a novel variant localized to mitochondria and early endosomes
Antigen processing: Ubiquitination & Proteasome degradation
Leber congenital amaurosis: genes, proteins and disease mechanisms
The role of calcium-independent phospholipase A2 in cardiolipin remodeling in the spontaneously hypertensive heart failure rat heart
The stem cell factor receptor/c-Kit as a drug target in cancer
Depalmitoylation of endothelial nitric-oxide synthase by acyl-protein thioesterase 1 is potentiated by Ca(2+)-calmodulin
triphopsphoric acid 1-xanthosin-5'-yl ester
Electron transport from NADPH to Ferredoxin
Recent advances in understanding leptin signaling and leptin resistance
Am. J. Physiol. Endocrinol. Metab. 297:E1247-59
The biochemistry and physiology of nucleotides
Metabolism of steroid hormones and vitamin D
Characterization of two human genes encoding acyl coenzyme A:cholesterol acyltransferase-related enzymes
Apoptosis and disease: a life or death decision
Virus-cell fusion as a trigger of innate immunity dependent on the adaptor STING
Hereditary disorders of connective tissue
The class II phosphoinositide 3-kinase PI3K-C2alpha is concentrated in the trans-Golgi network and present in clathrin-coated vesicles
Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 3775-3809
M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein
Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3
Orc6 involved in DNA replication, chromosome segregation, and cytokinesis.
Purification and functional characterization of aquaporin-8
How mitochondria produce reactive oxygen species
Control of muscle ryanodine receptor calcium release channels by proteins in the sarcoplasmic reticulum lumen
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book)
The Src homology 2 domain containing inositol 5-phosphatase SHIP2 is recruited to the epidermal growth factor (EGF) receptor and dephosphorylates phosphatidylinositol 3,4,5-trisphosphate in EGF-stimulated COS-7 cells
Tyrosine phosphorylation of MB-1, B29, and HS1 proteins in human B cells following receptor crosslinking
Aflatoxin B1-6,8-dialcohol [ChEBI:78575]
Differential recognition by CD28 of its cognate counter receptors CD80 (B7.1) and B70 (B7.2): analysis by site directed mutagenesis
Dynamic coupling of the putative coiled-coil domain of ORAI1 with STIM1 mediates ORAI1 channel activation
Post-transcriptional regulation of gene expression by degradation of messenger RNAs
Surprising versatility of Na+-glucose cotransporters: SLC5
Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes
Oxidative decarboxylation of pyruvate to acetyl CoA by pyruvate dehydrogenase
pyruvate + CoASH + NAD+ => acetylCoA + CO2 + NADH + H+
Acetyl-CoA + H2O + Oxaloacetate => Citrate + CoA
isocitrate + NADP+ => alpha-ketoglutarate + CO2 + NADPH + H+ [IDH2]
NADPH + NAD+ + H+ [cytosol] => NADP+ + NADH + H+ [mitochondrial matrix]
Oxidative decarboxylation of alpha-ketoglutarate to succinyl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
ADP + Orthophosphate + Succinyl-CoA <=> ATP + Succinate + CoA
xanthosine 5'-monophosphate (XMP) + L-glutamine + ATP + H2O => guanosine 5'-monophosphate (GMP) + L-glutamate + adenosine 5'-monophosphate (AMP) + pyrophosphate
XMP + L-Glutamine + ATP + H2O => GMP + L-Glutamate + AMP + pyrophosphate
inosine 5'-monophosphate (IMP) + NAD+ + H2O => xanthosine 5'-monophosphate (XMP) + NADH + H+
IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]
adenylosuccinate => adenosine 5'-monophosphate + fumarate
inosine 5'-monophosphate + L-aspartate + GTP => adenylosuccinate + guanosine 5'-diphosphate + orthophosphate
IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]
SUMO is transferred from E1 to E2 (UBE2I, UBC9)
The secondary structure of calcineurin regulatory region and conformational change induced by calcium/calmodulin binding
Clinical and biochemical manifestations of hyaluronidase deficiency
GCH1 reduces GTP to dihydroneopterin triphosphate
Cytosolic PYR is transported to the mitochondrial matrix by MPC1:MPC2
PYR + H+ (cytosol) => PYR + H+ (mitochondrial matrix)
(S)-Lactate + NAD+ <=> Pyruvate + NADH + H+
Pyruvate + NADH + H+ <=> (S)-Lactate + NAD+
The molecular basis of Sanfilippo syndrome type B
BLNK: molecular scaffolding through 'cis'-mediated organization of signaling proteins
Purification and properties of guanosine diphosphate hexose pyrophosphorylase from mammalian tissues
Proteases in MHC class I presentation and cross-presentation
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT2]
all-trans-decaprenyl diphosphate [ChEBI:61011]
L-1-pyrroline-5-carboxylate + NADPH + H+ => proline + NADP+
Molecular identification of cytosolic prostaglandin E2 synthase that is functionally coupled with cyclooxygenase-1 in immediate prostaglandin E2 biosynthesis
aspartate + glutamine + ATP <=> asparagine + glutamate + AMP + pyrophosphate [ASNS]
alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]
glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]
a-ketoisocaproate, a-keto b-methylvalerate, or a-ketoisovalerate + CoA + NAD+ => isovaleryl-CoA, a-methylbutyryl-CoA, or isobuyryl-CoA + CO2 + NADH + H+
Oxidative decarboxylation of branched-chain alpha-keto acids
alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA
beta-hydroxyisobutyryl-CoA + H2O => beta-hydroxyisobutyrate + CoA
Oxidative decarboxylation of alpha-ketoadipate to glutaryl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]
glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]
thioredoxin, oxidized + NADPH + H+ => thioredoxin, reduced + NADP+
regeneration of active (reduced) Thioredoxin
thioredoxin, oxidized (nucleus) <=> thioredoxin, oxidized (cytosol)
(d)NDP + ATP <=> (d)NTP + ADP [NME1,2,3]
(d)NTP + ADP <=> (d)NDP + ATP [NME1,2,3]
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]
thioredoxin, reduced (cytosol) <=> thioredoxin, reduced (nucleus)
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
(d)CDP or UDP + ADP <=> (d)CMP or UMP + ATP [CMPK1]
(d)CMP or UMP + ATP <=> (d)CDP or UDP + ADP [CMPK1]
dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
phosphorylation of dUMP or TMP to dUDP or TDP
Reduction of cytosolic ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O
Reduction of nuclear ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
glutaredoxin (oxidized) + glutathione (reduced) => glutaredoxin (reduced) + glutathione (oxidized)
glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]
amination of uridine 5'-triphosphate (UTP) to form cytidine 5'-triphosphate (CTP)
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS]
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS2]
Reduction of cytosolic ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (glutaredoxin)
NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O
guanine or hypoxanthine + PRPP => GMP or IMP + PPi [HPRT1]
Deamination of N6-methyl-AMP to form IMP
N6-methyl-AMP + H2O => IMP + methylamine
(2'-deoxy)adenosine + H2O => (2'-deoxy)inosine + NH3 [ADA]
(S)-dihydroorotate + ubiquinone => orotate + ubiquinol
oxidation of (S)-Dihydroorotate to form Orotate
dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate
carbamoyl phosphate and L-aspartate combine to form N-Carbamoyl-L-aspartate
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate
bicarbonate and glutamine combine to form carbamoyl phosphate
Preferential DNA repair of an active gene in human cells.
L13a-mediated translational silencing of Ceruloplasmin expression
The content of pentose-cycle intermediates in liver in starved, fed ad libitum and meal-fed rats.
Hailey-Hailey disease is caused by mutations in ATP2C1 encoding a novel Ca(2+) pump
Concerted action of two cation filters in the aquaporin water channel
Formation and metabolism of prebeta-migrating, lipid-poor apolipoprotein A-I
Expression of the AQP-1 water channel in normal human tissues: a semiquantitative study using tissue microarray technology
A yeast chromosomal origin of DNA replication defined by multiple functional elements.
Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy
The Akt activation inhibitor TCN-P inhibits Akt phosphorylation by binding to the PH domain of Akt and blocking its recruitment to the plasma membrane
Protein phosphatase 2Cepsilon is an endoplasmic reticulum integral membrane protein that dephosphorylates the ceramide transport protein CERT to enhance its association with organelle membranes
Characterization of ceramide synthase 2: tissue distribution, substrate specificity, and inhibition by sphingosine 1-phosphate
Mechanisms of transcription-coupled DNA repair.
Chapter 3 Activation of TRP Channels in Mammalian Systems
The copper transporter (Ctr) family of Cu+ uptake systems
3'-Phosphoadenylyl sulfate [ChEBI:17980]
Characterization of the rat aflatoxin B1 aldehyde reductase gene, AKR7A1. Structure and chromosomal localization of AKR7A1 as well as identification of antioxidant response elements in the gene promoter
Homologous recombination repair of replication-independent double-strand breaks
Congenital Disorders of Glycosylation Overview
Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.
Class I MHC mediated antigen processing & presentation
beta-catenin destruction complex: insights and questions from a structural perspective
dolichyl D-mannosyl phosphate [ChEBI:15809]
eNOS, COX-2, and prostacyclin production are impaired in endothelial cells from diabetics
The human arginases and arginase deficiency
Structural changes in the calcium pump accompanying the dissociation of calcium
Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: facts and models
The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy
A role for the endoplasmic reticulum protein retrotranslocation machinery during crosspresentation by dendritic cells
Multistep regulation of DNA replication by Cdk phosphorylation of HsCdc6.
Detoxification of Reactive Oxygen Species
Synthesis of IP2, IP, and Ins in the cytosol
Expression cloning and characterization of a cDNA encoding a novel membrane protein required for the formation of O-acetylated ganglioside: a putative acetyl-CoA transporter
Magnesium transporters: properties, regulation and structure
Comprehending the complex connection between PKCbeta, TAK1, and IKK in BCR signaling
The human homolog of the rat inositol phosphate multikinase is an inositol 1,3,4,6-tetrakisphosphate 5-kinase
Activating and inhibitory functions of DAP12
Tuberculosis: what we don't know can, and does, hurt us
PI is phosphorylated to PI4P by PI4KA/2B at the ER membrane
Toxic proteins released from mitochondria in cell death
PI3P is phosphorylated to PI(3,4)P2 by PIP4K2/5K1 at the plasma membrane
PI(3,4,5)P3 is dephosphorylated to PI(3,4)P2 by INPP5[2] at the plasma membrane
PI4KB binds to ARF1/3:GTP at the Golgi membrane
PI is phosphorylated to PI4P by PI4KA/2A/2B at the Golgi membrane
PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane
PI is phosphorylated to PI4P by PI4KB at the Golgi membrane
A novel microtubule-based motor protein (KIF4) for organelle transports, whose expression is regulated developmentally
Latent infection of Homo sapiens with Mycobacterium tuberculosis
PI4P is dephosphorylated to PI by SYNJ at the plasma membrane
Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct
PI5P is phosphorylated to PI(4,5)P2 by PIP4K2A/B at the plasma membrane
Adapters in the organization of mast cell signaling
PI(3,5)P2 is dephosphorylated to PI5P by SYNJ/MTM[1] at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI3P by SYNJ at the plasma membrane
PI3P is dephosphorylated to PI by SYNJ/MTM[1] at the plasma membrane
A defect in dolichol phosphate biosynthesis causes a new inherited disorder with death in early infancy
Activation of linoleic acid to linoleoyl-CoA
Nicotinate phosphoribosyltransferase of human erythrocytes. Purification and properties.
Elongation of docosapentaenoyl-CoA to tetracosapentaenoyl-CoA
Elongation of eicosapentaenoyl-CoA to docosapentaenoyl-CoA
Elongation of stearidonoyl-CoA to eicosatetraenoyl-CoA
Activation of alpha-linolenic acid to alpha-linolenoyl-CoA
Arteriosclerosis, Thrombosis, and Vascular Biology 28:e162
Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers
Increased adhesion and aggregation of platelets lacking cyclic guanosine 3',5'-monophosphate kinase I
2-MAG is transacylated to DAG by PNPLA2/3
A novel pantothenate kinase gene (PANK2) is defective in Hallervorden-Spatz syndrome
ETA is phosphorylated to PETA by CHK/ETNK
2-MAG and DAG are transacylated to TAG by PNPLA2/3
PETA and CTP are condensed to CDP-ETA by PCY2
CDP-ETA and DAG are converted to PE by CEPT1/EPT1
PE is hydrolyzed to 1-acyl LPE by PLA2[3]
PE is hydrolyzed to 1-acyl LPE by PLA2[2]
Superoxide production and electron transport in mitochondrial oxidation of dihydroorotic acid.
Lysosomal disorders: from storage to cellular damage
The Deleted in Colorectal Cancer netrin guidance system: a molecular strategy for neuronal navigation
CDP-Cho and DAG are converted to PC by CEPT1 at the ER membrane
PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
Cho is phosphorylated to PCho by CHK dimer
PC is hydrolyzed to 1-acyl LPC by PLA2[6]
PC is hydrolyzed to 1-acyl LPC by PLA2[5]
CDP-Cho and DAG are converted to PC by CHPT1 at the Golgi membrane
Molecular and evolutionary basis of the cellular stress response
NAGLU mutations underlying Sanfilippo syndrome type B
ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism
Pentose phosphate pathway (hexose monophosphate shunt)
Bi-directional routing of DNA mismatch repair protein human exonuclease 1 to replication foci and DNA double strand breaks
FGF signaling pathways in endochondral and intramembranous bone development and human genetic disease
5S-HpETE is reduced to 5S-HETE by GPX1/2/4
12R-HpETE is reduced to 12R-HETE by GPX1/2/4
12S-HpETE is reduced to 12S-HETE by GPX1/2/4
palmitoyl-CoA + serine => 3-ketosphinganine + CoASH + CO2
Functional characterization of ORCTL2--an organic cation transporter expressed in the renal proximal tubules
Elongation of gamma-lenolenoyl-CoA to dihomo-gamma-lenolenoyl-CoA
Elongation of arachidonyl-CoA to docosatetraenoyl-CoA
Elongation of docosatetraenoyl-CoA to tetracosatetraenoyl-CoA
Prostaglandin E synthase isomerizes PGH2 to PGE2
Characterization of the proteins of isolated human platelet alpha-granules. Evidence for a separate alpha-granule-pool of the glycoproteins IIb and IIIa.
Uncoupled eNOS favours the formation of superoxide
The cofactor BH4 is required for electron transfer in the eNOS catalytic cycle
PHB and all-E-10PrP2 are combined into DHB by COQ2
sphinganine + stearyl-CoA => dihydroceramide + CoASH
ADP-ATP translocase maintains a high ADP:ATP ratio in the matrix
MDMQ10H2 is methylated to DMQ10H2 by COQ5
Signal transduction via vascular endothelial growth factor (VEGF) receptors and their roles in atherogenesis
Isolation and characterization of a human thiamine pyrophosphokinase cDNA
Synaptojanin 1: localization on coated endocytic intermediates in nerve terminals and interaction of its 170 kDa isoform with Eps15
trans,trans-Farnesyl diphosphate [ChEBI:10700]
Expression and characterization of a human cDNA that complements the temperature-sensitive defect in dolichol kinase activity in the yeast sec59-1 mutant: the enzymatic phosphorylation of dolichol and diacylglycerol are catalyzed by separate CTP-mediated kinase activities in Saccharomyces cerevisiae
myo-Inositol hexakisphosphate [ChEBI:10603]
D-myo-Inositol 1,2,3,4,5,6-hexakisphosphate
myo-Inositol 1,2,3,4,5,6-hexakisphosphate
1D-myo-Inositol 1,2,3,4,5,6-hexakisphosphate
Developmental control of a G1-S transcriptional program in Drosophila
Molecular mechanisms of conduction and selectivity in aquaporin water channels
Molecular analysis of patients with beta-glucuronidase deficiency presenting as hydrops fetalis or as early mucopolysaccharidosis VII
HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells
Construction and expression of human aldolase A and B expression plasmids in Escherichia coli host
Molecular cloning of human thiamin pyrophosphokinase
ERIS, an endoplasmic reticulum IFN stimulator, activates innate immune signaling through dimerization
Proc. Natl. Acad. Sci. U.S.A. 106:8653-8
Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response
A stimulatory role for cGMP-dependent protein kinase in platelet activation
17beta-Hydroxyandrostan-3-one [ChEBI:793]
The identification of a phospholipase B precursor in human neutrophils
gamma -Secretase cleavage and nuclear localization of ErbB-4 receptor tyrosine kinase
A syndrome with congenital neutropenia and mutations in G6PC3
D-myo-Inositol 1,3,4,5,6-pentakisphosphate
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate [ChEBI:807]
Mycobacterium tuberculosis activates the DNA-dependent cytosolic surveillance pathway within macrophages
Telomere C-strand (Lagging Strand) Synthesis
Identification of HsORC4, a member of the human origin of replication recognition complex.
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
Normal human chromosomes have long G-rich telomeric overhangs at one end
Hereditary orotic aciduria and other disorders of pyrimidine metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2663-2704
Analysis of Gas6 in human platelets and plasma
Novel inositol polyphosphate 5-phosphatase localizes at membrane ruffles
HDL, ABC Transporters, and Cholesterol Efflux: Implications for the Treatment of Atherosclerosis
Cloning and characterization of the human phosphoinositide-specific phospholipase C-beta 1 (PLC beta 1)
The PtdIns3P phosphatase myotubularin is a cytoplasmic protein that also localizes to Rac1-inducible plasma membrane ruffles
Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex
Recombinational DNA repair and human disease.
Analysis of dolichol in human tissues by high pressure liquid chromatography
Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9
From birth to death: the complex lives of eukaryotic mRNAs
A transforming mutation in the pleckstrin homology domain of AKT1 in cancer
Lessons from photoreceptors: turning off G-protein signaling in living cells
Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
Zinc fluxes and zinc transporter genes in chronic diseases
Mechanisms underlying differential responses to FGF signaling
Phosphatidylinositol-4-phosphate 5-kinase isozymes catalyze the synthesis of 3-phosphate-containing phosphatidylinositol signaling molecules
Role of the CLOCK protein in the mammalian circadian mechanism
Clinical and genetic spectrum of pyruvate dehydrogenase deficiency: dihydrolipoamide acetyltransferase (E2) deficiency
Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
hMutSalpha forms an ATP-dependent complex with hMutLalpha and hMutLbeta on DNA
An interferon-induced protein with release factor activity is a tryptophanyl-tRNA synthetase
Presentation of cytosolic antigens via MHC class II molecules
Defective HLCS causes multiple carboxylase deficiency
Common and distinct elements in cellular signaling via EGF and FGF receptors
Desumoylation of homeodomain-interacting protein kinase 2 (HIPK2) through the cytoplasmic-nuclear shuttling of the SUMO-specific protease SENP1
Proinflammatory activities of leptin in non-autoimmune conditions
Depletion of intracellular calcium stores activates a calcium current in mast cells
Determination of the organisation of coding sequences within the iduronate sulphate sulphatase (IDS) gene
Ror-family receptor tyrosine kinases in noncanonical Wnt signaling: their implications in developmental morphogenesis and human diseases
Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V
Cellular signaling by fibroblast growth factor receptors
The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations
UDP-N-acetyl-D-glucosamine [ChEBI:16264]
Presynaptic phase of homologous DNA pairing and strand exchange
The receptor for advanced glycation end products (RAGE) is a cellular binding site for amphoterin. Mediation of neurite outgrowth and co-expression of rage and amphoterin in the developing nervous system
Mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1) in patients with a pyruvate dehydrogenase complex deficiency
Aquaporin-7 and glycerol permeability as novel obesity drug-target pathways
Activation and detoxication of aflatoxin B1
Uroporphyrinogen decarboxylase: complete human gene sequence and molecular study of three families with hepatoerythropoietic porphyria
Metabolism of carotenoids and retinoids related to vision
Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches
Mutations in TMEM76* cause mucopolysaccharidosis IIIC (Sanfilippo C syndrome)
Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
Mini-review: Specificity and expression of CIITA, the master regulator of MHC class II genes
The type 1 insulin-like growth factor receptor pathway
A novel role for human Nfs1 in the cytoplasm: Nfs1 acts as a sulfur donor for MOCS3, a protein involved in molybdenum cofactor biosynthesis
Functional characterization and localization of AQP3 in the human colon
The ins and outs of IgE-dependent mast-cell exocytosis
(S)-1-Pyrroline-5-carboxylate [ChEBI:17388]
5-methyltetrahydrofolyl polyglutamate macromolecule
5-methyltetrahydrofolyl polyglutamate macromolecule [ChEBI:63907]
Indirect inhibition of mitochondrial dihydroorotate dehydrogenase activity by nitric oxide.
Peroxisome proliferator-activated receptors, coactivators, and downstream targets
Stabilization of beta-catenin by a Wnt-independent mechanism regulates cardiomyocyte growth
Proc. Natl. Acad. Sci. U.S.A. 100:4610-5
N-acetyl-D-glucosaminylphosphatidylinositol [ChEBI:15935]
cis-Delta(9,12)-octadecadienoyl-coenzyme A
The ARF1 GTPase-activating protein: zinc finger motif and Golgi complex localization
The Akt kinase signals directly to endothelial nitric oxide synthase
New initiation factor activity required for globin mRNA translation.
Structure and expression of a complementary DNA for the nuclear coded precursor of human mitochondrial ornithine transcarbamylase.
Nucleoside diphosphate kinase from human erythrocytes. Structural characterization of the two polypeptide chains responsible for heterogeneity of the hexameric enzyme
Protein kinase G mediates vascular endothelial growth factor-induced Raf-1 activation and proliferation in human endothelial cells
The interleukin 2 receptor. Functional consequences of its bimolecular structure
STING Recognition of Cytoplasmic DNA Instigates Cellular Defense
A new biochemical subtype of the Sanfilippo syndrome: characterization of the storage material in cultured fibroblasts of Sanfilippo C patients
Diacylglycerol kinases: at the hub of cell signalling
A new pathway for synthesis of phosphatidylinositol-4,5-bisphosphate
T cell receptor signaling: beyond complex complexes
Molecular cloning and characterization of a novel phospholipase C, PLC-eta
ChEBI:11805 3-hydroxy-2-methylpropanoate
Polyamines: metabolism and implications in human diseases
Adhesion mechanisms in platelet function
Identification of a novel domain in two mammalian inositol-polyphosphate 5-phosphatases that mediates membrane ruffle localization. The inositol 5-phosphatase skip localizes to the endoplasmic reticulum and translocates to membrane ruffles following epidermal growth factor stimulation
Purification and characterization of homogeneous initiation factor M2A from rabbit reticulocytes.
Frataxin and mitochondrial FeS cluster biogenesis
Mechanisms of organelle transport and capture along proplatelets during platelet production
Identification of the human mitochondrial linoleoyl-coenzyme A monolysocardiolipin acyltransferase (MLCL AT-1)
Activating E17K mutation in the gene encoding the protein kinase AKT1 in a subset of squamous cell carcinoma of the lung
Mechanism and regulation of eukaryotic protein synthesis
Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
Making heads or tails of phospholipids in mitochondria
Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors
MHC II and the endocytic pathway: regulation by invariant chain
The crystal structure of human phosphoglucose isomerase at 1.6 A resolution: implications for catalytic mechanism, cytokine activity and haemolytic anaemia
Ectodomain cleavage of ErbB-4: characterization of the cleavage site and m80 fragment
Getting to the end: telomerase access in yeast and humans
The structure of human liver fructose-1,6-bisphosphate aldolase
Acta Crystallogr D Biol Crystallogr 57:1526-33
Neuregulin-2, a new ligand of ErbB3/ErbB4-receptor tyrosine kinases
Antiatherogenic Potential of gamma Linolenic Acid
A complete inventory of all enzymes in the eukaryotic methionine salvage pathway
Structural and functional properties of two mutants of lecithin-cholesterol acyltransferase (T123I and N228K)
Kinetics and mechanism of the reduction of ferricytochrome c by the superoxide anion
Purification, cloning, complementary DNA structure, and predicted amino acid sequence of human estradiol 17 beta-dehydrogenase
The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6p.
Overexpression of endothelial NO synthase induces angiogenesis in a co-culture model
Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5
Protein ligands to HuR modulate its interaction with target mRNAs in vivo
Genetic Analysis of Coenzyme Q Biosynthesis
Coenzyme Q: Molecular Mechanisms in Health and Disease (Book): 185-208
Synthesis of Leukotrienes (LT) and Eoxins (EX)
Opposing roles for ATF6alpha and ATF6beta in endoplasmic reticulum stress response gene induction
A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo.
Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)
Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
Activation of HER4 by heparin-binding EGF-like growth factor stimulates chemotaxis but not proliferation
Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin.
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
Cloning and characterization of the human beta-glucuronidase gene
At the beginning of this reaction, 1 molecule of 'ATAC B Complex' is present. At the end of this reaction, 1 molecule of 'U4 ATAC snRNP', and 1 molecule of 'ATAC C Complex' are present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'ATAC C Complex' is present. At the end of this reaction, 1 molecule of 'ATAC C Complex with lariat containing 5'-end cleaved mRNA' is present. This reaction takes place in the 'nucleus'.
The splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that are removed by the AT-AC spliceosome, which contains distinct snRNAs (U11, U12, U4atac, U6atac) that are structurally and functionally analogous to the major spliceosome. U5 snRNA as well as many of the protein factors appear to be conserved between the two spliceosomes.
The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing. Most of the mRNA is spliced by the major pathway, involving the U1, U2, U4, U5 and U6 snRNPs. A minor fraction, about 1 %, of the mRNAs are spliced via the U12 dependent pathway.
PERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintained in an inactive form by interaction of its luminal domain with BiP, an ER chaperone. BiP also binds unfolded proteins and so BiP dissociates from PERK when unfolded proteins accumulate in the ER. Dissociated PERK monomers spontaneously form homodimers and the homodimeric form of PERK possesses kinase activity in its cytosolic C-terminal domain. The kinase specifically phosphorylates the translation factor eIF2alpha at Ser52, resulting in an arrest of translation. Thus translation of proteins targeted to the ER is downregulated. The translation arrest also causes depletion of Cyclin D1, a rapidly turned over protein. The depletion of Cyclin D1 in turn causes arrest of the cell cycle in G1 phase.
The Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER during times of unusually high secretion activity. Analysis of mutants with altered UPR, however, shows that the UPR is also required for normal development and function of secretory cells. One level at which the URP operates is transcriptional and translational regulation: mobilization of ATF6 and IRE1 leads to increased transcription of genes encoding chaperones, and mobilization of PERK (pancreatic eIF2alpha kinase, EIF2AK3) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis. These three regulatory pathways are annotated here.
Docosapentaenoic acid (22:5, n-3), an elongation metabolite of eicosapentaenoic acid (20:5, n-3), is a potent stimulator of endothelial cell migration on pretreatment in vitro
Prostaglandins Leukot Essent Fatty Acids 54:319-25
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
The U4atac/U6atac enters the spliceosome and U6atac snRNA forms base pairing interactions with the 5' ss and also forms base pairing interactions with U12 and U4atac is partially displaced. U5 snRNP, the only snRNP common to both the major and minor splicing pathways, also joins the spliceosome to form the B complex and interacts with nucleotides within the 3' end of the exon flanking the 5' ss.
The Aspariagine Synthetase (ASNS) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
Defective MTR causes methylmalonic aciduria and homocystinuria type cblG
Central insulin and leptin-mediated autonomic control of glucose homeostasis
The metabolism of 7,10,13,16,19-docosapentaenoic acid to 4,7,10,13,16,19-docosahexaenoic acid in rat liver is independent of a 4-desaturase
HARS (cytosolic histidyl tRNA synthetase) catalyzes the reaction of histidine, tRNA(His), and ATP to form His-tRNA(His), AMP, and pyrophosphate (Lee et al. 2002).
QARS (cytosolic glutaminyl tRNA synthetase) catalyzes the reaction of glutamine, tRNA(Gln), and ATP to form Gln-tRNA(Gln), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex. The same gene encodes both the cytosolic and mitochondrial QARS enzymes (Lamour et al. 1994).
GARS (cytosolic glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54 residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot Marie Tooth disease and distal spinal muscular atrophy, two diseases characterized by axonal dysfunction (Antonellis et al. 2006)
Interaction between succinyl CoA synthetase and the heme-biosynthetic enzyme ALAS-E is disrupted in sideroblastic anemia
CARS (cytosolic cysteinyl tRNA synthetase) catalyzes the reaction of cysteine, tRNA(cys), and ATP to form Cys-tRNA(Cys), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homomultimer, probably a dimer (Davidson et al. 2001).
Multifunctional EPRS (cytosolic glutamyl prolyl tRNA synthetase) catalyzes the reaction of glutamate, tRNA(Glu), and ATP to form Glu tRNA(Glu), AMP, and pyrophosphate. The same enzyme also catalyzes the charging of tRNA(Pro) with proline. The enzyme is found in the cell as a component of the mutienzyme aminoacyl tRNA synthetase complex (Kaiser et al. 1994).
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
NARS (cytosolic asparaginyl tRNA synthetase) catalyzes the reaction of asparagine, tRNA(Asn), and ATP to form Asn-tRNA(Asn), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Beaulande et al. 1998).
DARS (cytosolic aspartyl tRNA synthetase) catalyzes the reaction of aspartate, tRNA(Asp), and ATP to form Asp-tRNA(Asp), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Escalante and Yang 1993).
AARS (cytosolic alanyl tRNA synthetase) catalyzes the reaction of alanine, tRNA(ala), and ATP to form Ala tRNA(Ala), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a monomer (Shiba et al. 1995). A mutation in the editing domain of the mouse Aars gene results in misincorporation of non-cognate amino acids into cellular proteins. This is associated with protein misfolding in Purkinje cells and a phenotype consistent with human ataxia (Lee et al. 2006).
RARS (cytosolic arginyl tRNA synthetase) catalyzes the reaction of arginine, tRNA(Arg), and ATP to form Arg-tRNA(Arg), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Ling et al. 2005).
Co-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. Thus the time that it takes for pol II to synthesize each intron defines a minimal time and distance along the gene in which splicing factors can be recruited. The time that it takes for pol II to reach the end of the gene defines the maximal time in which splicing could occur co-transcriptionally. Thus, the kinetics of transcription can affect the kinetics of splicing.Any covalent change in a primary (nascent) mRNA transcript is mRNA Processing. For successful gene expression, the primary mRNA transcript needs to be converted to a mature mRNA prior to its translation into polypeptide. Eucaryotic mRNAs undergo a series of complex processing reactions; these begin on nascent transcripts as soon as a few ribonucleotides have been synthesized during transcription by RNA Polymerase II, through the export of the mature mRNA to the cytoplasm, and culminate with mRNA turnover in the cytoplasm.
Identification of 14 novel GLB1 mutations, including five deletions, in 19 patients with GM1 gangliosidosis from South America
Basic Medical Biochemistry: A Clinical Approach, 2nd ed (Book): 527
The GAP gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GSK3A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The HYOU1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The KDELR3 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The PDIA5 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins
The ATP6VOD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DDX11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DNAJB11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DNAJB9 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Recent progress in structure-function analyses of Nramp proton-dependent metal-ion transporters
IRE1-alpha is a single-pass transmembrane protein that resides in the endoplasmic reticulum (ER) membrane. The C-terminus of IRE1-alpha is located in the cytosol; the N-terminus is located in the ER lumen. In unstressed cells IRE1-alpha exists in an inactive heterodimeric complex with BiP such that BiP in the ER lumen binds the N-terminal region of IRE1-alpha. Upon accumulation of unfolded proteins in the ER, BiP binds the unfolded protein and the IRE1-alpha:BiP complex dissociates. The dissociated IRE1-alpha then forms homodimers. Initially the luminal N-terminal regions pair. This is followed by trans-autophosphorylation of IRE1-alpha at Ser724 in the cytosolic C-terminal region. The phosphorylation causes a conformational change that allows the dimer to bind ADP, causing a further conformational change to yield back-to-back pairing of the cytosolic C-terminal regions of IRE1-alpha. The fully paired IRE1-alpha homodimer has endoribonuclease activity and cleaves the mRNA encoding Xbp-1. A 26 residue polyribonucleotide is released and the 5' and 3' fragments of the original Xbp-1 mRNA are rejoined. The spliced Xbp-1 message encodes Xbp-1 (S), a potent activator of transcription. Xbp-1 (S) together with the ubiquitous transcription factor NF-Y bind the ER Stress Responsive Element (ERSE) in a number of genes encoding chaperones. Recent data suggest that the IRE1-alpha homodimer can also cleave specific subsets of mRNAs, including the insulin (INS) mRNA in pancreatic beta cells.
Once dissociated from BiP, PERK (EIF2AK3) monomers form homodimers, the active form of the protein.
The WIPI1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
Xbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotrimer, binds the CCAAT portion of the ERSE and together the IRE1-alpha: NF-Y complex activates transcription of a set of chaperone genes including DNAJB9, EDEM, RAMP4, p58IPK, and others. This results in an increase in protein folding activity in the ER.
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
The C-terminal domain of PERK (EIF2AK3) has kinase activity when PERK homodimerizes. PERK kinase specifically phosphorylates Ser52 of eIF2-alpha, causing an arrest in translation. The result is that translation of ER-targeted proteins is halted on ribosomes in the vicinity of activated PERK. The general arrest of translation results in the loss of short-lived proteins such as Cyclin D1, causing an arrest of the cell cycle in G1.
The SRPR gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The Sec31A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The TSPYL2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SRPRB gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SYVN1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
KARS (mitochondrial lysyl tRNA synthetase) catalyzes the reaction of lysine, tRNA(Lys), and ATP to form Lys-tRNA(Lys), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer. The same gene encodes both cytosolic and mitochondrial KARS enzymes (Shiba et al. 1997).
MARS2 (mitochondrial methionyl tRNA synthetase) catalyzes the reaction of methionine, mitochondrial tRNA(Met), and ATP to form Met-tRNA(Met), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Spencer et al. 2004).
YARS2 (mitochondrial tyrosyl tRNA synthetase) catalyzes the reaction of tyrosine, mitochondrial tRNA(Tyr), and ATP to form Tyr-tRNA(Tyr), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Bonnefond et al. 2005).
WARS2 (mitochondrial tryptophanyl tRNA synthetase) catalyzes the reaction of tryptophan, mitochondrial tRNA(Trp), and ATP to form Trp-tRNA(Trp), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Jorgensen et al. 2000).
Mitochondrial PPA2 (pyrophosphatase (inorganic) 2) catalyzes the hydrolysis of pyrophosphate to yield two molecules of orthophosphate. The enzyme requires Mg++ for activity (Curbo et al. 2006). The enzyme is inferred to be a homodimer by analogy to its cytosolic isoform.
VARS2 (mitochondrial valyl tRNA synthetase) catalyzes the reaction of valine, mitochondrial tRNA(val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The VARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
Induction of CHOP expression by amino acid limitation requires both ATF4 expression and ATF2 phosphorylation
PARS2 (mitochondrial prolyl tRNA synthetase) catalyzes the reaction of proline, mitochondrial tRNA(Pro), and ATP to form Pro-tRNA(Pro), AMP, and pyrophosphate. The PARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
FARS2 (mitochondrial phenylalanyl tRNA synthetase) catalyzes the reaction of phenylalanine, mitochondrial tRNA(Phe), and ATP to form Phe-tRNA(Phe), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a monomer (Bullard et al. 1999).
TARS2 (mitochondrial threonyl tRNA synthetase) catalyzes the reaction of threonine, mitochondrial tRNA(Thr), and ATP to form Thr-tRNA(Thr), AMP, and pyrophosphate. The TARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
SARS2 (mitochondrial seryl tRNA synthetase) catalyzes the reaction of serine, mitochondrial tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. SARS2 is a class II tRNA synthetase inferred from the biochemical properties of its bovine homologue to function as a dimer (Yokogawa et al. 2000).
The sites and topology of mitochondrial superoxide production
Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
A mitogen-activated protein kinase-dependent signaling pathway in the activation of platelet integrin alpha IIbbeta3
Mutations in the MMAA gene in patients with the cblA disorder of vitamin B12 metabolism
tRNA synthetases catalyze the ligation of tRNAs to their cognate amino acids in an ATP-dependent manner. The reaction proceeds in two steps. First, amino acid and ATP form an aminoacyl adenylate molecule, releasing pyrophosphate. The aminoacyl adenylate remains associated with the synthetase enzyme where, in the second step it reacts with tRNA to form aminoacyl tRNA and AMP. The rapid hydrolysis of pyrophosphate makes these reactions essentially irreversible under physiological conditions (Fersht and Kaethner 1976a). Specificity of the tRNA charging reactions is achieved both by specific recognition of amino acid and tRNA substrates by the synthetase, and by an editing process in which incorrect aminoacyl adenylate molecules (e.g., valyl adenylate associated with isoleucyl tRNA synthetase) are hydrolyzed rather than conjugated to tRNAs in the second step of the reaction (Baldwin and Berg 1966a,b; Fersht and Kaethner 1976b). The tRNA synthetases can be divided into two structural classes based on conserved amino acid sequence features (Burnbaum and Schimmel 1991). A single synthetase mediates the charging of all of the tRNA species specific for any one amino acid but, with three exceptions, glycine, lysine, and glutamine, the synthetase that catalyzes aminoacylation of mitochondrial tRNAs is encoded by a different gene than the one that acts on mitochondrial tRNAs. Both mitochondrial and cytosolic tRNA synthetase enzymes are encoded by genes in the nuclear genome. A number of tRNA synthetases are known to have functions distinct from tRNA charging (reviewed by Park et al. 2005). Additionally, mutations in several of the tRNA synthetases, often affecting protein domains that are dispensable in vitro for aminoacyl tRNA synthesis, are associated with a diverse array of neurological and other diseases (Antonellis and Green 2008; Park et al. 2008). These findings raise interest into the role of these enzymes in human development and disease.
Transcription of miRNA genes. Most miRNAs are transcribed by RNA polymerase II. The miRNAs may be autonomous transcription units or they may be located in other transcripts, including locations within introns and other untranslated regions. Of the polymerase II transcribed miRNAs, about 60% are located in introns of protein coding genes, 12 % are in introns of non-coding RNAs, 18% are in exons of non-coding RNAs, and 10% uncertain. A second class of miRNA genes are associated with Alu and other repetitive elements and are cotranscribed with these elements by RNA polymerase III. There are currently only a few proven examples of polymerase III transcribed miRNAs.
Mitochondrial tRNA synthetases act in the mitochondrial matrix to catalyze the reactions of tRNAs encoded in the mitochondrial genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate (Schneider et al. 2000). The synthetase enzymes that catalyze these reactions are all encoded in the nuclear genome. In three cases, glycine, lysine, and glutamine, a single gene encodes two enzyme isoforms, one cytosolic and one mitochondrial. All other mitochondrial tRNA synthetases are encoded by genes different from the ones encoding the corresponding cytosolic enzymes.
Superoxide can reduce cytochrome c in the intermembrane space (Wegerich et al. 2013, and inferred from other mammals in Butler et al. 1975, Koppenol et al. 1976, Butler et al. 1982). Superoxide has been shown in rat and mouse mitochondria to be released into the intermembrane space by the complex III of the respiratory chain (Han et al. 2001, Muller et al. 2004).
Vitamin B12 transport from food to the body's cells--a sophisticated, multistep pathway
Glutathione reductase (GSR) in the mitochondrial matrix regenerates reduced glutathione from oxidized glutathione and NADPH (Berkholz et al. 2008).
Mn superoxide dismutase (SOD2) is located in the mitochondrial matrix where it catalyzes the reaction of two molecules of superoxide (O2-.) to form one molecule of oxygen (O2) and one molecule of hydrogen peroxide (H2O2). Data from mouse liver indicate that respiratory complex I leaks superoxide into the matrix and respiratory complex III leaks superoxide into both the matrix and the intermembrane space (Muller et al. 2004). Because of its negative charge superoxide is unable to cross membranes, however hydrogen peroxide, a product of SOD2, is released from mitochondria to the cytosol in proportion to the proton potential (inferred from rat heart mitochondria in Boveris et al. 2006, Korshunov et al. 1997).
Many biosynthetic reactions are coupled to the cleavage of ATP to yield AMP and pyrophosphate. These reactions are typically freely reversible when carried out with purified substrates and enzymes in vitro. In vivo, however, the pyrophosphate is rapdily and essentially irreversibly hydrolyzed by a ubiquitous inorganic pyrophosphatase. This hydrolysis has the effect of pulling the first reaction strongly in the direction of biosynthesis, at the expense of two high-energy phosphate bonds. Studies of human cells have identified two forms of the enzyme, one localized to the cytosol and the other to the mitochondrial matrix (Raja et al. 1981).
5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
Gene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are processed. Most annotation is centered on the generation of messenger RNAs (mRNAs) by regulated RNA polymerase II (PolII) transcription, although the activities of PolI and PolIII are also covered briefly, as are some aspects of microRNA generation and function. Aspects of mRNA synthesis annotated here include the assembly of transcription factor complexes and their role in targeting specific genes for transcription, PolII-mediated transcription (RNA synthesis) itself, and the co- and post-translational processing of this RNA, via capping, splicing, and 3'-cleavage and polyadenylation to yield mature mRNA molecules that are exported from the nucleus. mRNA editing and nonsense-mediated decay are also annotated. Processes leading to mRNA breakdown are described: deadenylation-dependent mRNA decay, microRNA-mediated RNA cleavage, and regulation of mRNA stability by proteins that bind AU-rich elements. Other pathways included here are tRNA aminoacylation and snRNP assembly.
In this module, the biology of various types of regulatory non-coding RNAs are described. Currently, biogenesis and functions of small interfering RNAs (siRNAs) and microRNAs are annotated.
Biogenesis of microRNAs (miRNAs) can be summarized in five steps (reviewed in Ketting 2011, Nowotny and Yang 2009, Kim et al. 2009, Chua et al. 2009, Hannon and He 2004): 1. Transcription. miRNA transcripts may come from autonomously transcribed genes, they may be contained in cotranscripts with other genes, or they may be located in introns of host genes. Most miRNAs are transcribed by RNA polymerase II, however a few miRNAs originate as RNA polymerase III cotranscripts with neighboring repetitive elements. The initial transcript, termed a primary microRNA (pri-miRNA), contains an imperfectly double-stranded region within a hairpin loop. Longer sequences extend from the 5' and 3' ends of the hairpin and may also contain double-stranded regions. 2. Cleavage by Drosha. The 5' and 3' ends of the pri-miRNA are removed during endoribonucleolytic cleavage by the Drosha nuclease in a complex with the RNA-binding protein DGCR8 (the Microprocessor complex). The cleavage product is a short hairpin of about 60 to 70 nt called the pre-microRNA (pre-miRNA). 3. Nuclear export by Exportin-5. The resulting pre-miRNA is bound by Exportin-5 in a complex with Ran and GTP. The complex translocates the pre-miRNA through the nuclear pore into the cytoplasm. 4. Cleavage by Dicer. Once in the cytoplasm the pre-miRNA is bound and cleaved by the Dicer ribonuclease in complex with the RNA-binding protein TRBP (TAR binding protein). The product is an imperfectly double-stranded miRNA of about 21 to 23 nucleotides. At this stage the double-stranded miRNA has protruding single-stranded 3' ends of 2-3 nt. 5. Strand selection and incorporation into RNA-Induced Silencing Complex (RISC). At this stage the miRNA has two strands: the passenger strand, which will be removed and degraded, and the guide strand, which will be retained and guides the RISC to target mRNAs. An Argonaute protein is already bound to the Dicer:miRNA complex or subsequently binds the complex (the order is unknown). The human genome encodes 4 Argonaute proteins (AGO1 (EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4)), however only AGO2 (EIF2C2) can cleave target mRNAs with perfect or nearly perfect complementarity to the guide miRNA. In mammalian cells, such endogenous interactions are very rare; most miRNAs only cause translational repression. For complexes that contain AGO2, cleavage of the passenger strand of the double-stranded miRNA accompanies removal of the passenger strand. Complexes containing other Argonautes may use a helicase to remove the passenger strand but this is not fully known. The resulting single-stranded miRNA (the guide strand) remains in a complex containing Argonaute, Dicer, TRBP, and other proteins termed the RNA-induced Silencing Complex (RISC). The full set of proteins composing RISC is not yet known.
D-myo-Inositol 1,3,4,6-tetrakisphosphate
1D-myo-Inositol 1,3,4,6-tetrakisphosphate [ChEBI:809]
ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
ChEBI:16152 ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.
Calmodulin: a prototypical calcium sensor
LARS (cytosolic leucyl tRNA synthetase) catalyzes the reaction of leucine, tRNA(Leu), and ATP to form Leu-tRNA(Leu), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Ling et al. 2005).
IARS (cytosolic aspartyl tRNA synthetase) catalyzes the reaction of isoleucine, tRNA(Ile), and ATP to form Ile-tRNA(Ile), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Shiba et al. 1994).
MARS (cytosolic methionyl tRNA synthetase) catalyzes the reaction of methionine, tRNA(Met), and ATP to form Met-tRNA(Met), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Kaminska et al. 2001).
KARS (cytosolic lysyl tRNA synthetase) catalyzes the reaction of lysine, tRNA(Lys), and ATP to form Lys-tRNA(Lys), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex. The same gene encodes both cytosolic and mitochondrial KARS enzymes (Shiba et al. 1997).
SARS (cytosolic seryl tRNA synthetase) catalyzes the reaction of serine, tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Hartlein and Cusack 1995; Vincent et al. 1997).
Multifunctional EPRS (cytosolic glutamyl-prolyl tRNA synthetase) catalyzes the reaction of proline, tRNA(Pro), and ATP to form Pro-tRNA(Pro), AMP, and pyrophosphate. The same enzyme also catalyzes the charging of tRNA(Glu) with glutamate. The enzyme is found in the cell as a component of the mutienzyme aminoacyl-tRNA synthetase complex (Kaiser et al. 1994).
WARS (cytosolic tryptophanyl tRNA synthetase) catalyzes the reaction of tryptophan, tRNA(Trp), and ATP to form Trp-tRNA(Trp), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Bange et al. 1992; Rubin et al. 1991; Yu et al. 2004).
TARS (cytosolic threonyl tRNA synthetase) catalyzes the reaction of threonine, tRNA(Thr), and ATP to form Thr-tRNA(Thr), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Pan et al. 1982).
VARS (cytosolic valyl tRNA synthetase) catalyzes the reaction of valine, tRNA(Val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Vilalta et al. 1993).
YARS (cytosolic tyrosyl tRNA synthetase) catalyzes the reaction of tyrosine, tRNA(Tyr), and ATP to form Tyr tRNA(Tyr), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Yang et al. 2003). Mutations in the YARS gene are associated with dominant-intermediate Charcot-Marie-Tooth disease â a form of peripheral neuropathy characterized by axon and Schwann cell dysfunction (Jordanova et al. 2006).
Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase)
Cytosolic PPA1 (pyrophosphatase (inorganic) 1) catalyzes the hydrolysis of pyrophosphate to yield two molecules of orthophosphate. The enzyme, a homodimer, requires Mg++ for activity (Fisher et al. 1974; Pynes and Younathan 1967; Thuiller et al. 1978).
DARS2 (mitochondrial aspartyl tRNA synthetase) catalyzes the reaction of aspartate, mitochondrial tRNA(Asp), and ATP to form Asp tRNA(Asp), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Bonnefond et al. 2005). Homozygosity for DARS2 mutations is associated with leukoencephalopathy with brainstem and spinal cord involvement plus lactate elevation (Scheper et al 2007).
NARS2 (mitochondrial asparaginyl tRNA synthetase) catalyzes the reaction of asparagine, mitochondrial tRNA(Asn), and ATP to form Asn-tRNA(Asn), AMP, and pyrophosphate. The NARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
AARS2 (mitochondrial alanyl tRNA synthetase) catalyzes the reaction of alanine, mitochondrial tRNA(Ala), and ATP to form Ala-tRNA(Ala), AMP, and pyrophosphate. The AARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005).
HARS2 (mitochondrial histidyl tRNA synthetase) catalyzes the reaction of histidine, mitochondrial tRNA(His), and ATP to form His-tRNA(His), AMP, and pyrophosphate. The enzyme is a class II tRNA synthetase (O'Hanlon et al. 1995).
GARS (mitochondrial glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly-tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54-residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot-Marie-Tooth disease (Antonellis et al. 2007).
Analysis of GPIIb/IIIa receptor number by quantification of 7E3 binding to human platelets
QARS (mitochondrial glutaminyl tRNA synthetase) catalyzes the reaction of glutamine, tRNA(Gln), and ATP to form Gln-tRNA(Gln), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase. The same gene encodes both the cytosolic and mitochondrial QARS enzymes (Lamour et al. 1994).
EARS2 (mitochondrial glutamyl tRNA synthetase) catalyzes the reaction of glutamate, mitochondrial tRNA(Glu), and ATP to form Glu-tRNA(Glu), AMP, and pyrophosphate. The EARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
LARS2 (mitochondrial leucyl tRNA synthetase) catalyzes the reaction of leucine, mitochondrial tRNA(Leu), and ATP to form Leu-tRNA(Leu), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Bullard et al. 2000).
L-Glutamate 5-semialdehyde [ChEBI:17232]
Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.
Stable dimeric assembly of the second membrane-spanning domain of CFTR (cystic fibrosis transmembrane conductance regulator) reconstitutes a chloride-selective pore
Eukaryotic mRNA cap binding protein: purification by affinity chromatography on sepharose-coupled m7GDP.
Insulin/IGF-I and related signaling pathways regulate aging in nondividing cells: from yeast to the mammalian brain
A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis
A tyrosine-phosphorylated carboxy-terminal peptide of the fibroblast growth factor receptor (Flg) is a binding site for the SH2 domain of phospholipase C-gamma 1
Localization, regulation and function of type II phosphatidylinositol 5-phosphate 4-kinases
Nitric oxide stimulates guanylate cyclase
The bisretinoids of retinal pigment epithelium
(7Z,10Z,13Z,16Z)-3-oxodocosatetraenoyl-CoA [ChEBI:63821]
From glycosylation disorders to dolichol biosynthesis defects: a new class of metabolic diseases
The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast.
Zippers make signals: NCAM-mediated molecular interactions and signal transduction
1-phosphatidyl-1D-myo-inositol 3-phosphate [ChEBI:17283]
MicroRNAs: genomics, biogenesis, mechanism, and function
AKT/PKB signaling: navigating downstream
Purification and kinetic properties of human erythrocyte Mg2+-dependent inorganic pyrophosphatase
Caspase cleavage product of BAP31 induces mitochondrial fission through endoplasmic reticulum calcium signals, enhancing cytochrome c release to the cytosol
The human Aquaporin-5 gene. Molecular characterization and chromosomal localization
Structural mechanism of muscle contraction
Mitotic lamin disassembly is triggered by lipid-mediated signaling
Identification and molecular characterization of acyl-CoA synthetase in human erythrocytes and erythroid precursors
Regulation of protein synthesis by hypoxia via activation of the endoplasmic reticulum kinase PERK and phosphorylation of the translation initiation factor eIF2alpha
Phase 1 - Functionalization of compounds
alpha-D-Glucose 6-phosphate [ChEBI:17665]
Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
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Cardiolipin hydrolysis by human phospholipases A2. The multiple enzymatic activities of human cytosolic phospholipase A2
The glucose-lactic acid cycle and gluconeogenesis
Cell lines from kidney proximal tubules of a patient with Lowe syndrome lack OCRL inositol polyphosphate 5-phosphatase and accumulate phosphatidylinositol 4,5-bisphosphate
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Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis
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Human acyl-CoA:diacylglycerol acyltransferase is a tetrameric protein
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Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
Triggering and amplifying pathways of regulation of insulin secretion by glucose
GSR catalyzes glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
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Mammalian class Sigma glutathione S-transferases: catalytic properties and tissue-specific expression of human and rat GSH-dependent prostaglandin D2 synthases
Diffusion of inactive Arf1-GDP from membrane
Coatomer:Arf1-GTP:GAP lattice formation on golgi membrane
Sculpting and pinching-off of Golgi vessicle
GAP Recruitment to the Coatomer:Arf1-GTP Complex
PRDX1,2,5 catalyze TXN reduced + H2O2 => TXN oxidized + 2H2O
PRDX5 reduces peroxynitrite to nitrite using TXN
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A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon
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cDNA cloning of human R-type pyruvate kinase and identification of a single amino acid substitution (Thr384----Met) affecting enzymatic stability in a pyruvate kinase variant (PK Tokyo) associated with hereditary hemolytic anemia
Diacylglycerol, when simplicity becomes complex
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New insights into the regulation of T cells by gamma(c) family cytokines
Recognition and association of DNA glycosylase with site containing an affected purine
Tyrosine residues in phospholipase Cgamma 2 essential for the enzyme function in B-cell signaling
Characterization of bovine endothelial nitric oxide synthase as a homodimer with down-regulated uncoupled NADPH oxidase activity: tetrahydrobiopterin binding kinetics and role of haem in dimerization
CLOCK/BMAL1 regulates human nocturnin transcription through binding to the E-box of nocturnin promoter
The enzymic chain elongation of fatty acids by rat-liver microsomes
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
Homologous recombinational repair of DNA ensures mammalian chromosome stability
Inborn errors of cobalamin absorption and metabolism
Am J Med Genet C Semin Med Genet 157:33-44
Metabolism of gammalinolenic acid in human neutrophils
The generation of insulin-containing secretory granules from proinsulin in the lumen of the endoplasmic reticulum (ER) can be described in 4 steps: formation of intramolecular disulfide bonds, formation of proinsulin-zinc-calcium complexes, proteolytic cleavage of proinsulin to yield insulin, translocation of the granules across the cytosol to the plasma membrane. Transcription of the human insulin gene INS is activated by 4 important transcription factors: Pdx-1, MafA, Beta2/NeuroD1, and E47. The transcription factors interact with each other at the promoters of the insulin gene and act synergistically to promote transcription. Expression of the transcription factors is upregulated in response to glucose. The preproinsulin mRNA is translated by ribosomes at the rough endoplasmic reticulum (ER) and the preproinsulin enters the secretion pathway by virtue of its signal peptide, which is cleaved during translation to yield proinsulin. Evidence indicates that the preproinsulin mRNA is stabilized by glucose. In the process annotated in detail here, within the ER, three intramolecular disulfide bonds form between cysteine residues in the proinsulin. Formation of the bonds is the spontaneous result of the conformation of proinsulin and the oxidizing environment of the ER, which is maintained by Ero1-like alpha The cystine bonded proinsulin then moves via vesicles from the ER to the Golgi Complex. High concentrations of zinc are maintained in the Golgi by zinc transporters ZnT5, ZnT6, and ZnT7 and the proinsulin forms complexes with zinc and calcium. Proinsulin-zinc-calcium complexes bud in vesicles from the trans-Golgi to form immature secretory vesicles (secretory granules) in the cytosol. Within the immature granules the endoproteases Prohormone Convertase 1/3 and Prohormone Convertase 2 cleave at two sites of the proinsulin and Carboxypeptidase E removes a further 4 amino acid residues to yield the cystine-bonded A and B chains of mature insulin and the C peptide, which will also be secreted with the insulin. The insulin-zinc-calcium complexes form insoluble crystals within the granule The insulin-containing secretory granules are then translocated across the cytosol to the inner surface of the plasma membrane. Translocation occurs initially by attachment of the granules to Kinesin-1, which motors along microtubules, and then by attachment to Myosin Va, which motors along the microfilaments of the cortical actin network. A pancreatic beta cell contains about 10000 insulin granules of which about 1000 are docked at the plasma membrane and 50 are readily releasable in immediate response to stimulation by glucose or other secretogogues. Docking is due to interaction between the Exocyst proteins EXOC3 on the granule membrane and EXOC4 on the plasma membrane. Exocytosis is accomplished by interaction between SNARE-type proteins Syntaxin 1A and Syntaxin 4 on the plasma membrane and Synaptobrevin-2/VAMP2 on the granule membrane. Exocytosis is a calcium-dependent process due to interaction of the calcium-binding membrane protein Synaptotagmin V/IX with the SNARE-type proteins.
After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the internal peptide bond cleavages that activate proenzymes, the attachment of oligosaccharide moieties to membrane-bound and secreted proteins, the attachment of lipid or glycolipid moieties that serve to anchor proteins to cellular membranes, and the vitamin K-dependent attachment of carboxyl groups to glutamate residues.
The BIP (HSPA5) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Peptide hormones are cleaved from larger precursors in the secretory system (endoplasmic reticulum, Golgi apparatus, secretory granules) of the cell. After secretion peptide hormones are modified and degraded by extracellular proteases.
The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
The Endoplasmin (HSP90B1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
Cyclic nucleotides and phosphodiesterases in platelets
SUMO is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). UBC9 is the only known E2 enzyme for SUMO and on certain substrates such as RanGAP1 may act without the requirement of an E3 ligase.
Small Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Hay 2013, Hannoun et al. 2010, Gareau and Lima 2010, Wilkinson and Henley 2010, Wang and Dasso 2009). Proteomic methods have yielded estimates of hundreds of target proteins. Targets are mostly located in the nucleus and therefore SUMOylation disproportionately affects gene expression. SUMOs are initially translated as proproteins possessing extra amino acid residues at the C-terminus which are removed by the SUMO processing endoproteases SENP1,2,5 (Hay 2007). Different SENPs have significantly different efficiencies with different SUMOs. The processing exposes a glycine residue at the C-terminus that is activated by ATP-dependent thiolation at cysteine-173 of UBA2 in a complex with SAE1, the E1 complex. The SUMO is transferred from E1 to cysteine-93 of a single E2 enzyme, UBC9 (UBE2I). UBC9 with or, in some cases, without an E3 ligase conjugates the glycine C-terminus of SUMO to an epsilon amino group of a lysine residue on the target protein. SUMO2 and SUMO3 may then be further polymerized, forming chains. SUMO1 is unable to form polymers. Conjugated SUMO can act as a biinding site for proteins possessing SUMO interaction motifs (SIMs) and can also directly affect the formation of complexes between the target protein and other proteins. Conjugated SUMOs are removed by cleavage of the isopeptide bond by processing enzymes SENP1,2,3,5. The processing enzymes SENP6 and SENP7 edit chains of SUMO2 and SUMO3.
The initial translation products of SUMO1, SUMO2, and SUMO3 are precursors that have extra amino acid residues at the C-terminus (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010, Hay 2007). SUMO1 has 4 extra residues, SUMO2 has 2 extra residues, and SUMO3 has 11 extra residues. Proteolytic cleavage by SUMO peptidases (SENPs) removes the propeptide and leaves diglycine residues at the C-terminus. Each SENP has distinct preferences for certain SUMOs. SENP1 has highest activity on SUMO1; SENP2 and SENP5 have highest activity on SUMO2 (Shen et al. 2006, Reverter and Lima 2006, Mikolajczyk et al. 2007). SENP1 and SENP2 are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006) and SENP5 is predominantly nucleolar (Di Bacco et al. 2006, Gong and Yeh 2006), therefore the processing reactions are believed to occur in the nucleus. The processed SUMO is then activated by formation of a thioester bond with a cysteine residue of an E1 enzyme, UBA2 (SAE2) in a complex with SAE1. SUMO is then transferred from the E1 enzyme to an E2 enzyme, UBC9 (UBE2I).
Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit
Conversion of Phosphatidylcholine to Phosphatidylglycerol with Phospholipase D and glycerol
The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO3 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO3 to yield pyrophosphate and a transient intermediate, SUMO3 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO2 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO2 to yield pyrophosphate and a transient intermediate, SUMO2 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO1 and cysteine-173 of UBA2 (Desterro et al. 1999, Okuma et al. 1999, Werner et al. 2009, Olsen et al. 2010, Wang and Chen 2010). ATP reacts with the C-terminal glycine residue of SUMO1 to yield pyrophosphate and a transient intermediate, SUMO1 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
Structural determinants of water permeation through aquaporin-1
SUMO1, 2, and 3 are initially expressed as propeptides containing extra residues at the C-terminus. (SUMO1 has 4 residues, SUMO2 has 2 residues, and SUMO3 has 11 residues,) SENP1, 2, and 5 are endoproteases that process the precursors to produce the mature peptides (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). SENP1 processes SUMO1 with greater efficiency than SUMO2 or SUMO3. SENP2 and SENP5 process SUMO2 with greater efficiency than SUMO1 or SUMO3 (Gong and Yeh 2006, Mikolajczyk et al. 2007). SENP1 shuttles between the cytosol and nuceoplasm and is predominantly nuclear (Bailey and O'hare 2004, Kim et al. 2005). SENP2 also shuttles (Itahana et al. 2006) and is mainly located on nucleoplasmic filaments of the nuclear pore complex (Hang and Dasso 2002, Zhang et al. 2002). SENP5 is located mostly in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
SUMO3 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Tatham et al. 2001, Werner et al. 2009).
SUMO2 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Tatham et al. 2001, Werner et al. 2009).
SUMO1 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Desterro et al. 1999, Okuma et al. 1999, Tatham et al. 2003, Lois and Lima 2005, Wang et al. 2007, Werner et al. 2009). The UbL domain of E1 recruits E2 into proximity for the transfer of SUMO (Lois and Lima 2005, Wang et al. 2009),
The UBA2:SAE1 complex catalyzes the formation of a thioester linkage between the C-terminal glycine of the mature SUMO and a cysteine residue (cysteine-173) in UBA2 (SAE2) (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). During the process the C-terminal glycine residue of SUMO is reacted with ATP to yield pyrophosphate and a transient intermediate, SUMO adenylate. The SUMO adenylate then reacts with the thiol group of the cysteine residue of UBA2 (Olsen et al. 2010).
Human phosphoribosylpyrophosphate synthetase
The SUMO3 precursor has 11 extra residues at the C-terminus which can be removed endoproteolytically by SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Gong and Yeh 2006, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). Overall, processing of SUMO3 is the lowest of any SUMO (Mikolajczyk et al. 2007). SENP1 and SENP2 shuttle between the nucleus and cytosol and are predominantly nuclear (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006). SENP5 is located in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
The SUMO2 precursor has 2 extra residues at the C-terminus which can be removed endoproteolytically by SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Gong and Yeh 2006, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). SENP2 and SENP5 have highest activity on SUMO2, however the processing activity of SENP1 is higher overall (Mikolajczyk et al. 2007). SENP1 and SENP2 shuttle between the nucleus and cytosol and are predominantly nuclear (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006). SENP5 is located in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
Control of pyrimidine biosynthesis in human lymphocytes. Simultaneous increase in activities of glutamine-utilizing carbamyl phosphate synthetase and aspartate transcarbamylase in phytohemagglutinin-stimulated human peripheral lymphocytes and their enzyme co-purification
Subunit structures and stoichiometries of human DNA fragmentation factor proteins before and after induction of apoptosis
FYVE-DSP2, a FYVE domain-containing dual specificity protein phosphatase that dephosphorylates phosphotidylinositol 3-phosphate
1,2-diacyl-sn-glycero-3-phosphocholine [ChEBI:16110]
HDL as a target in the treatment of atherosclerotic cardiovascular disease
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Molecular mechanism of an oncogenic mutation that alters membrane targeting: Glu17Lys modifies the PIP lipid specificity of the AKT1 PH domain
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Dihydroxyacetone phosphate [ChEBI:16108]
The mechanism of a peptide bond requires the movement of three protons. First the deprotonation of the ammonium ion generates a reactive amine, allowing a nucleophilic attack on the carbonyl group. This is followed by the loss of a proton from the reaction intermediate, only to be taken up by the oxygen on the leaving group (from the end of the amino acid chain bound to the tRNA in the P-site). The peptide bond formation results in the net loss of one water molecule, leaving a deacylated-tRNA in the P-site, and a nascent polypeptide chain one amino acid larger in the A-site. For the purpose of illustration, the figures used in the section show one amino acid being added to a peptidyl-tRNA with a growing peptide chain.
At the beginning of this reaction, 1 molecule of 'eEF2', and 1 molecule of 'GTP' are present. At the end of this reaction, 1 molecule of 'eEF2:GTP' is present. This reaction takes place in the 'cytosol'.
The eEF1B complex binds to eEF1A and regulates its activity by catalyzing the release of GDP. Subsequently, GTP is able to bind eEF1A allowing the formation of the ternary complex (eEF1A-GTP-aa-tRNA).In metazoans eEF1 protein family is composed of four subunits: eEF1A and eEF1B alpha, beta, and gamma (formerly EF-1alpha, EF-1beta, EF-1delta, and EF-1gamma, respectively). Both eEF1B alpha and eEF1B beta function as nucleotide exchange proteins. eEF1B gamma associates with eEF1B alpha and stimulates its exchange activity. This process is illustrated below with a GTP molecule in white and eEF1A protein in yellow.The three subunits of eEF1B are also shown.
3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
The process for translation of a protein destined for the endoplasmic reticulum (ER) branches from the canonical cytoslic translation process at the point when a nascent polypeptide containing a hydrophobic signal sequence is exposed on the surface of the cytosolic ribosome:mRNA:peptide complex. The signal sequence mediates the interaction of this complex with a cytosolic signal recognition particle (SRP) to form a complex which in turn docks with an SRP receptor complex on the ER membrane. There the ribosome complex is transferred from the SRP complex to a translocon complex embedded in the ER membrane and reoriented so that the nascent polypeptide protrudes through a pore in the translocon into the ER lumen. Translation, which had been halted by SRP binding, now resumes, the signal peptide is cleaved from the polypeptide, and elongation proceeds, with the growing polypeptide oriented into the ER lumen.
The binding of eEF1A:GTP to aminoacyl tRNA (aa-tRNA) results in the formation of a ternary complex (eEF1A:GTP:aa-tRNA). Human eEF1A and rabbit eEF1A are 100% identical, and prokaryotic homologue of eEF1A (EF-Tu) shows 59% identity in the GTP-binding domain.This process is illustrated below with: a GTP molecule in white and eEF1A protein in yellow.
The cycle of elongation starts with an empty ribosomal A-site and the peptidyl-tRNA in the P-site. eEF1A is activated by GTP binding and allows for the subsequent binding of aminoacyl-tRNA (aa-tRNA).This process is illustrated below with a GTP molecule in white and eEF1A protein in yellow.
Once the correct codon-anticodon match occurs between the mRNA and aa-tRNA, the decoding event triggers GTP hydrolysis on eEF1A. The resulting conformational change releases the aa-tRNA to the A-site, and GDP bound form of eEF1A is released from the ribosome. This process is illustrated below with: an amino acyl-tRNA with an amino acid,a peptidyl-tRNA with a growing peptide and a ribosome with A,P and E sites to accommodate these two forms of tRNA.
Evidence for the presence of phospholipid hydroperoxide glutathione peroxidase in human platelets: implications for its involvement in the regulatory network of the 12-lipoxygenase pathway of arachidonic acid metabolism
Once the correct codon-anticodon match occurs between the mRNA and aa-tRNA, the decoding event triggers GTP hydrolysis on eEF1A. The resulting conformational change releases the aa-tRNA to the A-site, and GDP bound form eEF1A is released from the ribosome. Insight into the mechanics of this system has been obtained from earlier works with rabbit reticulocytes and the E.coli system. This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide and a ribosome with A,P and E sites to accommodate these two forms of tRNA.
Following peptide bond formation, GTP-bound eEF2 catalyzes the translocation of the deacylated tRNA in the P-site and the peptidyl-tRNA in the A-site (the pre-translocation state) into the E- and P- sites (the post-translocation state), respectively. Thus, the mRNA advances by three bases to expose the next codon in the A-site. After translocation, GDP-bound eEF2 leaves the ribosome to allow another round of elongation. eEF2 is reactivated by the release of GDP and binds GTP for subsequent rounds. This process is illustrated below with a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH and a ribosome with A,P and E sites to accommodate these three forms of tRNA is also shown.
The A- and P-sites of the ribosome positions the aa-tRNA and peptidyl-tRNA such that a nucleophilic attack can occur between the amine group of the A-site aa-tRNA and the carbonyl group of the growing peptide chain on the P-site tRNA, resulting in the formation of a peptide bond. The carboxyl end of the peptide chain is uncoupled from the tRNA molecule in the P-site and forms a new peptide bond with the amino acid that is in the A-site. This process is illustrated below with: a peptidyl-tRNA with a growing peptide,a deacylated tRNA with an -OH and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
IFI16 is an innate immune sensor for intracellular DNA
TriC/CCT forms a binary complex with unfolded alpha- or beta-tubulin (Frydman et al., 1992; Gao et al., 1993). The tubulin folding intermediates produced by TriC are unstable (Gao et al., 1993). Five additional protein cofactors (cofactor A-E) are required for the generation of properly folded alpha- and beta-tubulin and for the formation of alpha/beta-tubulin heterodimers (Gao et al., 1993) (Tian et al., 1997, Cowan and Lewis 2001).
Group II chaperonins enclose substrate proteins following substrate binding through the formation of a "built- in" lid over the central cavity. Upon ATP binding, lid formation is triggered by the transition state of ATP hydrolysis (Meyer, et al., 2003). In the case of CCT-mediated tubulin folding, one or more rounds of ATP hydrolysis are likely required before the association of non-exchangeable GTP with chaperonin-bound alpha tubulin.
Please note that this reaction was inferred from experiments performed using Saccharomyces cerevisiae.
The translation elongation cycle adds one amino acid at a time to a growing polypeptide according to the sequence of codons found in the mRNA. The next available codon on the mRNA is exposed in the aminoacyl-tRNA (aa-tRNA) binding site (A site) on the 30S subunit. A: Ternary complexes of aa -tRNA:eEF1A:GTP enter the ribosome and enable the anticodon of the tRNA to make a codon/anticodon interaction with the A-site codon of the mRNA. B: Upon cognate recognition, the eEF1A:GTP is brought into the GTPase activating center of the ribosome, GTP is hydrolyzed and eEF1A:GDP leaves the ribosome. C: The peptidyl transferase center of ribosome catalyses the formation of a peptide bond between the incoming amino acid and the peptide found in the peptidyl-tRNA binding site (P site). D: In the pre-translocation state of the ribosome, the eEF2:GTP enters the ribosome, physically translocating the peptidyl-tRNA out of the A site to P site and leaves the ribosome eEF2:GDP. This action of eEF2:GTP accounts for the precise movement of the mRNA by 3 nucleotides.Consequently, deacylated tRNA is shifted to the E site. A ribosome associated ATPase activity is proposed to stimulate the release of deacylated tRNA from the E site subsequent to translocation (Elskaya et al., 1991). In this post-translocation state, the ribosome is now ready to receive a new ternary complex. This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH, and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
At the beginning of this reaction, 1 molecule of 'eEF1B alpha', 1 molecule of 'eEF1B gamma', and 1 molecule of 'eEF1B beta' are present. At the end of this reaction, 1 molecule of 'eEF1B complex' is present. This reaction takes place in the 'cytosol'.
The interaction between CCT and unfolded target proteins is thought to occur when CCT is in its ADP-bound state. ADP is then exchanged for ATP in CCT.
Protein synthesis is accomplished through the process of translation of an mRNA sequence into a polypeptide chain. This process can be divided into three distinct stages: initiation, elongation and termination. During the initiation phase, the two subunits of the ribosome are brought together to the translation start site on the mRNA where the polypeptide chain is to begin. Extension of the polypeptide chain occurs when a specific aminoacyl-tRNA, as determined by the template mRNA, binds an elongating ribosome. The protein chain is released from the ribosome when any one of three stop codons in the relevant reading frame on the mRNA is reached. Individual reactions at each one of these stages are catalyzed by a number of initiation, elongation and release factors, respectively.
The arrival of any of the three stop codons (UAA, UAG and UGA) into the ribosomal A-site triggers the binding of a release factor (RF) to the ribosome and subsequent polypeptide chain release. In eukaryotes, the RF is composed of two proteins, eRF1 and eRF3. eRF1 is responsible for the hydrolysis of the peptidyl-tRNA, while eRF3 provides a GTP-dependent function. The ribosome releases the mRNA and dissociates into its two complex subunits, which can reassemble on another molecule to begin a new round of protein synthesis. It should be noted that at present, there is no factor identified in eukaryotes that would be the functional equivalent of the bacterial ribosome release (or recycling) factor, RRF, that catalyzes dissociation of the ribosome from the mRNA following release of the polypeptide
GM1-gangliosidosis (genetic beta-galactosidase deficiency): identification of four mutations in different clinical phenotypes among Japanese patients
Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:346-9
After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the vitamin K-dependent attachment of carboxyl groups to glutamate residues and the conversion of lysine residues to hypusine.
The reaction of EIF5A, spermidine, and NAD+ to form EIF5A(Dhp), 1,3-diaminopropane, and NADH + H+ is reversible in vitro. Under physiological conditions, the reverse reaction is probably minimized by the rapid, irreversible conversion of FIF5A(Dhp) to EIF5A(Hyp).
Cytosolic deoxyhypusine synthase catalyzes the reaction of EIF5A protein, spermidine, and NAD+ to convert lysine-50 of EIF5A to deoxyhypusine, generating 1,3-diaminopropane and NADH + H+ in the process (Park 2006). Although the reaction is reversible, the reverse reaction is probably minimized under physiological conditions by the rapid, irreversible conversion of EIF5A(Dhp) to EIF5A(Hyp).
Cytosolic eIF5A undergoes a unique two-step post-translational modification at Lys 50 via deoxyhypusine (Dhp) to hypusine (Hyp). In the first step deoxyhypusine synthase transfers the aminobutyl group of spermidine to the epsilon-amino group of lysine 50, using NAD+ as a cofactor. Hydroxylation of the C2 of the newly added moiety in the second step is catalyzed by deoxyhypusine hydroxylase/monooxygenase with molecular oxygen as the source. The molecular function of eIF5A is unknown, but the protein is required for viability in eukaryotic cells and its normal function requires hypusinylation. eIF5A is the only protein known to undergo hypusinylation (Park 2006).
Cytosolic deoxyhypusine hydroxylase catalyzes the irreversible conversion of peptidyl-deoxyhypusine to peptidyl-hypusine. The only known substrate for this enzyme is the modified lysine at residue 50 of eIF5A (Kang et al. 2007; Kim et al. 2006).
In the case of actin and tubulin folding, and perhaps other substrates, the emerging polypeptide chain is transferred from the ribosome to TRiC via Prefoldin (Vainberg et al., 1998).
adenosine 5'-monophosphate [ChEBI:16027]
Nucleotide-independent transfer of beta-actin from prefoldin to CCT occurs when prefoldin binds to CCT (Vainberg et al., 1998). Following ATP- dependent folding within CCT (Gao et al., 1992), beta-actin is released as a soluble, monomeric protein.
Due to the crowded envirnoment within the cell, many proteins must interact with molecular chaperones to attain their native conformation (reviewed in Young et al., 2004). Chaperones recognize and associate with proteins in their non-native state and facilitate their folding by stabilizing the conformation of productive folding intermediates. Chaperones that take part broadly in de novo protein folding, such as the Hsp70s and the chaperonins, facilitate the folding process through cycles of substrate binding and release regulated by their ATPase activity (see Young et al., 2004; Spiess et al., 2004; Bigotti and Clarke, 2008).
The eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and Willison, 2008). CCT/TRiC is an example of a type II chaperonin, defined (in contrast to type I) as functioning in the absence of a cochaperonin. TriC/CCT is a multisubunit toroidal complex that forms a cylinder containing two back-to-back stacked rings enclosing a cavity where substrate folding occurs in an ATP dependent process (reviewed in Altschuler and Willison, 2008 ). CCT/TriC contains eight paralogous subunits that are conserved throughout eukaryotic organisms (Leroux and Hartl 2000; Archibald et al. 2001; Valpuesta et al. 2002). CCT-mediated folding of non-native substrate protein involves capture through hydrophobic contacts with multiple chaperonin subunits followed by transfer of the protein into the central ring cavity where it folds. Although folding is initiated within this central cavity, only 5%-20% of proteins that are released have partitioned to the native state. The remaining portion is then recaptured by other chaperonin molecules (Cowan and Lewis 2001). This cycling process may be repeated multiple times before a target protein partitions to the native state. In the cell, binding to CCT occurs via presentation of target protein bound to upstream chaperones. During translation, the emerging polypeptide chain may be transferred from the ribosome to CCT via the chaperone Prefoldin (Vainberg et al., 1998) or the Hsp70 chaperone machinery (Melville et al., 2003). While the majority of CCT substrates ultimately partition to the native state as soluble, monomeric proteins, alpha and beta tubulin are unusual in that they require additional cofactors that are required to assemble the tubulin heterodimer (Cowan and Lewis 2001).
Glucosamine-fructose 6-phosphate aminotransferases 1 and 2 (GFPT1,2) are the first and rate-limiting enzymes in the hexosamine synthesis pathway, and thus formation of hexosamines like N-acetylglucosamine (GlcNAc). These enzymes probably plays a role in limiting the availability of substrates for the N- and O- linked glycosylation of proteins (McKnight et al. 1992, Oki et al. 1999). GFPT1 and 2 are required for normal functioning of neuromuscular synaptic transmission. Defects in GFPT1 leads to altered muscle fibre morphology and impaired neuromuscular junction development (Senderek et al. 2011).
Dolichol is a polyisoprenol lipid comprised of five-carbon isoprene units linked linearly in a head-to-tail fashion. Almost all eukaryotic membranes contain dolichol and its phosphorylated form is used in the N-glycosylation of proteins where it is used as an anchor for the N-glycan sugar to the ER membrane, and as an initiation point for the synthesis. Dolichol biosynthesis occurs on the cytoplasmic face of the ER membrane, which is where N-glycosylation occurs too, so is perfectly placed to serve as a substrate for this process. Dolichyl phosphate can be obtained either from direct phosphorylation of dolichol, formed in a series of reactions from mevalonate 5-pyrophosphate, or a salvage reaction by de-phosphorylation of dolichyl diphosphate, released at the end of N-glycan biosynthesis (Cantagrel & Lefeber 2011).
Dolichol kinase (DOLK, TMEM15) mediates the phosphorylation of dolichol (DCHOL) to form dolichyl phosphate (DOLP) in the ER membrane (Fernandez et al. 2002). Defects in DOLK cause congenital disorder of glycosylation type 1M (CDG1M aka dolichol kinase deficiency; MIM:610768), a severe mutisystem disorder characterised by under-glycosylated serum glycoproteins which results in nervous system under-development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Death occurs in early life (Kranz et al. 2007).
Polyprenol reductase (SRD5A3), resident on the endoplasmic reticulum membrane, mediates the reduction of the alpha-isoprene unit of polyprenol (pPNOL) to form dolichol (DCHOL) in a NADPH-dependent manner (Cantagrel et al. 2010). Defects in SRD5A3 cause congenital disorder of glycosylation 1q (SRD5A3-CDG, CDG1Q; MIM:612379), a neurodevelopmental disorder characterised by under-glycosylated serum glycoproteins resulting in nervous system development, psychomotor retardation, hypotonia, coagulation disorders and immunodeficiency (Cantagrel et al. 2010, Kasapkara et al. 2012). Defects in SRD5A3 can also cause Kahrizi syndrome (KHRZ; MIM:612713), a neurodevelopmental disorder characterised by mental retardation, cataracts, coloboma, kyphosis, and coarse facial features (Kahrizi et al. 2011).
The ER membrane-associated enzyme dehydrodolichyl diphosphate synthase (DHDDS) mediates the sequential head-to-tail cis addition of multiple isopentyl pyrophosphate (IPP) molecules to farnesyl pyrophosphate (E,E-FPP) to produce polyprenol pyrophosphate (pPPP) (Shridas et al. 2003). Dolichol in humans contain homologues ranging from 17-23 isoprene units, the most common homologues contain 19 or 20 isoprene units (Freeman et al. 1980). Defects in DHDDS cause retinitis pigmentosa 59 (RP59; MIM:613861), a pigment retinopathy, characterised by retinal pigment deposits (visible on fundus examination) and primary loss of rod photoreceptors followed by secondary loss of cone photoreceptors. Sufferers typically have night vision blindness and loss of mid to peripheral vision. As the condition progresses, they lose far peripheral vision and eventually central vision (Zuchner et al. 2011).
Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of eleven reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring. As a nascent protein fated to become GPI-anchored moves into the lumen of the endoplasmic reticulum, it is attacked by a transamidase complex that cleaves it near its carboxy terminus and attaches an acylated GPI moiety. The GPI moiety is deacylated, yielding a protein-GPI conjugate that can be efficiently transported to the Golgi apparatus.
Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of nine reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring. This pathway is shown in the figure. Two additional reactions, not shown, allow the synthesis of variant forms of GPI, one with an additional mannose residue and one with an additional ethanolamine (Tauron et al. 2004; Shishioh et al. 2005). These variant GPI molecules may be used for tissue-specific protein modifications, or may function independently. The steps of GPI synthesis were first identified by isolating large numbers of mutant cell lines that had lost the ability to express GPI anchored proteins on their surfaces. Somatic cell hybrid analyses of these lines allowed the definition of complementation groups corresponding to distinct mutated genes, and cDNAs corresponding to normal forms of these genes were identified on the basis of their abilities to restore normal cell surface protein expression in mutant cells. Co-precipitation experiments with tagged cloned proteins have allowed the identification of additional proteins involved in GPI anchor biosynthesis.
In the eighth reaction of GPI synthesis, a third mannose residue is added, catalyzed by PIG-B (Takahashi et al. 1996).
In the second step of GPI synthesis, N-acetylglucosaminyl-PI is hydrolyzed to yield glucosaminyl-PI and acetate. The phosphatidylinositol (PI) derivatives involved in this reaction are located in the endoplasmic reticulum membrane, as is the PIG-L enzyme that catalyzes it (Sharma et al. 1999; Pottekat and Menon 2004).
In the fourth step of GPI synthesis, an acyl group (typically palmitate) is transferred from acyl CoA to glucosaminyl-PI. Mutagenesis and cloning studies suggest that a single protein, PIG-W, catalyzes this reaction (Murakami et al. 2003).
Molecular aspects of the adenine nucleotide carrier from mitochondria
Calcium, as the ion Ca2+, is essential in many biological processes. The majority of Ca2+ in many organisms is bound to phosphates which form skeletal structures and also buffer Ca2+ levels in extracellular fluids (typically 1 millimolar). Intracellular free Ca2+, by contrast, is 10,000 times lower than the outside of the cell (typically 10 micromolar). This concentration gradient is used to import Ca2+ into cells where it acts as a second messenger.
The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. PLC hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions.
When dissociated Galpha-GTP and Gbeta-gamma can activate or inhibit different signalling cascades and effector proteins. The precise pathways depends on the identity of the alpha and beta/gamma subtypes.
PP2B (calcineurin) is a calcium-dependent, calmodulin-stimulated protein phosphatase. It comprises of two components; a catalytic subunit and a regulatory subunit which confers calcium sensitivity to the complex. PP2B is in equilibrium between active and inactive forms. Because the affinity of calmodulin for the active form is higher than for the inactive form, it stabilises PP2B.
Dopamine- and cAMP-regulated phosphoprotein, Mr 32 kDa (DARPP-32), was identified as a major target for dopamine and protein kinase A (PKA) in striatum. Recent advances now indicate that regulation DARPP-32 phosphorylation provides a mechanism for integrating information arriving at dopaminoceptive neurons, in multiple brain regions, via a variety of neurotransmitters, neuromodulators, neuropeptides, and steroid hormones. Activation of PKA or PKG stimulates DARPP-32 phosphorylation at Thr34, converting DARPP-32 into a potent inhibitor of protein phosphatase-1 (PP-1). DARPP-32 is also phosphorylated at Thr75 by Cdk5, converting DARPP-32 into an inhibitor of PKA. Thus, DARPP-32 has the unique property of being a dual-function protein, acting either as an inhibitor of PP-1 or of PKA.
Opioids are chemical substances similar to opiates, the active substances found in opium (morphine, codeine etc.). Opioid action is mediated by the receptors for endogenous opioids; peptides such as the enkephalins, the endorphins or the dynorphins. Opioids possess powerful analgesic and sedative effects, and are widely used as pain-killers. Their main side-effect is the rapid establishment of a strong addiction. Opioids receptors are G-protein coupled receptors (GPCR). There are four classes of receptors: mu (MOR), kappa (KOR) and delta (DOR), and the nociceptin receptor (NOP).
Gastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic factor for gastrointestinal epithelial cells. Gastrin has two biologically active peptide forms, G34 and G17.Gastrin gene expression is upregulated in both a number of pre-malignant conditions and in established cancer through a variety of mechanisms. Depending on the tissue where it is expressed and the level of expression, differential processing of the polypeptide product leads to the production of different biologically active peptides. In turn, acting through the classical gastrin cholecystokinin B receptor CCK-BR, its isoforms and alternative receptors, these peptides trigger signalling pathways which influence the expression of downstream genes that affect cell survival, angiogenesis and invasion (Wank 1995, de Weerth et al. 1999, Grabowska & Watson 2007)
G protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors in humans, accounting for more than 1% of the protein-coding capacity of the human genome. All known GPCRs share a common architecture of seven membrane-spanning helices connected by intra- and extracellular loops. The extracellular loops contain two highly-conserved cysteine residues that form disulphide bonds to stabilize the structure of the receptor. They recognize diverse messengers such as light, odorants, small molecules, hormones and neurotransmitters. Most GPCRs act as guanine nucleotide exchange factors; activated by ligand binding, they promote GDP-GTP exchange on associated heterotrimeric guanine nucleotide-binding (G) proteins. There are two models for GPCR-G Protein interactions: 1) ligand-GPCR binding first, then binding to G Proteins; 2) "Pre-coupling" of GPCRs and G Proteins before ligand binding (review Oldham WM and Hamm HE, 2008). These in turn activate effector enzymes or ion channels. GPCRs are involved in a range of physiological roles which include the visual sense, smell, behavioural regulation, functions of the autonomic nervous system and regulation of the immune system and inflammation. GPCRs are divided into 6 classes based on sequence homology and functional similarity; the main mammalian families are classes A/1-C/3; Class A/1 (Rhodopsin-like) Class B/2 (Secretin receptor family) Class C/3 (Metabotropic glutamate/pheromones) Class D/4 (fungal mating pheromone receptors) Class E/5 (cAMP receptors) Class F/6 (Frizzled/Smoothened) Here, those Class A/1 (Rhodopsin-like) receptors that bind peptide ligands have been annotated. The binding events mediated by other classes of receptors, as well as the downstream events triggered by receptor-ligand interactions will be annotated in future releases of Reactome.
Dephosphorylated NFAT-calcineurin (CaN) complex translocates to nucleus, where it activates transcription (Okamura et al, 2000; Demjek et al, 2006; Saneyoshi et al, 2002; reviewed in Hogan et al, 2003).
A number of so called non-canonical WNT ligands have been shown to promote intracellular calcium release upon FZD binding. This beta-catenin-independent WNT pathway acts through heterotrimeric G proteins and promotes calcium release through phophoinositol signaling and activation of phosphodiesterase (PDE). Downstream effectors include the calcium/calmodulin-dependent kinase II (CaMK2) and PKC (reviewed in De, 2011). The WNT Ca2+ pathway is important in dorsoventral polarity, convergent extension and organ formation in vertebrates and also has roles in negatively regulating 'canonical' beta-catenin-dependent transcription. Non-canonical WNT Ca2+ signaling is also implicated in inflammatory response and cancer (reviewed in Kohn and Moon, 2005; Sugimura and Li, 2010).
Aquaporin-3 water channel localization and regulation in rat kidney
Defective BTD causes biotidinase deficiency
Phosphorylated IGF1R binds and phosphorylates SHC1 (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). Phosphorylated SHC then binds GRB:SOS, which activates RAS-RAF-MAPK signaling.
The phosphorylated type 1 insulin-like growth factor receptor phosphorylates IR1, IRS2, IRS4 and possibly other IRS/DOK family members (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). The phosphorylated IRS proteins serve as scaffolds that bind the effector molecules PI3K and GRB2:SOS. PI3K then activates PKB (AKT) signaling while GRB2:SOS activates RAS-RAF-MAPK signaling.
Humans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelial cell line C57MG and to induce secondary axis formation in Xenopus (Wong et al, 1994; Du et al, 1995). So-called canonical WNTs, including Wnt1, 3, 3a and 7, initiate signaling pathways that destabilize the destruction complex and allow beta-catenin to accumulate and translocate to the nucleus where it promotes transcription (reviewed in Saito-Diaz et al, 2013). Non-canonical WNTs, including Wnt 2, 4, 5a, 5b, 6, 7b, and Wnt11 activate beta-catenin-independent responses that regulate many aspects of morphogenesis and development, often by impinging on the cytoskeleton (reviewed in van Amerongen, 2012). Two of the main beta-catenin-independent pathways are the Planar Cell Polarity (PCP) pathway, which controls the establishment of polarity in the plane of a field of cells, and the WNT/Ca2+ pathway, which promotes the release of intracellular calcium and regulates numerous downstream effectors (reviewed in Gao, 2012; De, 2011).
WNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Saito-Diaz et al, 2013; MacDonald et al, 2009). The pathway is named for the WNT ligands, a large family of secreted cysteine-rich glycoproteins. At least 19 WNT members have been identified in humans and mice with distinct expression patterns during development (reviewed in Willert and Nusse, 2012). These ligands can activate at least three different downstream signaling cascades depending on which receptors they engage. In the so-called 'canonical' WNT signaling pathway, WNT ligands bind one of the 10 human Frizzled (FZD) receptors in conjunction with the LRP5/6 co-receptors to activate a transcriptional cascade that controls processes such as cell fate, proliferation and self-renenwal of stem cells. Engagement of the FZD-LRP receptor by WNT ligand results in the stabilization and translocation of cytosolic beta-catenin to the nucleus where it is a co-activator for LEF (lymphoid enhancer-binding factor)- and TCF (T cell factor) -dependent transcription. In the absence of WNT ligand, cytosolic beta-catenin is phosphorylated by a degradation complex consisting of glycogen synthase kinase 3 (GSK3), casein kinase 1 (CK1), Axin and Adenomatous polyposis coli (APC), and subsequently ubiquitinated and degraded by the 26S proteasome (reviewed in Saito-Diaz et al, 2013; Kimmelman and Xu, 2006). In addition to the beta-catenin-dependent transcriptional response, WNT signaling can also activate distinct non-transcriptional pathways that regulate cell migration and polarity. These beta-catenin-independent 'non-canonical' pathways signal through Frizzled receptors independently of LRP5/6, or occur through the tyrosine kinase receptors ROR and RYK (reviewed in Veeman et al, 2003; James et al, 2009). Non-canonical WNT pathways are best studied in Drosophila where the planar cell polarity (PCP) pathway controls the orientation of wing hairs and eye facets, but are also involved in processes such as convergent extension, neural tube closure, inner ear development and hair orientation in vertebrates and mammals(reviewed in Seifert and Mlodzik, 2007; Simons and Mlodzik, 2008). In the PCP pathway, binding of WNT ligand to the FZD receptor leads to activation of small Rho GTPases and JNK, which regulate the cytoskeleton and coordinate cell migration and polarity (reviewed in Lai et al, 2009; Schlessinger et al, 2009). In some cases, a FZD-WNT interaction increases intracellular calcium concentration and activates CaMK II and PKC; this WNT calcium pathway promotes cell migration and inhibits the canonical beta-catenin dependent transcriptional pathway (reviewed in Kuhl et al, 2000; Kohn and Moon, 2005; Rao et al 2010). Binding of WNT to ROR or RYK receptors also regulates cell migration, apparently through activation of JNK or SRC kinases, respectively, however the details of these pathways remain to be worked out (reviewed in Minami et al, 2010). Although the WNT signaling pathways were originally viewed as discrete, linear pathways controlled by defined subsets of 'canonical' or 'non-canonical' ligands and receptors, the emerging evidence is challenging this notion. Instead, the specificity and the downstream response appear to depend on the particular cellular context and vary with species, tissue and stage of development (reviewed in van Amerongen and Nusse, 2009; Rao et al, 2010).
Leptin (LEP, OB, OBS), a circulating adipokine, and its receptor LEPR (DB, OBR) control food intake and energy balance and are implicated in obesity-related diseases (recently reviewed in Amitani et al. 2013, Dunmore and Brown 2013, Cottrell and Mercer 2012, La Cava 2012, Marroqui et al. 2012, Paz-Filho et al. 2012, Denver et al. 2011, Lee 2011, Marino et al. 2011, Morton and Schwartz 2011, Scherer and Buettner 2011, Shan and Yeo 2011, Wauman and Tavernier 2011, Dardeno et al. 2010, Bjorbaek 2009, Morris and Rui 2009, Myers et al. 2008), including cancer (Guo et al. 2012), inflammation (Newman and Gonzalez-Perez 2013, Iikuni et al. 2008), and angiogenesis (Gonzalez-Perez et al. 2013). The identification of spontaneous mutations in the leptin gene (ob or LEP) and the leptin receptor gene (Ob-R, db or LEPR) genes in mice opened up a new field in obesity research. Leptin was discovered as the product of the gene affected by the ob (obesity) mutation, which causes obesity in mice. Likewise LEPR is the product of the gene affected by the db (diabetic) mutation. Leptin binding to LEPR induces canonical (JAK2/STATs; MAPK/ERK 1/2, PI-3K/AKT) and non-canonical signaling pathways (PKC, JNK, p38 MAPK and AMPK) in diverse cell types. The binding of leptin to the long isoform of LEPR (OB-Rl) initiates a phosphorylation cascade that results in transcriptional activation of target genes by STAT5 and STAT3 and activation of the PI3K pathway(not shown here), the MAPK/ERK pathway, and the mTOR/S6K pathway. Shorter LEPR isoforms with truncated intracellular domains are unable to activate the STAT pathway, but can transduce signals by way of activation of JAK2, IRS-1 or ERKs, including MAPKs. LEPR is constitutively bound to the JAK2 kinase. Binding of LEP to LEPR causes a conformational change in LEPR that activates JAK2 autophosphorylation followed by phosphorylation of LEPR by JAK2. Phosphorylated LEPR binds STAT3, STAT5, and SHP2 which are then phosphorylated by JAK2. Phosphorylated JAK2 binds SH2B1 which then binds IRS1/2, resulting in phosphorylation of IRS1/2 by JAK2. Phosphorylated STAT3 and STAT5 dimerize and translocate to the nucleus where they activate transcription of target genes (Jovanovic et al. 2010). SHP2 activates the MAPK pathway. IRS1/2 activate the PI3K/AKT pathway which may be the activator of mTOR/S6K. Several isoforms of LEPR have been identified (reviewed in Gorska et al. 2010). The long isoform (LEPRb, OBRb) is expressed in the hypothalamus and all types of immune cells. It is the only isoform known to fully activate signaling pathways in response to leptin. Shorter isoforms (LEPRa, LEPRc, LEPRd, and a soluble isoform LEPRe) are able to interact with JAK kinases and activate other pathways, however their roles in energy homeostasis are not fully characterized.
Signal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such as hormones and growth factors, or reacting to other types of stimuli, such as light. Stimulation of transmembrane receptors leads to their conformational change which propagates the signal to the intracellular environment by activating downstream signaling cascades. Depending on the cellular context, this may impact cellular proliferation, differentiation, and survival. On the organism level, signal transduction regulates overall growth and behavior. Receptor tyrosine kinases (RTKs) transmit extracellular signals by phosphorylating their protein partners on conserved tyrosine residues. Some of the best studied RTKs are EGFR (reviewed in Avraham and Yarden, 2011), FGFR (reviewed in Eswarakumar et al, 2005), insulin receptor (reviewed in Saltiel and Kahn, 2001), NGF (reviewed in Reichardt, 2006), PDGF (reviewed in Andrae et al, 2008) and VEGF (reviewed in Xie et al, 2004). RTKs frequently activate downstream signaling through RAF/MAP kinases (reviewed in McKay and Morrison, 2007 and Wellbrock et al 2004), AKT (reviewed in Manning and Cantley, 2007) and PLC- gamma (reviewed in Patterson et al), which ultimately results in changes in gene expression and cellular metabolism. Receptor serine/threonine kinases of the TGF-beta family, such as TGF-beta receptors (reviewed in Kang et al. 2009) and BMP receptors (reviewed in Miyazono et al. 2009), transmit extracellular signals by phosphorylating regulatory SMAD proteins on conserved serine and threonine residues. This leads to formation of complexes of regulatory SMADs and SMAD4, which translocate to the nucleus where they act as transcription factors. WNT receptors transmit their signal through beta-catenin. In the absence of ligand, beta-catenin is constitutively degraded in a ubiquitin-dependent manner. WNT receptor stimulation releases beta-catenin from the destruction complex, allowing it to translocate to the nucleus where it acts as a transcriptional regulator (reviewed in MacDonald et al, 2009 and Angers and Moon, 2009). WNT receptors were originally classified as G-protein coupled receptors (GPCRs). Although they are structurally related, GPCRs primarily transmit their signals through G-proteins, which are trimers of alpha, beta and gamma subunits. When a GPCR is activated, it acts as a guanine nucleotide exchange factor, catalyzing GDP to GTP exchange on the G-alpha subunit of the G protein and its dissociation from the gamma-beta heterodimer. The G-alpha subunit regulates the activity of adenylate cyclase, while the gamma-beta heterodimer can activate AKT and PLC signaling (reviewed in Rosenbaum et al. 2009, Oldham and Hamm 2008, Ritter and Hall 2009). NOTCH receptors are activated by transmembrane ligands expressed on neighboring cells, which results in cleavage of NOTCH receptor and release of its intracellular domain. NOTCH intracellular domain translocates to the nucleus where it acts as a transcription factor (reviewed in Kopan and Ilagan, 2009). Integrins are activated by extracellular matrix components, such as fibronectin and collagen, leading to conformational change and clustering of integrins on the cell surface. This results in activation of integrin-linked kinase and other cytosolic kinases and, in co-operation with RTK signaling, regulates survival, proliferation and cell shape and adhesion (reviewed in Hehlgans et al, 2007) . Besides inducing changes in gene expression and cellular metabolism, extracellular signals that trigger the activation of Rho GTP-ases can trigger changes in the organization of cytoskeleton, thereby regulating cell polarity and cell-cell junctions (reviewed in Citi et al, 2011).
After autophosphorylation the type 1 insulin-like growth factor receptor (IGF1R) binds and phosphorylates scaffold proteins, IRS1/2/4 and SHC1, which in turn bind effectors possessing enzymatic activity (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, and Siddle et al. 2012). IRS1/2/4 can bind both PI3K (via the p85 subunit of PI3K) and the GRB2:SOS complex. PI3K activates PKB (AKT, AKT1) signaling. GRB:SOS stimulates RAS to exchange GDP for GTP leading to activation of RAF and MAPK.
Binding of IGF1 (IGF-I) or IGF2 (IGF-II) to the extracellular alpha peptides of the type 1 insulin-like growth factor receptor (IGF1R) triggers the activation of two major signaling pathways: the SOS-RAS-RAF-MAPK (ERK) pathway and the PI3K-PKB (AKT) pathway (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parella et al. 2010, Annunziata et al. 2011, Siddle et al. 2012, Holzenberger 2012).
80S monosomes dissociate into 40S and 60S ribosomal subunits. eIF1A promotes this dissociation.
The 80S ribosome dissociates into free 40S (small) and 60S (large) ribosomal subunits. Each ribosomal subunit is constituted by several individual ribosomal proteins and rRNA.
The ternary complex forms upon binding of the initiator methionyl-tRNA to the active eIF2:GTP complex.
The ternary complex (Met-tRNAi:eIF2:GTP) binds to the complex formed by the 40S subunit, eIF3 and eIF1A, to form the 43S complex. eIF1A promotes binding of the ternary complex to the 40S subunit within 43S. The initiator methionyl-tRNA from the ternary complex is positioned at the ribosomal P site.
Binding of the methionyl-tRNA initiator to the active eIF2:GTP complex results in the formation of the ternary complex. Subsequently, this Met-tRNAi:eIF2:GTP (ternary) complex binds to the complex formed by the 40S subunit, eIF3 and eIF1A, to form the 43S complex.
The factor eIF4E within the eIF4F (cap-binding) complex directly binds the 5'-cap on eukaryotic mRNAs. Note that the mRNA is in complex with cytoplasmic proteins constituting an mRNP complex.
Activation of eIF2 through direct binding of GTP.
1D-myo-Inositol 1,4,5,6-tetrakisphosphate
1D-myo-Inositol 1,4,5,6-tetrakisphosphate [ChEBI:811]
D-myo-Inositol 1,4,5,6-tetrakisphosphate
Once the 60S subunit joins the translation initiation complex, eIF5B hydrolyzes its GTP and is released from the now 80S monosome. The fully assembled 80s ribosome is now ready to start elongation of the polypeptide chain.
The cap-binding complex is constituted by the initiation factors eIF4A, eIF4G and eIF4E. First, eIF4E must be released from the inactive eIF4E:4E-BP complex. Then eIF4A interacts with eIF4G, and eIF4E binds to the amino-terminal domain of eIF4G, resulting in the formation of the cap-binding complex eIF4F. eIF4A together with eIF4B or eIF4H is thought to unwind RNA secondary structures near the 5'-end of the mRNA. The translation initiation complex is formed when the 43S complex binds the cap-bound mRNA.
The mRNA-bound ribosomal complex moves along the 5'-untranslated region (5'-UTR) of the mRNA from its initial site to the initiation codon to form a 48S complex, in which the initiation codon (AUG) is base paired to the anticodon of the Met-tRNAi. It is not known whether eIF4A (or another ATPase, such as DED1) facilitates scanning by melting mRNA secondary structures or by actively propelling the ribosome.
The AUG initiation codon in the mRNA is recognized by base pairing with the anticodon of the Met-tRNAi. This reaction requires eIF1, eIF1A, eIF2 and eIF5.
The 80S ribosome bound to the mRNA moves along the mRNA molecule from its initial site to the initiation codon and forms a 48S complex, in which the initiation codon is base paired to the anticodon of the Met-tRNAi. Proper recognition of the AUG initiation codon depends on base pairing with the anticodon of the Met-tRNAi and requires eIF1, eIF1A, eIF2 and eIF5.
Structure and function of the radical enzyme ribonucleotide reductase
Facilitative Na+-independent glucose transporters
The active eIF2:GTP complex may be formed by direct binding of GTP to free eIF2 or by GDP-GTP exchange on the eIF2:GDP:eIF2B complex. The eIF2:GDP complex binds eIF2B forming an eIF2:GDP:eIF2B intermediate complex. eIF2B is a guanine nucleotide releasing factor required to cause GDP release so that a new GTP molecule can bind and activate eIF2. Phosphorylated eIF2:GDP sequesters all eIF2B as an inactive complex, and thus, reuse of eIF2 is inhibited as a consequence of the tight bond it forms with eIF2B, which prevents nucleotide exchange. Therefore, in the absence of free eIF2B, excess eIF2 remains in its inactive GDP-bound form and protein synthesis slows dramatically.
Translation initiation is a complex process in which the Met-tRNAi initiator, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the start codon of an mRNA. The basic mechanism for this process can be described as a series of five steps: 1) formation of a pool of free 40S subunits, 2) formation of the ternary complex (Met-tRNAi/eIF2/GTP), and subsequently, the 43S complex (comprising the 40S subunit, Met-tRNAi/eIF2/GTP, eIF3 and eIF1A), 3) activation of the mRNA upon binding of the cap-binding complex eIF4F, and factors eIF4A, eIF4B and eIF4H, with subsequent binding to the 43S complex, 4) ribosomal scanning and start codon recognition, and 5) GTP hydrolysis and joining of the 60S ribosomal subunit.
Inactive eIF2:GDP binds eIF2B to form an eIF2:GDP:eIF2B intermediate.
eIF2B is a guanine nucleotide releasing factor that is required to cause GDP release so that a new GTP molecule can bind and activate eIF2, so that it can be reused.
Joining of the 60S subunit to form the 80S ribosome is catalyzed by the presence of GTP-bound eIF5B.
Hydrolysis of eIF2-GTP occurs after the Met-tRNAi has recognized the AUG. This reaction is catalyzed by eIF5 (or eIF5B) and is thought to cause dissociation of all other initiation factors and allow joining of the large 60S ribosomal subunit. The 60S subunit joins - a reaction catalyzed by eIF5 or eIF5B - resulting in a translation-competent 80S ribosome. Following 60S subunit joining, eIF5B hydrolyzes its GTP and is released from the 80S ribosome, which is now ready to start elongating the polypeptide chain.
The SRP receptor in the the endoplasmic reticulum (ER) membrane binds via its alpha subunit to the the SRP54 subunit of the Signal Recognition Particle (SRP), which itself is bound to a ribosome:mRNA:polypeptide complex. This interaction tethers the ribosome to the ER membrane, oriented so that the nacent polypeptide will traverse the ER membrane and enter the ER lumen. This process has been characterized in detail in cultured canine cells; this human event is inferred by homology from its canine counterpart.
As the signal peptide of the nascent protein enters the lumen of the endoplasmic reticulum (ER), the signal peptide is recognized and cleaved by the ER membrane-associated Signal Peptidase. Translation of the protein then proceeds to completion.
Initiation of translation in the majority of eukaryotic cellular mRNAs depends on the 5'-cap (m7GpppN) and involves ribosomal scanning of the 5' untranslated region (5'-UTR) for an initiating AUG start codon. Therefore, this mechanism is often called cap-dependent translation initiation. Proximity to the cap, as well as the nucleotides surrounding an AUG codon, influence the efficiency of the start site recognition during the scanning process. However, if the recognition site is poor enough, scanning ribosomal subunits will ignore and skip potential starting AUGs, a phenomenon called leaky scanning. Leaky scanning allows a single mRNA to encode several proteins that differ in their amino-termini. Merrick (2010) provides an overview of this process and hghlights several features of it that remain incompletely understood. Several eukaryotic cell and viral mRNAs initiate translation by an alternative mechanism that involves internal initiation rather than ribosomal scanning. These mRNAs contain complex nucleotide sequences, called internal ribosomal entry sites, where ribosomes bind in a cap-independent manner and start translation at the closest downstream AUG codon. Initiation on several viral and cellular mRNAs is cap-independent and is mediated by binding of the ribosome to internal ribosome entry site (IRES) elements. These elements are often found in characteristically long structured regions on the 5'-UTR of an mRNA that may or may not have regulatory upstream open reading frames (uORFs). Both of these features on the 5'-end of the mRNA hinder ribosomal scanning, and thus promote a cap-independent translation initiation mechanism. IRESs act as specific translational enhancers that allow translation initiation to occur in response to specific stimuli and under the control of different trans-acting factors, as for example when cap-dependent protein synthesis is shut off during viral infection. Such regulatory elements have been identified in the mRNAs of growth factors, protooncogenes, angiogenesis factors, and apoptosis regulators, which are translated under a variety of stress conditions, including hypoxia, serum deprivation, irradiation and apoptosis. Thus, cap-independent translational control might have evolved to regulate cellular responses in acute but transient stress conditions that would otherwise lead to cell death, while the same mechanism is of major importance for viral mRNAs to bypass the shutting-off of host protein synthesis after infection. Encephalomyocarditis virus (EMCV) and hepatitis C virus exemplify two distinct mechanisms of IRES-mediated initiation. In contrast to cap-dependent initiation, the eIF4A and eIF4G subunits of eIF4F bind immediately upstream of the EMCV initiation codon and promote binding of a 43S complex. Accordingly, EMCV initiation does not involve scanning and does not require eIF1, eIF1A, and the eIF4E subunit of eIF4F. Nonetheless, initiation on some EMCV-like IRESs requires additional non-canonical initiation factors, which alter IRES conformation and promote binding of eIF4A/eIF4G. Initiation on the hepatitis C virus IRES is simpler: a 43S complex containing only eIF2 and eIF3 binds directly to the initiation codon as a result of specific interaction of the IRES and the 40S subunit.
The synthesis of a protein destined for the endoplasmic reticulum starts with the canonical events of cytosolic translation initiation and proceeds to the point where a nascent polypeptide chain containing a signal sequence protrudes from the mRNA:ribosome complex. Merrick (2010) provides an overview of these events.
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Gap-filling DNA repair synthesis and ligation in GG-NER
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The citric acid (TCA) cycle and respiratory electron transport
Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay
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Determination of nitric oxide synthase cofactors: heme, FAD, FMN, and tetrahydrobiopterin
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Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE
Genomic organization, cDNA sequence, bacterial expression, and purification of human seryl-tRNA synthase
Role of platelet-derived growth factors in physiology and medicine
Assignment of human beta-galactosidase-A gene to 3p21.33 by fluorescence in situ hybridization
Mutations in the holocarboxylase synthetase gene HLCS
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Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms
Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy
Acta Crystallogr Sect F Struct Biol Cryst Commun 62:613-7
The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
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The biology of cyclic GMP-dependent protein kinases
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Specific inhibition of pyruvate transport in rat liver mitochondria and human erythrocytes by alpha-cyano-4-hydroxycinnamate
glucosaminylphosphatidylinositol [ChEBI:24275]
UDP-acetylglucosamine acts as a donor for the first two steps of the N-glycan precursor biosynthesis pathway, and is later used as a substrate for further modifications after the precursor has been attached to the protein. It is synthesized from fructose 6-phosphate, glutamine, acetyl-CoA, and UTP in four steps.
Cytosolic UAP1 catalyzes the reaction of N-acetyl-D-glucosamine 1-phosphate (GlcNAc1P) and UTP to UDP-N-acetyl-D-glucosamine and pyrophosphate. Structural studies indicate that the active form of the enzyme is a dimer (Peneff C et al, 2001).
Cytosolic PGM3 catalyzes the isomerization of N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P) to form N-acetyl-D-glucosamine 1-phosphate (GlcNAc1P) (Pang H et al, 2002).
GDP-mannose is the mannose donor for the first 5 mannose addition reactions in the N-glycan precursor synthesis, and also for the synthesis of Dolichyl-phosphate-mannose involved in other mannose transfer reactions. It is synthesized from fructose 6-phosphate and GTP in three steps.
Reactions for the synthesis of the small nucleotide-linked sugar substrates that are used in the synthesis of the N-glycan precursor and in the later steps of glycosylation are annotated here. All these nucleotide-linked sugar donors are synthesized in the cytosol; however, to participate in the later reactions of N-glycan precursor biosynthesis (when the glycan is oriented toward the lumen of the endoplasmic reticulum (ER)), these substrates must be attached to a dolichyl-phosphate molecule and then flipped toward the luminal side of the ER, through a mechanism which is still not known but which involves a different protein than the one that mediates the flipping of the LLO itself (Sanyal et al. 2008). Two of the genes encoding enzymes involved in these reactions, MPI and PMM2, are known to be associated with Congenital Disorders of Glycosylation (CDG) diseases of type I. Of these, CDG-Ia, associated with defects in PMM2, is the most frequent CDG disease reported.
The mechanism of mismatch repair and the functional analysis of mismatch repair defects in Lynch syndrome
Phosphomannomutases 1 and 2 (PMM1 and PMM2) catalyze the isomerization of mannose 6-phosphate (Man6P) to mannose 1-phosphate (Man1P) in the cytosol of cells (Wada & Sakamoto 1997, Matthijs et al. 1997). Mutations in the PMM2 gene are one of the causes of Jaeken syndrome. a disease of glycosylation, type CDGIa. (Matthijs et al. 1997b).
Cross-talk between the endocytic pathway and the endoplasmic reticulum in cross-presentation by MHC class I molecules
Mannose 1-phosphate is converted to GDP-Mannose by mannose-1-phosphate guanyltransferase alpha and beta forms (GMPPA/B). This enzyme had originally been characterized from rat and bovine sources (Verachtert H et al, 1966) and more recently from pig (Ning B and Elbein AD, 2000).
N-linked glycosylation commences with the 14-step synthesis of a dolichol lipid-linked oligosaccharide (LLO) consisting of 14 sugars (2 core GlcNAcs, 9 mannoses and 3 terminal GlcNAcs). This pathway is highly conserved in eukaryotes, and a closely related pathway is found in many eubacteria and Archaea. Mutations in the genes associated with N-glycan precursor synthesis lead to a diverse group of disorders collectively known as Congenital Disorders of Glycosylation (type I and II) (Sparks et al. 1993). The phenotypes of these disorders reflect the important role that N-glycosylation has during development, controlling the folding and the properties of proteins in the secretory pathway, and proteins that mediate cell-to-cell interactions or timing of development.
In the first step of N-glycan precursor (LLO) synthesis, N-acetylglucosamine is added, via an alpha-1,3 linkage, to a molecule of dolichyl phosphate, producing N-acetyl-D-glucosaminyl-diphosphodolichol (Eckert et al. 1998). This reaction is catalyzed by DPAGT1 (ALG7 in yeast), mutations in which are associated with CDG disorder type I-J (Wu et al. 2003). The dolichyl phosphate acts as an anchor for the LLO, so that subsequent sugar-addition reactions take place on a sugar anchored in the ER membrane.
A second N-acetylglucosamine is added to the N-glycan precursor via a beta-1,4 linkage. This reaction is catalyzed by the ALG13:ALG14 complex, in which ALG13 functions as the catalyst and ALG14 functions as a membrane anchor which recruits ALG13 to the cytosolic face of ER (Gao XD et al, 2005).
Biosynthetic studies of A2E, a major fluorophore of retinal pigment epithelial lipofuscin
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: a novel enzyme of the beta-lactamase fold family releasing anandamide and other N-acylethanolamines
Sar1p-GTP hydrolysis is increased 15-30-fold by Sec23p. Sar1p-GDP is released as a result of this hydrolysis and used in further vesicle sculpting cycles. Sar1p-GTP hydrolysis occurs at two critical points during the cycle, first (as represented here) as a proofreading step, insuring that the cargo is loaded. Later in the cycle Sar1p-GTP hydrolysis triggers the uncoating of the budded vesicle.
Sar1p-GTP recruits the cytoplasmic Sec23p-Sec24p complex. Though not represented in the subsequent steps, Sec23p-Sec24p would bind to members of the p24 protein family of possible cargo receptors, and together with Sar1p bind the appropiate v-SNARE, and Rab-GTP.
Once loaded the vesicles become fully sculpted, pinch off from the ER and bud into the cytosol.
Cytosolic Sec13p-Sec31p complexes bind to pre-bound Sec23p-Sec24p complexes.
Vesicle uncoating is triggered by Sar1p-GTP hydrolysis leaving only the vesicle cargo and the v-SNARE to target the vesicle to the Golgi membrane.
COPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the Golgi apparatus. COPII-coated vesicles were originally discovered in the yeast Saccharomyces cerevisiae using genetic approaches coupled with a cell-free assay. The mammalian counterpart of this pathway is represented here. Newly synthesized proteins destined for secretion are sorted into COPII-coated vesicles at specialized regions of the ER. These vesicles leave the ER, become uncoated and subsequently fuse with the Golgi apparatus membrane.
Secretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus.
At least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Marti­nez-Menarguez et al, 1999). The other is mediated by LMAN1/MCFD2, mannose-binding lectins that recognize a glycan signal (Zhang B et al, 2003).
N-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 revealed that about 50% of the proteins in the Swiss-Prot database at the time were N-glycosylated (Apweiler et al. 1999). It is now established that the majority of the proteins in the secretory pathway require glycosylation in order to achieve proper folding. The addition of an N-glycan to a protein can have several roles (Shental-Bechor & Levy 2009). First, glycans enhance the solubility and stability of the proteins in the ER, the golgi and on the outside of the cell membrane, where the composition of the medium is strongly hydrophilic and where proteins, that are mostly hydrophobic, have difficulty folding properly. Second, N-glycans are used as signal molecules during the folding and transport process of the protein: they have the role of labels to determine when a protein must interact with a chaperon, be transported to the golgi, or targeted for degradation in case of major folding defects. Third, and most importantly, N-glycans on completely folded proteins are involved in a wide range of processes: they help determine the specificity of membrane receptors in innate immunity or in cell-to-cell interactions, they can change the properties of hormones and secreted proteins, or of the proteins in the vesicular system inside the cell. All N-linked glycans are derived from a common 14-sugar oligosaccharide synthesized in the ER, which is attached co-translationally to a protein while this is being translated inside the reticulum. The process of the synthesis of this glycan, known as Synthesis of the N-glycan precursor or LLO, constitutes one of the most conserved pathways in eukaryotes, and has been also observed in some eubacteria. The attachment usually happens on an asparagine residue within the consensus sequence asparagine-X-threonine by an complex called oligosaccharyl transferase (OST). After being attached to an unfolded protein, the glycan is used as a label molecule in the folding process (also known as Calnexin/Calreticulin cycle) (Lederkremer 2009). The majority of the glycoproteins in the ER require at least one glycosylated residue in order to achieve proper folding, even if it has been shown that a smaller portion of the proteins in the ER can be folded without this modification. Once the glycoprotein has achieved proper folding, it is transported via the cis-Golgi through all the Golgi compartments, where the glycan is further modified according to the properties of the glycoprotein. This process involves relatively few enzymes but due to its combinatorial nature, can lead to several millions of different possible modifications. The exact topography of this network of reactions has not been established yet, representing one of the major challenges after the sequencing of the human genome (Hossler et al. 2006). Since N-glycosylation is involved in an great number of different processes, from cell-cell interaction to folding control, mutations in one of the genes involved in glycan assembly and/or modification can lead to severe development problems (often affecting the central nervous system). All the diseases in genes involved in glycosylation are collectively known as Congenital Disorders of Glycosylation (CDG) (Sparks et al. 2003), and classified as CDG type I for the genes in the LLO synthesis pathway, and CDG type II for the others.
The SUMO1 precursor has 4 extra residues at the C-terminus which can be removed endoproteolytically by either SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). Both SENP1 and SENP2 shuttle between the nucleus and cytoplasmic and both are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006).
Posttranslational modification of the AU-rich element binding protein HuR by protein kinase Cdelta elicits angiotensin II-induced stabilization and nuclear export of cyclooxygenase 2 mRNA
Distribution of AQP2 and AQP3 water channels in human tissue microarrays
Tetrahydrobiopterin biosynthesis, regeneration and functions
Resolution of D-loop structures through Holliday junction intermediates
NMD: RNA biology meets human genetic medicine
Mutant human adenosine deaminase alleles and their expression by transfection into fibroblasts
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Peptide binding and antigen presentation by class II histocompatibility glycoproteins
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Spatial expression patterns and biochemical properties distinguish a second myo-inositol monophosphatase IMPA2 from IMPA1
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Metabolism of stearidonic acid in human subjects: comparison with the metabolism of other n-3 fatty acids
The inositol hexakisphosphate kinase family. Catalytic flexibility and function in yeast vacuole biogenesis
Structural biology of shared cytokine receptors
Interactions of CD80 and CD86 with CD28 and CTLA4
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ChEBI:17526 1-phosphatidyl-1D-myo-inositol 4-phosphates
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A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS
Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions
gamma-L-Glutamyl-L-cysteine [ChEBI:17515]
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The DNA replication fork in eukaryotic cells.
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Isolation and chromosomal localization of a novel FMS-like tyrosine kinase gene
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The GPIb thrombin-binding site is essential for thrombin-induced platelet procoagulant activity
Cloning of a gene for a novel epithelium-specific cytosolic phospholipase A2, cPLA2delta, induced in psoriatic skin
Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code
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Three mammalian lipins act as phosphatidate phosphatases with distinct tissue expression patterns
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Differential transformation of mammary epithelial cells by Wnt genes
Nitric oxide: a physiologic messenger molecule
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Nitric oxide synthase lies downstream from vascular endothelial growth factor-induced but not basic fibroblast growth factor-induced angiogenesis
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Peripheral blood platelets express VEGF-C and VEGF which are released during platelet activation
The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells
Baillieres Clin Endocrinol Metab 7:551-86
Mutations in the facilitative glucose transporter GLUT10 alter angiogenesis and cause arterial tortuosity syndrome
NOD-like receptors: role in innate immunity and inflammatory disease
Folic acid: nutritional biochemistry, molecular biology, and role in disease processes
The human mismatch recognition complex hMSH2-hMSH6 functions as a novel molecular switch
Kinesin-14 family proteins HSET/XCTK2 control spindle length by cross-linking and sliding microtubules
Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference
The MutSalpha-proliferating cell nuclear antigen interaction in human DNA mismatch repair
Mechanism of action and in vivo role of platelet-derived growth factor
A human amphotropic retrovirus receptor is a second member of the gibbon ape leukemia virus receptor family
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
Identification and characterization of a cDNA encoding a long-chain cis-isoprenyltranferase involved in dolichyl monophosphate biosynthesis in the ER of brain cells
Biochem. Biophys. Res. Commun. 312:1349-56
STING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. Indeed, select pathogen-derived DNA or RNA were shown to activate STING in human and mouse cells (Ishikawa H and Barber GN 2008; Ishikawa H et al. 2009; Sun W et al. 2009; Prantner D et al. 2010). Importantly, in vitro studies have shown that STING is essential for Mycobacterium tuberculosis (Manzanillo PS et al. 2012), Plasmodium falciparum (Sharma S et al. 2011) and human immunodeficiency virus (HIV) induced type I IFN production [Yan N et al 2010]. Mycobacterium tuberculosis, plasmodium falciparum and HIV are three deadliest pathogens, which kill millions of people each year worldwide. STING has been also implicated in type I IFN response which was stimulated by fusion of viral and target-cell membrane in a manner independent of DNA, RNA and viral capsid [Holm CK et al 2012]. Under steady state conditions, STING is positioned at the translocon complex within the ER membrane. However upon stimulation with intracellular DNA it translocates from ER to perinuclear vesicles via the Golgi by mechanisms that remain unclear (Ishikawa H and Barber GN 2008; Sun W et al. 2009; Ishikawa H et al. 2009; Saitoh T et al. 2009). Mouse Sting trafficking in dsDNA-stimulated mouse embryonic fibroblasts (MEF) cells was found to depend on autophagy-related gene 9a (Atg9a) (Saitoh T et al. 2009). STING was reported to function as a signaling adaptor or coreceptor in response to cytosolic dsDNA (Unterholzner L et al. 2010; Zhang Z et al. 2011). STING was also shown to function as a direct DNA sensor to induce the innate immune response in human telomerase fibroblasts (hTERT-BJ1) and murine embryonic fibroblasts (MEFs) (Abe T et al. 2013). Additionally, STING is thought to function as a direct sensor of cyclic dinucleotides. STING was shown to interact directly with c-di-GMP in human embryonic kidney HEK293T cell lysates (Burdette DL et al. 2011). Once STING is stimulated, its C-terminus serves as a signaling scaffold to recruit IRF3 and TBK1, which leads to TBK1-dependent phosphorylation of IRF3 (Tanaka Y and Chen ZJ 2012). Mouse, but not human STING, can also bind vascular disrupting agents 5,6-dimethylxanthenone-4-acetic acid (DMXAA) and the antiviral small molecule 10-carboxymethyl-9-acridanone (CMA) to induce type I IFN production, suggesting a species-specific drug effect on the STING-mediated host response (Conlon J et al. 2013; Cavlar T et al. 2013).
The helicase DDX41 was shown to sense exogenous DNA in human and mouse cells (Zhang Z et al. 2011, Parvatiyar K et al. 2012). DDX41 was also reported to sense and interact with bacterial secondary messengers cyclic di-GMP or cyclic di-AMP (Parvatiyar K et al. 2012). Mutagenesis analysis with DDX41 deletion constructs revealed that the central DEAD-box domain of DDX41 mediated the binding with DNA (Zhang Z et al. 2011, Parvatiyar K et al. 2012). Knockdown of DDX41 or STING in human cells (THP-1 and PBMC cells) and mouse dendritic cells significantly reduced the cytokine production in response to pathogen-derived DNA or poly(dG:dC) (Zhang Z et al. 2011, Parvatiyar K et al. 2012). DDX41 localized together with STING in the cytoplasm when both DDX41 and STING were co-expressed in HEK293T cells (Zhang Z et al. 2011). Mouse Ddx41 was found to bind Sting and Tbk1 in both resting and poly(dA:dT)-stimulated mouse splenic myeloid dendritic cell (D2SC mDCs) (Zhang Z et al. 2011). Ddx41-Sting interaction was also observed in c-di-GMP- or c-di-AMP-treated D2SC cells (Parvatiyar K et al. 2012). Moreover, knockdown of Ddx41 or Sting inhibited phosphorylation of Tbk1, Irf3, p65 subunit of NF-kappaB and other signal transducers in DNA-stimulated mouse bone marrow-derived (BMDCs) and D2SC cells (Zhang Z et al. 2011, Parvatiyar K et al. 2012). Collectively, these data suggest that DNA triggers DDX41 downstream signaling to type I interferon in a STING-dependent manner. The E3 ubiquitin ligase TRIM21 was reported to promote the K48-linked ubiquitination and degradation of DDX41 leading to downregulation of the type I interferon production in mouse mDC and human monocytes THP-1 (Zhang Z et al. 2013).
Several members of phospholipase A (PLA) are involved in phagocytosis. Macrophages express three classes of PLA2: secreted Ca-dependent (sPLA2), cytosolic Ca-dependent (cPLA2) and cytosolic Ca-independent (iPLA2) of which iPLA2 is involved in FCGR mediated arachidonic acid (AA) production. Aggregation of FCGR triggers phosphorylation and membrane translocation of iPLA2. Protein kinase C (PKC), ERK and p38MAPK seems to regulate iPLA2 in monocytes, neutrophils and macrophages. Phosphorylated iPLA2 then mediates production of AA and lysoophospholipids from phosphatidylcholine. iPLA2 inhibitors (bromoenol lactone) block AA release and phagocytosis which can be restored upon addition of exogenous AA, suggesting a critical role for iPLA2 in FCGR phagocytosis (Lennartz et al. 1993, Tay & Melendez). Release of AA by activated iPLA2 changes the physical characteristic of the membrane which may facilitate pseudopod extension.
Presence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon (IFN)-regulatory factors (DAI) (also called Z-DNA-binding protein 1, ZBP1), absent in melanoma 2 (AIM2), RNA polymerase III (Pol III), IFN-inducible protein IFI16, leucine-rich repeat flightless interacting protein-1 (LRRFIP1), DEAH-box helicases (DHX9 and DHX36), DEAD-box helicase DDX41, meiotic recombination 11 homolog A (MRE11), DNA-dependent protein kinase (DNA-PK), cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Detection of cytosolic DNA requires multiple and possibly redundant sensors leading to activation of the transcription factor NF-kappaB and TBK1-mediated phosphorylation of the transcription factor IRF3. Cytosolic DNA also activates caspase-1-dependent maturation of the pro-inflammatory cytokines interleukin IL-1beta and IL-18. This pathway is mediated by AIM2.
The innate immune system is the first line of defense against invading microorganisms, a broad specificity response characterized by the recruitment and activation of phagocytes and the release of anti-bacterial peptides. The receptors involved recognize conserved molecules present in microbes called pathogen-associated molecular patterns (PAMPs), and/or molecules that are produced as a result of tissue injury, the damage associated molecular pattern molecules (DAMPs). PAMPs are essential to the pathogen and therefore unlikely to vary. Examples are lipopolysaccharide (LPS), peptidoglycans (PGNs) and viral RNA. DAMPs include intracellular proteins, such as heat-shock proteins and extracellular matrix proteins released by tissue injury, such as hyaluronan fragments. Non-protein DAMPs include ATP, uric acid, heparin sulfate and dsDNA. The receptors for these factors are referred to collectively as pathogen- or pattern-recognition receptors (PRRs). The best studied of these are the membrane-associated Toll-like receptor family. Less well studied but more numerous are the intracellular nucleotide-binding domain, leucine rich repeat containing receptors (NLRs) also called nucleotide binding oligomerization domain (NOD)-like receptors, a family with over 20 members in humans and over 30 in mice. These recognise PAMPs/DAMPs from phagocytosed microorganisms or from intracellular infections (Kobayashi et al. 2003, Proell et al. 2008, Wilmanski et al. 2008). Some NLRs are involved in process unrelated to pathogen detection such as tissue homeostasis, apoptosis, graft-versus-host disease and early development (Kufer & Sansonetti 2011). Structurally NLRs can be subdivided into the caspase-recruitment domain (CARD)-containing NLRCs (NODs) and the pyrin domain (PYD)-containing NLRPs (NALPs), plus outliers including ice protease (caspase-1) activating factor (IPAF) (Martinon & Tschopp, 2005). In practical terms, NLRs can be divided into the relatively well characterized NOD1/2 which signal via RIP2 primarily to NFkappaB, and the remainder, some of which participate in macromolecular structures called Inflammasomes that activate caspases. Mutations in several members of the NLR protein family have been linked to inflammatory diseases, suggesting these molecules play important roles in maintaining host-pathogen interactions and inflammatory responses. Most NLRs have a tripartite structure consisting of a variable amino-terminal domain, a central nucleotide-binding oligomerization domain (NOD or NACHT) that is believed to mediate the formation of self oligomers, and a carboxy-terminal leucine-rich repeat (LRR) that detects PAMPs/DAMPs. In most cases the amino-terminal domain includes protein-interaction modules, such as CARD or PYD, some harbour baculovirus inhibitor repeat (BIR) or other domains. For most characterised NLRs these domains have been attributed to downstream signaling Under resting conditions, NLRs are thought to be present in an autorepressed form, with the LRR folded back onto the NACHT domain preventing oligomerization. Accessory proteins may help maintain the inactive state. PAMP/DAMP exposure is thought to triggers conformational changes that expose the NACHT domain enabling oligomerization and recruitment of effectors, though it should be noted that due to the lack of availability of structural data, the mechanistic details of NLR activation remain largely elusive. New terminology for NOD-like receptors was adopted by the Human Genome Organization (HUGO) in 2008 to standardize the nomenclature of NLRs. The acronym NLR, once standing for NOD-like receptor, now is an abbreviation of 'nucleotide-binding domain, leucine-rich repeat containing' protein. The term NOD-like receptor is officially outdated and replaced by NLRC where the C refers to the CARD domain. However the official gene symbols for NOD1 and NOD2 still contain NOD and this general term is still widely used.
In contrast to NOD1/2 some NLRPs function as large macromolecular complexes called 'Inflammasomes'. These multiprotein platforms control activation of the cysteinyl aspartate protease caspase-1 and thereby the subsequent cleavage of pro-interleukin 1B (pro-IL1B) into the active proinflammatory cytokine IL1B. Activation of caspase-1 is essential for production of IL1B and IL18, which respectively bind and activate the IL1 receptor (IL1R) and IL18 receptor (IL18R) complexes. IL1R and IL18R activate NFkappaB and other signaling cascades. As the activation of inflammasomes leads to caspase-1 activation, inflammasomes can be considered an upstream step of the IL1R and IL18R signaling cascades, linking intracellular pathogen sensing to immune response pathways mediated by Toll-Like Receptors (TLRs). Monocytes and macrophages do not express pro-IL1B until stimulated, typically by TLRs (Franchi et al. 2009). The resulting pro-IL1B is not converted to IL1B unless a second stimulus activates an inflammasome. This requirement for two distinct stimuli allows tight regulation of IL1B/IL18 production, necessary because excessive IL-1B production is associated with numerous inflammatory diseases such as gout and rheumatoid arthritis (Masters et al. 2009). There are at least four subtypes of the inflammasome, characterized by the NLRP. In addition the protein AIM2 can form an inflammasome. All activate caspase-1. NLRP1 (NALP1), NLRP3 (Cryopyrin, NALP3), IPAF (CARD12, NLRC4) and AIM2 inflammasomes all have clear physiological roles in vivo. NLRP2, NLRP6, NLRP7, NLRP10 and NLRP12 have been demonstrated to modulate caspase-1 activity in vitro but the significance of this is unclear (Mariathasan and Monack, 2007). NLRP3 and AIM2 bind the protein 'apoptosis-associated speck-like protein containing a CARD' (ASC, also called PYCARD), via a PYD-PYD domain interaction. This in turn recruits procaspase-1 through a CARD-CARD interaction. NLRP1 and IPAF contain CARD domains and can bind procaspase-1 directly, though both are stimulated by ASC. Oligomerization of NLRPs is believed to bring procaspases into close proximity, leading to 'induced proximity' auto-activation (Boatright et al. 2003). This leads to formation of the active caspase tetramer. NLRPs are generally considered to be cytoplasmic proteins, but there is evidence for cytoplasmic-nuclear shuttling of the family member CIITA (LeibundGut-Landmann et al. 2004) and tissue/cell dependent NALP1 expression in the nucleus of neurons and lymphocytes (Kummer et al. 2007); the significance of this remains unclear.
Advanced Glycosylation End- product-specific Receptor (AGER) also known as Receptor for Advanced Glycation End-products (RAGE) is a multi-ligand membrane receptor belonging to the immunoglobulin superfamily. It is considered to be a Pattern Recognition Receptor (Liliensiek et al. 2004). It recognizes a large variety of modified proteins known as advanced glycation/glycosylation endproducts (AGEs), a heterogenous group of structures that are generated by the Maillard reaction, a consequence of long-term incubation of proteins with glucose (Ikeda et al. 1996). Their accumulation is associated with diabetes, atherosclerosis, renal failure and ageing (Schmidt et al. 1999). The most prevalent class of AGE in vivo are N(6)-carboxymethyllysine (NECML) adducts (Kislinger et al. 1991). In addition to AGEs, AGER is a signal transduction receptor for amyloid-beta peptide (Ab) (Yan et al. 1996), mediating Ab neurotoxicity and promoting Ab influx into the brain. AGER also responds to the proinflammatory S100/calgranulins (Hofmann et al. 1999) and High mobility group protein B1 (HMGB1/Amphoterin/DEF), a protein linked to neurite outgrowth and cellular motility (Hori et al. 1995). The major inflammatory pathway stimulated by AGER activation is NFkappaB. Though the signaling cascade is unclear, several pieces of experimental data suggest that activation of AGER leads to sustained activation and upregulation of NFkappaB, measured as NFkappaB translocation to the nucleus, and increased levels of de novo synthesized NFkappaB (Bierhaus et al. 2001). As this is clearly an indirect effect it is represented here as positive regulation of NFkappaB translocation to the nucleus. AGER can bind ERK1/2 and thereby activate the MAPK and JNK cascades (Bierhaus et al. 2005).
In addition to AGER/RAGE, several other proteins have been identified as AGE-binding proteins. AGE binding proteins p60 and p90 (Yang et al. 1991) were subsequently identified as the Oligosaccharyl transferase 48 kDa subunit (Ost-48) and Glucosidease-2 subunit beta (Li et al. 1996). A third member was identified as Galectin-3 (Vlassara et al. 1995). These 3 proteins have been shown to be present on the plasma membrane of many cell types including vascular endothelium (Stitt et al. 1999). They have been designated AGE-R1, -R2 and -R3. Their suggested function is the removal and degradation of AGEs, but AGER-1 was found to negatively regulate AGER/RAGE (Lu et al. 2004), with kinetics that suggested a more complex interaction than simple competition for the same ligand.
Phagocytosis is one of the important innate immune responses that function to eliminate invading infectious agents. Monocytes, macrophages, and neutrophils are the professional phagocytic cells. Phagocytosis is a complex process involving the recognition of invading foreign particles by specific types of phagocytic receptors and the subsequent internalization of the particles. Fc gamma receptors (FCGRs) are among the best studied phagocytic receptors that bind to Fc portion of immunoglobulin G (IgG). Through their antigen binding F(ab) end, antibodies bind to specific antigen while their constant (Fc) region binds to FCGRs on phagocytes. The clustering of FCGRs by IgG antibodies on the phagocyte initiates a variety of signals, which lead, through the reorganisation of actin cytoskeleton and membrane remodelling, to the formation of pseudopod and phagosome. Fc gamma receptors are classified into three classes: FCGRI, FCGRII and FCGRIII. Each class of these FCGRs consists of several individual isoforms. Among all these isoforms FCGRI, FCGRIIA and FCGRIIIA, are able to mediate phagocytosis (Joshi et al. 2006, Garcia Garcia & Rosales 2002, Nimmerjahn & Ravetch 2006).
Phospholipases play an integral role in phagocytosis by generating essential second messengers. An early step in phagocytic signaling is the association of PIP2 and IP3 with the phagocytic cup. These are formed by the activity of phosphoinositol kinases and phospholipases. PI3K is has been shown to accumulate at phagocytic cups and converts PI (4,5)P2 to PI (3,4,5)P3. These phosphoinositides are capable of binding and increasing the activity of proteins that regulate the actin cytoskeleton. Phospholipases are lipid modifying enzymes that produce lipid mediators such as diacylglycerol (DAG), arachidonic acid (AA) and IP3. Phopsholipases PLA, PLC and PLD have been shown to be involved in antibody (IgG) mediated phagocytosis. The PLC product IP3 stimulates release of calcium from the endoplasmic reticulum. This Ca+2 concentration increase is greatest in the cytoplasm surrounding the phagocytic cup. Calcium is involved in the various stages of phagosome formation, including phagocytic ingestion and phagosome maturation.
Comparison of human B cell antigen receptor complexes: membrane-expressed forms of immunoglobulin (Ig)M, IgD, and IgG are associated with structurally related heterodimers
Mast cells (MC) are distributed in tissues throughout the human body and have long been recognized as key cells of type I hypersensitivity reactions. They also play important roles in inflammatory and immediate allergic reactions. Activation through FCERI-bound antigen-specific IgE causes release of potent inflammatory mediators, such as histamine, proteases, chemotactic factors, cytokines and metabolites of arachidonic acid that act on the vasculature, smooth muscle, connective tissue, mucous glands and inflammatory cells (Borish & Joseph 1992, Amin 2012, Metcalfe et al. 1993). FCERI is a multimeric cell-surface receptor that binds the Fc fragment of IgE with high affinity. On mast cells and basophils FCERI exists as a tetrameric complex consisting of one alpha-chain, one beta-chain, and two disulfide-bonded gamma-chains, and on dendritic cells, Langerhans cells, macrophages, and eosinophils it exists as a trimeric complex with one alpha-chain and two disulfide-bonded gamma-chains (Wu 2011, Kraft & Kinet 2007). FCERI signaling in mast cells includes a network of signaling molecules and adaptor proteins. These molecules coordinate ultimately leading to effects on degranulation, eicosanoid production, and cytokine and chemokine production and cell migration and adhesion, growth and survival. The first step in FCERI signaling is the phosphorylation of the tyrosine residues in the ITAM of both the beta and the gamma subunits of the FCERI by LYN, which is bound to the FCERI beta-chain. The phosphorylated ITAM then recruits the protein tyrosine kinase SYK (spleen tyrosine kinase) which then phosphorylates the adaptor protein LAT. Phosphorylated LAT (linker for activation of T cells) acts as a scaffolding protein and recruits other cytosolic adaptor molecules GRB2 (growth-factor-receptor-bound protein 2), GADS (GRB2-related adaptor protein), SHC (SRC homology 2 (SH2)-domain-containing transforming protein C) and SLP76 (SH2-domain-containing leukocyte protein of 76 kDa), as well as the exchange factors and adaptor molecules VAV and SOS (son of sevenless homologue), and the signalling enzyme phospholipase C gamma1 (PLC-gamma1). Tyrosoine phosphorylation of enzymes and adaptors, including VAV, SHC GRB2 and SOS stimulate small GTPases such as RAC, RAS and RAF. These pathways lead to activation of the ERK, JNK and p38 MAP kinases, histamine release and cytokine production. FCERI activation also triggers the phosphorylation of PLC-gamma which upon membrane localisation hydrolyse PIP2 to form IP3 and 1,2-diacylglycerol (DAG) - second messengers that release Ca2+ from internal stores and activate PKC, respectively. Degranulation or histamine release follows the activation of PLC-gamma and protein kinase C (PKC) and the increased mobilization of calcium (Ca2+). Receptor aggregation also results in the phosphorylation of adaptor protein NTAL/LAT2 which then recruits GAB2. PI3K associates with phosphorylated GAB2 and catalyses the formation of PIP3 in the membrane, which attracts many PH domain proteins like BTK, PLC-gamma, AKT and PDK. PI3K mediated activation of AKT then regulate the mast cell proliferation, development and survival (Gu et al. 2001).
The lipid raft resident adaptor molecules LAT1 and Non-T cell activation linker (NTAL), also known as linker for activation of B cells (LAB)/LAT2 are known participants in the regulation of mast cell calcium responses. Both LAT and NTAL are expressed and phosphorylated following engagement of FCERI on mast cells. NTAL is functionally and topographically different from LAT. There is a considerable debate on the role of NTAL in mast cell. Depending on the circumstances, NTAL appears to have a dual role as positive and negative regulator of MC responses elicited via FCERI. Studies conducted in bone marrow-derived mast cells (BMMCs) of mice lacking NTAL displayed enhanced FCERI-mediated tyrosine phosphorylation of several substrates, calcium response, degranulation, and cytokine production. This indicated that NTAL negatively regulates FCERI-mediated degranulation. However, in mice lacking both LAT and NTAL showed severe block in FCERI-mediated signaling than BMMCs deficient in LAT alone, suggesting that NTAL also shares a redundant function with LAT to play a positive role (Draberova et al. 2007, Orr & McVicar. 2011, Zhu et al. 2004, Volna et al. 2004). The major steps in NTAL mediated Ca+2 influx involves NTAL--> GAB2--> PI3K
Increase of intracellular calcium in mast cells is most crucial for mast cell degranulation. Elevation of intracellular calcium is achieved by activation of PLC-gamma. Mast cells express both PLC-gamma1 and PLC-gamma2 isoforms and activation of these enzymes leads to conversion of phosphatidylinositol 4,5-bisphosphate (PIP2) into inositol triphosphate (IP3) and diacylglycerol (DAG). The production of IP3 leads to mobilization of intracellular Ca+2, which later results in a sustained Ca+2 flux response that is maintained by an influx of extracellular Ca+2. In addition to degranulation, an increase in intracellular calcium concentration also activates the Ca2+/calmodulin-dependent serine phosphatase calcineurin. Calcineurin dephosphorylates the nuclear factor for T cell activation (NFAT) which exposes nuclear-localization signal sequence triggering translocation of the dephosphorylated NFAT-CaN complex to the nucleus. Once in the nucleus, NFAT regulates the transcription of several cytokine genes (Kambayashi et al. 2007, Hoth & Penner 1992, Ebinu et al. 2000, Siraganian et al).
Dephosphorylated NFAT-calcineurin (CaN) complex translocates to nucleus, where it activates transcription of several cytokine genes (e.g..IL2).
Calcineurin (CaN), also called protein phosphatase 2B (PP2B), is a calcium/Calmodulin (CaM)-dependent serine/threonine protein phosphatase. It exists as a heterodimer consisting of CaM-binding catalytic subunit CaN A chain and a Ca+2 binding regulatory CaN B chain. At low calcium concentrations, CaN exists in an inactive state, where the autoinhibitory domain (AID) binds to the active-site cleft. Upon an increase in calcium concentration CaM binds to Ca+2 ions and gets activated. Active CaM binds to CaN regulatory domain (RD) and this causes release of the AID and activation of the phosphatase (Rumi-Masante et al. 2012). Binding of calcium to CaN B regulatory chain also causes a conformational change of the RD of CaN A chain (Yang & Klee 2000).
Formation of the LAT signaling complex leads to activation of MAPK and production of cytokines. The sequence of events that leads from LAT to cytokine production has not been as clearly defined as the sequence that leads to degranulation. However, the pathways that lead to cytokine production require the guanine-nucleotide-exchange factors SOS and VAV that regulate GDP-GTP exchange of RAS. After its activation, RAS positively regulates the RAF-dependent pathway that leads to phosphorylation and, in part, activation of the mitogen-activated protein kinases (MAPKs) extracellular-signal-regulated kinase 1 (ERK1) and ERK2 (Gilfillan & Tkaczyk 2006).
FCERI aggregation has been shown to activate JNK as well as protein kinases upstream of JNK, such as MEKK1 (Mitogen-activated protein kinase/ERK Kinase Kinase-1) and JNK kinase (JNKK). PAK has been shown to be the upstream kinase involved in the activation of MEKK1, however no direct phosphorylation of MEKK1 by PAK is observed. Two threonine residues at positions 1400 and 1412 (analogous to 1381 and 1393 in mouse) in the activation loop of MEKK1 between the kinase subdomains VII and VIII are essential for its catalytic activity. The catalytic domain of MEKK1 is able to autophosphorylate these residues, enhancing its own activity.
DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008).
Mutations in PMM2, a phosphomannomutase gene on chromosome 16p13, in carbohydrate-deficient glycoprotein type I syndrome (Jaeken syndrome)
Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006).
In naive T cells, CD28 costimulation enhances cell cycle entry, potently stimulates expression of both the mitogenic lymphokine interleukin-2 (IL-2) and its receptor, and stimulates the activation of an antiapoptotic program. CD28 engages with one or both members of the B7 receptor family, B7.1 and B7.2. Upon ligand binding the tyrosines and proline-rich motifs present in the cytoplasmic tail of CD28 are phosphorylated by Lck or Fyn. Upon phosphorylation CD28 recruits and induces phosphorylation and activation of a more restricted set of intracellular signaling components that, together with those mobilized by the TCR, contribute to convert membrane-based biochemical and biophysical changes into gene activation events. Proteins like PI3K, Vav-1, Tec and Itk kinases, AKT, and the Dok-1 adaptor have been identified as elements of the CD28 signaling pathway by biochemical or genetic approaches or both.
PI3Ks can be activated by a number of different receptors, including the TcR (T cell receptor), co-stimulatory receptors (CD28), cytokine receptors and chemokine receptors. However, the specific roles of PI3Ks downstream of these receptors vary. CD28 contains the YMNM consensus PI3K-binding motif, and PI3K recruitment by CD28 contributes to or complements TCR-dependent PI3K signaling. Activation of PI3K promotes PIP3 production at the plasma membrane and several potential target molecules for this phospholipid have been implicated in PI3K pathways downstream of the TcR and CD28. Of these targets, at least Vav and Akt have been implicated in CD28 costimulation of T cell activation. AKT/PKB connects PI3K to signaling pathways that promote cytokine transcription, survival, cell-cycle entry and growth.
Nedd4 mediates ErbB4 JM-a/CYT-1 ICD ubiquitination and degradation in MDCK II cells
Mature B cells express IgM and IgD immunoglobulins which are complexed with Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) to form the B cell receptor (BCR) (Fu et al. 1974, Fu et al. 1975, Kunkel et al. 1975, Van Noesal et al. 1992, Sanchez et al. 1993, reviewed in Brezski and Monroe 2008). Binding of antigen to the immunoglobulin activates phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) in the cytoplasmic tails of Ig-alpha and Ig-beta by Src family tyrosine kinases, including LYN, FYN, and BLK (Nel et al. 1984, Yamanashi et al. 1991, Flaswinkel and Reth 1994, Saouaf et al. 1994, Hata et al. 1994, Saouaf et al. 1995, reviewed in Gauld and Cambier 2004, reviewed in Harwood and Batista 2010). The protein kinase SYK may also be involved in phosphorylating the ITAMs. The protein kinase SYK binds the phosphorylated immunoreceptor tyrosine-activated motifs (ITAMs) on the cytoplasmic tails of Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) (Wienands et al. 1995, Rowley et al. 1995, Tsang et al. 2008). The binding causes the activation and autophosphorylation of SYK (Law et al. 1994, Irish et al. 2006, Baldock et al. 2008, Tsang et al. 2008, reviewed in Bradshaw 2010). Activated SYK and other kinases phosphorylate BLNK (SLP-65, BASH) and BCAP. LYN and FYN phosphorylate CD19. Phosphorylated BLNK, BCAP, and CD19 serve as scaffolds which recruit effectors to the plasma membrane and assemble large complexes, the signalosomes. BCAP and CD19 recruit phosphoinositol 3-kinase (PI3K). BLNK recruits phospholipase C gamma (predominantly PLC-gamma2 in B cells, Coggeshall et al. 1992), NCK, BAM32, BTK, VAV1, and SHC. The effectors are phosphorylated by SYK and other kinases. Phosphorylated BCAP recruits PI3K, which is phosphorylated by a SYK-dependent mechanism (Kuwahara et al. 1996) and produces phosphatidylinositol-3,4,5-trisphosphate (PIP3). Phosphorylated CD19 likewise recruits PIP3K. PIP3 recruits BAM32 (Marshall et al. 2000) and BTK (de Weers et al. 1994, Baba et al. 2001) to the plasma membrane via their PH domains. PIP3 also recruits and activates PLC-gamma1 and PLC-gamma2 (Bae et al. 1998). BTK binds phosphorylated BLNK via its SH2 domain (Baba et al. 2001). BTK phosphorylates PLC-gamma2 (Rodriguez et al. 2001), which activates phospholipase activity (Carter et al. 1991, Roifman and Wang 1992, Kim et al. 2004, Sekiya et al. 2004). Phosphorylated BLNK recruits PLC-gamma, VAV, GRB2, and NCK (Fu and Chan 1997, Fu et al. 1998, Chiu et al. 2002). PLC-gamma hydrolyzes phosphatidylinositol-4,5-bisphosphate to yield inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (Carter et al. 1991, Kim et al. 2004). IP3 binds receptors on the endoplasmic reticulum and causes release of Ca2+ ions from the ER into the cytosol. The depletion of calcium from the ER in turn activates STIM1 to interact with ORAI and TRPC1 channels (and possibly other TRP channels) in the plasma membrane, resulting in an influx of extracellular calcium ions (Mori et al. 2002, Muik et al. 2008, Luik et al. 2008, Park et al. 2009).
Optimal activation of T-lymphocytes requires at least two signals. A primary one is delivered by the T-cell receptor (TCR) complex after antigen recognition and additional costimulatory signals are delivered by the engagement of costimulatory receptors such as CD28. The best-characterized costimulatory pathways are mediated by a set of cosignaling molecules belonging to the CD28 superfamily, including CD28, CTLA4, ICOS, PD1 and BTLA receptors. These proteins deliver both positive and negative second signals to T-cells by interacting with B7 family ligands expressed on antigen presenting cells. Different subsets of T-cells have very different requirements for costimulation. CD28 family mediated costimulation is not required for all T-cell responses in vivo, and alternative costimulatory pathways also exist. Different receptors of the CD28 family and their ligands have different regulation of expression. CD28 is constitutively expressed on naive T cells whereas CTLA4 expression is dependent on CD28/B7 engagement and the other receptor members ICOS, PD1 and BTLA are induced after initial T-cell stimulation. The positive signals induced by CD28 and ICOS molecules are counterbalanced by other members of the CD28 family, including cytotoxic T-lymphocyte associated antigen (CTLA)4, programmed cell death (PD)1, and B and T lymphocyte attenuator (BTLA), which dampen immune responses. The balance of stimulatory and inhibitory signals is crucial to maximize protective immune responses while maintaining immunological tolerance and preventing autoimmunity. The costimulatory receptors CD28, CTLA4, ICOS and PD1 are composed of single extracellular IgV-like domains, whereas BTLA has one IgC-like domain. Receptors CTLA4, CD28 and ICOS are covalent homodimers, due to an interchain disulphide linkage. The costimulatory ligands B71, B72, B7H2, B7H1 and B7DC, have a membrane proximal IgC-like domain and a membrane distal IgV-like domain that is responsible for receptor binding and dimerization. CD28 and CTLA4 have no known intrinsic enzymatic activity. Instead, engagement by their physiologic ligands B71 and B72 leads to the physical recruitment and activation of downstream T-cell effector molecules.
Mature B cells express IgM and IgD immunoglobulins which are complexed at the plasma membrane with Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) to form the B cell receptor (BCR) (Fu et al. 1974, Fu et al. 1975, Kunkel et al. 1975, Van Noesel et al. 1992, Sanchez et al. 1993, reviewed in Brezski and Monroe 2008). Binding of antigen to the immunoglobulin activates phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) in the cytoplasmic tails of Ig-alpha and Ig-beta by Src family tyrosine kinases, including LYN, FYN, and BLK (Nel et al. 1984, Yamanashi et al. 1991, Flaswinkel and Reth 1994, Saouaf et al. 1994, Hata et al. 1994, Saouaf et al. 1995, reviewed in Gauld and Cambier 2004, reviewed in Harwood and Batista 2010). The protein kinase SYK binds the phosphorylated immunoreceptor tyrosine-activated motifs (ITAMs) on the cytoplasmic tails of Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) (Wienands et al. 1995, Rowley et al. 1995, Tsang et al. 2008). The binding causes the activation and autophosphorylation of SYK (Law et al. 1994, Baldock et al. 2000, Irish et al. 2006, Tsang et al. 2008, reviewed in Bradshaw 2010). Activated SYK and other kinases phosphorylate BLNK (SLP-65), BCAP, and CD19 which serve as scaffolds for the assembly of large complexes, the signalosomes, by recruiting phosphoinositol 3-kinase (PI3K), phospholipase C gamma (predominantly PLC-gamma2 in B cells, Coggeshall et al. 1992), NCK, BAM32, BTK, VAV1, and SHC. The effectors are phosphorylated by SYK and other kinases. PLC-gamma associated with BLNK hydrolyzes phosphatidylinositol-4,5-bisphosphate to yield inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (Carter et al. 1991, Kim et al. 2004). IP3 binds receptors on the endoplasmic reticulum and causes release of calcium ions from the ER into the cytosol. The depletion of calcium from the ER in turn activates STIM1 to interact with ORAI and TRPC1 channels in the plasma membrane, resulting in an influx of extracellular calcium ions (Muik et al. 2008, Luik et al. 2008, Park et al. 2009, Mori et al. 2002). PI3K associated with BCAP and CD19 phosphorylates phosphatidylinositol 4,5-bisphosphate to yield phosphatidyinositol 3,4,5-trisphosphate. Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidylinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS is activated via RasGRP proteins, NF-AT is activated via calcineurin, and AKT (PKB) is activated via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidyinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS via RasGRP proteins, NF-AT via calcineurin, and AKT via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
Intracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T cells. The ubiquitin-26S proteasome system plays a central role in the generation of these class I MHC antigens. Ubiquitination is the mechanism of adding ubiquitin to lysine residues on substrate protein leading to the formation of a polyubiquitinated substrate. This process involves three classes of enzyme, an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase. Polyubiquitination through lysine-48 (K48) generally targets the substrate protein for proteasomal destruction. The protease responsible for the degradation of K48-polyubiquitinated proteins is the 26S proteasome. This proteasome is a two subunit protein complex composed of the 20S (catalytic core) and 19S (regulatory) proteasome complexes. The proteasome eliminates most of the foreign and non-functional proteins from the cell by degrading them into short peptides; only a small fraction of the peptides generated are of the correct length to be presented by the MHC class I system. It has been calculated that between 994 and 3122 protein molecules have to be degraded for the formation of a single, stable MHC class I complex at the cell surface, with an average effciency of 1 in 2000 (Kloetzel et al. 2004, Princiotta et al. 2003).
Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase.
The 26S proteasome complex consists of the 20S catalytic core particle which harbours the proteolytically active sites and the regulatory 19S particle which is responsible for substrate interaction. This process generates a vast number (perhaps hundreds) of different peptides, depending on the length and sequence of the substrate protein. Only a small fraction of these peptides (nearly 10%) form the exact length to be presented by class I MHC; most (approximately 70%) are too short to bind. The remaining proteasome products (10-20%) are N-terminally extended precursors that require additional cleavage by cytosolic aminopeptidases for presentation by MHC class I molecules.
The other TAP-dependent cross-presentation mechanism in phagocytes is the endoplasmic reticulum (ER)-phagosome model. Desjardins proposed that ER is recruited to the cell surface, where it fuses with the plasma membrane, underneath phagocytic cups, to supply membrane for the formation of nascent phagosomes (Gagnon et al. 2002). Three independent studies simultaneously showed that ER contributes to the vast majority of phagosome membrane (Guermonprez et al. 2003, Houde et al. 2003, Ackerman et al. 2003). The composition of early phagosome membrane contains ER-resident proteins, the components required for cross-presentation. This model is similar to the phagosome-to-cytosol model in that Ag is translocated to cytosol for proteasomal degradation, but differs in that antigenic peptides are translocated back into the phagosome (instead of ER) for peptide:MHC-I complexes. ER fusion with phagosome introduces molecules that are involved in Ag transport to cytosol (Sec61) and proteasome-generated peptides back into the phagosome (TAP) for loading onto MHC-I. Through extensive biochemical assays, fluorescent imaging and electron microscopy-based experiments, most of the evidence in favor of ER-phagocytosis has been challenged (Touret et al. 2005a/b). Using quantitative proteomics Roger and Foster have shown that the percentage of PM and ER membranes on phagosomes 10 min after internalization was approximately 10% and 0.2% (Rogers et al. 2007). They concluded that ER contributes only a small part of phagosomal membranes. Although the ER-phagosome pathway is controversial, the concept remains attractive as it explains how peptide-receptive MHC-I molecules could intersect with a relatively high concentration of exogenous antigens, presumably a crucial prerequisite for efficient cross-presentation (Basha et al. 2008).
Proteasomes are usually localized to the cytoplasm but are also present in the nucleus and ER. Houde et al. (2003) investigated the distribution of proteasomes in J774 macrophages and observed them on phagosomes. The proteasomes present on phagosomes may not come directly from ER, but instead assemble on phagosomes to play a function at a precise point during phagolysosomal biogenesis. Houde et al. also observed polyubiquitinated proteins on the cytoplasmic side of phagosomes and highlighted the link between the ubiquitination process and proteasomal degradation; translocated peptides are ubiquitinated and processed by the proteasome complex assembled on the cytoplasmic side of phagosomes, leading to the generation of MHC class I binding peptides.
Igf-I signaling and effects on longevity
Nestle Nutr Workshop Ser Pediatr Program 68:237-45; discussion 246-9
MHC class I molecules generally present peptide antigens derived from proteins synthesized by the cell itself to CD8+ T cells. However, in some circumstances, antigens from extracellular environment can be presented on MHC class I to stimulate CD8+ T cell immunity, a process termed cross-presentation (Rock & Shen. 2005). Cross-presentation/cross-priming is the ability of antigen presenting cells (APCs) to present exogenous antigens on MHC class I molecules to CD8+ T lymphocytes. Among all the APCs, Dendritic cells (DC) are the dominant antigen cross presenting cell types in vivo, although macrophages and B cells appear to cross present model antigens in vitro with a low degree of efficiency (Amigorena & Savina. 2010, Ackermann & Peter Cresswell. 2004). Compared to macrophages, DCs have low levels of lysosomal proteases and exhibit limited lysosomal degradation (Delamarre et al. 2005). This limited proteolysis of internalized antigens by DCs might contribute to their high efficiency for cross presentation (Monua & Trombetta. 2007). APCs acquire the exogenous antigens through endocytic mechanisms, especially phagosomes for particulate/cell-associated antigens and endosomes for soluble protein antigens. There does not seem to be a unique pathway for cross-presentation but rather different potential mechanisms of cross-presentation have been proposed. These proposed pathways can be classified according to the location where two key events occur: 1) processing of the antigenic protein and 2) loading of the processed peptide on to MHC I molecule (Blanchard & Shastri. 2010). Based on the requirement for TAP and cytosolic proteases two mechanisms have been described, a cytosolic pathway (TAP-dependent and proteasome-dependent) or a vacuolar pathway (TAP- and proteasome-independent) (Blanchard & Shastri. 2010, Amigorena & Savina. 2010). Regarding peptide-loading, MHC I could be loaded in the ER or in the phagosome and recycled to cell surface (Blanchard & Shastri. 2010). Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading. The outcome of the cross presentation can be either tolerance or immunity (Rock & Shen. 2005).
Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading.
Exogenous antigens are thought to be processed for cross-presentation in much the same manner as endogenous proteins once they enter the cytosolic pathway (Rock et al. 2010). Immunoproteasome components are the major proteases involved in generating the antigenic fragments. The precurssor peptides are further trimmed by cytosolic aminopeptidases and shuttled to ER through TAP for MHC class I loading.
Adaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with remarkable diversity tailored to recognize aspects of particular pathogens or antigens. During infection, dendritic cells (DC) which act as sentinels in the peripheral tissues recognize and pick up the pathogen in the form of antigenic determinants and then process these antigens and present them to T cells. These T cells of appropriate specificity respond to the antigen, and either kill the pathogen directly or secrete cytokines that will stimulate B lymphocyte response. B cells provide humoral immunity by secreting antibodies specific for the pathogen or antigen.
Antigen presenting cells (APCs) such as B cells, dendritic cells (DCs) and monocytes/macrophages express major histocompatibility complex class II molecules (MHC II) at their surface and present exogenous antigenic peptides to CD4+ T helper cells. CD4+ T cells play a central role in immune protection. On their activation they stimulate differentiation of B cells into antibody-producing B-cell blasts and initiate adaptive immune responses. MHC class II molecules are transmembrane glycoprotein heterodimers of alpha and beta subunits. Newly synthesized MHC II molecules present in the endoplasmic reticulum bind to a chaperone protein called invariant (Ii) chain. The binding of Ii prevents the premature binding of self antigens to the nascent MHC molecules in the ER and also guides MHC molecules to endocytic compartments. In the acidic endosomal environment, Ii is degraded in a stepwise manner, ultimately to free the class II peptide-binding groove for loading of antigenic peptides. Exogenous antigens are internalized by the APC by receptor mediated endocytosis, phagocytosis or pinocytosis into endocytic compartments of MHC class II positive cells, where engulfed antigens are degraded in a low pH environment by multiple acidic proteases, generating MHC class II epitopes. Antigenic peptides are then loaded into the class II ligand-binding groove. The resulting class II peptide complexes then move to the cell surface, where they are scanned by CD4+ T cells for specific recognition (Berger & Roche 2009, Zhou & Blum 2004, Watts 2004, Landsverk et al. 2009).
Antigen processing and loading on to MHC class II molecules occurs in late endocytic/lysosomal vesicles, where epitopes which require extensive proteolytic processing are generated (Bryant & Ploegh 2003). These late endosome/lysosomal-like compartments are enriched in MHC II and are referred to as MIICs (MHC class II compartments) (Peters et al. 1991). A variety of lysosomal proteases like cathepsins S, D, B etc. and Asparaginyl endopeptidase (AEP) are suggested to be involved in the processing of antigens to generate CD4+ T cell epitopes (Deusing et al. 1998, Shi et al. 1999, Pluger et al. 2002, Watts et al. 2005). An initial cleavage by endopeptidases (AEP) would be necessary to unlock the antigen and allow further trimming of the ends by exopeptidases (Cathepsins). In the acidic environment of the lysosome, cathepsins are generally activated by autocatalytic cleavage of a propeptide which otherwise blocks the active site.
Major histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular bacteria or tumor-associated antigens. They bind peptide fragments of these proteins and presenting them to CD8+ T cells at the cell surface. This enables cytotoxic T cells to identify and eliminate cells that are synthesizing abnormal or foreign proteins. MHC class I is a trimeric complex composed of a polymorphic heavy chain (HC or alpha chain) and an invariable light chain, known as beta2-microglobulin (B2M) plus an 8-10 residue peptide ligand. Represented here are the events in the biosynthesis of MHC class I molecules, including generation of antigenic peptides by the ubiquitin/26S-proteasome system, delivery of these peptides to the endoplasmic reticulum (ER), loading of peptides to MHC class I molecules and display of MHC class I complexes on the cell surface.
The NLRP3 (Cryopyrin) inflammasome is currently the best characterized. It consists of NLRP3, ASC (PYCARD) and procaspase-1; CARD8 (Cardinal) is also suggested to be a component. It is activated by a number of pathogens and bacterial toxins as well as diverse PAMPs, danger-associated molecular patterns (DAMPS) such as hyaluronan and uric acid, and exogenous irritants such as silica and asbestos (see Table S1 Schroder & Tschopp, 2010). Mutations in NLRP3 which lead to constitutive activation are linked to the human diseases Muckle-Wells syndrome, familial cold autoinflammatory syndrome and NOMID (Ting et al. 2006), characterized by skin rashes and other symptoms associated with generalized inflammation. The cause of these symptoms is uncontrolled IL-1 beta production. Multiple studies have shown that activation of the NLRP3 inflammasome by particulate activators (e.g. Hornung et al. 2008) requires phagocytosis, but this is not required for the response to ATP, which is mediated by the P2X7 receptor (Kahlenberg & Dubyak, 2004) and appears to involve the pannexin membrane channel (Pellegrin & Suprenenant 2006). Direct binding of activators to NLRP3 has not been demonstrated and the exact process of activation is unclear, though it is speculated to involve changes in conformation that free the NACHT domain for oligomerization (Inohara & Nunez 2001, 2003).
Differences between the trypanosomal and human GlcNAc-PI de-N-acetylases of glycosylphosphatidylinositol membrane anchor biosynthesis
The presence of reactive oxygen species (ROS) leads to the oxidation of thioredoxin and consequent release of TXNIP (Zhou et al. 2010). The source of the ROS is unclear but they are known to be essential for caspase-1 activation (Cruz et al. 2007) and are produced in response to all known NLRP3 activators (Dostert et al. 2008, Zhou et al. 2010). The freed TXNIP binds NLRP3 and is proposed to activate the NLRP3 inflammasome, explaining how ROS can bring about NLRP3 activation.
The ubiquitin ligaseâassociated protein SGT1 (SUGT1) has two putative HSP90 binding domains, a tetratricopeptide repeat and a p23-like CHORD and Sgt1 (CS) domain. The CS domain of human SGT1 physically interacts with HSP90. SGT1 and related proteins are believed to recruit heat shock proteins to multiprotein assemblies (Lee et al. 2004).
Molecular physiology of bestrophins: multifunctional membrane proteins linked to best disease and other retinopathies
MSH2:MSH6 (MutSalpha) binds single base mismatches and unpaired loops of 1-2 nucleotides (reviewed in Edelbrock et al. 2013). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta), which mediates repair of larger mismatches, and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). The MSH6 subunit is responsible for binding the mismatch, which activates MSH2:MSH6 to exchange ADP for ATP, adopt the conformation to allow movement on the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 has endonucleolytic activity and makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
The latent endonuclease activity of MLH1:PMS2 (MutLalpha) is activated by interaction with MSH2:MSH3 (MutSbeta) (Zhang et al. 2005, and inferred from activation of MLH1:PMS2 by MSH2:MSH6). MLH1:PMS2 makes a nick in the strand of DNA that will be repaired (Kadyrov et al. 2006).
After being activated by a mismatch, MSH2:MSH6 (MutSalpha) recruits MLH1:PMS2 (MutLalpha) to form a ternary complex with mismatched DNA (Gu et al. 1998, Blackwell et al. 2001, Plotz et al. 2002). As inferred from yeast, multiple MLH1:PMS2 complexes may be loaded at each mismatch (Hombauer et al. 2011). MSH2:MSH6 and MLH1:PMS2 interact with PCNA (Gu et al. 1998, Clark et al. 2000, Kleczkowska et al. 2001, Zhang et al. 2005, Constantin et al. 2005, Iyer et al. 2008, Masih et al. 2008, Iyer et al. 2010). The binding sites for MLH1:PMS2 and PCNA are distinct on MSH2:MSH6 so it is possible that both can bind simultaneously (Iyer et al. 2010). The interaction with PCNA appears to direct the orientation of the repair complex so as to determine which strand will be used as template and which strand will be repaired. In vivo, the recently replicated strand is repaired. In vitro, the strand containing a nick is repaired (Zhang et al. 2005, Constantin et al. 2005), possibly due to the ability of the nick to orient the loading of PCNA onto DNA by RFC (Pluciennik et al. 2010).
Human mucopolysaccharidosis IIID: clinical, biochemical, morphological and immunohistochemical characteristics
The latent endonuclease activity of MLH1:PMS2 (MutLalpha) is activated by interaction with MSH2:MSH6 and PCNA (Kadyrov et al 2006). MLH1:PMS2 makes a nick in the replicated strand of DNA. As inferred from yeast, more than one MLH1:PMS2 may bind per MSH2:MSH6 (Hombauer et al. 2011). Strand selection of the nick is determined by interaction with PCNA, though the exact mechanism is unknown (Pluciennik et al 2010).
EXO1 interacts with MSH2 and MLH1 (and therefore is presumed to interact with their respective heterodimers MSH2:MSH6 and MLH1:PMS2), forming a ternary complex with MLH1:PMS2 (Nielsen et al. 2004). EXO1 also interacts with PCNA in S phase (Nielsen et al. 2004, Zhang et al. 2005, Constantin et al. 2005, Knudsen et al. 2007, Liberti et al. 2011)
LIG1 (DNA ligase I) catalyzes the formation of a phosphodiester bond between a 3' hydroxyl group and a 5' phosphate group to form an intact DNA strand (Bhat and Grossman 1986). ATP is hydrolyzed to AMP and pyrophosphate in a reaction mechanism that involves adenylylation of a lysine residue of the enzyme, transfer of the adenylyl group to the 5' phosphate of DNA, and nick sealing by nucleophilic attack of the 3' hydroxyl group on the adenylylated 5' phosphate (Taylor et al. 2011, reviewed in Tomkinson et al. 2006). RPA stimulates the activity of LIG1 about 15-fold (Ranalli et al. 2002). LIG1 is recruited to repair sites by interaction with PCNA (Mortusewicz et al. 2006). Ligation is the final step in mismatch repair (Zhang et al. 2005, Constantin et al. 2005).
The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Impairment of the ability for TC-NER results in the onset of a severe hereditary disorder called Cockayne's syndrome, an autosomal recessive disease characterized by hypersensitivity to UV light . Many types of helix distorting lesions can block the movement of elongating RNA Pol II leading to its stalling and subsequent triggering of repair mechanisms. The repair of DNA damage in active genes occurs much faster compared to the repair in non-transcribed genomic regions (via GG-NER). Also, the non-transcribed strand of the same gene is repaired at a similar rate as that of non-transcribed genomic regions. The transcriptional responses to DNA damage in terms of stalling of Pol II, its displacement from the lesion site etc. are not well elucidated. The following annotation in GK provides an overall picture of TC-NER and will be updated as and when new insights are obtained about these crucial steps.
NER was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recovery of DNA synthesis and cell survival. Deficient NER processes have been identified from the cells of cancer-prone patients with different variants of xeroderma pigmentosum (XP), trichothiodystrophy (TTD), and Cockayne's syndrome. These XP cells exhibited an ultraviolet radiation hypersensitivity leading to a hypermutability response to UV, offering a direct connection between deficient NER, increased mutations, and cancer. While the NER pathway in prokaryotes is unique, the pathway utilized in yeast and higher eukaryotes is highly conserved and includes a variety of proteins that interact to form complexes. NER is involved in the repair of bulky adducts in DNA, such as UV-induced photo lesions [of both 6-4 photoproducts (6-4 pps) and cyclobutane pyrimidine dimer (CPDs)], intrastrand cross-links, large chemical adducts formed from exposure to aflatoxin, benzopyrene and other genotoxic agents. Specific proteins have been identified that participate in base damage recognition, cleavage of the damaged strand on both sides of the lesion, excision of the oligonucleotide bearing the lesion, and accessory proteins necessary for efficient function. Polymerization and ligation restore the strand to its original state. NER consists of two related pathways called global genomic repair (GG-NER) and transcription-coupled NER (TC-NER). The pathways differ in the way in which DNA damage is initially recognized, but the majority of the participating molecules are shared between these two branches of NER. GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Several of the proteins involved in NER are key components of the basal transcription complex TFIIH. NER proteins have also been shown to interact with the 19S regulatory subunit of the proteasome, suggesting a role in cellular regulation signal pathways. The establishment of mutant mouse models for NER genes and other DNA repair-related genes have been useful in demonstrating the associations between NER defects and cancer.
The MSH2:MSH6 (MutSalpha) heterodimer binds single base mismatches and insertion or deletion loops (IDLs) of 1-2 bases (Drummond et al. 1997, Genschel et al. 1998, Gradia et al. 2000, Zhang et al. 2005, Constantin et al. 2005, Tian et al. 2009, reviewed in Edelbrock et al. 2013). The MSH6 subunit contains a Phe-X-Glu motif that binds the mismatched base (Dufner et al 2000, Warren et al. 2007). During replication most nuclear MSH2:MSH6 is observed to colocalize with PCNA via an interaction between PCNA and MSH6 at replication forks during S phase (Kleczkowska et al. 2001), presumably coupling mismatch repair to DNA replication. The MSH6 subunit of MSH2:MSH6 also binds histone H3 methylated at lysine-36, which is enriched in chromatin during G1 and early S phase (Li et al. 2013).
After binding a mismatch, the MSH2:MSH6 (MutSalpha) heterodimer exchanges ADP for ATP, which alters its conformation to a sliding clamp or molecular switch able to diffuse in one direction along duplex DNA (Gradia et al. 1997, Blackwell et al. 1998, Gradia et al. 1999, Gradia et al. 2000). Each heterodimer can bind 2 molecules of ATP or ADP or a combination of ADP and ATP. The affinities and hydrolysis rates of the binding sites differ (Tian et al. 2009, Heinen et al. 2011). However, the exact location of a given adenosine at a given binding location and the conferred function is unclear but believed to control downstream events. Hydrolysis of the ATP by MSH2:MSH6 is not required for mismatch binding but is required for subsequent mismatch repair (Gu et al. 1998, Tian et al. 2009, Geng et al. 2012).
Defective CD320 causes methylmalonic aciduria
Transcriptional map of 170-kb region at chromosome 11p15.5: identification and mutational analysis of the BWR1A gene reveals the presence of mutations in tumor samples
Molecular characterization of a phospholipase D generating anandamide and its congeners
The TCR is a multisubunit complex that consists of clonotypic alpha/beta chains noncovalently associated with the invariant CD3 delta/epsilon/gamma and TCR zeta chains. T cell activation by antigen presenting cells (APCs) results in the activation of protein tyrosine kinases (PTKs) that associate with CD3 and TCR zeta subunits and the co-receptor CD4. Members of the Src kinases (Lck), Syk kinases (ZAP-70), Tec (Itk) and Csk families of nonreceptor PTKs play a crucial role in T cell activation. Activation of PTKs following TCR engagement results in the recruitment and tyrosine phosphorylation of enzymes such as phospholipase C gamma1 and Vav as well as critical adaptor proteins such as LAT, SLP-76 and Gads. These proximal activation leads to reorganization of the cytoskeleton as well as transcription activation of multiple genes leading to T lymphocyte proliferation, differentiation and/or effector function.
Protection against aflatoxin B1-induced cytotoxicity by expression of the cloned aflatoxin B1-aldehyde reductases rat AKR7A1 and human AKR7A3
On recruitment to plasma membrane PLC-gamma1 then hydrolyses PIP2 producing two second messengers, diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). IP3 induces a transient increase in intracellular free Ca++, while DAG is a direct activator of protein kinase C (PKC theta). These process have been implicated in many cellular physiological functions like cell proliferation, cell growth and differentiation.
In addition to serving as a scaffold via auto-phosphorylation, ZAP-70 also phosphorylates a restricted set of substrates following TCR stimulation - including LAT and SLP-76. These substrates have been recognized to play pivotal role in TCR signaling by releasing second messengers. When phosphorylated, LAT and SLP-76 act as adaptor proteins which serve as nucleation points for the construction of a higher order signalosome: GADS, PLC-gamma1 and GRB2 bind to the LAT on the phosphorylated tyrosine residues (steps 8 and 13). SLP-76 and SOS are then moved to the signalosome by interacting with the SH3 domains of GRB2 and GADS via their proline rich sequences (step 9). Three SLP-76 acidic domain N-term tyrosine residues are phosphorylated by ZAP-70, once SLP-76 binds to GADS (step 10). These phospho-tyrosine residues act as binding sites to the SH2 domains of PLC-gamma1, Vav and Itk (steps 11 and 12). PLC-gamma1 is activated by dual phosphorylation on the tyrosine residues at positions 771, 783 and 1254 by Itk and ZAP-70 (step 14). Phosphorylated PLC-gamma1 subsequently detaches from LAT and SLP-76 and translocates to the plasma membrane by binding to phosphatidylinositol-4,5-bisphosphate (PIP2) via its PH domain (step 15). PLC-gamma1 goes on to hydrolyse PIP2 to second messengers DAG and IP3. These second messengers are involved in PKC and NF-kB activation and calcium mobilization (step 16).
In this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
Activated PLA-gamma1 translocates to the plasmamembrane and interacts with the inositol ring of the membrane bound phosphatidylinositol 4,5-bisphosphate (PIP2) with its PH domain.
DNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. These cellular mechanisms that must cope with the plethora of DNA base pair adducts that arise. DNA damage can arise spontaneously in the cellular milieu through chemical alteration of base nucleotides or as a consequence of errors during DNA replication. For example, it is well known that normal cellular pH and temperature offer an environment, which is hostile to the integrity of DNA and its nucleotide components. Additionally, DNA damage may be induced in response to environmental exposures, including exposure to physical agents such as ionizing or ultraviolet (UV) radiation. Finally, specific chemical agents are known to alkylate or cross-link DNA bases, produce bulky adducts on DNA bases, or break DNA phosphate-sugar backbone. The pioneering work from a number of laboratories have elucidated the basic mechanisms underlying distinct DNA repair pathways that include nucleotide excision repair (NER), base excision repair (BER), DNA strand break repair (DSBR), direct reversal of DNA damage, and the replication past DNA lesions by specialized DNA bypass polymerases (bypass replication). Defects in most of these repair pathways have been associated with one or more specific human diseases. Additionally, the repair of damaged DNA is intimately associated with a number of other distinct cellular processes such as DNA replication, DNA recombination, cell cycle checkpoint arrest, and other basic cellular mechanisms as outlined herein.
Layers of smooth muscle cells can be found in the walls of numerous organs and tissues within the body. Smooth muscle tissue lacks the striated banding pattern characteristic of skeletal and cardiac muscle. Smooth muscle is triggered to contract by the autonomic nervous system, hormones, autocrine/paracrine agents, local chemical signals, and changes in load or length. Actin:myosin cross bridging is used to develop force with the influx of calcium ions (Ca2+) initiating contraction. Two separate protein pathways, both triggered by calcium influx contribute to contraction, a calmodulin driven kinase pathway, and a caldesmon driven pathway. Recent evidence suggests that actin, myosin, and intermediate filaments may be far more volatile then previously suspected, and that changes in these cytoskeletal elements along with alterations of the focal adhesions that anchor these proteins may contribute to the contractile cycle. Contraction in smooth muscle generally uses a variant of the same sliding filament model found in striated muscle, except in smooth muscle the actin and myosin filaments are anchored to focal adhesions, and dense bodies, spread over the surface of the smooth muscle cell. When actin and myosin move across one another focal adhesions are drawn towards dense bodies, effectively squeezing the cell into a smaller conformation. The sliding is triggered by calcium:caldesmon binding, caldesmon acting in an analogous fashion to troponin in striated muscle. Phosphorylation of myosin light chains also is involved in the initiation of an effective contraction.
MSH2:MSH3 (MutSbeta) binds unpaired loops of 2 or more nucleotides (Palombo et al. 1996, Genschel et al. 1998). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta) and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). Binding of the mismatch activates MSH2:MSH3 to exchange ADP for ATP, adopt the conformation to allow movement along the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
Expression of aquaporin 8 in colonic epithelium with diarrhoea-predominant irritable bowel syndrome
The mismatch repair (MMR) system corrects single base mismatches and small insertion and deletion loops (IDLs) of unpaired bases. MMR is primarily associated with DNA replication and is highly conserved across prokaryotes and eukaryotes. MMR consists of the following basic steps: a sensor (MutS homologue) detects a mismatch or IDL, the sensor activates a set of proteins (a MutL homologue and an exonuclease) that select the nascent DNA strand to be repaired, nick the strand, exonucleolytically remove a region of nucleotides containing the mismatch, and finally a DNA polymerase resynthesizes the strand and a ligase seals the remaining nick (reviewed in Kolodner and Marsischkny 1999, Iyer et al. 2006, Li 2008, Fukui 2010, Jiricny 2013). Humans have 2 different MutS complexes. The MSH2:MSH6 heterodimer (MutSalpha) recognizes single base mismatches and small loops of one or two unpaired bases. The MSH2:MSH3 heterodimer (MutSbeta) recognizes loops of two or more unpaired bases. Upon binding a mismatch, the MutS complex becomes activated in an ATP-dependent manner allowing for subsequent downstream interactions and movement on the DNA substrate. (There are two mechanisms proposed: a sliding clamp and a switch diffusion model.) Though the order of steps and structural details are not fully known, the activated MutS complex interacts with MLH1:PMS2 (MutLalpha) and PCNA, the sliding clamp present at replication foci. The role of PCNA is multifaceted as it may act as a processivity factor in recruiting MMR proteins to replicating DNA, interact with MLH1:PMS2 and Exonuclease 1 (EXO1) to initiate excision of the recently replicated strand and direct DNA polymerase delta to initiate replacement of bases. MLH1:PMS2 makes an incision in the strand to be repaired and EXO1 extends the incision to make a single-stranded gap of up to 1 kb that removes the mismatched base(s). (Based on assays of purified human proteins, there is also a variant of the mismatch repair pathway that does not require EXO1, however the mechanism is not clear. EXO1 is almost always required, it is possible that the exonuclease activity of DNA polymerase delta may compensate in some situations and it has been proposed that other endonucleases may perform redundant functions in the absence of EXO1.) RPA binds the single-stranded region and a new strand is synthesized across the gap by DNA polymerase delta. The remaining nick is sealed by DNA ligase I (LIG1). Concentrations of MMR proteins MSH2:MSH6 and MLH1:PMS2 increase in human cells during S phase and are at their highest level and activity during this phase of the cell cycle (Edelbrock et al. 2009). Defects in MSH2, MSH6, MLH1, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC, also known as Lynch syndrome) (reviewed in Martin-Lopez and Fishel 2013).
Human homologue of murine tumor rejection antigen gp96: 5'-regulatory and coding regions and relationship to stress-induced proteins
EXO1 interacts with MSH2 and MLH1 (and therefore is presumed to interact with their respective heterodimers MSH2:MSH3 and MLH1:PMS2), forming a ternary complex with MLH1:PMS2 (Nielsen et al. 2004). EXO1 also interacts with PCNA in S phase (Nielsen et al. 2004, Zhang et al. 2005, Constantin et al. 2005, Knudsen et al. 2007, Liberti et al. 2011)
Fcgamma receptor (FCGR) dependent phagocytosis
Isolation of a 45-kDa fragment from the kinesin heavy chain with enhanced ATPase and microtubule-binding activities
Complete amino acid sequence of human phosphoglycerate kinase. Cyanogen bromide peptides and complete amino acid sequence.
Regulation of mRNA stability by proteins that bind AU-rich elements
Neuregulin-3 (NRG3): a novel neural tissue-enriched protein that binds and activates ErbB4
Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein
Tyrosine phosphorylation of phospholipase C induced by membrane immunoglobulin in B lymphocytes
Defective CUBN causes hereditary megaloblastic anemia 1
Diseases associated with visual transduction
Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.
Participation of the microsomal CDP-diglycerides in the mitochondrial biosynthesis of phosphatidylglycerol
The role of autophosphorylation sites on PDGF receptors are to provide docking sites for downstream signal transduction molecules which contain SH2 domains. The SH2 domain is a conserved motif of around 100 amino acids that can bind a phosphorylated tyrosine residue. These downstream molecules are activated upon binding to, or phosphorylated by, the receptor kinases intrinsic to PDGF receptors. Some of the dowstream molecules are themselves enzymes, such as phosphatidylinositol 3'-kinase (PI3K), phospholipase C (PLC-gamma), the Src family of tyrosine kinases, the tyrosine phosphatase SHP2, and a GTPase activating protein (GAP) for Ras. Others such as Grb2 are adaptor molecules which link the receptor with downstream catalytic molecules.
Neurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. They signal through two types of receptors: TRK tyrosine kinase receptors (TRKA, TRKB, TRKC), which specifically interact with the different neurotrophins, and p75NTR, which interacts with all neurotrophins. TRK receptors are reported in a variety of tissues in addition to neurons. p75NTRs are also widespread. Neurotrophins and their receptors are synthesized as several different splice variants, which differ in terms of their biological activities. The nerve growth factor (NGF) was the first growth factor to be identified and has served as a model for studying the mechanisms of action of neurotrophins and growth factors. The mechanisms by which NGF generates diverse cellular responses have been studied extensively in the rat pheochromocytoma cell line PC12. When exposed to NGF, PC12 cells exit the cell cycle and differentiate into sympathetic neuron-like cells. Current data show that signalling by the other neurotrophins is similar to NGF signalling.
Trk receptors signal from the plasma membrane and from intracellular membranes, particularly from early endosomes. Signalling from the plasma membrane is fast but transient; signalling from endosomes is slower but long lasting. Signalling from the plasma membrane is annotated here. TRK signalling leads to proliferation in some cell types and neuronal differentiation in others. Proliferation is the likely outcome of short term signalling, as observed following stimulation of EGFR (EGF receptor). Long term signalling via TRK receptors, instead, was clearly shown to be required for neuronal differentiation in response to neurotrophins.
PI3K/AKT signalling is a major regulator of neuron survival. It blocks cell death by both impinging on the cytoplasmic cell death machinery and by regulating the expression of genes involved in cell death and survival. In addition, it may also use metabolic pathways to regulate cell survival.The PI3K/AKT pathway also affects axon diameter and branching (Marcus et al, 2002) and regulates small G proteins like RhoA (Vanhaesebroeck, B and Waterman, MD, 1999), which control the behaviour of the F-actin cytoskeleton. Moreover, through its connection with the TOR pathway, it promotes translation of a subset of mRNAs.
DNA polymerase switching: II. Replication factor C abrogates primer synthesis by DNA polymerase alpha at a critical length.
DNA polymerase switching: I. Replication factor C displaces DNA polymerase alpha prior to PCNA loading.
3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
all-trans-4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
3-decaprenyl-4-hydroxy-5-methoxybenzoic acid [ChEBI:50776]
all-trans-3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
3-decaprenyl-4,5-dihydroxybenzoic acid [ChEBI:50775]
all-trans-3-decaprenyl-4,5-dihydroxybenzoic acid
all-trans-3,4-dihydroxy-5-decaprenylbenzoic acid
The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
In normal development vascular endothelial growth factors (VEGFs) are crucial regulators of vascular development during embryogenesis (vasculogenesis) and blood-vessel formation in the adult (angiogenesis). In tumor progression, activation of VEGF pathways promotes tumor vascularization, facilitating tumor growth and metastasis. Abnormal VEGF function is also associated with inflammatory diseases including atherosclerosis, and hyperthyroidism. The members of the VEGF and VEGF-receptor protein families have distinct but overlapping ligand-receptor specificities, cell-type expression, and function. VEGF-receptor activation in turn regulates a network of signaling processes in the body that promote endothelial cell growth, migration and survival (Hicklin and Ellis, 2005; Shibuya and Claesson-Welsh, 2006). Molecular features of the VGF signaling cascades are outlined in the figure below (from Olsson et al. 2006; Nature Publishing Group). Tyrosine residues in the intracellular domains of VEGF receptors 1, 2,and 3 are indicated by dark blue boxes; residues susceptible to phosphorylation are numbered. A circled R indicates that phosphorylation is regulated by cell state (VEGFR2), by ligand binding (VEGFR1), or by heterodimerization (VEGFR3). Specific phosphorylation sites (boxed numbers) bind signaling molecules (dark blue ovals), whose interaction with other cytosolic signaling molecules (light blue ovals) leads to specific cellular (pale blue boxes) and tissue-level (pink boxes) responses in vivo. Signaling cascades whose molecular details are unclear are indicated by dashed arrows. DAG, diacylglycerol; EC, endothelial cell; eNOS, endothelial nitric oxide synthase; FAK, focal adhesion kinase; HPC, hematopoietic progenitor cell; HSP27, heat-shock protein-27; MAPK, mitogen-activated protein kinase; MEK, MAPK and ERK kinase; PI3K, phosphatidylinositol 3' kinase; PKC, protein kinase C; PLCgamma, phospholipase C-gamma; Shb, SH2 and beta-cells; TSAd, T-cell-specific adaptor. In the current release, the first events in these cascades - the interactions between VEGF proteins and their receptors - are annotated. Details of signaling events and their biological outcome, concisely illustrated in the image below, will be available in future versions of this pathway.
Stem cell factor (SCF) is a growth factor with membrane bound and soluble forms. It is expressed by fibroblasts and endothelial cells throughout the body, promoting proliferation, migration, survival and differentiation of hematopoetic progenitors, melanocytes and germ cells.(Linnekin 1999, Ronnstrand 2004, Lennartsson and Ronnstrand 2006). The receptor for SCF is KIT, a tyrosine kinase receptor (RTK) closely related to the receptors for platelet derived growth factor receptor, colony stimulating factor 1 (Linnekin 1999) and Flt3 (Rosnet et al. 1991). Four isoforms of c-Kit have been identified in humans. Alternative splicing results in isoforms of KIT differing in the presence or absence of four residues (GNNK) in the extracellular region. This occurs due to the use of an alternate 5' splice donor site. These GNNK+ and GNNK- variants are co-expressed in most tissues; the GNNK- form predominates and was more strongly tyrosine-phosphorylated and more rapidly internalized (Ronnstrand 2004). There are also splice variants that arise from alternative usage of splice acceptor site resulting in the presence or absence of a serine residue (Crosier et al., 1993). Finally, there is an alternative shorter transcript of KIT expressed in postmeiotic germ cells in the testis which encodes a truncated KIT consisting only of the second part of the kinase domain and thus lackig the extracellular and transmembrane domains as well as the first part of the kinase domain (Rossi et al. 1991). Binding of SCF homodimers to KIT results in KIT homodimerization followed by activation of its intrinsic tyrosine kinase activity. KIT stimulation activates a wide array of signalling pathways including MAPK, PI3K and JAK/STAT (Reber et al. 2006, Ronnstrand 2004). Defects of KIT in humans are associated with different genetic diseases and also in several types of cancers like mast cell leukaemia, germ cell tumours, certain subtypes of malignant melanoma and gastrointestinal tumours.
VEGFR2 stimulates ERK not via GRB2-SOS-RAS, but via pY1175-dependent phosphorylation of PLC gamma and subsequent activation of PKCs. PKC plays an important mediatory role in the proliferative Ras/Raf/MEK/ERK pathway. PKC alpha can intersect the Ras/Raf/MEK/ERK cascade at the level of Ras (Clark et al. 2004) or downstream of Ras through direct phosphorylation of Raf (Kolch et al. 1993). VEGF stimulation leads to Ras activation in a Ras-guanine nucleotide exchange factor (GEF) independent mechanism. It rather relies on modulating the regulation of Ras-GTPase activating protein (GAP) than regulation of Ras-GEFS (Wu et al. 2003).
Angiogenesis is the formation of new blood vessels from preexisting vasculature. One of the most important proangiogenic factors is vascular endothelial growth factor (VEGF). VEGF exerts its biologic effect through interaction with transmembrane tyrosine kinase receptors VEGFR, selectively expressed on vascular endothelial cells. VEGFA signaling through VEGFR2 is the major pathway that activates angiogenesis by inducing the proliferation, survival, sprouting and migration of endothelial cells (ECs), and also by increasing endothelial permeability (Lohela et al. 2009, Shibuya & Claesson-Welsh 2006, Claesson-Welsh & Welsh, 2013). The critical role of VEGFR2 in vascular development is highlighted by the fact that VEGFR2-/- mice die at E8.5-9.5 due to defective development of blood islands, endothelial cells and haematopoietic cells (Shalaby et al. 1995).
The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis
Platelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary endothelial cells and neurons.The PDGF family of growth factors is composed of four different polypeptide chains encoded by four different genes. The classical PDGF chains, PDGF-A and PDGF-B, and more recently discovered PDGF-C and PDGF-D. The four PDGF chains assemble into disulphide-bonded dimers via homo- or heterodimerization, and five different dimeric isoforms have been described so far; PDGF-AA, PDGF-AB, PDGF-BB, PDGF-CC and PDGF-DD. It is notable that no heterodimers involving PDGF-C and PDGF-D chains have been described. PDGF exerts its effects by binding to, and activating, two protein tyrosine kinase (PTK) receptors, alpha and beta. These receptors dimerize and undergo autophosphorylation. The phosphorylation sites then attract downstream effectors to transduct the signal into the cell.
The free radical nitric oxide (NO), produced by endothelial NO synthase (eNOS), is an important vasoactive substance in normal vascular biology and pathophysiology. It plays an important role in vascular functions such as vascular dilation and angiogenesis (Murohara et al. 1998, Ziche at al. 1997). NO has been reported to be a downstream mediator in the angiogenic response mediated by VEGF, but the mechanism by which NO promotes neovessel formation is not clear (Babaei & Stewart 2002). Persistent vasodilation and increase in vascular permeability in the existing vasculature is observed during the early steps of angiogenesis, suggesting that these hemodynamic changes are indispensable during an angiogenic processes. NO production by VEGF can occur either through the activation of PI3K or through a PLC-gamma dependent manner. Once activated both pathways converge on AKT phosphorylation of eNOS, releasing NO (Lin & Sessa 2006). VEGF also regulates vascular permeability by promoting VE-cadherin endocytosis at the cell surface through a VEGFR-2SrcVav2RacPAK signalling axis.
Transmembrane transport of small molecules
ERBB2:ERBB3 and ERBB2:ERBB4cyt1 heterodimers activate PI3K signaling by direct binding of PI3K regulatory subunit p85 (Yang et al. 2007, Cohen et al. 1996, Kaushansky et al. 2008) to phosphorylated tyrosine residues in the C-tail of ERBB3 (Y1054, Y1197, Y1222, Y1224, Y1276 and Y1289) and ERBB4 CYT1 isoforms (Y1056 in JM-A CYT1 isoform and Y1046 in JM-B CYT1 isoform). Regulatory subunit p85 subsequently recruits catalytic subunit p110 of PI3K, resulting in the formation of active PI3K, conversion of PIP2 to PIP3, and PIP3-mediated activation of AKT signaling (Junttila et al. 2009, Kainulainen et al. 2000). Heterodimers of ERBB2 and EGFR recruit PI3K indirectly, through GRB2:GAB1 complex (Jackson et al. 2004), which again leads to PIP3-mediated activation of AKT signaling.
ERBB2:EGFR and ERBB2:ERBB4 can directly recruit GRB2:SOS1 complex through phosphorylated C-tail tyrosines of EGFR (Y1068 and Y1086) and ERBB2 (Y1139) that serve as docking sites for GRB2 (Xie et al. 1995, Sepp-Lorenzino et al. 1996), which, again, results in SOS1-mediated guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinases (Janes et al. 1994, Sepp-Lorenzino et al. 1996).
DARPP-32: an integrator of neurotransmission
ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000). ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example. In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR. In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1. In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
Activation of PLCG1 signaling is observed only in the presence of ERBB2:EGFR heterodimers, with PLCG1 binding to phosphorylated tyrosine Y992 and Y1173 in the C-tail of EGFR (Chattopadhyay et al. 1999), and potentially Y1023 in the C-tail of ERBB2 (Fazioli et al. 1991, Cohen et al. 1996).
All ERBB2 heterodimers, ERBB2:EGFR, ERBB2:ERBB3 and ERBB2:ERBB4, are able to activate RAF/MAP kinase cascade by recruiting SHC1 (Pinkas-Kramarski et al. 1996, Sepp-Lorenzino et al. 1996) to phosphorylated C-tail tyrosine residues in either EGFR (Y1148 and Y1173), ERBB2 (Y1196, Y1221, Y1222 and Y1248), ERBB3 (Y1328) or ERBB4 (Y1188 and Y1242 in JM-A CYT1 isoform, Y1178 and Y1232 in JM-B CYT1 isoform, Y1172 and Y1226 in JM-A CYT2 isoform). SHC1 recruitment is followed by phosphorylation (Segatto et al. 1993, Soler et al. 1994), and the phosphorylated SHC1 recruits GRB2:SOS1 complex (Xie et al. 1995), which leads to SOS1-mediated guanyl-nucleotide exchange on RAS (Xie et al. 1995) and downstream activation of RAF and MAP kinases.
The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA
Eukaryotic protein synthesis: still a mystery
G protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it has become clear that this greatly oversimplifies the complexities of GPCR signaling (see Gurevich & Gurevich, 2008). The beta:gamma G-protein dimer is also involved in downstream signaling (Smrcka, 2008), and some receptors form part of metastable complexes of receptor and accessory proteins such as the arrestins. GPCRs are involved in many diverse signaling events (Kristiansen 2004), using a variety of pathways that include modulation of adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK.
All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000).
The CYT1 isoforms of ERBB4 possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K - PIK3R1 (Kaushansky et al. 2008, Cohen et al. 1996). Binding of PIK3R1 to CYT1 isoforms of ERBB4 is followed by recruitment of the p110 catalytic subunit of PI3K (PIK3CA), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000).
ERBB4, also known as HER4, belongs to the ERBB family of receptors, which also includes ERBB1 (EGFR i.e. HER1), ERBB2 (HER2 i.e. NEU) and ERBB3 (HER3). Similar to EGFR, ERBB4 has an extracellular ligand binding domain, a single transmembrane domain and a cytoplasmic domain which contains an active tyrosine kinase and a C-tail with multiple phosphorylation sites. At least three and possibly four splicing isoforms of ERBB4 exist that differ in their C-tail and/or the extracellular juxtamembrane regions: ERBB4 JM-A CYT1, ERBB4 JM-A CYT2 and ERBB4 JM-B CYT1 (the existence of ERBB4 JM-B CYT2 has not been confirmed). ERBB4 becomes activated by binding one of its seven ligands, three of which, HB-EGF, epiregulin EPR and betacellulin BTC, are EGF-like (Elenius et al. 1997, Riese et al. 1998), while four, NRG1, NRG2, NRG3 and NRG4, belong to the neuregulin family (Tzahar et al. 1994, Carraway et al. 1997, Zhang et al. 1997, Hayes et al. 2007). Upon ligand binding, ERBB4 forms homodimers (Sweeney et al. 2000) or it heterodimerizes with ERBB2 (Li et al. 2007). Dimers of ERBB4 undergo trans-autophosphorylation on tyrosine residues in the C-tail (Cohen et al. 1996, Kaushansky et al. 2008, Hazan et al. 1990, Li et al. 2007), triggering downstream signaling cascades. The pathway Signaling by ERBB4 only shows signaling by ERBB4 homodimers. Signaling by heterodimers of ERBB4 and ERBB2 is shown in the pathway Signaling by ERBB2. Ligand-stimulated ERBB4 is also able to form heterodimers with ligand-stimulated EGFR (Cohen et al. 1996) and ligand-stimulated ERBB3 (Riese et al. 1995). Dimers of ERBB4 with EGFR and dimers of ERBB4 with ERBB3 were demonstrated in mouse cell lines in which human ERBB4 and EGFR or ERBB3 were exogenously expressed. These heterodimers undergo trans-autophosphorylation, but their downstream signaling and physiological significance have not been studied. All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000). The CYT1 isoforms of ERBB4 also possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K (Kaushansky et al. 2008, Cohen et al. 1996), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000). Besides signaling as a transmembrane receptor, ligand activated homodimers of ERBB4 JM-A isoforms (ERBB4 JM-A CYT1 and ERBB4 JM-A CYT2) undergo proteolytic cleavage by ADAM17 (TACE) in the juxtamembrane region, resulting in shedding of the extracellular domain and formation of an 80 kDa membrane bound ERBB4 fragment known as ERBB4 m80 (Rio et al. 2000, Cheng et al. 2003). ERBB4 m80 undergoes further proteolytic cleavage, mediated by the gamma-secretase complex, which releases the soluble 80 kDa ERBB4 intracellular domain, known as ERBB4 s80 or E4ICD, into the cytosol (Ni et al. 2001). ERBB4 s80 is able to translocate to the nucleus, promote nuclear translocation of various transcription factors, and act as a transcription co-factor. In neuronal precursors, ERBB4 s80 binds the complex of TAB and NCOR1, helps to move the complex into the nucleus, and is a co-factor of TAB:NCOR1-mediated inhibition of expression of astrocyte differentiation genes GFAP and S100B (Sardi et al. 2006). In mammary cells, ERBB4 s80 recruits STAT5A transcription factor in the cytosol, shuttles it to the nucleus, and acts as the STAT5A co-factor in binding to and promoting transcription from the beta-casein (CSN2) promoter, and may be involved in the regulation of other lactation-related genes (Williams et al. 2004, Muraoka-Cook et al. 2008). ERBB4 s80 was also shown to bind activated estrogen receptor in the nucleus and act as its transcriptional co-factor in promoting transcription of some estrogen-regulated genes, such as progesterone receptor gene NR3C3 and CXCL12 i.e. SDF1 (Zhu et al. 2006). The C-tail of ERBB4 possesses several WW-domain binding motifs (three in CYT1 isoform and two in CYT2 isoform), which enable interaction of ERBB4 with WW-domain containing proteins. ERBB4 s80, through WW-domain binding motifs, interacts with YAP1 transcription factor, a known proto-oncogene, and may be a co-regulator of YAP1-mediated transcription (Komuro et al. 2003, Omerovic et al. 2004). The tumor suppressor WWOX, another WW-domain containing protein, competes with YAP1 in binding to ERBB4 s80 and prevents translocation of ERBB4 s80 to the nucleus (Aqeilan et al. 2005). ERBB4 s80 is also able to translocate to the mitochondrial matrix, presumably when its nuclear translocation is inhibited. Once in the mitochondrion, the BH3 domain of ERBB4, characteristic of BCL2 family members, may enable it to act as a pro-apoptotic factor (Naresh et al. 2006). Activation of ERBB4 in breast cancer cell lines leads to JNK-dependent increase in BRCA1 mRNA level and mitotic cell cycle delay, but the exact mechanism has not been elucidated (Muraoka-Cook et al. 2006). WW-domain binding motifs in the C-tail of ERBB4 play an important role in the downregulation of ERBB4 receptor signaling, enabling the interaction of intact ERBB4, ERBB4 m80 and ERBB4 s80 with NEDD4 family of E3 ubiquitin ligases WWP1 and ITCH. The interaction of WWP1 and ITCH with intact ERBB4 is independent of receptor activation and autophosphorylation. Binding of WWP1 and ITCH ubiquitin ligases leads to ubiquitination of ERBB4 and its cleavage products, and subsequent degradation through both proteasomal and lysosomal routes (Omerovic et al. 2007, Feng et al. 2009). In addition, the s80 cleavage product of ERBB4 JM-A CYT-1 isoform is the target of NEDD4 ubiquitin ligase. NEDD4 binds ERBB4 JM-A CYT-1 s80 (ERBB4jmAcyt1s80) through its PIK3R1 interaction site and mediates ERBB4jmAcyt1s80 ubiquitination, thereby decreasing the amount of ERBB4jmAcyt1s80 that reaches the nucleus (Zeng et al. 2009).
The classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gq participates in many other signalling events including direct interaction with RhoGEFs that stimulate RhoA activity and inhibition of PI3K. Both in vitro and in vivo, the G-protein Gq seems to be the predominant mediator of the activation of platelets.
A monoclonal antibody that appears to recognize the receptor for human T-cell growth factor; partial characterization of the receptor
Interleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but are now known to be produced by many other cells throughout the body. They have pleiotropic effects on cells which bind them, impacting processes such as tissue growth and repair, hematopoietic homeostasis, and multiple levels of the host defense against pathogens where they are an essential part of the immune system.
Interleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in vitro and was therefore named 'T cell growth factor' (TCGF). However, the generation of IL-2- and IL-2 receptor-deficient mice revealed that IL-2 also plays a regulatory role in the immune system by suppressing autoimmune responses. Two main mechanisms have been identified that explain this suppressive function: (1) IL-2 sensitizes activated T cells for activation-induced cell death (AICD) and (2) IL-2 is critical for the survival and function of regulatory T cells (Tregs), which possess potent immunosuppressive properties. IL-2 signaling occurs when IL-2 binds to the heterotrimeric high-affinity IL-2 receptor (IL-2R), which consists of alpha, beta and gamma chains. The IL-2R was identified in 1981 via radiolabeled ligand binding (Robb et al. 1981). The IL-2R alpha chain was identified in 1982 (Leonard et al.), the beta chain in 1986/7 (Sharon et al. 1986, Teshigawara et al. 1987) and the IL-2R gamma chain in 1992 (Takeshita et al.). The high affinity of IL-2 binding to the IL-2R is created by a very rapid association rate to the IL-2R alpha chain, combined with a much slower dissociation rate contributed by the combination of the IL-2R beta and gamma chains (Wang & Smith 1987). After antigen stimulation, T cells upregulate the high-affinity IL-2R alpha chain; IL-2R alpha captures IL-2 and this complex then associates with the constitutively expressed IL-2R beta and gamma chains. The IL-2R gamma chain is shared by several other members of the cytokine receptor superfamily including IL-4, IL-7, IL-9, IL-15 and IL-21 receptors, and consequently is often referred to as the Common gamma chain (Gamma-c). The tyrosine kinases Jak1 and Jak3, which are constitutively associated with IL-2R beta and Gamma-c respectively, are activated resulting in phosphorylation of three critical tyrosine residues in the IL-2R beta cytoplasmic tail. These phosphorylated residues enable recruitment of the adaptor molecule Shc, activating the MAPK and PI3K pathways, and the transcription factor STAT5. After phosphorylation, STAT5 forms dimers that translocate to the nucleus and initiate gene expression. While STAT5 activation is critical for IL-2 function in most cell types, the contribution of the PI3K/Akt pathway differs between distinct T cell subsets. In Tregs for example, PI3K/Akt is not involved in IL-2 signaling and this may explain some of the different functional outcomes of IL-2 signaling in Tregs vs. effector T cells.
AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes.
Release of phospho-SHC from the insulin receptor triggers a cascade of signalling events via SOS, RAF and the MAP kinases.
SHC is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving SOS, RAF and the MAP kinases.
Cytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concentrations. Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, to regulate cellular activity.
Humans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first critical hours and days of exposure to a new pathogen, our innate immune system.
IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in the future.
Autophosphorylation of the insulin receptor triggers a series of signalling events, mediated by SHC or IRS, and resulting in activation of the Ras/RAF and MAP kinase cascades. A second effect of the autophosphorylation of the insulin receptor is its internalisation into an endosome, which downregulates its signalling activity.
SOS is recruited to the plasma membrane and mediates activation of Ras.
Release of phospho-IRS from the insulin receptor triggers a cascade of signalling events via PI3K, SOS, RAF and the MAP kinases.
Polycystin-2 down-regulates cell proliferation via promoting PERK-dependent phosphorylation of eIF2alpha
The effect of the proton pump is to allow entry of [H+] ions into the lumen of the endosome. The net effect of this is to lower the pH of the lumen from pH 7.4 (the pH at the plasma membrane) to pH 6.0 (documented with studies using FITC-labeled insulin - a pH dependent fluorescence marker).
Insulin binding to its receptor results in receptor autophosphorylation on tyrosine residues and the tyrosine phosphorylation of insulin receptor substrates (e.g. IRS and Shc) by the insulin receptor tyrosine kinase. This allows association of IRSs with downstream effectors such as PI-3K via its Src homology 2 (SH2) domains leading to end point events such as Glut4 (Slc2a4) translocation. Shc when tyrosine phosphorylated associates with Grb2 and can thus activate the Ras/MAPK pathway independent of the IRSs. Signal transduction by the insulin receptor is not limited to its activation at the cell surface. The activated ligand-receptor complex initially at the cell surface, is internalised into endosomes itself a process which is dependent on tyrosine autophosphorylation. Endocytosis of activated receptors has the dual effect of concentrating receptors within endosomes and allows the insulin receptor tyrosine kinase to phosphorylate substrates that are spatially distinct from those accessible at the plasma membrane. Acidification of the endosomal lumen, due to the presence of proton pumps, results in dissociation of insulin from its receptor. (The endosome constitutes the major site of insulin degradation). This loss of the ligand-receptor complex attenuates any further insulin-driven receptor re-phosphorylation events and leads to receptor dephosphorylation by extra-lumenal endosomally-associated protein tyrosine phosphatases (PTPs). The identity of these PTPs is not clearly established yet. A discussion of candidates will be added in the near future.
Triggered by acidification of the endosome, insulin dissociates from the receptor and is degraded. The receptor is dephosphorylated and re-integrated into the plasma membrane, ready to be activated again by the binding of insulin molecules.
Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.
Signalling through Shc adaptor proteins appears to be identical for both NGF and EGF. It leads to a fast, but transient, MAPK/ERK activation, which is insufficient to explain the prolonged activation of MAPK found in NGF-treated cells.
RIT and RIN are two small guanine nucleotide binding proteins that share more than 50% sequence identity with RAS, including highly conserved core effector domains. Unlike RAS, the C termini of RIT and RIN lack a typical prenylation motif (CAAX, XXCC, or CXC) required for the association of RAS proteins with the plasma membrane. RIT is expressed in all tissues, whereas RIN is neuron-specific. They have similar signalling properties and are activated by NGF through unknown exchange factors. They signal to ERKs and p38 MAP kinase. They mainly lead to p38 activation via the BRAF-MEK kinase cascade.
Signaling by Vascular Epithelial Growth Factors (VEGF)
The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade.
ARMS (Ankyrin-Rich Membrane Spanning/Kidins 220) is a 220kD tetraspanning adaptor protein which becomes rapidly tyrosine phosphorylated by active Trk receptors. ARMS is another adaptor protein which is involved in the activation of Rap1 and the subsequent prolonged activation of the MAPK cascade.
After NGF binding, activated Trk receptors provide multiple docking sites for adaptor proteins and enzymes. Two docking proteins, the Ankyrin-Rich Membrane Spanning protein (ARMS/Kidins220) and Fibroblast growth factor receptor substrate 2 (Frs2), target signaling molecules in response to NGF stimulation and link receptor activation with the MAP kinase (also called the Extracellular signal-Regulated Kinase cascade, ERK) cascade, an essential process for growth factor-induced cell proliferation and differentiation. A feature of NGF signaling is the sustained activation of the MAPK cascade. This is achieved by the small G protein, Rap1 which binds to and activates B-Raf, an activator of the MAPK cascade. Rap1 is a member of the Ras family of G proteins and like all G proteins, Rap1 is in an inactive state when bound to GDP and is active when bound to GTP. A specific GEF (guanine nucleotide exchange factor) called C3G can activate Rap1 by exchanging GDP for GTP.
Neurotrophins utilize multiple pathways to activate ERKs (ERK1 and ERK2), a subgroup of the large MAP kinase (MAPK) family, from the plasma membrane. The major signalling pathways to ERKs are via RAS, ocurring from caveolae in the plasma membrane or from clathrin-coated vesicles, and via RAP1, taking place in early endosomes. Whereas RAS activation by NGF is transient, RAP1 activation by NGF is sustained for hours.
The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases.
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At the beginning of this reaction, 1 molecule of 'RAD51', and 1 molecule of '3' overhanging DNA at resected DSB ends' are present. At the end of this reaction, 1 molecule of 'RAD51:resected ends of DNA double-strand break' is present. This reaction takes place in the 'nucleus'.
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Localization of a thrombin-binding site on human platelet membrane glycoprotein Ib determined by a monoclonal antibody
Of the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of the numerous individual glycosylases, each of which recognizes and removes a specific modified base(s) from DNA. BER is responsible for the repair of the most prevalent types of DNA lesions, alterations, which arise intracellularly as a consequence of normal mitochondrial metabolism or by oxidative free radicals resulting from ionizing radiation, lipid peroxidation or activated phagocytic cells. BER is a two-step process initiated by one of the DNA glycosylases that recognizes a specific modified base(s) and removes that base through the catalytic cleavage of the glycosylic bond, leaving an abasic site without disruption of the phosphate-sugar DNA backbone. Subsequently, abasic sites are resolved by a series of enzymes that cleave the backbone, synthesize the replacement residue(s), and ligate the DNA strand. BER may occur by either a single-nucleotide replacement pathway or a multiple-nucleotide patch replacement pathway, depending on the structure of the terminal sugar phosphate residue. The glycosylases found in human cells recognize "foreign adducts" and not standard functional modifications such as DNA methylation.
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Resolution of AP sites can occur through the single-nucleotide replacement pathway or through the multiple-nucleotide patch replacement pathway.
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SUMO3:UBA2:SAE1 (name copied from entity in Homo sapiens)
While the single-nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the terminal sugar phosphate is such that it can not be cleaved through the AP lyase activity of DNA polymerase, POL Beta. Under these circumstances, a short stretch of residues containing the abasic site is excised and replaced (Dianov et al., 1999). Following DNA glycosylase mediated cleavage of the damaged base, the endonuclease APE1 is recruited to the site of damage where it cleaves the 5' side of the base-free deoxyribose residue. POL Beta then displaces the DNA glycosylase and synthesizes the first replacement residue. DNA polymerase, POL Delta replaces POL Beta and mediates the synthesis of several additional residues resulting in the displacement of a DNA flap containing the abasic sugar phosphate and 3' flanking residues. The flap structure is recognized and cleaved by the flap endonuclease, FEN1 and the replacement residues are then ligated by the DNA ligase, LIG1 (Klungland and Lindahl, 1997; Matsumoto et al., 1999).
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During removal of DNA patch containing abasic residue, DNA glycosylase is displaced by APE1 which endonucleolytically cleaves the 5' side of the base-free deoxyribose residue. POL Beta is recruited to the AP site where it mediates incorporation of the first replacement nucleotide. Association of POL delta with the AP site displaces POL Beta. DNA strand displacement synthesis then follows and flap structures are cleaved.
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At the beginning of this reaction, 1 molecule of 'PCNA', and 1 molecule of 'Flap endonuclease-1 ' are present. At the end of this reaction, 1 molecule of 'FEN1:PCNA complex' is present. This reaction takes place in the 'nucleus'.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594541
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596020
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596018
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_243651.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594542
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_251051.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596880
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_238052.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596876
RNA Polymerase II holoenzyme complex (unphosphorylated) (name copied from entity in Homo sapiens)
Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT
SUMO3:UBE2I (name copied from entity in Homo sapiens)
Depyrimidination of a damaged nucleotide is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apyrimidinic (AP) site.
SUMO2:UBE2I (name copied from entity in Homo sapiens)
Base excision repair is initiated by DNA glycosylases that hydrolytically cleave of the base-deoxyribose glycosyl bond of a damaged nucleotide residue releasing the damaged base (Lindahl and Wood, 1999).
SUMO1:C93-UBE2I (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'formamidopyrimidine', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
SUMO3:UBA2 (name copied from entity in Homo sapiens)
Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
Cloning and characterization of human agmatinase
RNA Polymerase II (unphosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
capped, methylated pre-mRNA:CBC Complex (name copied from entity in Homo sapiens)
ATAC A Complex (name copied from entity in Homo sapiens)
PERK dimer (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. At the end of this reaction, 1 molecule of 'cytosine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
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At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. At the end of this reaction, 1 molecule of 'Thymine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=75165
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site', and 1 molecule of '5,6-Dihydrouracil' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
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At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a formamidopyrimidine ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
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The circadian E-box: when perfect is not good enough
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a dihydrouracil' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. This reaction takes place in the 'nucleus'.
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TFIIF (name copied from entity in Homo sapiens)
Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a thymine glycol ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. This reaction takes place in the 'nucleus'.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_210242.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123470.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_249999.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596879
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596011
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Mechanism of the nucleotide exchange reaction in eukaryotic polypeptide chain initiation. Characterization of the guanine nucleotide exchange factor as a GTP-binding protein.
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snRNP Sm core complex (name copied from entity in Homo sapiens)
U11 snRNP (name copied from entity in Homo sapiens)
Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
SF3B (name copied from entity in Homo sapiens)
Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apurinic (AP) site.
U12 snRNP (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a cytosine glycol' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. This reaction takes place in the 'nucleus'.
U5 snRNP (name copied from entity in Homo sapiens)
U4 ATAC:U5:U6 ATAC Complex (name copied from entity in Homo sapiens)
U4 ATAC snRNP (name copied from entity in Homo sapiens)
U4 ATAC snRNP:U6 ATAC snRNP (name copied from entity in Homo sapiens)
A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase.
ATAC B Complex (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'MPG glycosylase:3-methyladenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site', and 1 molecule of '3-Methyladenine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
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ATAC C Complex (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MYH-bound apurinic/apyrimidinic site', and 1 molecule of '8-oxoguanine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MYH glycosylase'.
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The recognition and cleavage of an altered base by a DNA glycosylase is thought to involve the diffusion of the enzyme along the minor grove of the DNA molecule. The enzyme presumably compresses the backbone of the affected DNA strand at the site of damage. This compression is thought to result in an outward rotation of the damaged residue into a "pocket" of the enzyme that recognizes and cleaves the altered base (Parikh et al., 1998).
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U6 ATAC snRNP (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing a formamidopyrimidine ', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595979
At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site', and 1 molecule of 'formamidopyrimidine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594534
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5597060
At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. At the end of this reaction, 1 molecule of '8-oxoguanine', and 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8670.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241349.1
At the beginning of this reaction, 1 molecule of 'MPG glycosylase:hypoxanthine complex' is present. At the end of this reaction, 1 molecule of 'Hypoxanthine', and 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_245710.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595983
At the beginning of this reaction, 1 molecule of 'MPG glycosylase:ethenoadenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site', and 1 molecule of 'ethenoadenine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594535
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595981
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594533
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594532
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163085
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_202009.2
B-cell antigen receptor stimulation activates the human Bruton's tyrosine kinase, which is deficient in X-linked agammaglobulinemia
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TARS dimer (name copied from entity in Homo sapiens)
SARS dimer (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20218.2
GARS dimer (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595977
CARS dimer (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an adenine opposite to an 8-oxo guanine', and 1 molecule of 'MYH glycosylase' are present. At the end of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. This reaction takes place in the 'nucleus'.
KARS homodimer (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an 8-oxo guanine opposite to a cytosine', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. This reaction takes place in the 'nucleus'.
DARS homodimer (name copied from entity in Homo sapiens)
aminoacyl-tRNA synthetase multienzyme complex (name copied from entity in Homo sapiens)
Cytochrome P450s and other enzymes in drug metabolism and toxicity
WARS dimer (name copied from entity in Homo sapiens)
Nonsense-mediated decay of an mRNA can be triggered even if the termination codon does not precede an exon junction (Buhler et al. 2006, Eberle et al. 2008, Silva et al. 2008, Singh et al. 2008, Ivanov et al. 2008). UPF1 and PABP seem to modulate the efficiency of translation termination and PABP in the proximity of a termination codon prevents NMD likely by outcompeting UPF1 for interaction with eRF3 (Singh et al. 2008, Ivanov et al. 2008, Silva et al. 2008). Factors in the competition may be the length and secondary structure of the 3' UTR (Buhler et al. 2006, Eberle et al. 2008). UPF1 preferentially binds some but not all longer UTRs (Hogg and Goff 2010). Interaction of eRF3 with PABP stimulates ribosome dissociation and initiation of a new round of translation on the mRNA. Interaction of eRF3 with UPF1 appears to promote nonsense-mediated decay. It is possible but not yet demonstrated that all components of the SURF complex (SMG1, UPF1, eRF1, eRF3) are assembled on an mRNA without an exon junction complex and that UPF1 is phosphorylated by SMG1.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_212293.2
YARS dimer (name copied from entity in Homo sapiens)
During normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of translation to commence. Nonsense-mediated decay (NMD) is triggered if eRF3 at the ribosome interacts with UPF1, which may compete with PABP (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). An exon junction located 50-55 nt downstream of a termination codon is observed to enhance NMD. Exon-junction complexes (EJCs) are deposited on the mRNA during splicing in the nucleus, remain on mRNAs after transport to the cytosol, and are dislodged by the ribosome as it progresses along the mRNA during the pioneer round of translation (Gehring et al. 2009). EJCs contain the core factors eIF4A-III, Magoh-Y14, and CASC3 as well as the peripheral factors RNPS1, UPF2, and UPF3. UPF2 and UPF3 recruit UPF1 to eRF3 at the terminating ribosome. Thus an EJC downstream of a termination codon will not have been dislodged during translation and will recruit UPF1, triggering NMD. UPF1 is believed to form a complex containing SMG1, SMG8, and SMG9. In the key regulatory step of NMD SMG1 phosphorylates UPF1. The phosphorylated UPF1 then recruits either SMG6 or SMG5 and SMG7. SMG6 is itself an endoribonuclease that cleaves the mRNA. SMG5 and SMG7 do not have endoribonuclease activty, but are thought to recruit ribonucleases. Nonsense-mediated decay has been observed to involve deadenlyation, decapping, and both 5' to 3' and 3' to 5' exonuclease activities, but the exact degradative pathways taken by a given mRNA are not yet known. UPF1 also plays roles in Staufen-mediated decay, histone mRNA decay, telomere maintenance, genome integrity, and may play a role in normal termination of translation.
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PPA1 dimer (name copied from entity in Homo sapiens)
The Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Neu-Yilik and Kulozik 2008, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). In mammalian cells a termination codon can be recognized as premature if it precedes an exon-exon junction by at least 50-55 nucleotides or if it is followed by an abnormal 3' untranslated region (UTR). While length of the UTR may play a part, the qualifications for being "abnormal" have not been fully elucidated. Also, some termination codons preceding exon junctions are not degraded by NMD so the criteria for triggering NMD are not yet fully known (reviewed in Rebbapragada and Lykke-Andersen 2009). While about 30% of disease-associated mutations in humans activate NMD, about 10% of normal human transcripts are also degraded by NMD (reviewed in Stalder and Muhlemann 2008, Neu-Yilik and Kulozik 2008, Bhuvanagiri et al. 2010, Nicholson et al. 2010). Thus NMD is a normal physiological process controlling mRNA stability in unmutated cells. Exon junction complexes (EJCs) are deposited on an mRNA during splicing in the nucleus and are displaced by ribosomes during the first round of translation. When a ribosome terminates translation the A site encounters the termination codon and the eRF1 factor enters the empty A site and recruits eRF3. Normally, eRF1 cleaves the translated polypeptide from the tRNA in the P site and eRF3 interacts with Polyadenylate-binding protein (PABP) bound to the polyadenylated tail of the mRNA. During activation of NMD eRF3 interacts with UPF1 which is contained in a complex with SMG1, SMG8, and SMG9. NMD can arbitrarily be divided into EJC-enhanced and EJC-independent pathways. In EJC-enhanced NMD, an exon junction is located downstream of the PTC and the EJC remains on the mRNA after termination of the pioneer round of translation. The core EJC is associated with UPF2 and UPF3, which interact with UPF1 and stimulate NMD. Once bound near the PTC, UPF1 is phosphorylated by SMG1. The phosphorylation is the rate-limiting step in NMD and causes UPF1 to recruit either SMG6, which is an endoribonuclease, or SMG5 and SMG7, which recruit ribonucleases. SMG6 and SMG5:SMG7 recruit phosphatase PP2A to dephosphorylate UPF1 and allow further rounds of degradation. How EJC-independent NMD is activated remains enigmatic but may involve competition between PABP and UPF1 for eRF3.
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DARS2 dimer (name copied from entity in Homo sapiens)
Nonsense-mediated decay has been observed with mRNAs that do not have an exon junction complex (EJC) downstream of the termination codon (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Nicholson et al. 2010). In these cases the trigger is unknown but a correlation with the length of the 3' UTR has sometimes been seen. The current model posits a competition between PABP and UPF1 for access to eRF3 at the terminating ribosome (Ivanov et al. 2008, Singh et al. 2008, reviewed in Bhuvanagiri et al. 2010). Abnormally long 3' UTRs may prevent PABP from efficiently interacting with eRF3 and allow UPF1 to bind eRF3 instead. Long UTRs with hairpin loops may bring PABP closer to eRF3 and help evade NMD (Eberle et al. 2008). The pathway of degradation taken during EJC-independent NMD has not been elucidated. It is thought that phosphorylation of UPF1 by SMG1 and recruitment of SMG6 or SMG5 and SMG7 are involved, as with EJC-enhanced NMD, but this has not yet been shown.
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RNA metabolism consists of both mRNA degradative pathways and non-coding RNA metabolism. Non-coding RNA metabolism includes the processing and packaging of the small nuclear ribonucleoproteins (snRNPs).
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_192734.3
Once synthesized mRNA can be utilized until degraded. Degradation itself is the final mode of gene expression regulation.
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an ethenoadenine ', and 1 molecule of 'MPG glycosylase' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:ethenoadenine complex' is present. This reaction takes place in the 'nucleus'.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_125107.1
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing a 3-methyladenine', and 1 molecule of 'MPG glycosylase' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:3-methyladenine complex' is present. This reaction takes place in the 'nucleus'.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_247418.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1500646
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594543
At the beginning of this reaction, 1 molecule of 'MPG glycosylase', and 1 molecule of 'Double-strand DNA containing a hypoxanthine' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:hypoxanthine complex' is present. This reaction takes place in the 'nucleus'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594538
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The subcellular localization of acetyl-CoA carboxylase 2
SOD2 tetramer (name copied from entity in Homo sapiens)
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PPA2 dimer (name copied from entity in Homo sapiens)
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KARS dimer (name copied from entity in Homo sapiens)
YARS2 dimer (name copied from entity in Homo sapiens)
SARS2 dimer (name copied from entity in Homo sapiens)
SMG1 phosphorylates UPF1 in vitro and in vivo (Denning et al. 2001, Yamashita et al. 2001, Kashima et al. 2006). Serines 1073, 1078, 1096, and 1116 in isoform 2 (Serines 1084, 1089, 1107, 1127 in isoform 1) are phosphorylated in vitro and phosphorylation at serines 1078 and 1096 has been confirmed in vivo (Yamashita et al. 2001, Ohnishi et al. 2003, Kashima et al. 2006). UPF1 also contains additional serine and threonine residues that could be phosphorylated. SMG8 and SMG9 associate with SMG1 and regulate the kinase activity of SMG1 (Yamashita et al. 2009). The phosphorylation reaction is rate-limiting in nonsense-mediated decay and is therefore regarded as a licensing step (reviewed in Rebbapragada and Lykke-Andersen 2009). Phosphorylation is enhanced by the exon junction complex, which can interact with UPF1 via UPF2 and/or UPF3 (Kashima et al. 2006, Ivanov et al. 2008) or via Y14:Magoh (Ivanov et al. 2008). SMG8 and SMG9 bind SMG1 and regulate its kinase activity (Yamashita et al. 2009, Fernandez et al. 2011).
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Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases
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Interfacial kinetic and binding properties of the complete set of human and mouse groups I, II, V, X, and XII secreted phospholipases A2
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Adenosine triphosphate-adenosine-5'-monophosphate phosphotransferase from normal human liver mitochondria. Isolation, chemical properties, and immunochemical comparison with Duchenne muscular dystrophic serum aberrant adenylate kinase
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Polymerization is carried out by DNA polymerases, delta and epsilon.
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At the beginning of this reaction, 1 molecule of 'Stalled Pol II in TC-NER', and 1 molecule of 'repaired DNA template:nascent mRNA hybrid' are present. At the end of this reaction, 1 molecule of 'Active Pol II complex with repaired DNA template:mRNA hybrid' is present. This reaction takes place in the 'nucleus'.
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The 'road block' induced by the DNA damage to the transcription machinery triggers assembly of a transcription couple repair complex, whose composition and function are yet to fully understood. Damage recognition is achieved by the arrest of Pol II active complex. Subsequently various factors like CSA, CSB, TFIIH, XPG, XPF-ERCC1 complexes are recruited. The importance of active CSA and CSB are known from the mutation profile of the patients bearing the corresponding disease phenotypes. CSB can act as a 'repair-transcription uncoupling factor' that may use its DNA translocase activity to remove the Pol II activity from the lesion site. TFIIS may cleave up to 35 nucleotides from the 3' end of the nascent RNA product leading to the enhanced access to damage site on the corresponding template DNA.
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At the beginning of this reaction, 1 molecule of 'newly synthesized DNA fragment ', 1 molecule of 'DNA ligase I ', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with dual incisions' are present. At the end of this reaction, 1 molecule of 'repaired DNA template:nascent mRNA hybrid', and 1 molecule of 'DNA ligase I ' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA ligase activity' of 'DNA ligase I '.
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DNA Ligase 1 ligates the newly synthesized fragment to the gap in the template DNA.
Binding of XPC complex to the damaged site on the DNA substrate is followed by XPA and RPA recruitment. XPA is a metalloprotein that binds to different types of DNA damage. Binding of RPA, or Replicative protein A, a heterotrimer, initiates the formation of incision complex. This includes a serial assembly of the rest of the NER machinery consisting of TFIIH, XPG etc. Action of helicases in TFIIH complex opens up a bubble structure in the DNA template, exposing a fragment of DNA with lesion for endonuclease activity.
At the site of damage, the Pol II complex is arrested resulting in reduced levels of transcription. Several models have been proposed to explain the mechanism of this transcriptional downregulation. These include a. hyperphosphorylation of Pol II resulting in aborted entry to new pre-initiation complexes b. sequestration of TATA-binding proteins (TBP) c. enhanced use of TFIIH complexes for repair purposes precluding their use in transcription.
An active Pol II complex consisting mainly of the Pol II holoenzyme transcribes the damaged DNA template.
GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The three events that characterize NER are well characterized in GG-NER: damage recognition, bimodal incision of DNA via repair protein complex, resulting excision of DNA fragment with the lesion. Post-excision polymerization and ligation restore back the native chemistry and configuration to the damaged DNA.
The resultant gap is filled by polymerase activities of Pol delta and Pol epsilon. Accessory replication protein complexes of RPA, PCNA and RFC play a role in this synthesis. DNA Ligase 1 seals the gap restoring the covalent integrity of the repaired strand.
Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the itpa gene
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Once repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates of through synthesis-dependent strand-annealing.
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Homologous recombination repair of replication-independent double-strand breaks requires the activation of ATM followed by ATM mediated phosphorylation of DNA repair proteins. DNA repair and signaling proteins are then recruited to double-strand breaks. The ends of the DNA double strand breaks must be resectioned and RPA complexes associate with the resulting ssDNA. Homologous DNA pairing and strand exchange then occurs followed by DNA repair synthesis and resolution of D-loop structures.
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The HRR pathway is an "error free" DNA repair mechanism that utilizes information encoded by homologous sequence to repair double-strand breaks (DSBs). HRR acts on DSBs occurring within replicated DNA (replication-independent DSBs) or on DSBs that are generated at broken replication forks (replication-dependent DSBs). Repair by homologous recombination involves processing of the ends of the DNA double-strand break, homologous DNA pairing and strand exchange, repair DNA synthesis, and resolution of the heteroduplex molecules.
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Numerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-strand breaks (DSBs), one of the most dangerous type of DNA damage along with interstrand crosslinks, are caused by ionizing radiation or certain chemicals such as bleomycin, and occur normally during the processes of DNA replication, meiotic exchange, and V(D)J recombination. Two distinct mechanisms for DSB repair are the error-free homologous recombination repair (HRR) pathway and the error-prone nonhomologous end-joining (NHEJ) pathway. The choice of pathway may be determined by whether the DNA region has already replicated and the precise nature of the break. NHEJ functions at all stages of the cell cycle, but plays the predominant role in both the G1 phase and in S-phase regions of DNA that have not yet replicated (Rothkamm et al. 2003). HRR functions primarily in repairing both one-sided DSBs that arise at DNA replication forks and two-sided DSBs arising in S or G2-phase chromatid regions that have replicated.
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At the beginning of this reaction, 1 molecule of 'ERCC1, DNA excision repair protein', and 1 molecule of 'XPF protein' are present. At the end of this reaction, 1 molecule of 'ERCC1:XPF complex' is present. This reaction takes place in the 'nucleus'.
Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
UBA2:SAE1 (name copied from entity in Homo sapiens)
SUMO1:UBA2:SAE1 (name copied from entity in Homo sapiens)
The RAD51-ssDNA nucleoprotein filament is a right-hand helical nucleoprotein filament referred to as the presynaptic filament. This nucleoprotein complex contains a binding site for the double-stranded homologous DNA molecule with which it interacts during strand exchange. Loading of RAD51 onto ssDNA is thought to be facilitated by recombination mediator RAD52 (McIlwraith et al., 2000), RAD51 paralogs: RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3 (Sigurdsson et al., 2001), by the association of RAD52 with ssDNA (Parsons et al., 2000) and by the association of RAD51 with BRCA2 (Tarsounas et al., 2003).
SUMO1:UBA2 (name copied from entity in Homo sapiens)
Defective MUT causes methylmalonic aciduria mut type
Protease nexin-II (amyloid beta-protein precursor): a platelet alpha-granule protein
Sar1b:GTP:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from ssDNA, followed by the association of RAD51 with BRCA2, formation of RAD52 heptameric ring structure complexes on ssDNA, association of RAD52 with the RPA complex, association of RAD52 with ssDNA at resected ends of double-strand break and assembly of the RAD51-ssDNA nucleoprotein complex. Stable synaptic pairing between recombining DNA molecules involves the invasion of homologous duplex DNA by the processed single-stranded ends of the double-strand break, followed by displacement of the non-complimentary strand of the duplex. This results in the formation of a D-loop structure. Invasion of the heteroduplex DNA by RAD51 nucleoprotein filament involves the identification of a region of homology between these two molecules. The mechanism by which this occurs is not yet known. RAD51 catalyses the invasion of the nucleoprotein filament into homologous double-stranded DNA. Watson-Crick hydrogen bonding between the ssDNA within the nucleoprotein filament and the homologous strand of the invaded DNA duplex result in the displacement of the non-pairing strand (strand displacement) and formation of the D-loop structure (Sung et al., 2003). The RAD51 nucleoprotein filament has independent binding sites for the ssDNA strand upon which it assembles and the recombining homologous duplex DNA. The repair proteins RPA, RAD52, and RAD54 appear to promote RAD51 mediated invasion and homologous DNA pairing reaction (McIlwraith et al, 2000 and Sigurdsson et al., 2002). The conformation of the RAD52-ssDNA complex is thought to place the ssDNA on an exposed surface of the protein, in a configuration that may promote the DNA-DNA annealing of complementary DNA strands. RAD54 may function in the transient separation of the duplex DNA strands via its ATP hydrolysis-mediated DNA supercoiling function (Sigurdsson et al., 2002). Branch migration or strand exchange occurs as the complimentary duplex DNA strand is progressively taken up into the nucleoprotein filament to base pair with the invading single-strand sequence (Sung et al., 2003).
The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from ssDNA, followed by the association of RAD51 with BRCA2, formation of RAD52 heptameric ring structure complexes on ssDNA, association of RAD52 with the RPA complex, association of RAD52 with ssDNA at resected ends of double-strand break and assembly of the RAD51-ssDNA nucleoprotein complex.
Sar1b:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Following the synthesis of new DNA at resected 5' ends of the DSB, the heterologous DNA molecules may be ligated resulting in the formation of Holliday junctions. The Holliday structures are then cleaved resulting in reciprocal exchange of sequence between sister chromatids.
Sec23p:Sec24p Complex (name copied from entity in Homo sapiens)
Ligation of the crossed-strand intermediate results in the formation of Holliday structures with two crossovers. In humans, the identity of this ligase activity involved in this process is not known.
SUMO2:UBA2:SAE1 (name copied from entity in Homo sapiens)
SUMO2:UBA2 (name copied from entity in Homo sapiens)
Characterization of the advanced glycation end-product receptor complex in human vascular endothelial cells
Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay
Identification, purification and characterization of a novel phosphatidylinositol-specific phospholipase C, a third member of the beta subfamily
Constitutive PI3K/AKT Signaling in Cancer
Characterization of the localization and proteolytic activity of the SUMO-specific protease, SENP1
Glycogen and its metabolism: some new developments and old themes
XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
Cell surface heparin binding protein HIP
Reduced half-life of holocarboxylase synthetase from patients with severe multiple carboxylase deficiency
integral component of cytoplasmic side of endoplasmic reticulum membrane
PRDX1 dimer (name copied from entity in Homo sapiens)
PRDX2 dimer (name copied from entity in Homo sapiens)
Coatomer (name copied from entity in Homo sapiens)
Arf1-GTP (name copied from entity in Homo sapiens)
Coatomer:Arf1-GTP Complex (name copied from entity in Homo sapiens)
GTP hydrolysis and joining of the 60S ribosomal subunit
Extracellular-signal-regulated kinase signalling in neurons
HuR (ELAVL1) is a ubiquitous protein that binds AU-rich elements in mRNAs and acts to stabilize the mRNAs. HuR activity is controlled by phosphorylation, with PKC alpha and PCK delta enhancing the ability of HuR to bind and stabilize mRNAs. Binding of mRNAs occurs in the nucleus and HuR then interacts with the CRM1 export pathway to transfer the mRNA to the cytoplasm. The mechanism by which HuR shields the mRNA from degradation is unknown. HuR also regulates translation of some mRNAs, in some cases repressing translation and in some cases enhancing translation of bound mRNAs by recruiting them to polysomes. HuR binds and regulates mRNAs encoding Cyclooxygenase-2 (COX2, PTGS2), Cyclin A (CCNA, CCNA2), Cyclin D1 (CCND1), Cyclin B1 (CCNB1), CD83 antigen (CD83), and proto-oncogene c-Fos (FOS). HuR is a member of a family of proteins that also contains HuD (ELAVL4), HuB (ELAVL2), and HuC (ELAVL3). HuB, HuC, and HuD are specifically expressed in neural tissue. HuR participates in apoptosis. During lethal stress HuR becomes mostly cytoplasmic and is a target of Caspase-3 and Caspase-7. The cleavage products of HuR in turn promote apoptosis.
RNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-element binding proteins is regulated, usually by phosphorylation but also by subcellular localization.
The molecular mechanism of lead inhibition of human porphobilinogen synthase
After undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by the PAN2-PAN3 complex that shortens the poly(A) tail from about 200 adenosine residues to about 80 residues and one catalyzed by the CCR4-NOT complex or by the PARN enzyme that shortens the tail to about 10-15 residues. After deadenylation the mRNA is then hydrolyzed by either the 5' to 3' pathway or the 3' to 5' pathway. It is unknown what determinants target a mRNA to one pathway or the other. The 5' to 3' pathway is initiated by binding of the Lsm1-7 complex to the 3' oligoadenylate tail followed by decapping by the DCP1-DCP2 complex. The 5' to 3' exoribonuclease XRN1 then hydrolyzes the remaining RNA. The 3' to 5' pathway is initiated by the exosome complex at the 3' end of the mRNA. The exosome processively hydrolyzes the mRNA from 3' to 5', leaving only a capped oligoribonucleotide. The cap is then removed by the scavenging decapping enzyme DCPS.
HuR (ELAV1) phosphorylated on serine221 and serine158 binds COX-2 mRNA in the nucleus. The phosphorylation of serine 158 appears to affect RNA-binding while phosphorylation on serine 221 affects nucleocytoplasmic shuffling.
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SOD2:Mn2+ (name copied from entity in Homo sapiens)
HuR phosphorylated on ser221 and ser318 binds AU-rich regions of mRNAs. Phosphorylation on ser318 appears to affect RNA binding and phosphorylation of ser221 affects nucleocytoplasmic shuttling.
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HuR binds AU-rich elements of mRNAs. Bound HuR can form oligomers on longer AU-rich elements. Phosphorylated HuR binds mRNA more tightly than unphosphorylated HuR does.
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GSR holoenzyme (name copied from entity in Homo sapiens)
At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning. Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1. BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening. PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome. The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
GSR dimer (name copied from entity in Homo sapiens)
The Lsm1-7 complex forms a heptameric ring that binds the 3' oligoadenylated ends of mRNAs that have been deadenylated. The bound Lsm1-7 may prevent access of the exosome (a 3' to 5' exonuclease) to the 3' end and thereby direct the mRNA to the 5' to 3' exonuclease pathway. The yeast Lsm1-7 complex has a preference for oligoadenylated RNA compared to polyadenylated RNA, however other determinants of binding by Lsm1-7 are unknown.
Cytochrome c (reduced) (name copied from entity in Homo sapiens)
The XRN1 exoribonuclease hydrolyzes decapped mRNA from 5' to 3' and yields ribonucleotides having 5'-monophosphates. In yeast Xrn1 associates with the Lsm1-7 complex.
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Cytochrome c (oxidized) (name copied from entity in Homo sapiens)
Degradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-methylguanosine cap of the mRNA is hydrolyzed by the DCP1-DCP2 complex. Third, the 5' end of the decapped mRNA is attacked by the XRN1 exoribonuclease which digests the remainder of the mRNA from 5' to 3'. These processes may be physically connected by PATL1, the homolog of yeast Pat1, which stably binds the Lsm1-7 complex and interacts with the DCP1-DCP2 decapping complex and the Ccr4-NOT deadenylation complex (Ozgur et al. 2010).
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Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity
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Recruitment and regulation of phosphatidylinositol phosphate kinase type 1 gamma by the FERM domain of talin
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Complete sequencing and characterization of 21,243 full-length human cDNAs
REV-ERBA binds DNA elements very similar to those bound by the transcription activator RORA. RORAREV-ERBA bound to DNA and heme recruits the corepressors NCoR and HDAC3 to repress transcription. Thus REV-ERBA and RORA appear to compete to repress or activate genes, repectively.
As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003).
The ELOVL3 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Arf1-GDP (name copied from entity in Homo sapiens)
As a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are aspects of the roles of cell adhesion molecules in axonal guidance and myogenesis, of transcriptional regulation in hematopoiesis (specifically, B lymphopoiesis), pancreatic beta cell and white adipocyte differentiation, and molecular events of "nodal" signaling.
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Coatomer:Arf1-GTP:GAP Complex (name copied from entity in Homo sapiens)
The NOCTURNIN gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The NOCTURNIN gene shows circadian expression because the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds an E-box element in the NOCTURNIN promoter and activates transcription.
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Two transcription factors, PDX1 and HNF1A, play key roles in maintaining the gene expression pattern characteristic of mature beta cells in the endocrine pancreas. Targets of these regulatory molecules include genes encoding insulin, the GLUT2 glucose transporter, the liver- (and pancreas) specific form of pyruvate kinase and other transcription factors including HNF4A, HNF4G, and FOXA3. PDX1 expression in turn is controlled by the activities of MAFA, FOXA2, and PAX6, and negatively regulated via AKT (Chakrabarti and Mirmira 2003; Servitja and Ferrer 2004).
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The normal development of the pancreas during gestation has been intensively investigated over the past decade especially in the mouse (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003). Studies of genetic defects associated with maturity onset diabetes of the young (MODY) has provided direct insight into these processes as they take place in humans (Fajans et al. 2001). During embryogenesis, committed epithelial cells from the early pancreatic buds differentiate into mature endocrine and exocrine cells. It is helpful to schematize this process into four consecutive cellular stages, to begin to describe the complex interplay of signal transduction pathways and transcriptional networks. The annotations here are by no means complete - factors in addition to the ones described here must be active, and even for the ones that are described, only key examples of their regulatory effects and interactions have been annotated. It is also important to realize that in the human, unlike the mouse, cells of the different stages can be present simultaneously in the developing pancreas and the linear representation of these developmental events shown here is an over-simplification of the actual developmental process (e.g., Sarkar et al. 2008). The first stage of this process involves the predifferentiated epithelial cells of the two pancreatic anlagen that arise from the definitive endoderm at approximately somite stages 11-15 and undergo budding from somite stages 20-22. This period corresponds to gestational days 8.75-9.5 in the mouse, and 26 in the human. Pancreatic buds subsequently coalesce to form a single primitive gland, while concomitantly a ductal tree lined by highly proliferative epithelial cells is formed. A subset of such epithelial cells is thought to differentiate into either endocrine or acinar exocrine cells. A third cellular stage is defined by the endocrine-committed progenitors that selectively express the basic helix-loop-helix transcription factor NEUROG3. NEUROG3 is known to activate a complex transcriptional network that is essential for the specification of endocrine cells. Many transcription factors that are activated by NEUROG3 are also involved in islet-subtype cellular specification and in subsequent stages of differentiation of endocrine cells. This transient cellular stage thus leads to the generation of all known pancreatic endocrine cells, including insulin-producing beta-cells, and glucagon-producing alpha cells, the final stage of this schematic developmental process. The diagram below summarizes interactions that take place between transcription factors and transcription factor target genes during these cellular stages, and shows cases where there is both functional evidence that a transcription factor is required for the target gene to be expressed, and biochemical evidence that this interaction is direct. We also describe instances where a signaling pathway is known to regulate a transcription factor gene in this process, even if the intervening signaling pathway is not fully understood.
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Axon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, which senses the guidance cues in the environment through guidance cue receptors and responds by undergoing cytoskeletal changes that determine the direction of axon growth. Guidance cues present in the surrounding environment provide the necessary directional information for the trip. These extrinsic cues have been divided into attractive or repulsive signals that tell the growth cone where and where not to grow. Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules and their receptors that guide axons. These include netrins, Slits, semaphorins, and ephrins, and their cognate receptors, DCC and or uncoordinated-5 (UNC5), roundabouts (Robo), neuropilin and Eph. In addition, many other classes of adhesion molecules are also used by growth cones to navigate properly which include NCAM and L1CAM.
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The glucokinase (GCK) gene is transcribed and its mRNA is translated. GCK transcription is positively regulated by the activity of the NEUROD1 and PDX1 transcription factors. These events and interactions are inferred from corresponding ones studied in molecular detail in the mouse.
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Netrins are secreted proteins that play a crucial role in neuronal migration and in axon guidance during the development of the nervous system. To date, several Netrins have been described in mouse and humans: Netrin-1, -3/NTL2, -4/h and G-Netrins. Netrin-1 is the most studied member of the family and has been shown to play a crucial role in neuronal navigation during nervous system development mainly through its interaction with its receptors DCC and UNC5. Members of the Deleted in colorectal cancer (DCC) family- which includes DCC and Neogenin in vertebrates- mediate netrin-induced axon attraction, whereas the C. elegans UNC5 receptor and its four vertebrate homologs Unc5a-Unc5d mediate repulsion.
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The neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the nervous system. The role of NCAM in neural differentiation and synaptic plasticity is presumed to depend on the modulation of intracellular signal transduction cascades. NCAM based signaling complexes can initiate downstream intracellular signals by at least two mechanisms: (1) activation of FGFR and (2) formation of intracellular signaling complexes by direct interaction with cytoplasmic interaction partners such as Fyn and FAK. Tyrosine kinases Fyn and FAK interact with NCAM and undergo phosphorylation and this transiently activates the MAPK, ERK 1 and 2, cAMP response element binding protein (CREB) and transcription factors ELK and NFkB. CREB activates transcription of genes which are important for axonal growth, survival, and synaptic plasticity in neurons. NCAM1 mediated intracellular signal transduction is represented in the figure below. The Ig domains in NCAM1 are represented in orange ovals and Fn domains in green squares. The tyrosine residues susceptible to phosphorylation are represented in red circles and their positions are numbered. Phosphorylation is represented by red arrows and dephosphorylation by yellow. Ig, Immunoglobulin domain; Fn, Fibronectin domain; Fyn, Proto-oncogene tyrosine-protein kinase Fyn; FAK, focal adhesion kinase; RPTPalpha, Receptor-type tyrosine-protein phosphatase; Grb2, Growth factor receptor-bound protein 2; SOS, Son of sevenless homolog; Raf, RAF proto-oncogene serine/threonine-protein kinase; MEK, MAPK and ERK kinase; ERK, Extracellular signal-regulated kinase; MSK1, Mitogen and stress activated protein kinase 1; CREB, Cyclic AMP-responsive element-binding protein; CRE, cAMP response elements.
PIP2 hydrolysis appers to be an important mechanism for netrin-1 mediated neurite elongation. Netrin-1 alone could not elicit hydrolysis of PIP2 but depends on the stimulation of DCC and PLCgamma.
The levels of second messengers such as Ca+2, cAMP and cGMP may regulate the response of the growth cone to a particular cue. Netrin-1 as a guidance molecule depends on intracellular Ca+2 concentration, coactivation of PI3K and PLCgamma, and the type of response depends on the levels of cAMP. Netrin first stimulates its receptor DCC, resulting in the activation of the enzyme phospholipase C. This then produces the messenger molecules, inositol-1,4,5-trisphosphate (IP3) and DAG, which in turn causes the release of Ca+2 from intracellular stores. Ca+2 release from the stores then activates TRPC channels on the cell surface. DAG activates TRPC3 and TRPC6 in a direct, membrane delimited manner, and IP3 may activate TRPC channels by depleting the ER Ca+2 levels.
Chromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
The gene encoding SPO11 shares sequence similarity to TopoVI, a type II topoisomerase. SPO11 dimers cleave both strands of DNA. Each subunit of the dimer remains covalently attached to the 5' end of one strand of DNA via a phosphodiester linkage to a conserved tyrosine residue of SPO11. In addition to SPO11, work from budding yeast has shown a total of 7 proteins essential for double strand break formation. The mammalian ortholog of Mei4 (S. cerevisiae) as well as a mammalian-specific gene called Mei1 are essential to formation of meiotic double strand breaks.
Meiotic recombination exchanges segments of duplex DNA between chromosomal homologs, generating genetic diversity (reviewed in Handel and Schimenti 2010, Inagaki et al. 2010, Cohen et al. 2006). There are two forms of recombination: non-crossover (NCO) and crossover (CO). In mammals, the former is required for correct pairing and synapsis of homologous chromosomes, while CO intermediates called chiasmata are required for correct segregation of bivalents. Meiotic recombination is initiated by double-strand breaks created by SPO11, which remains covalently attached to the 5' ends after cleavage. SPO11 is removed by cleavage of single DNA strands adjacent to the covalent linkage. The resulting 5' ends are further resected to produce protruding 3' ends. The single-stranded 3' ends are bound by RAD51 and DMC1, homologs of RecA that catalyze a search for homology between the bound single strand and duplex DNA of the chromosomal homolog. RAD51 and DMC1 then catalyze the invasion of the single strand into the homologous duplex and the formation of a D-loop heteroduplex. Approximately 90% of heteroduplexes are resolved without crossovers (NCO), probably by synthesis-dependent strand annealing. The invasive strand is extended along the homolog and ligated back to its original duplex, creating a double Holliday junction. The mismatch repair proteins MSH4, MSH5 participate in this process, possibly by stabilizing the duplexes. The mismatch repair proteins MLH1 and MLH3 are then recruited to the double Holliday structure and an unidentified resolvase (Mus81? Gen1?) cleaves the junctions to yield a crossover. Crossovers are not randomly distributed: The histone methyltransferase PRDM9 recruits the recombination machinery to genetically determined hotspots in the genome and each incipient crossover somehow inhibits formation of crossovers nearby, a phenomenon called crossover interference. Each chromosome bivalent, including the X-Y body in males, has at least one crossover and this is required for meiosis to proceed correctly.
During meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing event of meiosis, pairs (bivalents) of homologous chromosomes in the form of sister chromatids are paired, synapsed along their regions of homologous DNA (reviewed in Yang and Wang 2009), and then segregated, resulting in haploid daughters containing sister chromatids paired at their centromeres (reviewed in Cohen et al. 2006, Handel and Schimenti 2010). The sister chromatids are then separated and segregated during meiosis II. Recombination between chromosomal homologues but not between sister chromatids occurs during prophase of meiosis I (reviewed in Inagaki et al. 2010). Though hundreds of recombination events are initiated, most are resolved without crossovers and only tens proceed to become crossovers. In mammals recombination events are required between homologues for normal pairing, synapsis, and segregation.
Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993).
Wnt regulation of planar cell polarity (PCP)
Origins and Mechanisms of miRNAs and siRNAs
Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase
Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase.
Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.
Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: alpha-glucosaminide N-acetyltransferase (HGSNAT) gene
After the primers are synthesized on the G-Rich strand, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
Telomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (Blackburn and Gall 1978; Moyzis et al. 1988; Meyne et al. 1989). The repeats at human telomeres are composed of TTAGGG sequences and stretch for several kilobase pairs. Another feature of telomeric DNA in many eukaryotes is a G-rich 3' single strand overhang, which in humans is estimated to be approximately 50-300 bases long (Makarov et al. 1997; Wright et al. 1997; Huffman et al. 2000). Telomeric DNA isolated from humans and several other organisms can form a lasso-type structure called a t-loop in which the 3' single-strand end is presumed to invade the double stranded telomeric DNA repeat tract (Griffith et al. 1999). Telomeric DNA is bound by multiple protein factors that play important roles in regulating telomere length and in protecting the chromosome end from recombination, non-homologous end-joining, DNA damage signaling, and unregulated nucleolytic attack (reviewed in de Lange 2005). DNA attrition can occur at telomeres, which can impact cell viability. Attrition can occur owing to the "end-replication problem", a consequence of the mechanism of lagging-strand synthesis (Watson 1972; Olovnikov 1973). Besides incomplete replication, nucleolytic processing also likely contributes to telomere attrition (Huffman et al. 2000). If telomeres become critically shortened, replicative senescence can result (Harley et al. 1990). Thus, in order to undergo multiple divisions, cells need a mechanism to replenish the sequence at their chromosome ends. The primary means for maintaining the sequence at chromosome ends in many eukaryotic organisms, including humans, is based on telomerase (Greider and Blackburn, 1985; Morin 1989). Telomerase is a ribonucleoprotein complex minimally composed of a conserved protein subunit containing a reverse transcriptase domain (telomerase reverse transcriptase, TERT) (Lingner et al. 1997; Nakamura et al. 1997) and a template-containing RNA (telomerase RNA component, TERC, TR, TER) (Greider and Blackburn, 1987; Feng et al 1995). Telomerase uses the RNA template to direct addition of multiple tandem repeats to the 3' G-rich single strand overhang. Besides extension by telomerase, maintenance of telomeric DNA involves additional activities, including C-strand synthesis, which fills in the opposing strand, and nucleolytic processing, which likely contributes to the generation of the 3' overhang.
The complementary strand is synthesized by the polymerase primase complex using conventional RNA priming.
Once the RNA-DNA primer is synthesized, replication factor C (RFC) initiates a reaction called "polymerase switching"; pol delta, the processive enzyme replaces pol alpha, the priming enzyme. RFC binds to the 3'-end of the RNA-DNA primer on the Primosome, to displace the pol alpha primase complex. The binding of RFC triggers the binding of the primer recognition complex.
The binding of the primer recognition complex involves the loading of proliferating cell nuclear antigen (PCNA). Replication Factor C transiently opens the PCNA toroid in an ATP-dependent reaction, and then allows PCNA to re-close around the double helix adjacent to the primer terminus. This leads to the formation of the "sliding clamp".
DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA. There have been reports that TRF1 inhibits this activity at telomeres, though the mechanism and physiological relevance of this inhibition remain to be elucidated.
Homologous DNA pairing and strand exchange
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A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling
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Structure-function analysis of the bestrophin family of anion channels
Eukaryotic translation initiation factor 4 gamma
26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide
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Eukaryotic translation initiation factor 1A, X-chromosomal
eukaryotic translation initiation factor 1A
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EGFR interacts with phospholipase C-gamma
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.
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ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex
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Molecular cloning, expression and catalytic activity of a human AKR7 member of the aldo-keto reductase superfamily: evidence that the major 2-carboxybenzaldehyde reductase from human liver is a homologue of rat aflatoxin B1-aldehyde reductase
Transport of inorganic cations/anions and amino acids/oligopeptides
Phospholipase C-gamma 1 and phospholipase C-gamma 2 are substrates of the B cell antigen receptor associated protein tyrosine kinase
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Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol
Endothelium-derived relaxing and contracting factors
Disassembly of exon junction complexes by PYM
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Type II phosphatidylinositol 4-kinase beta is a cytosolic and peripheral membrane protein that is recruited to the plasma membrane and activated by Rac-GTP
cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse
eukaryotic translation initiation factor 2, subunit 2
Eukaryotic translation initiation factor 2 subunit 2
eukaryotic translation initiation factor 2 beta subunit
translation initiation factor 2 alpha subunit
Eukaryotic translation initiation factor 2 subunit 1
translation initiation factor 2, subunit 1
Eukaryotic translation initiation factor 2 alpha subunit
Eukaryotic translation initiation factor 2 gamma subunit
eukaryotic translation initiation factor 2, subunit 3
Eukaryotic translation initiation factor 2 subunit 3
Insights into COPI coat assembly and function in living cells
Ribonucleoside-diphosphate reductase M2 chain
eukaryotic translation initiation factor 3 subunit 10
eukaryotic translation initiation factor 3 subunit 6
eukaryotic translation initiation factor 3 subunit 9
Eukaryotic translation initiation factor 3 subunit 4
eukaryotic translation initiation factor 3 subunit 5
eukaryotic translation initiation factor 3 subunit 8
Eukaryotic translation initiation factor 3 subunit 2
eukaryotic translation initiation factor 3 subunit 7
Multidrug resistance- associated protein MGr1-Ag
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Innate immune recognition of an AT-rich stem-loop DNA motif in the Plasmodium falciparum genome
The role of assembly in insulin's biosynthesis
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A quantitative model of human DNA base excision repair. I. Mechanistic insights
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Sulfotransferases in the bioactivation of xenobiotics
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Enhanced tyrosine phosphorylation in B lymphocytes upon complexing of membrane immunoglobulin
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A 40-bp RNA element that mediates stabilization of vascular endothelial growth factor mRNA by HuR
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Complementation cloning identifies CDG-IIc, a new type of congenital disorders of glycosylation, as a GDP-fucose transporter deficiency
The phosphatidylinositol 3-kinase/Akt signaling pathway modulates the endocrine differentiation of trophoblast cells
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
Deficiency of UDP-GlcNAc:Dolichol Phosphate N-Acetylglucosamine-1 Phosphate Transferase (DPAGT1) causes a novel congenital disorder of Glycosylation Type Ij
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A conserved family of enzymes that phosphorylate inositol hexakisphosphate
Regulation of nuclear processes by inositol polyphosphates
Molecular cloning and characterization of a novel 3'-phosphoadenosine 5'-phosphosulfate transporter, PAPST2
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Substrate specificity combined with stereopromiscuity in glutathione transferase A4-4-dependent metabolism of 4-hydroxynonenal
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Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones
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KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions
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'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
Epstein-Barr virus small RNA associated protein
'Mg2+ [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
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'ADP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
'GDP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
'ATP [nucleoplasm]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
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Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A
A third MRX family (MRX68) is the result of mutation in the long chain fatty acid-CoA ligase 4 (FACL4) gene: proposal of a rapid enzymatic assay for screening mentally retarded patients
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TAX-responsive enhancer element binding protein 107
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Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal, and respiratory tissues
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Gamma linolenic acid: an antiinflammatory omega-6 fatty acid
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Kinesin-14 proteins have a C-terminal motor domain. At least four members of the group (Dm Ncd, Sc KAR3, Cg CHO2, At KCBP) have been demonstrated to be minus-end directed motors (Walker et al. 1990), in contrast to the usual plus-end directed motility of other kinesin proteins. During spindle formation, Kinesin-14 cross-links antiparallel microtubules and slides them together (thereby generating inward forces) to balance the outward forces generated by plus-end-directed kinesins of the Kinesin-5 family. Kinesin-14 family members also gather microtubule minus-ends and focus them into spindle poles. Mutation or inhibition of Kinesin-14 family members often results in disordered or splayed meiotic spindle poles (Ambrose et al. 2005).
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Comparative mechanistic and substrate specificity study of inositol polyphosphate 5-phosphatase Schizosaccharomyces pombe Synaptojanin and SHIP2
RNA Polymerase II holoenzyme complex (hyperphosphorylated) (name copied from entity in Homo sapiens)
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Activation of phospholipase C enzymes results in the generation of second messengers of the phosphatidylinositol pathway. The events resulting from this pathway are a rise in intracellular calcium and activation of Protein Kinase C (PKC). Phospholipase C cleaves the phosphodiester bond in PIP2 to form 1,2 Diacylglycerol (DAG) and 1,4,5-inositol trisphosphate (IP3). IP3 opens Ca2+ channels in the platelet dense tubular system, raising intracellular Ca2+ levels. DAG is a second messenger that regulates a family of Ser/Thr kinases consisting of PKC isozymes (Nishizuka 1995). DAG achieves activation of PKC isozymes by increasing their affinity for phospholipid. Most PKC enzymes are also calcium-dependent, so their activation is in synergy with the rise in intracellular Ca2+. Platelets contain several PKC isoforms that can be activated by DAG and/or Ca2+ (Chang 1997).
Active Pol II transcription complex with damaged DNA hybrid (name copied from entity in Homo sapiens)
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Platelets function as exocytotic cells, secreting a plethora of effector molecules at sites of vascular injury. Platelets contain a number of distinguishable storage granules including alpha granules, dense granules and lysosomes. On activation platelets release a variety of proteins, largely from storage granules but also as the result of apparent cell lysis. These act in an autocrine or paracrine fashion to modulate cell signaling. Alpha granules contain mainly polypeptides such as fibrinogen, von Willebrand factor, growth factors and protease inhibitors that that supplement thrombin generation at the site of injury. Dense granules contain small molecules, particularly adenosine diphosphate (ADP), adenosine triphosphate (ATP), serotonin and calcium, all recruit platelets to the site of injury.
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After Platelet activation '78 kDa glucose-regulated protein' from the endoplasmic reticulum lumen is released in to the extracellular platelet releasate.
Platelet releasate contains a range of proteins that do not originate in specialized storage granules. In some cases platelet lysis may contribute to the presence of these proteins in the platelet relesate.
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Kinesin-8 is a plus-end-directed dimeric kinesin with an internal motor domain (Loughlin et al. 2008) that can depolymerize stable microtubuless specifically at their plus-ends (Pereira et al. 1997) in a length-dependent manner (Varga et al. 2006). Human kinesin-8 KIF18A is believed to promote chromosome congression by attenuating chromosome oscillation magnitudes (Stumpff et al. 2008).
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Kinesin-5 motors are bipolar homotetramers with two motor domains at each end, separated by a stalk/tail region (Cole et al. 1994). During mitosis, Kinesin-5 motors function near the spindle midzone to maintain pole to pole distance. Motor domains attach to microtubules from opposite poles and translocate towards the plus ends, thereby pushing the spindle poles apart (Kapitein et al. 2005). Kinesin-5 is also involved in axon growth (Myers & Baas 2007).
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F-actin-capping protein binds in a Ca2+-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits. Unlike other capping proteins (such as gelsolin and severin), they do not sever actin filaments.
Tissue-differential expression of two distinct genes for phosphoribosyl pyrophosphate synthetase and existence of the testic-specific transcript
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Platelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the platelet membrane (Ruggeri 2002). Intracellular signaling reactions then enhance the adhesive and procoagulant properties of tethered platelets or of platelets circulating in the proximity. Once platelets have adhered they degranulate, releasing stored secondary agents such as ADP, ATP, and synthesize thromboxane A2. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. Adenosine nucleotides signal through P2 purinergic receptors on the platelet membrane. ADP activates P2Y1 and P2Y12, which signal via both the alpha and gamma:beta components of the heterotrimeric G-protein (Hirsch et al. 2001, 2006), while ATP activates the ionotropic P2X1 receptor (Kunapuli et al. 2003). Activation of these receptors initiates a complex signaling cascade that ultimately results in platelet activation, aggregation and thrombus formation (Kahner et al. 2006). Integrin AlphaIIbBeta3 is the most abundant platelet receptor, with 40 000 to 80 000 copies per resting platelet, acting as a major receptor for fibrinogen and other adhesive molecules (Wagner et al. 1996). Activation of AlphaIIbBeta3 enhances adhesion and leads to platelet-platelet interactions, and thus aggregation (Philips et al. 1991). GP VI is the most potent collagen receptor initiating signal generation, an ability derived from its interaction with the FcRI gamma chain. This results in the phosphorylation of the gamma-chain by non-receptor tyrosine kinases of the Src family (1). The phosphotyrosine motif is recognized by the SH2 domains of Syk, a tyrosine kinase. This association activates the Syk enzyme, leading to activation (by tyrosine phosphorylation) of PLC gamma2 (2). Thrombin is an important platelet agonist generated on the membrane of stimulated platelets. Thrombin acts via cell surface Protease Activated Receptors (PARs). PARs are G-protein coupled receptors activated by a proteolytic cleavage in an extracellular loop (Vu, 1991) (3). Activated PARs signal via G alpha q (4) and via the beta:gamma component of the G-protein (5). Both stimulate PLC giving rise to PIP2 hydrolysis and consequent activation of PI3K (6). PLCgamma2 activation also gives rise to IP3 (7) which stimulates the IP3 receptor (8) leading to increased intracellular calcium. Platelet activation further results in the scramblase-mediated transport of negatively-charged phospholipids to the platelet surface. These phospholipids provide a catalytic surface (with the charge provided by phosphatidylserine and phosphatidylethanolamine) for the tenase complex (formed by the activated forms of the blood coagulation factors factor VIII and factor I).
MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1).
Spectrum of mutations in mut methylmalonic acidemia and identification of a common Hispanic mutation and haplotype
MLH1:PMS2 (name copied from entity in Homo sapiens)
MSH2:MSH6:ATP (name copied from entity in Homo sapiens)
MSH2:MSH6:ATP:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
MSH2:MSH6:ADP:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
MSH2:MSH6:ADP (name copied from entity in Homo sapiens)
Active Pol II complex with repaired DNA template:mRNA hybrid (name copied from entity in Homo sapiens)
Stalled Pol II in TC-NER (name copied from entity in Homo sapiens)
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Alpha granules contain mainly polypeptides such as fibrinogen, von Willebrand factor, growth factors and protease inhibitors that supplement thrombin generation at the site of injury. In addtion to their role in hemostasis, platelets also contain angiogenesis stimulators and inhibitors (Italiano et al. 2008).
Hydrolysis of phosphatidyl inositol-bisphosphate (PIP2) by phospholipase C (PLC) produces diacylglycerol (DAG) and inositol triphosphate (IP3). Both are potent second messengers. IP3 diffuses into the cytosol, but as DAG is a hydrophobic lipid it remains within the plasma membrane. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, while DAG activates the conventional and unconventional protein kinase C (PKC) isoforms, facilitating the translocation of PKC from the cytosol to the plasma membrane. The effects of DAG are mimicked by tumor-promoting phorbol esters. DAG is also a precursor for the biosynthesis of prostaglandins, the endocannabinoid 2-arachidonoylglycerol and an activator of a subfamily of TRP-C (Transient Receptor Potential Canonical) cation channels 3, 6, and 7.
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Primary megakaryocytes reveal a role for transcription factor NF-E2 in integrin alpha IIb beta 3 signaling
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During steady state conditions, cytoplasmic [Ca2+] is reduced by the accumulation of Ca2+ in intracellular stores and Ca2+ extrusion.
MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch and single strand incision (name copied from entity in Homo sapiens)
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Nitric Oxide (NO) inhibits smooth muscle cell proliferation and migration, oxidation of low-density lipoproteins, and platelet aggregation and adhesion. It can stimulate vasodilatation of the endothelium, disaggregation of preformed platelet aggregates and inhibits activated platelet recruitment to the aggregate. NO is synthesized from L-arginine by a family of isoformic enzymes known as nitric oxide synthase (NOS). Three isoforms, namely endothelial, neuronal, and inducible NOS (eNOS, nNOS, and iNOS, respectively), have been identified. The eNOS isoform is found in the endothelium and platelets. NO regulation of cyclic guanosine-3,5-monophosphate (cGMP), via activation of soluble guanylate cyclase, is the principal mechanism of negative control over platelet activity. Defects in this control mechanism have been associated with platelet hyperaggregability and associated thrombosis.
EXO1:MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch and single strand incision (name copied from entity in Homo sapiens)
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Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). Cyclooxygenase-2 (COX-2) and endothelial nitric oxide synthase (eNOS) are primarily expressed in endothelial cells. Both are important regulators of vascular function. Under normal conditions, laminar flow induces vascular endothelial COX-2 expression and synthesis of Prostacyclin (PGI2) which in turn stimulates endothelial Nitric Oxide Synthase (eNOS) activity. PGI2 and NO both oppose platelet activation and aggregation, as does the CD39 ecto-ADPase, which decreases platelet activation and recruitment by metabolizing platelet-released ADP.
MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 bases or more (name copied from entity in Homo sapiens)
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Ca2+ homeostasis is controlled by processes that elevate or counter the elevation of cytosolic Ca2+. During steady state conditions, cytoplasmic Ca2+ is reduced by the accumulation of Ca2+ in intracellular stores and by Ca2+ extrusion. The primary intracellular calcium store in platelets is the dense tubular system, the equivalent of the ER system in other cell types. Ca2+ is extruded by Ca2+-ATPases including plasma membrane Ca2+ ATPases (PMCAs) and sarco/endoplasmic reticulum Ca2+ -ATPase isoforms (SERCAs). Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
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The platelet GPIb complex (GP1b-IX-V) together with GPVI are primarily responsible for regulating the initial adhesion of platelets to the damaged blood vessel and platelet activation. The importance of GPIb is demonstrated by the bleeding problems in patients with Bernard-Soulier syndrome where this receptor is either absent or defective. GP1b-IX-V binds von Willebrand Factor (vWF) to resting platelets, particularly under conditions of high shear stress. This transient interaction is the first stage of the vascular repair process. Activation of GP1b-IX-V on exposure of the fibrous matrix following atherosclerotic plaque rupture, or in occluded arteries, is a major contributory factor leading to thrombus formation leading to heart attack or stroke. GpIb also binds thrombin (Yamamoto et al. 1986), at a site distinct from the site of vWF binding, acting as a docking site for thrombin which then activates Proteinase Activated Receptors leading to enhanced platelet activation (Dormann et al. 2000).
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14-3-3 family proteins can bind Raf1 and have been suggested to activate Raf1, but this has been refuted.
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Diacylglycerol kinases (DGKs) are intracellular lipid kinases that use ATP to phosphorylate diacylglycerol (DAG)., generating phosphatidic acid (PA). This lowers membrane DAG levels, regulating signalling proteins that require DAG for membrane association such as Protein Kinase C. PA is a signalling molecule that regulates Raf-1 and PKC zeta, and a substrate for the resynthesis of phosphatidylinositol.
The GPVI receptor is a complex of the GPVI protein with Fc epsilon R1 gamma (FcR). The Src family kinases Fyn and Lyn constitutively associate with the GPVI-FcR complex in platelets and initiate platelet activation through phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) in the FcR gamma chain, leading to binding and activation of the tyrosine kinase Syk. Downstream of Syk, a series of adapter molecules and effectors lead to platelet activation. The GPVI receptor signaling cascade is similar to that of T- and B-cell immune receptors, involving the formation of a signalosome composed of adapter and effector proteins. At the core of the T-cell receptor signalosome is the transmembrane adapter LAT and two cytosolic adapters SLP-76 and Gads. While LAT is essential for signalling to PLCgamma1 downstream of the T-cell receptor, the absence of LAT in platelets only impairs the activation of PLCgamma2, the response to collagen and GPVI receptor ligands remains sufficient to elicit a full aggregation response. In contrast, GPVI signalling is almost entirely abolished in the absence of SLP-76.
AGE adducts:Peptide (name copied from entity in Homo sapiens)
SUGT1:HSP90 (name copied from entity in Homo sapiens)
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AGE adducts:Peptide:AGER-1,2,3 (name copied from entity in Homo sapiens)
MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 or more bases and single strand incision (name copied from entity in Homo sapiens)
MSH2:MSH3:ATP (name copied from entity in Homo sapiens)
Activated PLC gamma1 bound to PIP2 (name copied from entity in Homo sapiens)
EXO1:MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 or more bases and single strand incision (name copied from entity in Homo sapiens)
Platelet-collagen interaction: is GPVI the central receptor?
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At the beginning of this reaction, 1 molecule of 'DNA polymerase alpha:primase:DNA polymerase alpha:origin complex', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon', and 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed RNA polymerase activity' of 'DNA polymerase alpha:primase'.
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Cyclin E - Cdk2 complexes control the transition from G1 into S-phase. In this case, the binding of p21Cip1/Waf1 or p27kip1 is inhibitory. Important substrates for Cyclin E - Cdk2 complexes include proteins involved in the initiation of DNA replication. The two Cyclin E proteins are subjected to ubiquitin-dependent proteolysis, under the control of an E3 ubiquitin ligase known as the SCF. Cyclin A - Cdk2 complexes, which are also regulated by p21Cip1/Waf1 and p27kip1, are likely to be important for continued DNA synthesis, and progression into G2. An additional level of control of Cdk2 is reversible phosphorylation of Threonine-14 (T14) and Tyrosine-15 (Y15), catalyzed by the Wee1 and Myt1 kinases, and dephosphorylation by the three Cdc25 phosphatases, Cdc25A, B and C.
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Progression through G1 and G1 to S-phase transition that initiates DNA synthesis involve many complexes that are regulated by RB1:E2F pathway. RB1:E2F pathway plays a key role in gene expression regulation in proliferating and differentiated cells. As a repressor, E2F remains bound to RB1; it can activate the expression of S-phase genes involved in DNA replication after the phosphorylation of RB1. E2F proteins regulate expression of genes involved in various processes thereby forming interlinks between cell cycle, DNA synthesis, DNA damage recognition etc. In this module, activation of replication related genes by E2F1 and two ways by which E2F1 regulates DNA replication initiation are annotated. Detailed connection between the E2F protein function and various pathways will be covered in future releases of Reactome.
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Mitochondrial respiratory chain-dependent generation of superoxide anion and its release into the intermembrane space
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At the beginning of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present. At the end of this reaction, 1 molecule of 'DNA polymerase alpha:primase', and 1 molecule of 'RNA primer-DNA primer:origin duplex with DNA damage' are present. This reaction takes place in the 'nucleus'.
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In S. cerevisiae, two ORC subunits, Orc1 and Orc5, both bind ATP, and Orc1 in addition has ATPase activity. Both ATP binding and ATP hydrolysis appear to be essential functions in vivo. ATP binding by Orc1 is unaffected by the association of ORC with origin DNA (ARS) sequences, but ATP hydrolysis is ARS-dependent, being suppressed by associated double-stranded DNA and stimulated by associated single-stranded DNA. These data are consistent with the hypothesis that ORC functions as an ATPase switch, hydrolyzing bound ATP and changing state as DNA unwinds at the origin immediately before replication. It is attractive to speculate that ORC likewise functions as a switch as human pre-replicative complexes are activated, but human Orc proteins are not well enough characterized to allow the model to be critically tested. mRNAs encoding human orthologs of all six Orc proteins have been cloned, and ATP-binding amino acid sequence motifs have been identified in Orc1, Orc4, and Orc5. Interactions among proteins expressed from the cloned genes have been characterized, but the ATP-binding and hydrolyzing properties of these proteins and complexes of them have not been determined.
DNA polymerase alpha:primase is comprised of four subunits, p180, p70, p58, and p49. The two primase subunits, p58 and p49, form a tight complex. The p49 subunit contains the DNA primase activity and one role of p58 appears to be tethering p49 to p180, the DNA polymerase catalytic subunit. The fourth subunit, p70, binds p180 and may tether the DNA polymerase alpha:primase complex to Cdc45.
At the beginning of this reaction, 1 molecule of 'origin of replication', and 1 molecule of 'DNA polymerase epsilon' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon:origin complex' is present.
The E2F family of transcription factors regulate the transition from the G1 to the S phase in the cell cycle. E2F activity is regulated by members of the retinoblastoma protein (pRb) family, resulting in the tight control of the expression of E2F-responsive genes. Phosphorylation of pRb by cyclin D:CDK complexes releases pRb from E2F, inducing E2F-targeted genes such as cyclin E.
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LAT and NTAL mediate immunoglobulin E-induced sustained extracellular signal-regulated kinase activation critical for mast cell survival
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While circularization of mRNA during translation initiation is thought to contribute to an increase in the efficiency of translation, it also appears to provide a mechanism for translational silencing. This might be achieved by bringing inhibitory 3' UTR-binding proteins into a position in which they interfere either with the function of the translation initiation complex or with the assembly of the ribosome (Mazumder et al 2001). Translational silencing of Ceruloplasmin (Cp) occurs 16 hrs after its induction by INF-gamma (Mazumder et al., 1997). Although the mechanism by which silencing occurs has not yet been determined, this process is mediated by the L13a subunit of the 60s ribosome and thought to require circularization of the Cp mRNA (Sampath et al., 2003; Mazumder et al., 2001; Mazumder et al., 2003). Between 14 and 16 hrs after INF gamma induction, the L13a subunit of the 60s ribosome is phosphorylated and released from the 60s subunit. Phosphorylated L13a then associates with the GAIT element in the 3' UTR of the Cp mRNA inhibiting its translation.
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Although the mechanism through which L13a prevents translation initiation has not been determined, Mazumder et al. (2003) have described four alternatives. L13a could (1) inhibit the function of eIF4F, (2) block the recruitment of the 43S preinitiation complex, (3) prevent scanning of the 43S complex to the initiation codon, or 4) interfere with joining of the 60S ribosomal subunit.
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E2F1 binds to E2F binding sites on the genome activating the synthesis of the target proteins. For annotation purposes, the reactions regulated by E2F1 are grouped under this pathway and information about the target genes alone are displayed for annotation purposes. Cellular targets for activation by E2F1 include thymidylate synthetase, Rir2, Dihydrofolate reductase, Cdc2, Cyclin A1, Cdc6 (DeGregori et al., 1995), Cdt1 (Yoshida and Inoue, 2004), CDC45 (Arata et al., 2000), CDC6 (Yan et al., 1998; Ohtani et al., 1998), Cyclin E (Ohtani et al., 1996), Emi1 (Hsu et al., 2002), and Orc1 (Ohtani et al., 1997). The activation of TK2 (Dnk1) and Cdc25A by E2F1 have been inferred from similar events in Drosophila (Duronio and O'Farrell, 1994;Reis and Edgar, 2004). Rir2 protein is involved in dNTP level regulation and activation of this enzyme results in higher levels of dNTPs in anticipation of S-phase. E2F activation of Rir2 has been shown also in Drosophila by Duronio and O'Farrell (1994). E2F1 activation of CDC45 is shown in mouse cells by using human E2F1 construct (Arata et al., 2000). Cyclin E is also transcriptionally regulated by E2F1. Cyclin E protein plays important role in the transition of G1 in S-phase by associating with Cdk2 (Ohtani et al., 1996). E2F activation of PCNA has been demonstrated in Drosophila (DeGregori et al., 1995) and in some human cells by using recombinant adenovirus constructs. E2F activation of Polymerase A (Pol A) has been demonstrated in some human cells. It has also been demonstrated in Drosophila by Ohtani and Nevins (1994). It has been observed in Drosophila that E2F1 regulated expression of Orc1 stimulates ORC1-6 complex formation and binding to the origin of replication (Asano and Wharton, 1999). Orc1-6 recruit Cdc6 and Cdt1 that are required to recruit the MCM2-7 replication helicases. E2F1 regulation incorporates a feedback mechanism where in Geminin can inhibit MCM2-7 recruitment of ORC1-6 complex by interacting with Cdc6/Cdt1. The activation of Cdc25A and TK2 (Dnk1) by E2F1 has been inferred from similar events in Drosophila (Duronio RJ, O'Farrell 1994; Reis and Edgar, 2004). E2F1 activates string (Cdc25) that in turn activates Cyclin B/Cdk1. A similar phenomenon has been observed in mouse NIH 3T3 cells and in Rat1 cells.
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Translational control mechanisms often involve interactions between the 3' - or 5' -untranslated regions (UTRs) of mRNA and RNA-binding proteins. One such mechanism requires circularization of the mRNA molecule involving protein-protein interactions between the mRNA termini (Mazumder et al., 2001). While the circularization of mRNA during translation initiation is thought to contribute to an increase in the efficiency of translation, it also appears to provide a mechanism for translational silencing. This might be achieved by bringing inhibitory 3' UTR-binding proteins into a position in which they interfere either with the function of the translation initiation complex or with the assembly of the ribosome.
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Megakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they undergo endoreduplication (polyploidisation) and expansion of cytoplasmic mass to cell sizes larger than 50-100 microns, and ploidy ranges up to 128 N. As MK's mature, the polyploid nucleus becomes horseshoe-shaped, the cytoplasm expands, and platelet organelles and the demarcation membrane system are amplified. Proplatelet projections form which give rise to de novo circulating platelets (Deutsch & Tomer 2006). The processes of megakaryocytopoiesis and platelet production occur within a complex microenvironment where chemokines, cytokines and adhesive interactions play major roles (Avecilla et al. 2004). Megakaryocytopoiesis is regulated at several levels including proliferation, differentiation and platelet release (Kaushansky 2003). Thrombopoietin (TPO/c-Mpl ligand) is the most potent cytokine stimulating proliferation and maturation of MK progenitors (Kaushansky 2005) but many other growth factors are involved. MK development is controlled by the action of multiple Transcriptin Factors, many MK-specific genes are co-regulated by GATA and friend of GATA (FOG), RUNX1 and ETS proteins. Nuclear factor erythroid 2 (NF-E2) which has an MK-erythroid specific 45-kDa subunit controls terminal MK maturation, proplatelet formation and platelet release (Schulze & Shivdasani 2004). NF-E2 deficient mice have profound thrombocytopenia (Shiraga et al. 1999). c-myb functions with p300 as a negative regulator of thrombopoiesis (Metcalf et al. 2005). During MK maturation, internal membrane systems, granules and organelles are assembled. Cytoplasmic fragmentation requires changes in the MK cytoskeleton and formation of organelles and channels. Individual organelles migrate from the cell body to the proplatelet ends, with approximately 30 percent of organelles/granules in motion at any given time (Richardson et al. 2005).
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Kinesins are a superfamily of microtubule-based motor proteins that have diverse functions in transport of vesicles, organelles and chromosomes, and regulate microtubule dynamics. There are 14 families of kinesins, all reprsented in humans. A standardized nomenclature was published in 2004 (Lawrence et al.).
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The L13a subunit of the 60s ribosome is phosphorylated about 16 hours after INF gamma induction by an unknown kinase. At this time, L13a is also released from the 60s subunit (Mazumder et al.,2003). It is unclear, however, whether phosphorylation occurs before or after the release of L13a. Here, phosphorylation is shown as occurring after release.
DNA containing an MPG-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
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Hemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). The chief trigger for the change in endothelial function that leads to the formation of a haemostatic thrombus is the loss of the endothelial cell barrier between blood and extracellular matrix components (Ruggeri 2002). Circulating platelets identify and discriminate areas of endothelial lesions; here, they adhere to the exposed sub endothelium. Their interaction with the various thrombogenic substrates and locally generated or released agonists results in platelet activation. This process is described as possessing two stages, firstly, adhesion - the initial tethering to a surface, and secondly aggregation - the platelet-platelet cohesion (Savage & Cattaneo et al. 2001). Three mechansism contribute to the loss of blood following vessel injury. The vessel constricts, reducing the loss of blood. Platelets adhere to the site of injury, become activated and aggregate with fibrinogen into a soft plug that limits blood loss, a process termed primary hemostasis. Proteins and small molecules are released from granules by activated platelets, stimulating the plug formation process. Fibrinogen from plasma forms bridges between activated platelets. These events initiate the clotting cascade (secondary hemostasis). Negatively-charged phospholipids exposed at the site of injury and on activated platelets interact with tissue factor, leading to a cascade of reactions that culminates with the formation of an insoluble fibrin clot.
hNTH1 glycosylase:cytosine glycol complex (name copied from entity in Homo sapiens)
DNA containing an hOGG1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hNTH1 glycosylase: foramidopyrimidine complex (name copied from entity in Homo sapiens)
All kinesins contain a motor domain or head, the position varies but it is structurally highly conserved (Kull et al. 1996, Sablin et al. 1996). The microtubule-binding site includes structural elements which interact with tubulin and undergo movement between the ADP and ATP bound states. The highly conserved switch I (SSRSH) and II (DLAGSE) motifs, which change in conformation during the ATP hydrolysis cycle, form a salt-bridge that, in myosin, closes the nucleotide-binding cleft, enabling the motor to hydrolyze ATP (Geeves & Holmes 1999). This closed conformation has now been seen in a crystal structure of the frog kinesin-5 Eg5 (Parke et al. 2010).
hNTH1 glycosylase:dihydrouracil complex (name copied from entity in Homo sapiens)
Kinesins consume ATP to power the motor which allows them to move along microtubules. The motor region contains highly conserved Switch 1 (SSRSH) and 2 (DLAGSE) motifs which change conformation during ATP hydrolysis (Rice et al. 1999). These form a salt-bridge that, in myosin, closes the nucleotide-binding cleft, enabling the motor to hydrolyze ATP (Geeves & Holmes 1999). This closed conformation has now been seen by cryo-electron microscopy in human conventional kinesin (Sindelar & Downing 2010) and in a crystal structure of the frog kinesin-5 Eg5 (Parke et al. 2010).
The complex route to MHC class I-peptide complexes
DNA containing a hNTH1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
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hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
RAD51:resected ends of DNA double-strand break (name copied from entity in Homo sapiens)
FEN1:PCNA complex (name copied from entity in Homo sapiens)
ERCC1:XPF complex (name copied from entity in Homo sapiens)
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Transcriptional control of megakaryocyte development
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After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
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The processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate. However, incorporation of an incorrect nucleotide does occur occasionally. Misincorporated nucleotides are removed by the 3' to 5' exonucleolytic proofreading capability of pol delta.
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PURIFICATION AND PROPERTIES OF GLUTATHIONE REDUCTASE OF HUMAN ERYTHROCYTES
At the start of the elongation phase of DNA replication, the Mcm2-7 complex may re-arrange to function as the replicative helicase associated with the replication fork. In general, a replicative helicase is associated with the replication fork and unwinds DNA ahead of the polymerase. In yeast, the Mcm proteins associate with origin DNA in G1 phase and then exit the origin upon replication initiation, consistent with moving out of the origin with the replication fork. The Mcm2-7 complex is a ring-shaped hexamer. Complexes of Mcm4, Mcm6 and Mcm7 proteins from humans or S. pombe display a modest ATP-dependent helicase activity in vitro. Consistent with the hypothesis that eukaryotic Mcm complexes function as helicases, an archaeal Mcm homolog is a ring-shaped double hexamer that has a processive DNA unwinding activity. Mcm proteins may have additional functions during elongation, as uninterrupted function of all six is required for replication fork progression in budding yeast. Mcm4,6,7 helicase activity may be negatively regulated in two ways. Mcm2, Mcm4, Mcm6, and Mcm7 also form a stable complex which, however, has no helicase activity, suggesting that Mcm2 inhibits DNA unwinding by Mcm4,6,7. In addition, phosphorylation of human Mcm4,6,7 complex by CDK inhibits its helicase activity.
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DNA Replication is regulated accurately and precisely by various protein complexes. Many members of the MCM protein family are assembled into the pre-Replication Complexes (pre-RC) at the end of M phase of the cell cycle. DNA helicase activity of some of the MCM family proteins are important for the unwinding of DNA and initiation of replication processes. This section contains four events which have been proved in different eukaryotic experimental systems to involve various proteins for this essential step during DNA Replication.
The MCM2-7 related protein, MCM8, is required to replicate chromosomal DNA in Xenopus egg extracts. MCM8 binds chromatin upon initiation of DNA synthesis. It may function as an helicase in the elongation step.
In budding yeast, all MCM proteins have been proved to be essential for elongation. The active form of this protein complex may be a heterohexamer. A subcomplex of MCM proteins consisting fo MCM4,6, and -7 has a weak helicase activity that may contribute to DNA unwinding.
At the beginning of this reaction, 1 molecule of 'ubiquitinated Orc1' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present. This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.
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At the beginning of this reaction, 1 molecule of 'CDC6', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'ADP', and 1 molecule of 'phosphorylated Cdc6' are present. This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'CDK'.
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In this reaction, 1 molecule of 'phosphorylated Cdc6' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
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At the beginning of this reaction, 1 molecule of 'ubiquitinated Cdc6' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present. This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.
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As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002).
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Small is beautiful: insulin-like growth factors and their role in growth, development, and cancer
DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA (Frick & Richardson 2002; Wang et al 1984).
At the beginning of this reaction, 1 molecule of 'dTTP', 1 molecule of 'dGTP', 1 molecule of 'dATP', 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex', and 1 molecule of 'dCTP' are present. At the end of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'DNA polymerase alpha:primase'.
In this reaction, 1 molecule of 'ubiquitinated Orc1' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
At the beginning of this reaction, 1 molecule of 'ubiquitin', and 1 molecule of 'phosphorylated Orc1' are present. At the end of this reaction, 1 molecule of 'ubiquitinated Orc1' is present. This reaction takes place in the 'nucleus'.
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The replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried out during a discrete temporal period known as the S (synthesis)-phase, and chromosome segregation occurs during a massive reorganization to cellular architecture at mitosis. Two gap-phases separate these major cell cycle events: G1 between mitosis and S-phase, and G2 between S-phase and mitosis. In the development of the human body, cells can exit the cell cycle for a period and enter a quiescent state known as G0, or terminally differentiate into cells that will not divide again, but undergo morphological development to carry out the wide variety of specialized functions of individual tissues. A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the activity of the catalytic subunit is dependent on binding to a cyclin partner. The human genome encodes several cyclins and several CDKs, with their names largely derived from the order in which they were identified. The oscillation of cyclin abundance is one important mechanism by which these enzymes phosphorylate key substrates to promote events at the relevant time and place. Additional regulatory proteins and post-translational modifications ensure that CDK activity is precisely regulated, frequently confined to a narrow window of activity.
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Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase.
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Finally, progression out of mitosis and division of the cell into two daughters (cytokinesis) requires the inactivation of Cyclin B - Cdc2 by ubiquitin-dependent proteolysis of Cyclin A and B, which is regulated by a large E3 ubiquitin ligase complex known as the Anaphase Promoting Complex (APC). The detailed annotation of the M/G1 transition will be completed in a later version of GK.
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Phosphate transporters: a tale of two solute carrier families
Two cofactors and cytoplasmic chaperonin are required for the folding of alpha- and beta-tubulin
DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both S. cerevisiae and humans has been demonstrated by chromatin immunoprecipitation experiments. In S. cerevisiae, pre-replicative complexes are assembled from late M to G1. In mammalian cells as well, pre-replicative complexes are assembled from late M to G1, as shown by biochemical fractionation and immunostaining. There are significant sequence similarities among some of the proteins in the pre-replicative complex. The ORC subunits Orc1, Orc4 and Orc5 are homologous to one another and to Cdc6. The six subunits of the Mcm2-7 complex are homologous to one another. In addition, Orc1, Orc4, Orc5, Cdc6, and the Mcm2-7 subunits, are members of the AAA+ superfamily of ATPases. Since the initial identification of these pre-RC components other factors that participate in this complex have been found, including Cdt1 in human, Xenopus, S. pombe, and S. cerevisiae cells.
Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells, but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7 association with the Cdt1:Cdc6:ORC:origin complex. In S. cerevisiae, Cdc6 protein is expressed late in the M phase of the cell cycle and, in cells with a prolonged G1 phase, late in G1. This protein has a short half-life, and is destroyed by ubiquitin-mediated proteolysis, mediated by the SCF complex. Human Cdc6 protein levels are reduced early in G1 but otherwise are constant throughout the cell cycle. Some reports have suggested that after cells enter S phase, Cdc6 is phosphorylated, excluded from the nucleus and subject to ubiquitination and degradation. Replenishing Cdc6 protein levels during G1 appears to be regulated by E2F transcription factors.
Ligand-induced, receptor-mediated dimerization and activation of EGF receptor
Mitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Finally, cytokinesis leads to cell division. The phase between two M phases is called the interphase; it encompasses the G1, S, and G2 phases of the cell cycle.
The path to perdition is paved with protons
During prophase, the chromatin in the nucleus condenses, and the nucleolus disappears. Centrioles begin moving to the opposite poles or sides of the cell. Some of the fibers that extend from the centromeres cross the cell to form the mitotic spindle.
The nuclear envelope breakdown (NEBD) happens in late prophase of mitosis and involves disassembly of the nuclear pore complex, depolymerization of the nuclear lamina, and clearance of nuclear envelope from chromatin. NEBD allows mitotic spindle microtubules to access condensed chromosomes at kinetochores and enables nuclear division and segregation of genetic material to two daughter cells. For a recent review, please refer to Guttinger et al. 2009.
The nuclear envelope breakdown in mitotic prophase involves depolymerisation of lamin filaments, the main constituents of the nuclear lamina. The nuclear lamina is located at the nuclear face of the inner nuclear membrane and plays and important role in the structure and function of the nuclear envelope (reviewed by Burke and Stewart 2012). Depolymerisation of lamin filaments, which consist of lamin homodimers associated through electrostatic interactions in head-to-tail molecular strings, is triggered by phosphorylation of lamins. While CDK1 phosphorylates the N-termini of lamins (Heald and McKeon 1990, Peter et al. 1990, Ward and Kirschner 1990, Mall et al. 2012), PKCs (PRKCA and PRKCB) phosphorylate the C-termini of lamins (Hocevar et al. 1993, Goss et al. 1994, Mall et al. 2012). PKCs are activated by lipid-mediated signaling, where lipins, activated by CTDNEP1:CNEP1R1 serine/threonine protein phosphatase complex, catalyze the formation of DAG (Gorjanacz et al. 2009, Golden et al. 2009, Wu et al. 2011, Han et al. 2012, Mall et al. 2012).
Lipin proteins LPIN1, 2, and 3, associated with the nuclear envelope, can each catalyze the hydrolysis of phosphatidate to yield 1,2-diacyl-glycerol and orthophosphate. The activities of LPIN1 and LPIN2 have been established experimentally (Grimsey et al. 2008); that of LPIN3 is inferred from its structural similarities both to its human paralogues and to its mouse ortholog (Donkor et al. 2007).
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Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation
At the end of this reaction, 1 molecule of 'Cdc6' is present.
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The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex.
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Licensing factors are removed from the origin by various means like biochemical modification (phosphorylation) or by physical association with other proteins. This pathway includes the annotations of events in which the fates of different proteins at the origin are outlined.
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DNA replication is regulated at various levels via ORC proteins. This pathway includes annotation of individual events that lead to the regulation of replication.
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Cardiolipin is synthesized on the matrix side of the inner membrane in rat liver mitochondria
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Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997).
Defective MMAA causes methylmalonic aciduria type cblA
DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues, the E type cyclins shared by the G1 and S phases, are destroyed and the levels of the mitotic cyclins rise.
The actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of the primer. The DNA replication preinitiation events begin in late M or early G1 phase.
The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments.
Removal of the flap by FEN-1 leads to the generation of a nick between the 3'-end of the upstream Okazaki fragment and the 5'-end of the downstream Okazaki fragment. DNA ligase I then seals the nicks between adjacent processed Okazaki fragments to generate intact double-stranded DNA.
The sodium phosphate cotransporter family SLC34
Pyruvate dehydrogenase E1 component beta subunit, mitochondrial precursor
pyruvate dehydrogenase E1 beta apoprotein
In vivo expression and functional characterization of the zinc transporter ZnT8 in glucose-induced insulin secretion
pyruvate dehydrogenase E1 alpha apoprotein
Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor
Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase
Transcription factors direct the development and function of pancreatic beta cells
CCT/TriC(ATP) (name copied from entity in Homo sapiens)
deoxyhypusine synthase tetramer (name copied from entity in Homo sapiens)
Sar1b:GTP Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p (name copied from entity in Homo sapiens)
PMM (PMM1), the human homologue of SEC53 or yeast phosphomannomutase, is localized on chromosome 22q13
The SLC2 family of facilitated hexose and polyol transporters
Sar1b:GDP Complex (name copied from entity in Homo sapiens)
DOHH:Fe++ (name copied from entity in Homo sapiens)
2xUAP1-2 (name copied from entity in Homo sapiens)
2xUAP1 (name copied from entity in Homo sapiens)
Citrate synthase, mitochondrial precursor
Isocitrate dehydrogenase 2 (NADP), mitochondrial
Dihydrolipoamide dehydrogenase, mitochondrial
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor
70 kDa mitochondrial autoantigen of primary biliary cirrhosis
Pyruvate dehydrogenase protein X component, mitochondrial precursor
Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex
pyruvate dehydrogenase complex X component (E3 binding protein)
nicotinamide nucleotide transhydrogenase
2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor
alpha-ketoglutarate dehydrogenase E1 apoenzyme
Inhibition of replication initiation of damaged DNA by RB1/E2F1
eEF1B:GDP exchange complex (name copied from entity in Homo sapiens)
eEF1B complex (name copied from entity in Homo sapiens)
IMP (inosine monophosphate) dehydrogenase 1
Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) (IMP dehydrogenase 1) (IMPDH-I) (IMPD 1)
Inosine-5'-monophosphate dehydrogenase 1
Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)
AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)
AMP deaminase 2 (EC 3.5.4.6) (AMP deaminase isoform L)
AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)
eEF1A:GTP (name copied from entity in Homo sapiens)
eEF1A:GTP:aminoacyl-tRNA complex (name copied from entity in Homo sapiens)
80S:aminoacyl tRNA:mRNA:eEF1A:GTP (name copied from entity in Homo sapiens)
eEF1A:GDP (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA:aminoacyl-tRNA (name copied from entity in Homo sapiens)
80S Ribosome:mRNA:peptidyl-tRNA with elongating peptide (name copied from entity in Homo sapiens)
eEF2:GTP (name copied from entity in Homo sapiens)
eEF2:GDP (name copied from entity in Homo sapiens)
CCT/TriC(ATP)-associated actin (name copied from entity in Homo sapiens)
Common themes in siRNA-mediated epigenetic silencing pathways
DNA mismatch repair: functions and mechanisms
GTP bound eRF3 (name copied from entity in Homo sapiens)
eRF3-GDP:eRF1:80S Ribosome:mRNA:tRNA Complex (name copied from entity in Homo sapiens)
CCT/TriC(ADP)-associated non-native tubulin (name copied from entity in Homo sapiens)
eRF3-GTP:eRF1:80S Ribosome:mRNA:peptidyl-tRNA Complex (name copied from entity in Homo sapiens)
eRF3-GDP:eRF1:80S Ribosome:mRNA:peptidyl-tRNA Complex (name copied from entity in Homo sapiens)
tubulin-GTP folding intermediate (name copied from entity in Homo sapiens)
CCT/TriC (ADP) associated actin (name copied from entity in Homo sapiens)
CCT/TriC(ADP) (name copied from entity in Homo sapiens)
CCT/TriC(ATP):unfolded tubulin complex (name copied from entity in Homo sapiens)
eIF2:GDP: eIF2B (name copied from entity in Homo sapiens)
ribosome:mRNA:polypeptide+signal (name copied from entity in Homo sapiens)
Genetic evidence that phosphatidylserine synthase II catalyzes the conversion of phosphatidylethanolamine to phosphatidylserine in Chinese hamster ovary cells
SRP receptor (name copied from entity in Homo sapiens)
SRP:polypeptide+signal:ribosome (name copied from entity in Homo sapiens)
40S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
eIF2:GDP (name copied from entity in Homo sapiens)
eIF2B subunits complex (name copied from entity in Homo sapiens)
eIF5B:GDP (name copied from entity in Homo sapiens)
eIF5B:GTP (name copied from entity in Homo sapiens)
Signal Peptidase (name copied from entity in Homo sapiens)
cleaved polypeptide:Translocon (name copied from entity in Homo sapiens)
membrane-bound ribosome:mRNA:cleaved polypeptide (name copied from entity in Homo sapiens)
SEC61 translocon (name copied from entity in Homo sapiens)
TRAP Complex (name copied from entity in Homo sapiens)
Translocon:TRAP (name copied from entity in Homo sapiens)
membrane-bound ribosome:mRNA:polypeptide+signal (name copied from entity in Homo sapiens)
DNA ligases: structure, reaction mechanism, and function
polypeptide+signal:Translocon (name copied from entity in Homo sapiens)
SRP receptor:SRP:ribosome:polypeptide+signal (name copied from entity in Homo sapiens)
Signal Recognition Particle (name copied from entity in Homo sapiens)
Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors
Calcineurin alpha regulatory subunit:Calcium (name copied from entity in Homo sapiens)
PPP3CA,B:Calmodulin (name copied from entity in Homo sapiens)
Calcineurin:Phosphorylated NFATC1,2,3 (name copied from entity in Homo sapiens)
NFAT:CaN:CaM (name copied from entity in Homo sapiens)
CaN:CaM:Ca2+ (name copied from entity in Homo sapiens)
CaN alpha regulatory:Ca2+ (name copied from entity in Homo sapiens)
Transcription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
At the beginning of this reaction, 1 molecule of '1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate' is present. At the end of this reaction, 1 molecule of '1D-myo-Inositol 1,4,5-trisphosphate', and 1 molecule of '1,2-Diacylglycerol' are present. This reaction is mediated by the 'phospholipase C activity' of 'Phosphorylated phospholipase C gamma 2'.
Calcineurin (CaN) (name copied from entity in Homo sapiens)
DDX41:DDX41 ligand (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'SUPT5H protein', and 1 molecule of 'SPT4H1 protein' are present. At the end of this reaction, 1 molecule of 'DSIF complex' is present. This reaction takes place in the 'nucleus'.
Calcineurin:Calmodulin (CaN:CaM) (name copied from entity in Homo sapiens)
At the beginning of this reaction, 1 molecule of 'FACT 140 kDa subunit', and 1 molecule of 'FACT 80 kDa subunit' are present. At the end of this reaction, 1 molecule of 'FACT complex' is present. This reaction takes place in the 'nucleus'.
PPP3CA,B:Fe3+:Zn2+ (name copied from entity in Homo sapiens)
Fatty acid, triacylglycerol, and ketone body metabolism
Protein Kinase G (PKG) is a homodimer held together by a leucine zipper present in the N terminus. Each member of the dimer has two cyclic GMP (cGMP) binding sites, one low affinity and one high affinity. PKG was first described in various arthropods. Mammals have two PKG genes, prkg1 and prkg2, that encode PKG1 (cGKI) and PKG2 (cGKII). The N terminus (the first 90-100 residues) of PKG1 is encoded by two alternatively spliced exons that produce the isoforms PKG1alpha and PKG1beta. Both are cytosolic. PKG1 is present in high concentrations (>0.1 µM) in all smooth muscles, platelets, cerebellum, hippocampus, dorsal root ganglia, neuromuscular endplate, and kidney. PKG1beta is the predominant PKG isoform in platelets. PKG1 is required for the inhibition of platelet activation by NO/cGMP. PKG2 is anchored at the plasma membrane by myristoylation of the N-terminal Gly-2 residue. PKG2 phosphorylates cystic fibrosis transmembrane conductance regulator.
Cyclic GMP phosphodiesterase are hydrolases selective for cAMP (PDE4, 7 and 8), cGMP (PDE5, 6 and 9) or able to hydrolyse both cAMP and cGMP (PDE1, 2, 3, 10 and 11). Â The dual-specificity PDEs allow for cross-regulation of the cAMP and cGMP pathways, e.g. PDE2 can hydrolyse both, but binding of cGMP to the regulatory GAF-B domain increases cAMP affinity and hydrolysis. PDE2, 3 and 5 are expressed in platelets.
Cyclic guanosine monophosphate (cGMP) is an important secondary messenger synthesized by guanylate cyclases. cGMP has effects on phosphodiesterases (PDE), ion-gated channels, and the cGMP-dependent protein kinases (cGK, Protein Kinase G or PKG). It is involved in regulation of several physiological functions including vasodilation, platelet aggregation and neurotransmission. Elevation of intracellular cGMP activates PKG (Haslam et al. 1999) which regulates several intracellular molecules and pathways including the vasodilator-stimulated phosphoprotein (VASP) (Halbrugge et al. 1990) and the ERK pathway (Hood and Granger 1998, Li et al. 2001). cGMP mediates nitric oxide (NO)-induced vascular smooth muscle relaxation (Furchgott and Vanhoutte 1989). Phosphodiesterase 5 (PDE5) hydrolyzes cGMP; the PDE5 inhibitor sildenafil (Viagra) increases intracellular cGMP and thereby can be used as a treatment for erectile dysfunction (Corbin and Francis 1999). The role of the cGMP and PKG in platelet activation was controversial as increases in platelet cGMP levels were observed in response to both platelet agonists (thrombin, ADP or collagen) and inhibitors (NO donors such as sodium nitroprusside), but it is currently accepted that PKG inhibits platelet activation (Haslam et al. 1999). Consistent with this, nitric oxide (NO) donors that inhibit platelet activation enhance intracellular cGMP (Haslam et al. 1999). cGMP also plays an important stimulatory role in GPIb-IX-mediated platelet activation. Platelet responses to cGMP have been proposed to be biphasic, consisting of an early stimulatory response that promotes platelet activation followed by a delayed platelet inhibition that serves to limit the size of platelet aggregates (Li et al 2003).
Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity
eIF4F:mRNP (name copied from entity in Homo sapiens)
48S complex (name copied from entity in Homo sapiens)
40S:eIF3:eIF1A (name copied from entity in Homo sapiens)
mRNP (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA:eIF5B:GTP (name copied from entity in Homo sapiens)
The kinetics of the reduction of cytochrome c by the superoxide anion radical
CaN catalytic alpha/beta:Zn++:Fe3+:CaM:Ca2+ (name copied from entity in Homo sapiens)
The major HMG-box-containing chromatin proteins HMGB1 and HMGB2 stimulate DNA cleavage by DFF40/CAD (Liu et al., 1998; Toh et al., 1998; Widlak et al., 2000). Changes in DNA conformation following HMG-box binding makes the substrate more accessible to cleavage by DFF40/CAD nuclease and thus may contribute to preferential linker DNA cleavage during apoptosis (Kalinowska-Herok and Widlak., 2008).
DNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed in Widlak and Garrard, 2005). In non-apoptotic cells, DFF is a nuclear heterodimer consisting of a 45 kD chaperone and inhibitor subunit (DFF45)/inhibitor of CAD (ICAD-L)] and a 40 kD nuclease subunit (DFF40/CAD)( Liu et al. 1997, 1998; Enari et al. 1998). During apoptosis, activated caspase-3 or -7 cleave DFF45/ICAD releasing active DFF40/CAD nuclease. The activity of DFF is tightly controlled at multiple stages. During translation, DFF45/ICAD, Hsp70, and Hsp40 proteins play a role in insuring the appropriate folding of DFF40 during translation(Sakahira and Nagata, 2002). The nuclease activity of DFF40 is enhanced by the chromosomal proteins histone H1, Topoisomerase II and HMGB1/2(Widlak et al., 2000). In addition, the inhibitors (DFF45/35; ICAD-S/L) are produced in stoichiometric excess (Widlak et al., 2003).
Apoptotic factors released from the mitochondria promote apoptosis through several different mechanisms. Cytochrome C participates in Apoptosome driven effector caspase activation while SMAC relieves IAP mediated caspase inhibition.
The intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stresses in the endoplasmic reticulum and death receptor stimulation. Following the reception of stress signals, proapoptotic BCL-2 family proteins are activated and subsequently interact with and inactivate antiapoptotic BCL-2 proteins. This interaction leads to the destabilization of the mitochondrial membrane and release of apoptotic factors. These factors induce the caspase proteolytic cascade, chromatin condensation, and DNA fragmentation, ultimately leading to cell death. The key players in the Intrinsic pathway are the Bcl-2 family of proteins that are critical death regulators residing immediately upstream of mitochondria. The Bcl-2 family consists of both anti- and proapoptotic members that possess conserved alpha-helices with sequence conservation clustered in BCL-2 Homology (BH) domains. Proapoptotic members are organized as follows: 1. "Multidomain" BAX family proteins such as BAX, BAK etc. that display sequence conservation in their BH1-3 regions. These proteins act downstream in mitochondrial disruption. 2. "BH3-only" proteins such as BID,BAD, NOXA, PUMA,BIM, and BMF have only the short BH3 motif. These act upstream in the pathway, detecting developmental death cues or intracellular damage. Anti-apoptotic members like Bcl-2, Bcl-XL and their relatives exhibit homology in all segments BH1-4. One of the critical functions of BCL-2/BCL-XL proteins is to maintain the integrity of the mitochondrial outer membrane.
PPP3CA,B,C:Fe3+:Zn2+:4xCa2+:CaM (name copied from entity in Homo sapiens)
Active steroid hormones are produced from the precursor cholesterol.The steps involved in the biosynthesis of the adrenal steroid hormones, corticosterone, cortisol, and aldosterone; and the gonadal steroid hormones, progesterone, estradiol, and testosterone are annotated here. The enzymes that catalyze these reactions fall into two major classes of proteins: the cytochrome P450 heme-containing proteins and the hydroxysteroid dehydrogenases.
PP2B catalytic (Fe3+, Zn2+) (name copied from entity in Homo sapiens)
Permeabilization of the outer mitochondrial membrane by pro-apoptotic BCL2 family proteins, such as BAK and BAX, allows cytochrome c eflux from the mitochondrial intermembrane space into the cytosol (Arnoult et al. 2003).
CaN catalytic alpha/beta:Zn++:Fe3+ (name copied from entity in Homo sapiens)
In the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucleus and other organelles, DNA fragmentation, chromatin condensation, cell shrinkage and cell detachment and membrane blebbing (reviewed in Fischer et al., 2003).
Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various apoptotic pathways are still being revealed today. The two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptors The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53. In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes.
DNA fragmentation in response to apoptotic signals is achieved through the activity of two apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in Widlak and Garrard, 2005). These endonucleases cleave chromatin producing 3'-hydroxyl groups and 5'-phosphate residues. 50-300 kb cleavage products are produced followed by internucleosomal DNA fragmentation. Although the activities of DFF and Endo G are similar, they reside in different locations within the cell and are regulated in different ways.
Adenoviral expression of the BAP31 cleavage product, p20 causes early release of Ca2+ from the ER, concomitant uptake of Ca2+ into mitochondria, and recruitment of Drp1 to the mitochondria (Breckenridge et al., 2003) . Drp1 mediates scission of the outer mitochondrial membrane, resulting in dramatic fragmentation and fission of the mitochondrial network .
ribonucleotide reductase M2B (TP53 inducible)
Ribonucleoside-diphosphate reductase M1 chain (EC 1.17.4.1) (Ribonucleotide reductase large chain)
Ribonucleoside-diphosphate reductase M1 chain
Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596093
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596057
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Glutathione reductase, mitochondrial precursor
non-metastatic cells 1, protein (NM23A) expressed in
Tumor metastatic process-associated protein
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Nucleoside diphosphate kinase, mitochondrial
non-metastatic cells 4, protein expressed in
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ornithine aminotransferase, mitochondrial
deoxythymidylate kinase (thymidylate kinase)
Adenylate kinase isoenzyme 2, mitochondrial
Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)
Identification of two tyrosine phosphoproteins, pp70 and pp68, which interact with phospholipase Cgamma, Grb2, and Vav after B cell antigen receptor activation
Myotubularin and MTMR2, phosphatidylinositol 3-phosphatases mutated in myotubular myopathy and type 4B Charcot-Marie-Tooth disease
Transcriptional induction of the human asparagine synthetase gene during the unfolded protein response does not require the ATF6 and IRE1/XBP1 arms of the pathway
The molecular genetic basis of muscle phosphoglycerate mutase (PGAM) deficiency
Ribonucleoside-diphosphate reductase M2 chain (EC 1.17.4.1) (Ribonucleotide reductase small chain)
glutaredoxin (thioltransferase), oxidized
Mucopolysaccharidosis type IVA (Morquio A disease): clinical review and current treatment
Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase
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IAP proteins: blocking the road to death's door
Coproporphyrinogen III oxidase, mitochondrial
5-aminolevulinate synthase, non-specific (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, non-specific, mitochondrial
5-aminolevulinate synthase, erythroid (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor
branched chain keto acid dehydrogenase E1, alpha polypeptide
branched chain keto acid dehydrogenase E1, beta polypeptide
Glutamate dehydrogenase 1, mitochondrial precursor
Glutamine- dependent asparagine synthetase
Asparagine synthetase (glutamine-hydrolyzing)
Reduction of alpha gamma-diketo and alpha-keto acids catalyzed by muscle preparations and by crystalline lactic dehydrogenase
Transport of glycerol from adipocytes to the liver by Aquaporins
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FGFR activation in skeletal disorders: too much of a good thing
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3-hydroxyisobutyryl-coenzyme A hydrolase
ornithine carbamoyltransferase, mitochondrial
dihydrolipoamide branched chain transacylase E2
Expression cloning of a human cDNA encoding folylpoly(gamma-glutamate) synthetase and determination of its primary structure
Transcription initiation protein SPT4 homolog 1
Chromatin-specific transcription elongation factor 80 kDa subunit
Recombination signal sequence recognition protein
Structure-specific recognition protein 1 (SSRP1) (Recombination signal sequence recognition protein) (T160) (Chromatin-specific transcription elongation factor 80 KDA subunit
Structure-specific recognition protein 1
Cyclic GMP-dependent protein kinases (PKGs)
Ways of dying: multiple pathways to apoptosis.
Dominant negative mechanism underlies autosomal dominant Stargardt-like macular dystrophy linked to mutations in ELOVL4
Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
Cytochrome c oxidase assembly protein COX15 homolog
Aflatoxin B1 aldehyde reductase member 4 ecNumber1.-.-.-/ecNumber
Aflatoxin B1 aldehyde reductase member 3 ecNumber1.-.-.-/ecNumber
Aflatoxin B1 aldehyde reductase member 2 ecNumber1.1.1.n11/ecNumber
NADPH:adrenodoxin oxidoreductase, mitochondrial
Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
Regulation of purine synthesis de novo in human fibroblasts by purine nucleotides and phosphoribosylpyrophosphate
Molecular mechanisms of megakaryocyte differentiation
Platelet releasate (inferred) cytosolic proteins
Mutations in PYCR1 cause cutis laxa with progeroid features
DNA containing an MYH-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hOGG1 glycosylase: formamidopyrimidine complex (name copied from entity in Homo sapiens)
hOGG1 glycosylase:8-oxo guanine complex (name copied from entity in Homo sapiens)
MYH glycosylase:adenine complex (name copied from entity in Homo sapiens)
MPG glycosylase:hypoxanthine complex (name copied from entity in Homo sapiens)
MPG glycosylase:ethenoadenine complex (name copied from entity in Homo sapiens)
MPG glycosylase:3-methyladenine complex (name copied from entity in Homo sapiens)
UPF1:eRF3 Complex on Translated mRNA (name copied from entity in Homo sapiens)
mRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction (name copied from entity in Homo sapiens)
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction (name copied from entity in Homo sapiens)
Proximal tubular handling of phosphate: A molecular perspective
Biosynthesis of tricarboxylic acids by carbon dioxide fixation; enzymatic mechanisms
Forearm blood flow during body temperature transients produced by leg exercise.
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
cGMP-dependent protein kinase 1, alpha isozyme
Temporal differences in the activation of three classes of non-transmembrane protein tyrosine kinases following B-cell antigen receptor surface engagement
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Intact AQP0 performs cell-to-cell adhesion
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Interfacial kinetic and binding properties of mammalian group IVB phospholipase A2 (cPLA2beta) and comparison with the other cPLA2 isoforms
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The SLC31 (Ctr) copper transporter family
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Importance of dietary gamma-linolenic acid in human health and nutrition
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A unified model for apical caspase activation
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Subunit interactions in the mammalian alpha-ketoglutarate dehydrogenase complex. Evidence for direct association of the alpha-ketoglutarate dehydrogenase and dihydrolipoamide dehydrogenase components.
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Mucopolysaccharidosis IV A: assignment of the human N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene to chromosome 16q24
Activation of phospholipase C-gamma by phosphatidylinositol 3,4,5-trisphosphate
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Activation of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease). Oligomerization and direct interaction with histone H1
The subcellular localization of an aquaporin-2 tetramer depends on the stoichiometry of phosphorylated and nonphosphorylated monomers
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E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
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Dihydroorotate dehydrogenase, mitochondrial precursor
Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (Fragment)
carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
CAD protein (Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carbamoyltransferase (EC 2.1.3.2); Dihydroorotase (EC 3.5.2.3))
Glutamine-dependent carbamoyl-phosphate synthase
Hypoxanthine-guanine phosphoribosyltransferase
Cyclic GMP phosphodiesterase-5: target of sildenafil
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Subcellular localization and secretion of factor V from human platelets
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Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
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cDNA sequence and gene locus of the human retinal phosphoinositide-specific phospholipase-C beta 4 (PLCB4)
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Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism
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The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1
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Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A
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Heme O and heme A are specifically synthesised for the heme-copper respiratory oxidases. Mitochondrial protoheme IX farnesyltransferase (COX10) mediates the transformation of protoheme IX (heme) and farnesyl diphosphate (FAPP) to heme O (Glerum & Tzagoloff 1994). COX10 is highly expressed in muscle, heart and brain (Murakami et al. 1997).
Ferrochelatase (FECH) catalyzes the insertion of ferrous iron into protoporphyrin IX (PRIN9) to form heme. FECH is localized on the matrix surface of the inner mitochondrial membrane and this reaction takes place within the mitochondrial matrix. The enzyme functions as a homodimer with each monomer containing a nitric oxide-sensitive 2Fe-2S cluster. Enzyme deficiency is associated with erythropoietic protoporphyria in vivo, and inhibition of ferrochelatase activity is a clinically important consequence of lead poisoning (Piomelli et al. 1987).
O2-dependent coproporpyrinogen oxidase (CPO) catalyzes the conversion of coproporphyrinogen III (COPRO3) to protoporphyrinogen IX (PPGEN9). The localization of the human enzyme to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Elder and Evans 1978). The human enzyme functions as a homodimer (Lee et al. 2005). Enzyme deficiency is associated with hereditary coproporphyria in vivo.
Cytosolic uroporphyrinogen decarboxylase (UROD) catalyzes the sequential removal of four carboxylic groups from the acetic acid side chains of uroporphyrinogen I (URO1) to form coproporphyrinogen I (COPRO1). UROD catalyzes this reaction less efficiently than the decarboxylation of uroporphyrinogen III (de Verneuil et al. 1983).
Cytosolic uroporphyrinogen decarboxylase (UROD) catalyzes the sequntial removal of four carboxylic groups from the acetic acid side chains of uroporphyrinogen III (URO3) to form coproporphyrinogen III (COPRO3) (de Verneuil et al. 1983). Human UROD is a dimer (Whitby et al. 1998). Heterogenous and homogenous deficiencies of UROD are associated with porphyria cutanea tarda and hepatoerythropoietic porphyria respectively in vivo (Moran-Jiminez et al. 1996).
Cytosolic porphobilinogen deaminase catalyzes the polymerization of four molecules of porphobilinogen (PBG) to generate hydroxymethylbilane (HMB), an unstable tetrapyrrole. This reaction is the first step in the formation of the tetrapyrrole macrocycle. Two isoforms of porphobilinogen deaminase are generated by alternative splicing, one expresssed in erythroid tissues and one ubiquitously expressed in the body. Deficiencies of both forms of PBG deaminase are associated with acute intermittent porphyria.
Porphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the name itself, porphyrin, is derived from the Greek word for purple. The aromatic character of porphyrins can be seen by NMR spectroscopy. Porphyrins readily combine with metals by coordinating them in the central cavity. Iron (heme) and magnesium (chlorophyll) are two well known examples although zinc, copper, nickel and cobalt form other known metal-containing phorphyrins. A porphyrin which has no metal in the cavity is called a free base. Some iron-containing porphyrins are called hemes (heme-containing proteins or hemoproteins) and these are found extensively in nature ie. hemoglobin. Hemoglobin is quantitatively the most important hemoprotein. The hemoglobin iron is the transfer site of oxygen and carries it in the blood all round the body for cell respiration. Other examples are cytochromes present in mitochondria and endoplasmic reticulum which takes part in electron transfer events, catalase and peroxidase whic protect the body against the oxidant hydrogen peroxide and tryptophan oxygenase which is present in intermediary metabolism. Hemoproteins are synthesized in all mammalian cells and the major sites are erythropoietic tissue and the liver. The processes by which heme is synthesized, transported, and metabolized are a critical part of human iron metabolism (Severance and Hamze 2009); here the core processes of heme biosynthesis and catabolism have been annotated.
ACSS1 (acyl-CoA synthetase short-chain family member 1) in the mitochondrial matrix catalyzes the reaction of acetate, coenzyme A, and ATP to form acetyl-CoA, AMP, and pyrophosphate (Schwer et al. 2006).
Heme A is the prosthetic group of cytochrome c oxidase, the terminal enzyme in the respiratory chain. It is formed by the action of cytochrome c oxidase assembly protein COX15 homolog (COX15) on heme O (Petruzzella et al. 1998, Antonicka et al. 2003). Defects in COX15 cause of mitochondrial complex IV deficiency (MT-C4D; MIM:220110), also called cytochrome c oxidase deficiency resulting in a disorder of the mitochondrial respiratory chain seen as heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs (Antonicka et al. 2003). Defects in COX15 also cause Leigh syndrome (LS; MIM:256000), an early-onset progressive neurodegenerative disorder characterised by the presence of focal, bilateral lesions in one or more areas of the central nervous system (Oquendo et al. 2004, Bugiani et al. 2005).
Eight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and glycine to form 5-aminolevulinate (ALA). The next four steps take place in the cytosol. Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG). The next two steps convert four molecules of PBG into the cyclic tetrapyrrole uroporphyringen III, which is then decarboxylated into coproporphyrinogen III. The last three steps occur in the mitochondria and involve modifications to the tetrapyrrole side chains and finally, insertion of iron. In addition to these synthetic steps, a spontaneous cytosolic reaction allows the formation of uroporphyringen I which is then enzymatically decarboxylated to coproporphyrinogen I, which cannot be metabolized further in humans. Also, lead can inactivate ALAD, the enzyme that catalyzes PBG synthesis, and ferrochelatase, the enzyme that catalyzes heme synthesis. The porphyrias are disorders that arise from defects in the enzymes of heme biosynthesis. Defective pathway enzymes after ALA synthase result in accumulated substrates which can cause either skin problems, neurological complications, or both due to their toxicity in higher concentrations. They are broadly classified as hepatic porphyrias or erythropoietic porphyrias, based on the site of the overproduction of the substrate. Each defect is described together with the reaction it affects.
Polyamines is a family of molecules (i.e. putrescine, spermine, spermidine) derived from ornithine according to a decarboxylation/condensative process. More recently, it has been demonstrated that arginine can be metabolised according to the same pathway leading to agmatine formation. Polyamines are essential for the growth, the maintenance and the function of normal cells. The complexity of their metabolism and the fact that polyamines homeostasis is tightly regulated support the idea that polyamines are essential to cell survival. Multiple abnormalities in the control of polyamines metabolism might be implicated in several pathological processes (Moinard et al., 2005). Legend for the following figure:
Methionine salvage is a sequential pathway of six reactions that create methionine from 5'-methylthioadenosine (MTA) which is a byproduct of polyamine biosynthesis in nearly all organisms. The process happens completely in the cytosol. It is important in humans for recycling of sulphur that has to be assimilated using energy. (Pirkov et al, 2008; Albers, 2009)
At the beginning of this reaction, 1 molecule of 'S-adenosylhomocysteine', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of 'adenosine', and 1 molecule of 'Homocysteine' are present. This reaction takes place in the 'cytosol' and is mediated by the 'adenosylhomocysteinase activity' of 'SAH hydrolase homotetramer'.
S-adenosylmethionine (SAM) is an essential metabolite in all cells. SAM is a precursor in the synthesis of polyamines. Methionine adenosyltransferase (MAT; EC 2.5.1.6) catalyzes the only known SAM biosynthetic reaction from methionine and ATP. In mammalian tissues, three different forms of MAT (MAT I, MAT III and MAT II) have been identified that are the product of two different genes (MAT1A and MAT2A). A third gene MAT2B has been identified and is known to be a part of MAT II heterotetramer complex.
The AMP-activated protein kinase pathway--new players upstream and downstream
In the last step MOB gets transaminated to methionine. The reaction was confirmed in yeast, where several transaminases catalyze it, which appears to be also the case in rat. At the moment, the human enzymes involved are unknown but due to homology to the respective enzyme in the parasite Crithidia fasciculata we feel supported to state that human GOT is probably one of the involved transaminases. (Berger et al, 2001)
Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein
5-Aminolevulinic acid dehydratase (ALAD aka porphobilinogen synthase, PBGS), catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen (PBG). The substrate that becomes the acetyl side chain-containing half of PBG is called A-side ALA; the half that becomes the propionyl side chains and the pyrrole nitrogen is called P-ALA (Jaffe 2004). PBG is the first pyrrole formed, the precursor to all tetrapyrrole pigments such as heme and chlorophyll. There are at least eight bonds that are made or broken during this reaction. The active form of the ALAD enzyme is an octamer complexed with eight Zn2+ ions, four that are strongly bound and four that are weakly bound. The four weakly bound ones are dispensible for enzyme activity in vitro (Bevan et al. 1980; Mitchell et al. 2001). Deficiencies of ALAD enzyme in vivo are associated with 5-aminolevulinate dehydratase-deficient porphyria (e.g., Akagi et al. 2000).
The main sulfur amino acids are methionine, cysteine, homocysteine and taurine. Of these, the first two are proteinogenic. This group of reactions contains all processes that 1) break down sulfur amino acids, 2) interconvert between them, and 3) synthesize them from solved sulfide which comes from sulfate assimilation and reduction. Only plants and microorganisms employ all processes. Humans cannot de novo synthesize any sulfur amino acid, nor convert cysteine to methionine (Brosnan & Brosnan, 2006).
This group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amino acids that are not essential components of the human diet; and 4) the synthesis of related nitrogen-containing molecules including carnitine and creatine. Transport of these molecuels across lipid bilayer membranes is annotated separately as part of the module on "transmembrane transport of small molecules".
The committed step for porphyrin synthesis is the formation of 5-aminolevulinate (ALA) by condensation of glycine (from the general amino acid pool) and succinyl-CoA (from the TCA cycle), in the mitochondrial matrix. The reaction is catalyzed by two different ALA synthases, one expressed ubiquitously (ALAS1) and the other only expressed in erythroid precursors (ALAS2). Both enzymes are expressed as homodimers and require pyridoxal 5-phosphate as a cofactor. No disease-causing mutations of ALAS1 have been recognised in humans. Mutations in ALAS2 cause X-linked sideroblastic anaemia (XLSA), characterised by a microcytic hypochromic anaemia.
Lead binds to ALAD enzyme displacing half the zinc ions essential for its catalytic activity and inactivating it. Lead is a major environmental toxin and this enzyme is one of its principal molecular targets (Jaffe et al. 2001).
Cytosolic serine hydroxymethyltransferase tetramer (SHMT1) catalyzes the reaction of 3-Hydroxy-N6,N6,N6-trimethyl-L-lysine to form glycine and 4-trimethylammoniobutanal (Hulse et al. 1978).
The urea cycle yields urea, the major form in which excess nitrogen is excreted from the human body, and the amino acid arginine (Brusilow and Horwich 2001). It consists of four reactions: that of ornithine and carbamoyl phosphate to form citrulline, of citrulline and aspartate to form argininosuccinate, the cleavage of argininosuccinate to yield fumarate and arginine, and the cleavage of arginine to yield urea and re-form ornithine. The carbamoyl phosphate consumed in this cycle is synthesized in the mitochondria from bicarbonate and ammonia, and this synthesis in turn is dependent on the presence of N-acetylglutamate, which allosterically activates carbamoyl synthetase I enzyme. The synthesis of N-acetylglutamate is stimulated by high levels of arginine. Increased levels of free amino acids, indicated by elevated arginine levels, thus stimulate urea synthesis. Two enzymes catalyze the hydrolysis of arginine to yield ornithine and urea. Cytosolic ARG1 is the canonical urea cycle enzyme. Mitochondrial ARG2 likewise catalyzes urea production from arginine and may have a substantial sparing effect in patients lacking ARG1 enzyme, so its reaction is annotated here although the role of ARG2 under normal physiological conditions remains unclear.
Arginase 2 (ARG2) trimer catalyzes the hydrolysis of arginine to form urea and ornithine (Cama et al. 2003). ARG2 is localized to the mitochondrion (Gotoh ea 1996). The enzyme is expressed in many tissues in addition to liver and while its function appears to mitigate the effects of ARG1 deficiency on urea synthesis, its normal physiological roles have not been fully defined (Iyer et al. 1998).
Cytosolic Arginase 1 (ARG1) trimer catalyzes the hydrolysis of arginine to yield ornithine and urea (DiCostanzo et al. 2005). Patients expressing mutated forms of the enzyme with diminished in vitro arginase activity can accumulate arginine to pathogenic levels in the blood (e.g., Uchino et al. 1995).
ATP-binding cassette (ABC) transporters in human metabolism and diseases
Human Sulfotransferases and Their Role in Chemical Metabolism
As it hydrolyzes a guanidino group within agmatine and also contains signature amino acid residues that act as ligand binding sites for the potential Mn(++) cofactor, agmatinase is classified as a member of the arginase superfamily (Morris, 2003).
Agmatine is an amine that is formed by decarboxylation of L-arginine by the enzyme arginine decarboxylase (ADC) and hydrolyzed by the enzyme agmatinase to putrescine. Agmatine binds to several target receptors in the brain and has been proposed as a novel neuromodulator (Reghunathan 2006). Agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation (Satriano, 2003).
Carnitine is synthesized in four steps from trimethyllysine (generated in turn by the S-adenosyl-methionine-mediated methylation of lysine residues in proteins, followed by protein hydrolysis). The enzymes that catalyze the first three steps of carnitine synthesis, converting trimethyllysine to gamma-butyrobetaine, are widely distributed in human tissues. The enzyme that catalyzes the last reaction, converting gamma-butyrobetaine to carnitine, is found only in liver and kidney cells, and at very low levels in brain tissues. Other tissues that require carnitine, such as muscle, are dependent on transport systems that mediate its export from the liver and uptake by other tissues (Kerner and Hoppel 1998).
Agmatine is polyamine formed by decarboxylation of L-arginine by arginine decarboxylase (ADC). Human ADC is a 460-amino acid protein that shows about 48% identity to mammalian ornithine decarboxylase (ODC) but has no ODC activity.
L-ornithine is converted into putrescine by ODC holoenzyme complex.Putrescine is subsequent used for polyamine synthesis.
Spermidine synthase is one of four enzymes in the polyamine-biosynthetic pathway and carries out the final step of spermidine biosynthesis. This enzyme catalyzes the conversion of putrescine to spermidine using decarboxylated S-adenosylmethionine as the cofactor.
Mitochondrial glutamate dehydrogenase 1 (GLUD1) catalyzes the reversible reaction of 2-oxoglutarate, NAD(P)H + H+, and ammonia to form glutamate and NAD(P)+ (Fang et al. 2002). Mature GLUD1 protein lacks the 53 aminoterminal residues of the nascent protein (Julliard and Smith 1979), which function as a mitochondrial import signal. The active form of the enzyme is a hexamer, allosterically activated by ADP and inhibited by GTP (Fang et al. 2002; Smith et al. 2002).
These reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four amino acids for glucose synthesis under fasting conditions. These reactions also provide a means to collect nitrogen, both as ammonia and as amino groups, and direct it towards urea synthesis. Transamination, the conversion of an amino acid to the corresponding alpha-keto acid coupled to the conversion of a molecule of alpha-ketoglutarate to glutamate, is the first step in the catabolism of most amino acids. Transamination reactions are freely reversible so they also provide a means to balance concentrations of various amino acids and alpha-keto (2-oxo) acids in the cytosol.
Mitochondrial glutamate dehydrogenase 1 (GLUD1) catalyzes the reversible reaction of glutamate and NAD(P)+ to form 2-oxoglutarate, NAD(P)H + H+, and ammonia (Fang et al. 2002). Mature GLUD1 protein lacks the 53 aminoterminal residues of the nascent protein (Julliard and Smith 1979), which function as a mitochondrial import signal. The active form of the enzyme is a hexamer, allosterically activated by ADP and inhibited by GTP (Fang et al. 2002; Smith et al. 2002).
The mitochondrial nranched-chain alpha-ketoacid dehydrogenase (BKCD) complex catalyzes the reactions of alpha-ketoisocaproate, alpha-keto beta-methylvalerate, or aalpha-ketoisovalerate with CoA and NAD+ to form isovaleryl-CoA, a-methylbutyryl-CoA, or isobuyryl-CoA, respectively, and CO2 and NADH (Chuang and Shih 2001). While bovine and microbial BCKD complexes have been characterized most extensively (Reed and Hackert 1990), structural studies of individual components and subcomplexes of human BKCD have confirmed their structures and roles in the overall oxidative carboxylation process, and have related these features to the disruptive effects of mutations on branched-chain amino acid metabolism in vivo: E1a and E1b components - AEvarsson et al. 2000; E2 - Chang et al. 2002; E3- Brautigam et al. 2005. In addition, structural studies have confirmed the lipoylation of lysine residue 44 in E2 protein (Chang et al. 2002) and the loss of an aminoterminal mitochondrial transport sequence from mature E3 protein (Bruatigam et al. 2005). Loss of mitochondrial transport sequences from proteins E1a, E1b, and E2 has been domstrated by sequence analysis (Wynn et al. 1999).
Mitochondrial acetyl-CoA acetyltransferase (ACAT1) catalyzes the reaction of alpha-methyl-acetoacetyl-CoA and CoA to form propionyl-CoA and acetyl-CoA. Structural studies have shown the active enzyme to be a tetramer of ACAT1 polypeptides whose aminoterminal 34 residues, a mitochondrial targeting sequence, have been removed (Haapalainen et al. 2007).
Mitochondrial 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) catalyzes the hydrolysis of beta-hydroxyisobutyryl-CoA to form beta-hydroxyisobutyrate (3-hydroxy-2-methylpropanoate) and CoA (Hawes et al. 1996).
The branched-chain amino acids, leucine, isoleucine, and valine, are all essential amino acids (i.e., ones required in the diet). They are major constituents of muscle protein. The breakdown of these amino acids starts with two common steps catalyzed by enzymes that act on all three amino acids: reversible transamination by branched-chain amino acid aminotransferase, and irreversible oxidative decarboxylation by the branched-chain ketoacid dehydrogenase complex. Isovaleryl-CoA is produced from leucine by these two reactions, alpha-methylbutyryl-CoA from isoleucine, and isobutyryl-CoA from valine. These acyl-CoA's undergo dehydrogenation, catalyzed by three different but related enzymes, and the breakdown pathways then diverge. Leucine is ultimately converted to acetyl-CoA and acetoacetate; isoleucine to acetyl-CoA and succinyl-CoA; and valine to succinyl-CoA. Under fasting conditions, substantial amounts of all three amino acids are generated by protein breakdown. In muscle, the final products of leucine, isoleucine, and valine catabolism can be fully oxidized via the citric acid cycle; in liver they can be directed toward the synthesis of ketone bodies (acetoacetate and acetyl-CoA) and glucose (succinyl-CoA) (Chuang & Shih 2001, Sweetman & Williams 2001).
The mitochondrial alpha-ketoglutarate dehydrogenase complex catalyzes the reaction of alpha-ketoadipate, CoASH, and NAD+ to form glutaryl-CoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of alpha-ketoadipate catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the glutaryl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998). While all of the human proteins are known as predicted protein products of cloned genes, direct experimental evidence for their functions is available only for E3 (DLD) (Brautigam et al. 2005).
In humans, most catabolism of L-lysine normally proceeds via a sequence of seven reactions which feeds into the pathway for fatty acid catabolism. In the first two reactions, catalyzed by a single enzyme complex, lysine is combined with alpha-ketoglutarate to form saccharopine, which in turn is cleaved and oxidized to yield glutamate and alpha-ketoadipic semialdehyde. The latter molecule is further oxidized to alpha-ketoadipate. Alpha-ketoadipate is oxidatively decarboxylated by the alpha-ketoglutarate dehydrogenase complex (the same enzyme complex responsible for the conversion of alpha-ketoglutarate to succinyl-CoA in the citric acid cycle), yielding glutaryl-CoA. Glutaryl-CoA is converted to crotonyl-CoA, crotonyl-CoA is converted to beta-hydroxybutyryl-CoA, and beta-hydroxybutyryl-CoA is converted to acetoacetyl-CoA. The products of lysine catabolism are thus exclusively ketogenic; i.e., under starvation conditions they can be used for the synthesis of ketone bodies, beta-hydroxybutyrate and acetoacetate, but not for the net synthesis of glucose (Cox 2001; Goodman and Freeman 2001).
Mitochondrial ornithine transcarbamoylase (OTC) catalyzes the reaction of ornithine and carbamoyl phosphate to form citrulline (Horwich et al. 1984). The enzyme is a homotrimer (Shi et al. 2001).
Cytosolic ITPA dimer catalyzes the reaction of dITP and water to form dIMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of dITP is thought to prevent its incorporation into DNA, which would be mutagenic (Lin et al. 2001; Abolhassani et al. 2010).
Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis
Cytosolic ITPA dimer catalyzes the reaction of XTP and water to form XMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of XTP is thought to prevent its incorporation into mRNA, which would lead to aberrant protein synthesis (Lin et al. 2001; Abolhassani et al. 2010).
Cytosolic asparagine synthase (ASNS) catalyzes the reaction of aspartate, glutamine, and ATP to form asparagine, glutamate, AMP, and pyrophosphate. Studies of the recombinant protein expressed in E. coli suggest that the active form of the enzyme is a dimer (Van Heeke and Schuster 1989).
Pyrroline-5-carboxylate reductase 1 (PYCR1) catalyzes the reaction of (S)-1-pyrroline-5-carboxylate with NADPH + H+ to form proline and NADP+ (Merrill et al. 1989). The active enzyme is a homodecamer (Meng et al. 2006). Recent immunofluoresence studies show that PYCR1 colocalizes with mitochondrial markers including pyrroline 5-carboxylate synthase in cultured human fibroblasts (Reversade et al. 2009).
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Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of glutamate semialdehyde and glutamate to form ornithine and alpha-ketoglutarate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Vallee and Simell 2001).
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Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of ornithine and alpha-ketoglutarate to form glutamate semialdehyde and glutamate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Valle and Simell 2001).
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Mitochondrial glutamate oxaloacetate transaminase 2 (aspartate aminotransferase 2 - GOT2) catalyzes the reversible reaction of aspartate and 2-oxoglutarate (alpha-ketoglutarate) to form oxaloacetate and glutamate (Martini et al. 1985). The active form of the enzyme is inferred to be a dimer with one molecule of pyridoxal phosphate associated with each monomer.
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Cytosolic aspartate aminotransferase (glutamate oxaloacetate transaminase 1 - GOT1) catalyzes the reversible reaction of oxaloacetate and glutamate to form aspartate and 2-oxoglutarate (alpha-ketoglutarate) (Doyle et al. 1990). Unpublished crystallographic data (PBD 3IIO) suggest the enzyme is a homodimer.
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Vitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only in limited amounts by human cells. Vitamins are classified according to their solubility, either fat-soluble or water-soluble. The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases. The metabolism of water-soluble vitamins and of vitamin D are annotated in Reactome.
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Nucleotides and their derivatives are used for short-term energy storage (ATP, GTP), for intra- and extra-cellular signaling (cAMP; adenosine), as enzyme cofactors (NAD, FAD), and for the synthesis of DNA and RNA. Most dietary nucleotides are consumed by gut flora; the human body's own supply of these molecules is synthesized de novo. Additional metabolic pathways allow the interconversion of nucleotides, the salvage and reutilization of nucleotides released by degradation of DNA and RNA, and the catabolism of excess nucleotides (Rudolph 1994). These pathways are regulated to control the total size of the intracellular nucleotide pool, to balance the relative amounts of individual nucleotides, and to couple the synthesis of deoxyribonucleotides to the onset of DNA replication (S phase of the cell cycle). These pathways are also of major clinical interest as they are the means by which nucleotide analogues used as anti-viral and anti-tumor drugs are taken up by cells, activated, and catabolized (Weilin and Nordlund 2010). As well, differences in nuclotide metabolic pathways between humans and aplicomplexan parasites like Plasmodium have been exploited to design drugs to attack the latter (Hyde 2007). The movement of nucleotides and purine and pyrimidine bases across lipid bilayer membranes, mediated by SLC transporters, is annotated as part of the module "transmembrane transport of small molecules".
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Cytosolic glutathione reductase catalyzes the reaction of glutathione (oxidized) and NADPH + H+ to form two molecules of glutathione (reduced) and NADP+ (Scott et al. 1963, Loos et al. 1976). Deficiency of glutathione reductase can cause hemolytic anemia.
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
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Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While the high ratio of ATP to ADP concentrations in the cytosol normally favors the conversion of (d)NDP and ATP to (d)NTP and ADP, the reversibility of the reactions and the overlapping substrate specificities of the enzymes suggest that this group of reverse reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleoside di- and tri-phosphates in the pool.
An array of kinases catalyze the reversible phosphorylation of nucleotide monophosphates to form nucleotide diphosphates and triphosphates. Nucleoside monophosphate kinases catalyze the reversible phosphorylation of nucleoside and deoxynucleoside 5'-monophosphates to form the corresponding nucleoside 5'-diphosphates. Most appear to have restricted specificities for nucleoside monophosphates, and to use ATP preferentially (Van Rompay et al. 2000; Anderson 1973; Noda 1973). The total number of human enzymes that catalyze these reactions in vivo is not clear. In six cases, a well-defined biochemical activity has been associated with a purified protein, and these are annotated here. However, additional nucleoside monophosphate kinase-like human proteins have been identified in molecular cloning studies whose enzymatic activities are unknown, and several distinctive nucleoside monophosphate kinase activities detected in cell extracts, e.g., a GTP-requiring adenylate kinase activity (Wilson et al. 1976) and one or more guanylate kinase activities (Jamil et al. 1975) have not been unambiguously associated with specific human proteins. The nucleoside monophosphates against which each of the six well-characterized enzymes is active is shown in the table (Van Rompay et al. 2000). All six efficiently use ATP as a phosphate donor, but have some activity with other nucleoside triphosphates as well in vitro. The high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions under most conditions. All of these phosphorylation reactions are freely reversible in vitro when carried out with purified enzymes and substrates, having equilibrium constants near 1. In vivo, high ratios of ATP to ADP are likely to favor the forward direction of these reactions, i.e., the conversion of (d)NMP and ATP to (d)NDP and ADP. At the same time, the reversibility of the reactions and the overlapping substrate specificities of the enzymes raises the possibility that this group of reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleotides in the pool: if any one molecule builds up to unusually high levels, multiple routes appear to be open not only to dispose of it but to use it to increase the supply of less abundant nucleotides. Ribonucleotide reductase catalyzes the synthesis of deoxyribonucleotide diphosphates from ribonucleotide diphosphates.
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail, but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
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Cytosolic thioredoxin reductase catalyzes the reaction of thioredoxin, oxidized and NADPH + H+ to form thioredoxin, reduced and NADP+ (Urig et al. 2006).
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In this reaction, 1 molecule of 'thioredoxin, oxidized' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
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Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While cytosolic nucleoside diphosphate kinases can efficiently use several nucleotide triphosphates as a phosphate donor, the high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions and only reactions with ATP as the phosphate donor are annotated. All of these phosphorylation reactions are freely reversible in vitro (Parks and Agarwal 1973; Schaertl et al. 1998), but the high ratio of ATP to ADP concentrations in the cytosol should favor the conversion of (d)NDP and ATP to (d)NTP and ADP.
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In this reaction, 1 molecule of 'Thioredoxin' is translocated from cytosol to nucleoplasm. This movement of the molecule occurs through the 'nuclear pore'.
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Cytosolic ITPA dimer catalyzes the reaction of ITP and water to form IMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of ITP is thought to prevent its incorporation into mRNA, which would lead to aberrant protein synthesis (Lin et al. 2001; Abolhassani et al. 2010).
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The formation of a disulfide cross-link between the two subunits demonstrates the dimeric structure of the mitochondrial oxoglutarate carrier
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Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction of either dUDP or TDP with ADP to form dUMP or TMP. The active form of the enzyme is a homodimer (Lee and Cheng 1977).
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Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction of either dUMP or TMP with ATP to form dUDP or TDP. The active form of the enzyme is a homodimer (Lee and Cheng 1977).
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Cytosolic UMP-CMP kinase (CMPK1) catalyzes the reversible reaction of CDP, dCDP, or UDP and ADP to form CMP, dCMP, or UMP and ATP (Liou et al. 2002; Scott and Wright 1979).
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Cytosolic UMP-CMP kinase (CMPK1) catalyzes the reversible reaction of CMP, dCMP, or UMP and ATP to form CDP, dCDP, or UDP and ADP (Liou et al. 2002; Scott and Wright 1979).
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Cytosolic ribonucleotide reductase catalyzes the reduction of adenine, guanine, cytidine, and uridine ribonucleoside 5'-diphosphates to form the corresponding deoxyribonucleoside 5'-diphosphates, coupled to the oxidation of thioredoxin (Holmgren 1989; Eklund et al. 2001). Ribonucleotide reductase is a tetramer of two large and two small subunits (Shao et al. 2004; Zhou et al. 2005). The overall activity of the enzyme is regulated allosterically: ATP binding is stimulatory while dATP binding is inhibitory (Reichard et al. 2000). The reducing equivalents needed for ribonucleotide reductase activity can be provided by either of two small proteins, glutaredoxin and thioredoxin (Holmgren 1989; Sun et al. 1998). Both are re-reduced with NADPH as the donor of reducing equivalents, and so are active in catalytic amounts. The relative contributions of glutaredoxin and thioredoxin in vivo are unknown.
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Cytosolic ribonucleotide reductase catalyzes the reduction of adenine, guanine, cytidine, and uridine ribonucleoside 5'-diphosphates to form the corresponding deoxyribonucleoside 5'-diphosphates, coupled to the oxidation of glutaredoxin (Eklund et al. 2001). Ribonucleotide reductase is a tetramer of two large and two small subunits (Shao et al. 2004; Zhou et al. 2005). The overall activity of the enzyme is regulated allosterically: ATP binding is stimulatory while dATP binding is inhibitory (Reichard et al. 2000). The reducing equivalents needed for ribonucleotide reductase activity can be provided by either of two small proteins, glutaredoxin and thioredoxin (Holmgren 1989; Sun et al. 1998). Both are re-reduced with NADPH as the donor of reducing equivalents, and so are active in catalytic amounts. The relative contributions of glutaredoxin and thioredoxin in vivo are unknown.
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Cytosolic CTP synthase 2 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005; van Kuilenberg et al. 2000). Unpublished X-ray crystallographic data suggest that the enzyme is a tetramer (PDB 3IHL). Both CTPS2 and a second human gene product, CPTS, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
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Cytosolic CTP synthase 1 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005). The active form of the enzyme is a tetramer (Kursala et al. 2006). Both CTPS and a second human gene product, CPTS2, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
Cytosolic glutaredoxin (oxidized) and glutathione (reduced) react to form glutaredoxin (reduced) and glutathione (oxidized) (Padilla et al. 1995).
Deoxyribonucleotides needed for DNA repair are synthesized de novo by the reduction of ribonucleoside 5'-diphosphates. This reaction is catalyzed by a nuclear form of ribonucleotide reductase active throughout the cell cycle. The reducing equivalents needed for these reactions can be provided directly by thioredoxin.
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The juxtamembrane region of the EGF receptor functions as an activation domain
Subcellular localization and lysophospholipase/transacylation activities of human group IVC phospholipase A2 (cPLA2gamma)
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The events of human purine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of inosine 5'-monophosphate (IMP), the biosynthesis of other purine ribo- and deoxyribonucleotides, purine salvage reactions, and purine catabolism (Watts 1974). De novo synthesis of inosine 5'-monophosphate (IMP). The purine ribonucleotide IMP is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP). Purine biosynthesis [interconversion]. Purine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from IMP and from guanosine and adenosine ribo- and deoxyribonucleotide monophosphates generated in salvage reactions. Purine salvage reactions. Purine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Purine catabolism. The purine bases guanine and hypoxanthine are degraded to uric acid, which is excreted from the body.
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The synthesis of N-carbamoyl L-aspartate from carbamoyl phosphate and L-aspartate is catalyzed by the aspartate carbamoyltansferase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
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The synthesis of carbamoyl phosphate from glutamine, bicarbonate, and ATP is catalyzed by the carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states, as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
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Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate (orotic acid). The enzyme is located in the inner mitochondrial membrane oriented so that cytosolic dihydroorotate molecules have access to it, and orotate is released into the cytosol. The reducing equivalents generated by the reaction are transferred by ubiquinone (Coenzyme Q) to the electron transport chain within the inner mitochondrial membrane. There is no evidence for the involvement of NAD+ as an acceptor of reducing equivalents in this reaction in mammalian cells (Jones 1980). In contrast, the reaction catalyzed by the enzyme isolated from the anaerobic bacterium Clostridium oroticum requires NAD+ as a cofactor but also proceeds strongly in the direction of dihydroorotate synthesis consistent with the greater electronegativity of NAD+ (Lieberman and Kornberg 1953). Early studies of purified rat liver enzyme by Forman and Kennedy suggested the presence of flavin mononucleotide and iron-sulfur complexes as cofactors. More recent work by Bader, Beuneu, and their colleagues with recombinant human protein expressed in insect cells has confirmed the presence of flavin mononucleotide, at a stoichiometry of one molecule per molecule of apoenzyme but suggests that iron-sulfur complexes, if indeed they are involved in the oxidation and electron transport process, are not an integral part of the dihydroorotate dehydrogenase holoenzyme.
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The synthesis of dihydroorotate from N-carbamoyl L-aspartate is catalyzed by the dihydroorotase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein. This activity has not been directly demonstrated in experimental studies of the purified human protein, but has been inferred from the behavior of the purified hamster protein and the high degree of sequence similarity between the cloned hamster and human genes (Iwahana et al. 1996). Also on the basis of this similarity, the active human protein is annotated as a hexamer (Lee et al. 1985).
The pyrimidine orotate (orotic acid) is synthesized in a sequence of four reactions, deriving its atoms from glutamine, bicarbonate, and aspartate. A single multifunctional cytosolic enzyme catalyzes the first three of these reactions, while the last one is catalyzed by an enzyme associated with the inner mitochondrial membrane. In two further reactions, catalyzed by a bifunctional cytosolic enzyme, orotate reacts with 1-phosphoribosyl 5-pyrophosphate (PRPP) to yield orotidine 5'-monophosphate, which is decarboxylated to yield uridine 5'-monophosphate (UMP). While several individual reactions in this pathway are reversible, other irreversible reactions drive the pathway in the direction of UMP biosynthesis in the normal cell. All reactions are thus annotated here only in the forward direction. This pathway has been most extensively analyzed at the genetic and biochemical level in hamster cell lines. All three enzymes have also been purified from human sources, however, and the key features of these reactions have been confirmed from studies of this human material (Jones 1980; Webster et al. 2001). All other pyrimidines are synthesized from UMP. The reactions annotaed here, catalyzed by dCMP deaminase and dUTP diphosphatase yield dUMP, which in turn is converted to TMP by thymidylate synthase.
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Cytosolic thymidylate synthase catalyzes the reaction of dUMP and N5,N10-methylene tetrahydrofolate to form TMP and dihydrofolate (Davisson et al. 1989). The enzyme is a homodimer (Phan et al. 2001).
Biosynthesis of diphosphopyridine nucleotide. II. Enzymatic aspects.
Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of AMP and ATP to form two molecules of ADP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
The events of human pyrimidine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of the pyrimidine ring and its conversion to uridine 5'-monophosphate (UMP), the biosynthesis of other pyrimidine ribo- and deoxyribonucleotides, pyrimidine salvage reactions, and pyrimidine catabolism (Loffler et al. 2005). De novo synthesis of the pyrimidine ring and its conversion to UMP. The pyrimidine base orotate is synthesized from glutamine, bicarbonate, and aspartate. Orotate reacts with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) and is then decarboxylated to form the pyrimidine nucleotide UMP. Pyrimidine biosynthesis [interconversion]. Pyrimidine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from UMP and from pyrimidine ribonucleotide monophosphates generated in salvage reactions. Pyrimidine salvage reactions. Pyrimidine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Pyrimidine catabolism. The pyrimidine bases thymine and uracil are degraded to beta-aminoisobutyrate and beta-alanine, respectively, which are excreted from the body.
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Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of two molecules of ADP to form AMP and ATP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
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The E3 ubiquitin ligase WWP1 selectively targets HER4 and its proteolytically derived signaling isoforms for degradation
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Cleavage preferences of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease) on naked DNA and chromatin substrates
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The NMR solution structure of human glutaredoxin in the fully reduced form
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Clamping down on clamps and clamp loaders--the eukaryotic replication factor C.
Transport to the Golgi and subsequent modification
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Glycerol-3-phosphate dehydrogenase 1-like protein
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Glycerol-3-phosphate dehydrogenase (NAD+), cytoplasmic
MicroRNAs: small RNAs with a big role in gene regulation
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Gene duplication and the evolution of group II chaperonins: implications for structure and function
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acyl-CoA synthetase long-chain family member 1
acyl-CoA synthetase long-chain family member 5
Identification of a specific telomere terminal transferase activity in Tetrahymena extracts
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The role of CDP-diacylglycerol synthetase and phosphatidylinositol synthase activity levels in the regulation of cellular phosphatidylinositol content
Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.
Elongation of very long chain fatty acids protein 6
Elongation of very long chain fatty acids protein 7
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Elongation of very long chain fatty acids protein 1
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Elongation of very long chain fatty acids protein 4
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Elongation of very long chain fatty acids protein 5
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Elongation of very long chain fatty acids protein 2
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Elongation of very long chain fatty acids protein 3
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PC and PE synthesis: mixed micellar analysis of the cholinephosphotransferase and ethanolaminephosphotransferase activities of human choline/ethanolamine phosphotransferase 1 (CEPT1)
Translational control by the 3'-UTR: the ends specify the means
A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1
Direct observation of single kinesin molecules moving along microtubules
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 2
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4
Function in protein folding of TRiC, a cytosolic ring complex containing TCP-1 and structurally related subunits
Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate [ChEBI:37393]
1,2-Diacyl-sn-glycero-3-phospho-sn-glycerol 3'-phosphate
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphates
3(3-Phosphatidyl-)L-glycerol 1-phosphate
3(3-sn-Phosphatidyl)-sn-glycerol 1-phosphate
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate
Peptide hormone expression and precursor processing
Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule
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Essential role for Gab2 in the allergic response
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2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial ecNumber2.1.1.114/ecNumber
ADP,ATP carrier protein, heart/skeletal muscle isoform T1
E2F mediated regulation of DNA replication
Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
Structural basis of the suppressed catalytic activity of wild-type human glutathione transferase T1-1 compared to its W234R mutant
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Idiopathic chronic megaloblastic anemia in children
Early phagosomes in dendritic cells form a cellular compartment sufficient for cross presentation of exogenous antigens
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An associated molecule, p64, with IL-2 receptor beta chain. Its possible involvement in the formation of the functional intermediate-affinity IL-2 receptor complex
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Regulation of gene expression in beta cells
Presenilin-dependent ErbB4 nuclear signaling regulates the timing of astrogenesis in the developing brain
Mutations in the gene for the E1beta subunit: a novel cause of pyruvate dehydrogenase deficiency
How nucleotide excision repair protects against cancer.
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII
Post-proteasomal antigen processing for major histocompatibility complex class I presentation
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CDP-diacylglycerol--inositol 3-phosphatidyltransferase
The exogenous pathway for antigen presentation on major histocompatibility complex class II and CD1 molecules
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CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
Diacylglycerol cholinephosphotransferase 1
Calcium-independent phospholipase A2-gamma
Selectivity in post-translational biotin addition to five human carboxylases
Choline-phosphate cytidylyltransferase A
Choline-phosphate cytidylyltransferase B
Phosphatidylserine decarboxylase proenzyme Chain B
Phosphatidylserine decarboxylase proenzyme Chain A
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Choline/ethanolaminephosphotransferase 1
Ethanolamine-phosphate cytidylyltransferase
Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia
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Calcium-independent phospholipase A2-epsilon
Patatin-like phospholipase domain-containing protein 3
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Patatin-like phospholipase domain-containing protein 2
Acetyl-CoA acetyltransferase, mitochondrial
The human glutathione transferase alpha locus: genomic organization of the gene cluster and functional characterization of the genetic polymorphism in the hGSTA1 promoter
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Thioredoxin reductase, cytoplasmic precursor
Thioredoxin reductase, cytoplasmic precursor (EC 1.8.1.9) (TR)
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Role of aquaporin-7 and aquaporin-9 in glycerol metabolism; involvement in obesity
Genetic depletion of the malin E3 ubiquitin ligase in mice leads to lafora bodies and the accumulation of insoluble laforin
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The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex
The nuclear lamins: flexibility in function
Human 1-D-myo-inositol-3-phosphate synthase is functional in yeast
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VEGF receptor expression and signaling in human bladder tumors
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Discovery of the aquaporins and development of the field
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The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
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Mechanism of B-cell receptor-induced phosphorylation and activation of phospholipase C-gamma2
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Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle
Type beta transforming growth factor in human platelets: release during platelet degranulation and action on vascular smooth muscle cells
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Immunological and inflammatory functions of the interleukin-1 family
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Horror autoinflammaticus: the molecular pathophysiology of autoinflammatory disease (*)
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Completion of mammalian lagging strand DNA replication using purified proteins.
Replication protein A stimulates proliferating cell nuclear antigen-dependent repair of abasic sites in DNA by human cell extracts.
Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver
Am J Physiol Gastrointest Liver Physiol 279:G178-85
ARE-mRNA degradation requires the 5'-3' decay pathway
Aflatoxin B1 aldehyde reductases (AKR7A2, AKR7A3 and AKR7L) are dimeric, cytosolic, NADPH-dependent enzymes able to catalyse the reduction of aflatoxin B1 dialdehyde (AFBDHO) to aflatoxin B1-6,8-dialcohol (AFBDOH) (Ellis et al. 2003, Bodreddigari et al. 2008, Ireland et al. 1998). AKRs can turnover a vast range of substrates, including drugs, carcinogens, and reactive aldehydes. They play central roles in the metabolism of these agents, leading to either their bioactivation or detoxication (Jin & Penning 2007). The dialcohol is excreted in urine by conjugation with glucuronide (not shown here).
Phase II of biotransformation is concerned with conjugation, that is using groups from cofactors to react with functional groups present or introduced from phase I on the compound. The enzymes involved are a set of transferases which perform the transfer of the cofactor group to the substrate. The resultant conjugation results in greatly increasing the excretory potential of compounds. Although most conjugations result in pharmacological inactivation or detoxification, some can result in bioactivation. Most of the phase II enzymes are located in the cytosol except UDP-glucuronosyltransferases (UGT), which are microsomal. Phase II reactions are typically much faster than phase I reactions therefore the rate-limiting step for biotransformation of a compound is usually the phase I reaction. Phase II metabolism can deal with all the products of phase I metabolism, be they reactive (Type I substrate) or unreactive/poorly active (Type II substrate) compounds. With the exception of glutathione, the conjugating species needs to be made chemically reactive after synthesis. The availability of the cofactor in the synthesis may be a rate-limiting factor in some phase II pathways as it may prevent the formation of enough conjugating species to deal with the substrate or it's metabolite. As many substrates and/or their metabolites are chemically reactive, their continued presence may lead to toxicity.
Glutathione S-Transferases (GSTs; EC 2.5.1.18) are another major set of phase II conjugation enzymes. They can be found in the cytosol as well as being microsomal membrane-bound. Cytosolic GSTs are encoded by at least 5 gene families (alpha, mu, pi, theta and zeta GST) whereas membrane-bound enzymes are encoded by single genes. Soluble GSTs are homo- or hetero-dimeric enzymes (approximately 25KDa subunits) which can act on a wide range of endogenous and exogenous electrophiles. GSTs mediate conjugation using glutathione (GSH), a tripeptide synthesized from its precursor amino acids gamma-glutamate, cysteine and glycine. A generalized reaction is RX + GSH -> HX + GSR Glutathione conjugates are excreted in bile and converted to cysteine and mercapturic acid conjugates in the intestine and kidneys. GSH is the major, low molecular weight, non-protein thiol synthesized de novo in mammalian cells. As well as taking part in conjugation reactions, GSH also has antioxidant ability and can metabolize endogenous and exogenous compounds. The nucleophilic GSH attacks the electrophilic substrate forming a thioether bond between the cysteine residue of GSH and the electrophile. The result is generally a less reactive and more water-soluble conjugate that can be easily excreted. In some cases, GSTs can activate compounds to reactive species such as certain haloalkanes and haloalkenes. Substrates for GSTs include epoxides, alkenes and compounds with electrophilic carbon, sulfur or nitrogen centres. There are two types of conjugation reaction with glutathione: displacement reactions where glutathione displaces an electron-withdrawing group and addition reactions where glutathione is added to activated double bond structures or strained ring systems.
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Localization of phosphatidylinositol phosphate kinase IIgamma in kidney to a membrane trafficking compartment within specialized cells of the nephron
The combination of glutamate, cysteine and ATP is required to form glutathione. The steps involved in the synthesis and recycling of glutathione are outlined (Meister, 1988).
The glutathione S-transferases (GSTs) catalyze the nucleophilic attack by reduced glutathione (GSH) on nonpolar compounds that contain an electrophilic carbon, nitrogen, or sulphur atom. Their substrates include halogenonitrobenzenes, arene oxides, quinones, and alpha, beta-unsaturated carbonyls. Three major families of proteins are widely distributed in nature. Two of these, the cytosolic and mitochondrial GST, comprise soluble enzymes that are only distantly related whilst the third family comprises microsomal GST, referred to as membrane-associated proteins in eicosanoid and glutathione (MAPEG) metabolism. At least 16 cytosolic GST subunits exist in human which are all in a dimeric form. Based on amino acid sequence similarities, seven classes of cytosolic GST are recognized in mammalian species; Alpha, Mu, Pi, Sigma, Theta, Omega, and Zeta (25). As well as being homodimers, the Alpha and Mu classes are also able to form heterodimers so a large number of isozymes are possible from all cytosolic GST subunits (Sinning et al. 1993, LeTrong et al. 2002, Ahmad et al. 1993, Pastore et al. 1998, Tars et al. 2010, Bruns et al. 1999, Balogh et al. 2010, Morel et al. 2002, Li et al. 2005, Patskovsky et al. 2006, Raghunathan et al. 1994, Patskovsky et al. 1999, Comstock et al. 1994, Board et al. 2000, Zhou et al. 2011, Zhou et al. 2012, Sun et al. 2011, Tars et al. 2006, Rossjohn et al. 1998, Polekhina et al. 2001, Inoue et al. 2003). Typical electrophilic substrates are chosen as examples for which the majority of the cytosolic GST isozymes act on.
Methylation is a common but minor pathway of Phase II conjugation compared to glucuronidation or sulfonation. The cofactor used in methylation conjugation is S-adenosylmethionine (SAM). SAM is the second most widely used enzyme substrate after ATP and is involved in a wide range of important biological processes. SAM is sythesized from methionine's reaction with ATP, catalyzed by methionine adenosyltransferase (MAT). There are two genes, MAT1A and MAT2A, which encode for two homologous MAT catalytic subunits, 1 and 2. During conjugation with nucleophilic substrates, the methyl group attached to the sulfonium ion of SAM is transferred to the substrate forming the conjugate. SAM, having lost the methyl moiety, is converted to S-adenosylhomocysteine (SAH). SAH can be hydrolyzed to form adenosine and homocysteine. Homocysteine can either be converted to glutathione or methylated to form methionine, thus forming the starting point for SAM synthesis and completing the cycle. Fuctional groups attacked are phenols, catechols, aliphatic and aromatic amines and sulfhydryl-containing groups. The enzymes that catalyze the transfer of the methyl group to these functional groups are the methyltransferases (MT). MTs are small, cytosolic, monomeric enzymes that utilize SAM as a methyl donor. There are many MTs but the best studied ones are named on the basis of their prototypical substrates: COMT (catechol O-methyltransferase), TPMT (thiopurine methyltransferase), TMT (thiol methyltransferase), HNMT (histamine N-methyltransferase) and NNMT (nicotinamide N-methyltransferase). An example of each enzyme mentioned is given. In each case, a typical substrate for the enzyme is shown.
In the second step in the formation of glutathione, gamma-glutamylcysteine ligates with glycine to form glutathione (Gali and Board, 1995; ).
Phase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conjugating species with which to react with. Many xenobiotics are lipophilic and almost chemically inert (e.g. PAHs) so would not necessarily undergo a phase 2 reaction. Making them more chemically reactive would facilitate their excretion but also increases their chance of reacting with cellular macromolecules (e.g. proteins, DNA). There is a fine balance between producing a more reactive metabolite and conjugation reactions. There are two groups of enzymes in phase 1 - oxidoreductases and hydrolases. Oxidoreductases introduce an oxygen atom into or remove electrons from their substrates. The major oxidoreductase enzyme system is called the P450 monooxygenases. Other systems include flavin-containing monooxygenases (FMO), cyclooxygenases (COX) and monoamine oxidases (MAO). Hydrolases hydrolyse esters, amides, epoxides and glucuronides.
Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgi apparatus and mediates the sulfonation of proteoglycans. The second, annotated here, is cytosolic and mediates the sulfonation of a diverse array of small molecules, increasing their solubilities in water and modifying their physiological functions. There are probably thirteen or more human cytosolic SULT enzymes; eleven of these have been purified and characterized enzymatically, and are annotated here (Blanchard et al. 2004; Gamage et al. 2005). These enzymes appear to be active as dimers. Their substrate specificities are typically broad, and not related in an obvious way to their structures; indeed, apparently orthologous human and rodent SULT enzymes can have different substrate specificities (Glatt 2000), and none has been exhaustively characterized. The substrates listed in the table and annotated here are a sample of the known ones, chosen to indicate the range of activity of these enzymes and to capture some of their known physiologically important targets. Absence of a small molecule - enzyme pair from the table, however, may only mean that it has not yet been studied.
Ethanol and related alcohols can be ingested as part of the diet and are formed by microorganisms in the intestinal tract. Ethanol oxidation to acetate occurs primarily in liver cells in a multistep process first described by Racker (1949). First, in the cytosol, ethanol is oxidized to acetaldehyde, with the formation of NADH. Second, in the mitochondrion, acetaldehyde is oxidized to acetate with the formation of NADH. Finally, acetate in the mitochondrion can be condensed with coenzyme A to form acetyl CoA. Polymorphisms in the enzymes catalyzing the first two steps are associated with variation in the efficiency of alcohol catabolism in human populations (Chen et al. 1999; Lange et al. 1976; Jornvall 1985). The molecular mechanism by which cytosolic acetaldehyde enters the mitochondrial matrix is not known (Lemasters 2007). Cytosolic enzymes capable of oxidizing acetaldehyde to acetate have also been identified and characterized in vitro (Inoue et al. 1979) so a purely cytosolic pathway for ethanol oxidation to acetate and conversion to acetyl-CoA can be annotated. The role of this pathway in vivo is unclear, though limited attempts to correlate deficiencies in the cytosolic enzyme with alcohol intolerance have yielded suggestive data (Yoshida et al. 1989). Additional peroxisomal and microsomal pathways for the oxidation of ethanol to acetaldehyde have been described; their physiological significance is unclear and they are not annotated here.
Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. The processes of energy metabolism can be classified into two groups according to whether they involve carbohydrate-derived or lipid-derived molecules, and within each group it is useful to distinguish processes that mediate the breakdown and oxidation of these molecules to yield energy from ones that mediate their synthesis and storage as internal energy reserves. Synthetic reactions are conveniently grouped by the chemical nature of the end products, such as nucleotides, amino acids and related molecules, and porphyrins. Detoxification reactions (biological oxidations) are likewise conveniently classified by the chemical nature of the toxin. At the same time, all of these processes are tightly integrated. Intermediates in reactions of energy generation are starting materials for biosyntheses of amino acids and other compounds, broad-specificity oxidoreductase enzymes can be involved in both detoxification reactions and biosyntheses, and hormone-mediated signaling processes function to coordinate the operation of energy-generating and energy-storing reactions and to couple these to other biosynthetic processes.
Abacavir is a nucleoside analogue reverse transcriptase inhibitor with antiretroviral activity, widely used in combination with other drugs to treat HIV-1 infection (Yuen et al. 2008). Its uptake across the plasma membrane is mediated by organic cation transporters SLC22A1, 2, and 3; the transport proteins ABCB1 and ABCG2 mediate its efflux. Abacavir itself is a prodrug. Activation requires phosphorylation by a cytosolic adenosine phosphotransferase and deamination by ADAL deaminase to yield carbovir monophosphate. Cytosolic nucleotide kinases convert carbovir monophosphate to carbovir triphosphate, the active HIV reverse transcriptase inhibitor. Abacavir can be glucuronidated or oxidized to a 5'-carboxylate; these are the major forms in which it is excreted from the body.
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Water permeability and characterization of aquaporin-11
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NADPH, ferredoxin reductase (FDXR, Adrenodoxin reductase), and ferredoxins (FDX1, FDX1L) comprise a short electron transport chain that provides electrons for biosynthesis of iron-sulfur clusters and steroid hormones (Sheftel et al. 2010, Shi et al. 2012, reviewed in Grinberg et al. 2000, Lambeth et al. 1982).
Iron-sulfur (Fe-S) proteins are localized in the cytosol, nucleus, and mitochondria of mammalian cells (reviewed in Stemmler et al. 2010, Rouault 2012, Bandyopadhyay et al. 2008, Lill 2009, Lill et al. 2012). Fe-S protein biogenesis in the mitochondrial matrix involves the iron-sulfur cluster (ISC) assembly machinery. Ferrous iron is transported across the inner mitochondrial membrane into the mitochondrial matrix by Mitoferrin-1 (SLC25A37) and Mitoferrin-2 (SLC25A28). (Mitoferrin-1 is enriched in erythroid cells while Mitoferrin-2 is ubiquitous.) Frataxin binds ferrous iron in the mitochondrial matrix. The cysteine desulfurase NFS1 in a subcomplex with ISD11 provides the sulfur by converting cyteine into alanine and forming a persulfide which is used for cluster formation on ISCU, the scaffold protein. Interaction between NFS1 and ISD11 is necessary for desulfurase activity. Frataxin binds to a complex containing NFS1, ISD11, and ISCU and is proposed to function as an iron donor to ISCU or as an allosteric switch that activates sulfur transfer and Fe-S cluster assembly (Tsai and Barondeau 2010). Cluster formation also involves the electron transfer chain ferredoxin reductase and ferredoxin. ISCU initially forms clusters containing 2 iron atoms and 2 sulfur atoms ([2Fe-2S] clusters). They are released by the function of HSP70-HSC20 chaperones and the monothiol glutaredoxin GLRX5 and used for assembly of [2Fe-2S] proteins. Assembly of larger clusters such as [4Fe-4S] clusters may involve the function of ISCA1, ISCA2, and IBA57. The clusters are transferred to apo-enzymes such as the respiratory complexes, aconitase, and lipoate synthase through dedicated targeting factors such as IND1, NFU1, and BOLA3.
Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of abacavir monophosphate and water to form carbovir monophosphate and cyclopropylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
Abacavir activation proceeds steps of phosphorylation, deamination to yield carbovir monophosphate, and phosphorylation of the latter compound to yield the triphosphate. In addition, abacavir can be conjugated with glucuronide or oxidized to its 5'-carboxylate derivative, the two major forms in which it is excreted from the body (Yuen et al. 2008).
Aflatoxins are among the principal mycotoxins produced as secondary metabolites by the molds Aspergillus flavus and Aspergillus parasiticus that contaminate economically important food and feed crops (Wild & Turner 2002). Aflatoxin B1 (AFB1) is the most potent naturally occurring carcinogen known and is also an immunosuppressant. It is a potent hepatocarcinogenic agent in many species, and has been implicated in the etiology of human hepatocellular carcinoma. Poultry, especially turkeys, are extremely sensitive to the toxic and carcinogenic action of AFB1 present in animal feed, resulting in multi-million dollar losses to the industry. Discerning the biochemical and molecular mechanisms of this extreme sensitivity of poultry to AFB1 will help with the development of new strategies to increase aflatoxin resistance (Rawal et al. 2010, Diaz & Murcia 2011). AFB1 has one major genotoxic metabolic fate, conversion to AFXBO, and several others that are less mutagenic but that can still be quite toxic, causing [X, Y, and Z]. AFB1 can be oxidised to the toxic AFB1 exo 8,9 epoxide (AFXBO) product by several cytochrome P450 enzymes, especially P450 3A4 in the liver. This 8,9 epoxide can react with the N7 atom of a guanyl base of DNA to produce adducts by intercalating between DNA base pairs. The exo epoxide is unstable in solution, however, and can react spontaneously to form a diol that is no longer reactive with DNA. The diol product in turn undergoes base-catalysed rearrangement to a dialdehyde that can react with protein lysine residues. AFB1 can also be metabolised to products (AFQ1, AFM1, AFM1E) which have far less genotoxic consequences than AFB1. The main route of detoxification of AFB1 is conjugation of its reactive 8,9-epoxide form with glutathione (GSH). This reaction is carried out by trimeric glutathione transferases (GSTs), providing a chemoprotective mechanism against toxicity. Glutathione conjugates are usually excreted as mercapturic acids in urine (Guengerich et al. 1998, Hamid et al. 2013). The main metabolic routes of aflatoxin in humans are described here.
All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common. The very nature of many chemicals that make them suitable for uptake by these routes, in other words their lipophilicty (favours fat solubility) is also the main reason organisms have developed mechanisms that convert them to hydrophilic (favours water solubility) compounds which are readily excreted via bile and urine. Otherwise, lipophilic chemicals would accumulate in the body and overwhelm defense mechanisms. This process is called biotransformation and is catalyzed by enzymes mainly in the liver of higher organisms but a number of other organs have considerable ability to process xenobiotica such as kidneys, gut and lungs. As well as xenobiotics, many endogenous compounds are commonly eliminated by this process. This mechanism is of ancient origin and a major factor for its development in animals is plants. Most animals are plant eaters and thus are subject to a huge variety of chemical compounds which plants produce to stop themselves being eaten. This complex set of enzymes have several features which make them ideal for biotransformation; (1) metabolites of the parent chemical are usually made more water soluble so it favours rapid excretion via bile and urine (2) the enzymes possess broad and overlapping specificity to be able to deal with newly exposed chemicals (3) metabolites of the parent generally don't have adverse biological effects. In the real world however, all these criteria have exceptions. Many chemicals are transformed into reactive metabolites. In pharmacology, the metabolites of some parent drugs exert the desired pharmacological effect but in the case of polycyclic aromatic hydrocarbons (PAHs), which can undergo epoxidation, it results in the formation of an electrophile which can attack proteins and DNA. Metabolism of xenobiotica occurs in several steps called Phase 1 (functionalization) and Phase 2 (conjugation). To improve water solubility, a functional group is added to or exposed on the chemical in one or more steps (Phase 1) to which hydrophilic conjugating species can be added (Phase 2). Functional groups can either be electrophilic (epoxides, carbonyl groups) or nucleophilic (hydroxyls, amino and sulfhydryl groups, carboxylic groups) (see picture). Once chemicals undergo functionalization, the electrophilic or nucleophilic species can be detrimental to biological systems. Electrophiles can react with electron-rich macromolecules such as proteins, DNA and RNA by covalent interaction whilst nucleophiles have the potential to interact with biological receptors. That's why conjugation is so important as it mops up these potentially reactive species. Many chemicals, when exposed to certain metabolizing enzymes can induce those enzymes, a process called enzyme induction. The effect of this is that these chemicals accelerate their own biotransformation and excretion. The reverse is also true where some chemicals cause enzyme inhibition. Some other factors that alter enzyme levels are sex, age and genetic predisposition. Between species, there can be considerable differences in biotransformation ability which is a problem faced by drug researchers interpreting toxicological results to humans.
Two electrons and one proton are transferred from NADPH to the FAD moiety of ferredoxin reductase. A proton from the medium is also taken up by ferredoxin reductase.
Two electrons are transferred from reduced ferredoxin reductase (FDXR, adrenodoxin reductase) to two ferredoxin-1 or ferredoxin-1L (FDX1, FDX1L) molecules, each of which binds one electron. Two protons are released during the reaction.
Gamma-linolenoyl-CoA (6,9,12-20:3(n-6)) is rapidly elongated to dihomo-gamma-linolenoyl-CoA (DGL-CoA; 8,11,14-20:3(n-6)) by the action of C18-PUFA-specific elongase 5 (ELOVL5). Two carbon atoms are added during this reaction. DGL-CoA later undergoes desaturation to form arachidonic acid (AA, 5,8,11,14-20:4(n-6)). Depending on the cell type, DGL-CoA can also be metabolized by cyclooxygenases and lipoxygenases to produce anti-inflammatory eicosanoids (prostaglandins of series 1 (PGE1) and 15-hydroxyeico- satrienoic acid (15-HETrE)). GLA and these two oxidative metabolites exert clinical effects in a variety of diseases, including suppression of chronic inflammation, vasodilation and lowering of blood pressure, inhibition of platelet aggregation and thrombosis. (Fan et al. 2001, Fan & Chapkin 1998, Kapoor & Huang. 2006)
The dietary essential fatty acid (EFA) linoleic acid (LA) is activated to a high energy form known as linoleoyl-CoA by the action of long-chain acyl-CoA synthetases (ACSLs). Thioesterification of long-chain fatty acids into their acyl-CoA derivatives is considered to be the first committed step in fatty acid metabolism. Formation of acyl-CoA allows an otherwise non-reactive fatty acid to participate in biosynthetic or catabolic pathways. This acyl CoA form is converted to its longer-chain polyunsaturated products by a series of desaturation and elongation reactions (Ellis et al. 2010, Watkins 2008).
CD28 costimulation: a source of Vav-1 for TCR signaling with the help of SLP-76?
Alpha-linolenic acid (ALA, 18:3(n-3)) is an omega-3 fatty acid, supplied through diet as it cannot be synthesized by humans. ALA has an important role in human health. It is converted to long chain more unsaturated n-3 fatty acids by a series of alternating desaturation and elongation reactions. Omega-3 products of ALA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) reduce inflammation and may help lower risk of chronic diseases, such as heart disease and arthritis. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The alpha-linolenic acid pathway involves the following steps: 18:3(n-3)--> 18:4(n-3)-->20:4(n-3)-->20:5(n-3)-->22:5(n-3)-->24:5(n-3)-->24:6(n-3)-->22:6(n-3). Two desaturation enzymes are involved in this process: delta-6 desaturase that converts 18:3(n-3) to 18:4(n-3) and 24:5(n-3) to 24:6(n-3) respectively, delta-5 desaturase 20:4(n-3) to 20:5(n-3). (Sprecher 2002).
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Linoleic acid (LA, 18:2(n-6)) is an omega-6 fatty acid obtained through diet, mainly from vegetable oils. Omega-6 fatty acids helps stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The linoleic acid pathway involves the following steps: 18:2(n-6)-->18:3(n-6)--> 20:3(n-6)-->20:4(n-6)-->22:4(n-6)-->24:4(n-6)-->24:5(n-6)-->22:5(n-6). Two desaturation enzymes are involved in this process: delta-6 desaturase which converts 18:2(n-6) to 18:3 (n-6) and 24:4(n-6) to 24:5(n-6) respectively, and delta-5 desaturase which converts 20:3(n-6) to 20:4(n-6). (Sprecher 2002).
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There are two major classes of polyunsaturated fatty acids (PUFAs): the omega-3 (n-3) and the omega-6 (n-6) fatty acids, where the number corresponds to the position of the first double bond proximate to the methyl end of the fatty acid. Omega-3 and omega-6 fatty acids are considered essential fatty acids. Humans cannot synthesize them, instead they are supplied through diet. Linoleic acid (LA, 18:2(n-6)), a major component of omega-6 fatty acids and alpha-linolenic acid (ALA, 18:2(n-3)) a major component of omega-3 fatty acids are the two main dietary essential fatty acids (EFAs) in humans. ALA and LA obtained from diet are converted in the body into their longer chain and more unsaturated omega-3 and omega-6 products by a series of desaturation and elongation steps. Metabolism of ALA and LA to their corresponding products is mediated via common enzyme systems. In humans ALA is finally converted to docosahexaenoic acid (DHA, C22:6(n-3)), and LA is converted to docosapentaenoic acid (DPA, C22:5(n-6)). The intermediary omega-3 and omega-6 series fatty acids play a significant role in health and disease by generating potent modulatory molecules for inflammatory responses, including eicosanoids (prostaglandins, and leukotrienes), and cytokines (interleukins) and affecting the gene expression of various bioactive molecules (Kapoor & Huang 2006, Sprecher 2002, Burdge 2006).
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Arachidonyl-CoA undergoes a two-carbon chain elongation on the carboxyl end to form docosatetraenoyl-CoA (DTA-CoA/Adrenic acid/7,10,13,16-docosatetraenoic acid (7,10,13,16-22:4(n-6)). This reaction is catalyzed by the enzymes ELOVL5 or ELOVL2. Malanoyl-CoA provides the additional two carbons required for elongation. Docosatetraenoyl-CoA is further metabolized by cyclooxygenases (COX), lipoxygenases (LO) and cytochrome P450s (CYP450s) to dihomo (DH) eicosanoids (Kopf et al. 2010, Leonard et al. 2004).
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Docosatetraenoyl-CoA is elongated to tetracosatetraenoyl-CoA (TTA-CoA, 9,12,15,18-tetracosatetraenoic acid, 9,12,15,18-24:4(n-6)) by the elongase enzyme ELOVL2.
The bioactive prostaglandin (PG) signalling molecules, including PGA2, PGE2, PGF2a, and PGI2 (prostacyclin) are synthesised from arachidonic acid and its products by various prostaglandin synthase type enzymes. Prostaglandin H2 (PGH2) is the starting point for the synthesis of Thromboxanes (TXs) (Buczynski et al. 2009, Vance & Vance 2008). PGs and TXs are collectively known as the prostanoids. Two enzymes, PTGS1 and 2 (COX1 and 2) both catalyze the two-step conversion of arachidonic acid to PGH2. PTGS1 is constitutively expressed in many cell types while PTGS2 is induced in response to stress and mediates the syntheses of prostaglandins associated with pain, fever, and inflammation. Aspirin irreversibly inactivates both enzymes (though it acts more efficiently on PTGS1), explaining both its antiinflammatory effects and side effects like perturbed gastic acid secretion. Drugs like celecoxib, by specifically inhibiting PTGS2, have a strong anti-inflammatory effect with fewer side effects. These PTGS2-specific drugs, however, probably because of their effects on the balance of prostaglandin synthesis in platelets and endothelial cells, can also promote blood clot formation (Buczynski et al. 2009; Stables & Gilroy 2011).
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Prostaglandin E2 (PGE2) is the most abundant prostanoid in the body and is a major mediator of inflammation in diseases such as osteoarthritis and rheumatoid arthritis. The product of arachidonic acid, prostaglandin H2 (PGH2) serves as the substrate for the isomerization to PGE2. The conversion is carried out by prostaglandin E synthase (PGES), of which there are three forms. Two are membrane-bound enzymes and are designated as mPGES-1 (functionally linked with COX-2) and mPGES-2 (golgi membrane-associated, functionally coupled with both COX-1 and COX-2). The other is cytosolic (cPGES, PTGES3) and functionally linked to COX-1 to produce PGE2 immediately. In this reaction, cPGES is used for conversion of PGH2 to PGE2.
Prostaglandin D2 (PGD2) is a structural isomer of prostaglandin E2 (PGE2). There is a 9-keto and 11-hydroxy group on PGE2 with these substituents reversed on PGD2. PGD2 is formed by two evolutionarily distinct, but functionally convergent, prostaglandin D synthases: lipocalin-type prostaglandin-D synthase aka Prostaglandin-H2 D-isomerase (PTDGS) and hematopoietic prostaglandin D synthase (HPGDS). One of the main differences between these two proteins is that HPGDS requires glutathione (GSH) for catalysis while PTDGS can function without this cofactor. Here, HPGDS with GSH promotes the isomerisation of prostaglandin H2 (PGH2) to prostaglandin D2 (PGD2) (Jowsey et al. 2001, Inoue et al. 2003).
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Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants.
At the plasma membrane, phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (PIP4K2A) and beta (PIP4K2B) homodimers and heterodimers (Clarke et al. 2010) phosphorylate phosphatidylinositol 5-phosphate (PI5P) to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). The following lists the above proteins with their corresponding literature references: PIP4K2A (Rameh et al. 1997, Clarke et al. 2008) and PIP4K2B (Rameh et al. 1997).
At the plasma membrane, synaptojanin-1 aka Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1) (Guo et al. 1999), -2 (SYNJ2) and some myotubularins (MTMs) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 5-phosphate (PI5P). The MTMs involved are: myotubularin (MTM1) (Cao et al. 2007, Tronchere et al. 2004, Schaletzky et al. 2003, Laporte et al. 2002) and myotubularin-related proteins 1 (MTMR1) (Tronchere et al. 2004), 3 (MTMR3) (Walker et al. 2001, Lorenzo et al. 2005), 6 (MTMR6) (Schaletzky et al. 2003, Choudhury et al. 2006), and 14 (MTMR14) (Tosch et al. 2006).
At the plasma membrane, synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 aka Synaptojanin-1 (SYNJ1) (Guo et al. 1999, Mani et al. 2007, Johenning et al. 2004) and -2 (SYNJ2) (Malecz et al. 2000) dephosphorylate phosphatidylinositol 4-phosphate (PI4P) phosphatidylinositol (PI). The SAC1 domains of SYNJ1 and SYNJ2 demonstrate 4-phosphatase activity.
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ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases.
At the plasma membrane, subsequent phosphorylation of phosphatidylinositol 4-phosphate (PI4P) produces phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) while the actions of various other kinases and phosphatases produces phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Zhang et al. 1997, Gurung et al. 2003, Guo et al. 1999, Vanhaesebroeck et al. 1997, Tolias et al. 1998, Schaletzky et al. 2003, Kim et al. 2002, Clarke et al. 2010).
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Phosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 4-phosphate (PI4P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate PI(3,4)P2, phosphatidylinositol 4,5-bisphosphate PI(4,5)P2, phosphatidylinositol 3,5-bisphosphate PI(3,5)P2, and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). These seven phosphoinositides, which are heterogeneously distributed within cells, can serve as signature components of different intracellular compartment membranes and so help to mediate specificity of membrane interactions. Phosphoinositide levels are tightly regulated spatially and temporally by the action of various kinases and phosphatases whilst PI(4,5)P2 is also a substrate for phospholipase C. The differential localisation of each of these enzymes on specific compartment membranes ensures maintenance of the heterogeneous distribution of phosphoinositides despite the continuous membrane flow from one compartment to another. PI is primarily synthesised in the endoplasmic reticulum from where the phospholipid is exported to other compartments via membrane traffic or via cytosolic phospholipid transfer proteins. Phosphorylation of PI to PI4P primarily occurs in the Golgi, where PI4P plays an important role in the biogenesis of transport vesicles such as the secretory vesicle involved in its transport to the plasma membrane. At this place, PI4P has a major function acting as a precursor of PI(4,5)P2, which is located predominantly at this membrane. PI(4,5)P2 binds and regulates a wide range of proteins that function on the cell surface and serves as a precursor for second messengers. Additionally, it helps define this membrane as a target for secretory vesicles, functions as a coreceptor in endocytic processes, and functions as a cofactor for actin nucleation. At the plasma membrane, PI(4,5)P2 is further phosphorylated to PI(3,4,5)P3, another phosphoinositide with important signalling functions including stimulating cell survival and proliferation. The inositol 3-phosphatase, phosphatase and tensin homolog (PTEN) regenerates PI (4,5)P2, while the 5-phosphatases convert PI(3,4,5)P3 into the phosphoinositide, PI(3,4)P2, propagating the signal initiated by PI(3,4,5)P3. PI(3,4)P2 is further dephosphorylated in the endocytic pathway by inositol 4-phosphatases to PI3P, the signature phosphoinositide of the early endosomal compartment and a ligand for numerous endosomal proteins. However, the bulk of PI3P is generated directly in the endosomes by phosphorylation of PI. The subsequent endosomal phosphorylation of PI3P to PI(3,5)P2 is believed to generate docking sites for recruitment of cytosolic factors responsible for the control of outgoing traffic from the endosomes. The main localisation and function of the low abundance phosphoinositide PI5P, that can be generated by several pathways, remains to be determined (Krauss & Haucke 2007, Leventis & Grinstein 2010, Roth 2004, Gees et al. 2010, De Matteis & Godi 2004, van Meer et al. 2008, Vicinanza et al. 2008, Lemmon 2008, Kutaleladze 2010, Robinson & Dixon 2006, Blero et al. 2007, Liu & Bankaitis 2010, McCrea & De Camilli 2009, Vicinanza et al. 2008, Di Paolo & De Camilli, 2006).
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Phospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such as choline. These molecules are a major constituent of cellular membranes, where their diverse structures and asymmetric distributions play major roles in determining membrane properties (Dowhan 1997). The four major classes of phospholipids in human plasma membranes are phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, and sphingomyelin. The first three are derivatives of glycerol while sphingomyelin is a derivative of serine. Here, pathways for the metabolism of glycerophospholipids, phosphphatidylinositol (PI), and sphingolipids are annotated.
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In the first step the precursor apha-linolenic (9,12,15-18:3(n-3)) acid is activated to a high energy form known as alpha-linolenoyl-CoA (9Z,12Z,15Z-octadecatrienoyl-CoA) by the iron enzyme long-chain-fatty-acid-CoA-ligase (acyl-CoA synthetase 1, ACSL1) and coenzyme A.
SDA-CoA (6,9,12,15-18:4(n-3)) is rapidly elongated by two carbon atoms to 8,11,14,17-eicosatetraenoyl-CoA (8,11,14,17-20:4(n-3), ETA-CoA). The NADPH-consuming enzyme long-chain fatty acyl elongase (ELOVL5) mediates this reaction which and adds malonyl-CoA to the SDA-CoA and releases carbon dioxide and free CoA (Leonard et al. 2004).
Eicosapentaenoyl-CoA (EPA-CoA) is transformed to docosapentaenoyl-CoA (DPA-CoA/clupanodonic acid; 7,10,13,16,19-22:5(n-3)) by addition of two carbon atoms from malanoyl-CoA. This reaction is catalyzed by the enzymes ELOVL5/2 (Leonard et al. 2004). DPA is quite high in seal oil and may act as an anti-atherogenic factor. DPA has 10-fold greater endothelial cell migration ability than EPA, which is important in wound-healing processes. DPA may act as a precursor for production of the DPA-related D-series of resolvins or neuroprotectins (Kaur et al. 2011).
Docosapentaenoyl-CoA is elongated to tetracosapentaenoyl-CoA (9,12,15,18,21-24:5(n-3)) by the enzyme ELOVL2.
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Adrenic acid metabolites as endogenous endothelium-derived and zona glomerulosa-derived hyperpolarizing factors
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (COQ5) catalyses the C-methyltransferase conversion of 2-methoxy-6-decaprenyl-1,4-benzoquinol (MDMQ10H2) to 6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol (DMQ10H2). This reaction is inferred from the equivalent reaction in yeast (Barkovich et al. 1997).
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3,4-dihydroxy-5-decaprenylbenzoic acid (DHDB) to 3-methoxy-4-hydroxy-5-decaprenylbenzoic acid (MHDB) (Jonassen & Clarke 2000).
4-hydroxybenzoate polyprenyltransferase, mitochondrial (COQ2) catalyses the combination of 4-hydroxybenzoic acid, aka para-hydroxybenzoic acid (PHB) with the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) to form 3-decaprenyl-4-hydroxybenzoic acid (DHB) (Forsgren et a l. 2004, Tekle et al. 2008). This reaction is irreversible and occurs in the mitochondria.
Sphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid base in mammals. Amide linkage of a fatty acid to sphingosine yields ceramides. Esterification of phosphocholine to ceramides yields sphingomyelin, and ceramide glycosylation yields glycosylceramides. Introduction of sialic acid residues yields gangliosides. These molecules appear to be essential components of cell membranes, and intermediates in the pathways of sphingolipid synthesis and breakdown modulate processes including apoptosis and T cell trafficking. While sphingolipids are abundant in a wide variety of foodstuffs, these dietary molecules are mostly degraded by the intestinal flora and intestinal enzymes. The body primarily depends on de novo synthesis for its sphingolipid supply (Hannun and Obeid 2008; Merrill 2002). De novo synthesis proceeds in four steps: the condensation of palmitoyl-CoA and serine to form 3-ketosphinganine, the reduction of 3-ketosphinganine to sphinganine, the acylation of sphinganine with a long-chain fatty acyl CoA to form dihydroceramide, and the desaturation of dihydroceramide to form ceramide. Other sphingolipids involved in signaling are derived from ceramide and its biosynthetic intermediates. These include sphinganine (dihydrosphingosine) 1-phosphate, phytoceramide, sphingosine, and sphingosine 1-phosphate. Sphingomyelin is synthesized in a single step in the membrane of the Golgi apparatus from ceramides generated in the endoplasmic reticulum (ER) membrane and transferred to the Golgi by CERT (ceramide transfer protein), an isoform of COL4A3BP that is associated with the ER membrane as a complex with PPM1L (protein phosphatase 1-like) and VAPA or VAPB (VAMP-associated proteins A or B). Sphingomyelin synthesis appears to be regulated primarily at the level of this transport process through the reversible phosphorylation of CERT (Saito et al. 2008).
The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
Pancreatic beta cells integrate signals from several metabolites and hormones to control the secretion of insulin. In general, glucose triggers insulin secretion while other factors can amplify or inhibit the amount of insulin secreted in response to glucose. Factors which increase insulin secretion include the incretin hormones Glucose-dependent insulinotropic polypeptide (GIP and glucagon-like peptide-1 (GLP-1), acetylcholine, and fatty acids. Factors which inhibit insulin secretion include adrenaline and noradrenaline. Increased blood glucose levels from dietary carbohydrate play a dominant role in insulin release from the beta cells of the pancreas. Glucose catabolism in the beta cell is the transducer that links increased glucose levels to insulin release. Glucose uptake and glycolysis generate cytosolic pyruvate; pyruvate is transported to mitochondria and converted both to oxaloacetate which increases levels of TCA cycle intermediates, and to acetyl-CoA which is oxidized to CO2 via the TCA cycle. The rates of ATP synthesis and transport to the cytosol increase, plasma membrane ATP-sensitive inward rectifying potassium channels (KATP channels) close, the membrane depolarizes, and voltage-gated calcium channels in the membrane open (Muoio and Newgard 2008; Wiederkehr and Wollheim 2006). Elevated calcium concentrations near the plasma membrane cause insulin secretion in two phases: an initial high rate within minutes of glucose stimulation and a slow, sustained release lasting longer than 30 minutes. In the initial phase, 50-100 insulin granules already docked at the membrane are exocytosed. Exocytosis is rendered calcium-dependent by Synaptotagmin V/IX, a calcium-binding membrane protein located in the membrane of the docked granule, although the exact action of Synapototagmin in response to calcium is unknown. Calcium also causes a translocation of reserve granules within the cell towards the plasma membrane for release in the second, sustained phase of secretion. Human cells contain L-type (continually reopening), P/Q-type (long burst), R-type (long burst), and T-type (short burst) calcium channels and these partly account for differences between the two phases of secretion. Other factors that distinguish the two phases are not yet fully known (Bratanova-Tochkova et al. 2002; Henquin 2000; MacDonald et al. 2005).
Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase
Lipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphingolipids, eicosanoids, cholesterol, bile salts, steroid hormones, and fat-soluble vitamins. They function as a major source of energy (fatty acids, triacylglycerols, and ketone bodies), are major constituents of cell membranes (cholesterol and phospholipids), play a major role in their own digestion and uptake (bile salts), and participate in numerous signaling and regulatory processes (steroid hormones, eicosanoids, phosphatidylinositols, and sphingolipids). Because of their poor solubility in water, most lipids in extracellular spaces in the human body are found as complexes with specific carrier proteins. Regulation of the formation and movement of these lipoprotein complexes is a critical aspect of human lipid metabolism, and lipoprotein abnormalities are associated with major human disease processes including atherosclerosis and diabetes. The central steroid in human biology is cholesterol, obtained from animal fats consumed in the diet or synthesized de novo from acetyl-coenzyme A. (Vegetable fats contain various sterols but no cholesterol.) Cholesterol is an essential constituent of lipid bilayer membranes and is the starting point for the biosyntheses of bile acids and salts, steroid hormones, and vitamin D. Bile acids and salts are mostly synthesized in the liver. They are released into the intestine and function as detergents to solubilize dietary fats. Steroid hormones are mostly synthesized in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). At the same time, chronically elevated cholesterol levels in the body are associated with the formation of atherosclerotic lesions and hence increased risk of heart attacks and strokes. The human body lacks a mechanism for degrading excess cholesterol, although an appreciable amount is lost daily in the form of bile salts and acids that escape recycling. Aspects of lipid metabolism currently annotated in Reactome include lipid digestion, mobilization, and transport; fatty acid, triacylglycerol, and ketone body metabolism; peroxisomal lipid metabolism; phospholipid and sphingolipid metabolism; cholesterol biosynthesis; bile acid and bile salt metabolism; and steroid hormone biosynthesis.
A family of antiport, ATP-ADP translocases, preferentially export ATP from the matrix while importing ADP from the cytosol, thereby maintaining a high ADP:ATP ratio in the matrix. When there are increased energy demands on the body, such as under heavy exercise, cytosolic ADP rises and is exchanged with mitochondrial matrix ATP via the transmembrane ADP:ATP translocase. Increased ADP causes the proton-motive force to be discharged and protons enter via ATPase, thereby regenerating the ATP pool. There are 3 isoforms of translocases in humans; isoform 1 is the heart/skeletal muscle form, isoform 2 is the fibroblast form and isoform 3 is the liver form. All isoforms exist as homodimers. The translocase can adopt 2 different conformations, called the CATR (carboxyatractyloside) and BA (bongkrekic acid) conformations. Amongst the endogenous nucleotides, only ADP and ATP can trigger the rapid conversion between the CATR and BA conformations. The reaction can be summed as below: ADPout + ATPin <-> ADPin + ATPout
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3-demethylubiquinol-10 (DeMQ10H2) to ubiquinol-10 (Q10H2) (Jonassen & Clarke 2000).
The length of the polyisoprenoid chain of ubiquinone aka coenzyme Q (Q), varies depending on the species involved: it is 6 in budding yeast, Saccharomyces cerevisiae, (Q6) and 10 in humans (Q10). Most ubiquinone is naturally reduced to ubiquinol (Q10H2 in humans) and it is this form which dominates in most human tissues. It functions as an ubiquitous coenzyme in redox reactions and its ability both to associate with complexes I and III of the electron transport chain and to move freely in the inner mitochondrial membrane are central to its role in electron transport. In eukaryotes ubiquinones/ubiquinols are also found in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. Ubiquinol/ubiquinone is synthesized in the following way. Initially, the polyisoprenoid tail is assembled by a polyprenyl diphosphate synthase. Next, 4 hydroxybenzoate polyprenyltransferase (COQ2) catalyses the formation of the covalent linkage between the benzoquinone head group and the tail to produce 4 hydroxy 3 polyprenyl benzoic acid intermediate (DHB, 3 decaprenyl 4 hydroxybenzoic acid in humans). There follows modifications of the aromatic ring starting with hydroxylation, followed by O methylation, and decarboxylation to form the 2 methoxy 6 polyprenyl phenol intermediate (DMPhOH ; 2 methoxy 6 decaprenylphenol in humans). Following this, two additional methylations, one C methylation, and one O methylation step, finally generate the fully substituted hydroquinone, ubiquinol (Szkopinska 2000, Kagan & Quinn 2000, Tran & Clarke 2007, Kawamukai 2009).
Leukotrienes (LTs) are biologically active molecules formed in response to inflammatory stimuli. They cause contraction of bronchial smooth muscles, stimulation of vascular permeability, and attraction and activation of leukocytes. LTs were discovered in 1938 and were termed the "slow release substance" (SRS) until their structures were determined in 1979 and they were then renamed to leukotrienes. LTs are derived from arachidonic acid through action by arachidonate 5-lipoxygenase (ALOX5). Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are generated as products derived from leukotriene A4 (LTA4). Eoxins are generated from leukotrienes (LTs) and resemble cysteinyl leukotrienes but have a different three-dimensional structure (Murphy & Gijon 2007, Hammarstrom 1983, MA.Claesson 2009, Vance & Vance 2008, Buczynski et al. 2009).
Leukotriene A4 hydrolase (LTA4H) is a monomeric, soluble enzyme that catalyzes the hydrolysis of the allylic epoxide leukotriene A4 (LTA4) to the dihydroxy acid leukotriene B4 (LTB4) (Radmark et al. 1984, McGee & Fitzpatrick 1985).
5-hydroperoxy-eicosatetraenoic acid (5-HpETE), 5-hydroxyeicosatetraenoic acid (5S-HETE) and 5-oxo-eicosatetraenoic acid (5-oxoETE) are formed after the initial step of arachidonic acid oxidation by arachidonate 5-lipoxygenase (ALOX5) (Buczynski et al. 2009, Vance & Vance 2008).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) reduce 5-hydroperoxyeicosatetraenoic acid (5-HpETE) to 5-hydroxyeicosatetraenoic acid (5-HETE) in the presence of glutathione (GSH). This reaction is inferred from the event in rabbit involving the protein GPX1 (Chiba et al. 1999).
On the biosynthesis and biological role of eoxins and 15-lipoxygenase-1 in airway inflammation and Hodgkin lymphoma
Prostaglandins Other Lipid Mediat 89:120-5
SPTLC (serine palmitoyltransferase) enzyme complexes associated with the endoplasmic reticulum membrane catalyze the reaction of palmitoyl-CoA and serine to form 3-ketosphinganine. SPTLC2 and SPTLC3 polypeptides exhibit enzyme activity when either is complexed with SPTLC1. SPTLC1 and 2 are abundant and widely expressed in human tissues, while SPTLC3 is expressed only in a smaller group of tissues and at variable levels. Results of studies in which siRNA was used to reduce levels of the three endogenous mRNAs differentially suggest that SPTLC2 and 3 both encode active serine palmitoyltransferases (Hornemann et al. 2006). Neither human nor mouse SPTLC1 has detectable enzyme activity, but the protein has an essential function, as mutations that disrupt it are associated with hereditary neuropathy (Dawkins et al. 2001). Studies of mouse and hamster proteins support the hypothesis that heterodimerization with SPTLC1 stabilizes SPTLC2 (or 3) and mediates its localization to the endoplasmic reticulum membrane (Hanada et al. 2000; Weiss and Stoffel 1997). Analyses of complexes extracted from human placenta, and of cultured human cells over-expressing various SPTLC constructs, suggest that these heterodimers may associate into larger complexes (Hanada et al. 2000; Weiss and Stoffel 1997; Hornemann et al. 2006, 2007).
LASS (âlongevity assurance homologâ, also known as ceramide synthase, CerS) enzymes associated with the endoplasmic reticulum membrane catalyze the reaction of sphinganine (dihydrosphingosine) and a long-chain fatty acyl CoA such as stearyl-CoA to form a dihydroceramide and CoASH (Pewzner-Jung et al. 2006). Six human LASS genes have been identified; they differ in the identities of the fatty acyl CoAs that they use most efficiently as substrates (Lahiri and Futerman 2005; Laviad et al. 2008).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12R-hydroperoxy-eicosatetraenoic acid (12R-HpETE) to 12R-hydro-eicosatetraenoic acid (12R-HETE).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE) to 12S-hydro-eicosatetraenoic acid (12S-HETE). GPXs are selenoenzymes that are responsible for reducing the cellular peroxide. Cellular GPXs compete with hepoxilins A3 (HXA3) synthase for 12S-HpETE as substrate either to produce 12S-HETE or to convert to HXA3, respectively.
The 12-eicosatetraenoic acids: 12-hydroperoxy-eicosatetraenoic acid (12-HpETE), 12-hydroxyeicosatetraenoic acid (12-HETE) and 12-oxo-eicosatetraenoic acid (12-oxoETE) are formed after the initial step of arachidonic acid oxidation by the arachidonate 12 and 15 lipoxygenases (ALOX12, ALOX12B and ALOX15 respectively). This part of the pathway is bifurcated at the level of 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE), which can either be reduced to 12S-hydro-eicosatetraenoic acid (12S-HETE) or converted to hepoxilins (Buczynski et al. 2009, Vance & Vance 2008).
Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonic acid (all-cis 5,8,11,14-eicosatetraenoic acid) that is released from membrane phospholipids. Once released, arachidonic acid is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoic acids (Buczynski et al. 2009, Vance & Vance 2008). Levels of free arachidonic acid in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonic acid. The enzymes involved in arachidonic acid metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize. Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
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A three-domain structure of kinesin heavy chain revealed by DNA sequence and microtubule binding analyses
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Intracellular zinc homeostasis and zinc signaling
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Feedback regulation of EGFR signalling: decision making by early and delayed loops
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ditrans,polycis-polyprenol [ChEBI:67132]
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Phospholipase Czeta causes Ca2+ oscillations and parthenogenetic activation of human oocytes
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At the endoplasmic reticulum (ER) membrane, phosphatidylinositol (PI) and phosphatidylinositol 4-phosphate (PI4P) are interconverted (Wong et al. 1997, Gehrmann et al. 1999, Wei et al. 2002, Rohde et al. 2003).
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At the plasma membrane, synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 aka synaptojanin-1 (SYNJ1) (Guo et al. 1999, Mani et al. 2007) and -2 (SYNJ2) (Malecz et al. 2000) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P).
At the plasma membrane, synaptojanin-1 aka Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1) (Guo et al. 1999), -2 (SYNJ2) and some myotubularins (MTMs) dephosphorylate phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol (PI). The MTMs involved are: myotubularin (MTM1) (Cao et al. 2007, Tronchere et al. 2004, Schaletzky et al. 2003, Laporte et al. 2002, Kim et al. 2002) and myotubularin-related proteins 1 (MTMR1) (Kim et al. 2002, Tronchere et al. 2004), 3 (MTMR3) (Kim et al. 2002, Zhao et al. 2001, Walker et al. 2001, Lorenzo et al. 2005), 6 (MTMR6) (Schaletzky et al. 2003, Kim et al. 2002, Choudhury et al. 2006), and 14 (MTMR14) (Tosch et al. 2006).
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At the plasma membrane, phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (PIP4K2A) and beta (PIP4K2B) homodimers and heterodimers (Clarke et al. 2010), along with phosphatidylinositol-4-phosphate 5-kinase type-1 alpha (PIP5K1A), beta (PIP5K1B), and gamma (PIP5K1C) phosphorylate phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2). The following lists the above proteins with their corresponding literature references: PIP4K2A (Zhang et al. 1997, Rameh et al. 1997, Clarke et al. 2008), PIP4K2B (Zhang et al. 1997, Rameh et al. 1997), PIP5K1A (Zhang et al. 1997, Tolias et al. 1998), PIP5K1B (Zhang et al. 1997, Tolias et al. 1998), and PIP5K1C (Wenk et al. 2001, Di Paolo et al. 2002).
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At the plasma membrane, phosphatidylinositol 5-phosphatases dephosphorylate phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) to phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2). The phosphatidylinositol 5-phosphatases involved are: inositol polyphosphate 5-phosphatase K (INPP5K) aka SKIP (Ijuin et al. 2000, Gurung et al. 2003), phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) aka PIPP (Gurung et al. 2003, Mochizuki & Takenawa 1999), phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 1 (INPP5D) aka SHIP1 (Drayer et al. 1995, Kavanaugh et al. 1996, Dunant et al. 2000), and phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2 (INPPL1) aka SHIP2 (Habib et al. 1998, Wisniewski et al. 1999, Pesesse et al. 2001).
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At the plasma membrane, Synaptojanin-1 (SYNJ1) and -2 (SYNJ2), inositol polyphosphate 5-phosphatase K (INPP5K) aka SKIP, phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) aka PIPP dephosphorylate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) to form phosphatidylinositol 4-phosphate (PI4P). SYNJ1/2 both have an N-terminal Sac1-like domain, a central 5-phosphatase domain and a C-terminal proline-rich segment, with this latter part being the most divergent part of the protein sequence. The following lists the above proteins with their corresponding literature references: SYNJ1 (Johenning et al. 2004, Haffner et al. 1997, Guo et al. 1999, Mani et al. 2007), SYNJ2 (Malecz et al. 2000), INPP5K (Injuin et al. 2000, Gurung et al. 2003), and INPP5J (Gurung et al. 2003, Mochizuki & Takenawa 1999).
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At the Golgi membrane, phosphatidylinositol 4-phosphate (PI4P) is primarily generated from phosphorylation of phosphatidylinositol (PI). Other phosphoinositides are also generated by the action of various kinases and phosphatases such as: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Godi et al. 1999, Minogue et al. 2001, Rohde et al. 2003, Sbrissa et al. 2007, Sbrissa et al. 2008, Domin et al. 2000, Arcaro et al. 2000).
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At the Golgi membrane, activated phosphatidylinositol 4-kinase beta (PI4KB) complexed to ADP-ribosylation factor 1/3 (ARF1/3) phosphorylates phosphatidylinositol (PI) to phosphatidylinositol 4-phosphate (PI4P) (Suzuki et al. 1997).
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At the Golgi membrane, ADP-ribosylation factor 1 and 3 (ARF1 and ARF3) complexed to GTP bind to phosphatidylinositol 4-kinase beta (PI4KB) and activate it (Haynes et al. 2007, Wong et al. 1997, Godi et al. 1999).
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At the Golgi membrane, phosphatidylinositol 4-kinase alpha (PI4KA) (Gehrmann et al. 1999, Godi et al. 1999), or phosphatidylinositol 4-kinase type 2-alpha/beta (PI4K2A/B) (Balla et al. 2002, Minogue et al. 2001, Wei et al. 2002) phosphorylate phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P).
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At the endoplasmic reticulum (ER) membrane, phosphatidylinositol 4-kinase alpha (PI4KA) (Wong et al. 1997, Gehrmann et al. 1999) or phosphatidylinositol 4-kinase type 2-beta (PI4K2B) (Wei et al. 2002) phosphorylate phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P).
Glycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids act as precursors of lipid mediators such as platelet-activating factor and eicosanoids. Cellular membranes contains a distinct composition of various glycerophospholipids such as phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), cardiolipin (CL), lysophosphatidic acid (LPA) and lysobisphosphatidic acid (also known as bis(monoacylglycerol) hydrogen phosphate - BMP). Glycerophospholipids are first formed by the de novo (Kennedy) pathway using fatty acids activated as acyl-CoA donors. However, the acyl groups of glycerophospholipids are highly diverse and distributed in an asymmetric manner. Saturated and monounsaturated fatty acids are usually esterified at the sn-1 position, whereas polyunsaturated acyl groups are esterified at the sn-2 position. Subsequent acyl chain remodeling (Lands cycle) generates the diverse glycerophospholipid composition and asymmetry characteristic of cell membranes. In the de novo pathway of glycerophospholipid biosynthesis, lysophosphatidic acid (LPA) is initially formed from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT), then PA is metabolized into two types of glycerol derivatives. The first is diacylglycerol (DAG) which is converted to triacylglycerol (TAG), PC, and PE. Subsequently, PS is synthesized from PC or PE. The second is cytidine diphosphate-diacylglycerol (CDP-DAG), which is processed into PI, PG, CL, and BMP. Each glycerophospholipid is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by an acyltransferase. Most of the glycerophospholipids are synthesized at the endoplasmic reticulum (ER), however, some, most notably cardiolipin, and BMP are synthesized in the mitochondrial and endosomal membranes respectively. Since the most of the glycerophospholipids are found in all membrane compartments, there must be extensive network of transport of glycerophospholipids from one membrane compartment to another via various mechanisms including diffusion through the cytosol, formation of transportation complexes, and diffusion via membrane contact sites (MCS) (Osman et al. 2011, Lebiedzinska et al. 2009, Lev 2010, Scherer & Schmitz 2011, Orso et al. 2011, Hermansson et al. 2011, Vance & Vance 2008).
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Phosphatidylglycerol (PG) is synthesised at the inner mitochondrial (IM) membrane, phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG), which in turn is converted with glycerol-3-phosphate (G3P) into phosphatidylglycerophosphate (PGP) and cytidine monophosphate (CMP). Finally, PGP is dephosphorylated to PG. In addition, PG can be synthesised at the endoplamic reticulum (ER) membrane when phospholipase D transphosphatidylates phosphatidylcholine (PC) with glycerol to displace choline (Cho) and form PG (Piazza & Marmer 2007, Stuhne-Sekalec et al. 1986, Lykidis et al. 1997, Cao & Hatch 1994).
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At the inner mitochondrial (IM) membrane, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (PGS1) converts cytidine diphosphate-diacylglycerol (CDP-DAG) and glycerol-3-phosphate (G3P) to phosphatidylglycerophosphate (PGP) and cytidine monophosphate (CMP). This event is inferred from rats. The enzyme PGS1 has been characterized in humans (Ota et al. 2004).
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Acyl chain remodeling of cardiolipin (CL) occurs in the inner mitochondria membranes (IM) via hydrolysis by phopholipases and subsequent reacylation by acyltransferases. At the endoplasmic reticulum (ER) membrane the situation is more complicated with monolysocardiolipin (MLCL) involved in hydrolysis and subsequent reacylation back to CL (Zachman et al. 2010, Malhotra et al. 2009, Xu et al. 2003, Taylor & Hatch 2009, Cao et al. 2004, Zhao et al. 2009, Buckland et al. 1998).
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At the inner mitochondrial membrane (IM), calcium-independent phospholipase A2 gamma (PLA2G6) hydrolyzes, removing one of the acyl chains, cardiolipin (CL) to form monolysocardiolipin (MLCL). This reaction is inferred from rats. PLA2G6 has also been characterized in humans (Larsson et al. 1998, Ma et al. 1999, Larsson Forsell et al. 1999).
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At the endoplasmic reticulum (ER) membrane, CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) converts cytidine diphosphate-diacylglycerol (CDP-DAG) and inositol (Ins) into phosphatidylinositol (PI) and cytidine monophosphate (CMP) (Lykidis et al. 1997).
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At the endoplasmic reticulum (ER) membrane, phosphatidate cytidylyltransferase 1 (CDS1) converts phosphatidic acid (PA) and cytidine triphosphate (CTP) into cytidine diphosphate-diacylglycerol (CDP-DAG). Both ER and mitochondrial membranes have the capability to synthesize cytidine diphosphate-diacylglycerol (CDP-DAG) with phosphatidate cytidylyltransferase 1 and 2 (CDS1 and CDS2) (Lykidis et al. 1997). However, transport of CDP-DAG between organelles cannot be ruled out (Stuhne-Sekalec et al. 1986).
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At the inner mitochondrial (IM) membrane, phosphatidate cytidylyltransferase 2 (CDS2) converts phosphatidic acid (PA) and cytidine triphosphate (CTP) into cytidine diphosphate-diacylglycerol (CDP-DAG). Both ER and mitochondrial membranes have the capability to synthesise cytidine diphosphate-diacylglycerol (CDP-DAG) with phosphatidate cytidylyltransferase 1 and 2 (CDS1 and CDS2) (Lykidis et al. 1997, Schlame & Haldar 1993). However, transport of CDP-DAG between organelles cannot be ruled out (Stuhne-Sekalec et al. 1986).
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Phosphatidylinositol (PI) is synthesized when phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG) followed by conversion into PI and cytidine monophosphate (CMP) (Stuhne-Sekalec et al 1986, Lykidis et al. 1997).
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A synopsis of the unconjugated acidic transamination metabolites of phenylalanine in phenylketonuria
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The Protein Biosynthesis Elongation Cycle
Translational Control of Gene Expression89-127
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Biochemical analysis of the human mismatch repair proteins hMutS? MSH2(G674A)-MSH6 and MSH2-MSH6(T1219D)
Cross-linking of B cell antigen receptor-related structure of pre-B cell lines induces tyrosine phosphorylation of p85 and p110 subunits and activation of phosphatidylinositol 3-kinase
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New insights into an old problem: ternary complex (Met-tRNAf.eIF.GTP) formation in animal cells.
Post-transcriptional control of gene expression. J.E. McCarty and M.F.Tuite (eds).521-526
Pathway and mechanism of initiation of protein synthesis.
Translational Control of Gene Expression. (Sonenberg, Hershey and Mathews, eds.)33-88
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T cell antigen-receptor signal transduction
Genetic approaches to translation initiation in Saccharomyces cerevisiae.
Translational Control of Gene Expression. N. Sonenberg, J.W. Hershey and M.B. Mathews (eds.)487-502
Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes
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Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit.
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Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12
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Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription
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Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities
Kinesin-2 is a motor for late endosomes and lysosomes
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Molybdenum cofactor biosynthesis and deficiency
Active site remodelling accompanies thioester bond formation in the SUMO E1
Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine
MicroRNA genes are transcribed by RNA polymerase II
The enzymes and control of eukaryotic mRNA turnover
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function
Mitochondrial 2-oxoglutarate/malate carrier protein
6-phosphogluconate dehydrogenase, decarboxylating
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Characterization of a human gene conferring sensitivity to infection by gibbon ape leukemia virus
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Subcellular localization and targeting of N-acetylglucosaminyl phosphatidylinositol de-N-acetylase, the second enzyme in the glycosylphosphatidylinositol biosynthetic pathway
How MHC class II molecules acquire peptide cargo: biosynthesis and trafficking through the endocytic pathway
Localization by fluorescence in situ hybridization of the human functional beta-glucuronidase gene (GUSB) to 7q11.21 --> q11.22 and two pseudogenes to 5p13 and 5q13
Aspartate aminotransferase, mitochondrial precursor
aspartate aminotransferase, mitochondrial, apoenzyme monomer
Anti-apoptotic signaling by the interleukin-2 receptor reveals a function for cytoplasmic tyrosine residues within the common gamma (gamma c) receptor subunit
glyceraldehyde-3-phosphate dehydrogenase, testis-specific, monomer
Glyceraldehyde 3-phosphate dehydrogenase, liver
glyceraldehyde-3-phosphate dehydrogenase monomer
glyceraldehyde 3-phosphate dehydrogenase, muscle
Vertebrate agmatinases: what role do they play in agmatine catabolism?
Agmatine: at the crossroads of the arginine pathways
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Mitochondrial tRNA import: are there distinct mechanisms?
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Probable lysosomal cobalamin transporter
Phosphopantothenoylcysteine decarboxylase
Factor VIII-related antigen in human blood platelets: localization and release by thrombin and collagen
Molecular identification of a novel mammalian brain isoform of acyl-CoA:lysophospholipid acyltransferase with prominent ethanolamine lysophospholipid acylating activity, LPEAT2
MTABC3, a novel mitochondrial ATP-binding cassette protein involved in iron homeostasis
Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations
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Herp is dually regulated by both the endoplasmic reticulum stress-specific branch of the unfolded protein response and a branch that is shared with other cellular stress pathways
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FAD1 flavin adenine dinucleotide synthetase homolog
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phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
Activation of the pre-replicative complex
Enzymes and reactions at the eukaryotic DNA replication fork.
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Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.
Regulation of Glucokinase by Glucokinase Regulatory Protein
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The Mammalian synaptonemal complex: a scaffold and beyond
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N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
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Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney
DNA mismatch repair in eukaryotes and bacteria
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Subcellular localization and properties of alkaline inorganic pyrophosphatase in human polymorphonuclear leucocytes
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Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family
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Mutations in the catalytic subunit of class IA PI3K confer leukemogenic potential to hematopoietic cells
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Analysis of phosphoinositide binding domain properties within the myotubularin-related protein MTMR3
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The extended protein kinase C superfamily
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Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis
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Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine
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Subcellular locations of phosphatidylinositol 4-kinase isoforms
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BH2 may compete with BH4 to bind eNOS, uncoupling eNOS leading to the formation of superoxide rather than nitric oxide. BH2, the oxidised form of BH4, cannot contribute electrons to heme in the reductase domain of eNOS, thereby uncoupling it from arginine oxidation and producing superoxide from oxygen instead (Vasquez-Vivar et al. 2002).
Nitric oxide (NO) is produced from L-arginine by the family of nitric oxide synthases (NOS) enzymes, forming the free radical NO and citrulline as byproduct. The cofactor tetrahydrobiopterin (BH4) is an essential requirement for the delivery of an electron to the intermediate in the catalytic cycle of NOS.
Docosapentaenoic acid (22:5n-3): a review of its biological effects
The cofactor tetrahydrobiopterin (BH4) ensures endothelial nitric oxide synthase (eNOS) couples electron transfer to L-arginine oxidation (Berka et al. 2004). During catalysis, electrons derived from NADPH transfer to the flavins FAD and FMN in the reductase domain of eNOS and then on to the ferric heme in the oxygenase domain of eNOS. BH4 can donate an electron to intermediates in this electron transfer and is oxidised in the process, forming the BH3 radical. This radical can be reduced back to BH4 by iron, completing the cycle and forming ferrous iron again. Heme reduction enables O2 binding and L-arginine oxidation to occur within the oxygenase domain (Stuehr et al. 2009).
HSP90 serves as a scaffold to promote productive interaction between AKT1 and eNOS. Due to the proximity of these proteins once complexed with HSP90, AKT1 phosphorylates eNOS at Ser1177. When Ser1177 is phosphorylated, the level of NO production is elevated two- to three-fold above basal level.
ChREBP (Carbohydrate Response Element Binding Protein) is a large multidomain protein containing a nuclear localization signal near its amino terminus, polyproline domains, a basic helix-loop-helix-leucine zipper domain, and a leucine-zipper-like domain (Uyeda et al., 2002). Its dephosphorylation in response to molecular signals associated with the well-fed state allows it to enter the nucleus, interact with MLX protein, and bind to ChRE DNA sequence motifs near Acetyl-CoA carboxylase, Fatty acid synthase, and Pyruvate kinase (L isoform) genes (Ishi et al.2004). This sequence of events is outlined schematically in the picture below (adapted from Kawaguchi et al. (2001) - copyright (2001) National Academy of Sciences, U.S.A.).
Old and new generation lipid mediators in acute inflammation and resolution
Many hormones that affect individual physiological processes including the regulation of appetite, absorption, transport, and oxidation of foodstuffs influence energy metabolism pathways. While insulin mediates the storage of excess nutrients, glucagon is involved in the mobilization of energy resources in response to low blood glucose levels, principally by stimulating hepatic glucose output. Small doses of glucagon are sufficient to induce significant glucose elevations. These hormone-driven regulatory pathways enable the body to sense and respond to changed amounts of nutrients in the blood and demands for energy. Glucagon and Insulin act through various metabolites and enzymes that target specific steps in metabolic pathways for sugar and fatty acids. The processes responsible for the long-term control of fat synthesis and short term control of glycolysis by key metabolic products and enzymes are annotated in this module as six specific pathways: Pathway 1. Glucagon signalling in metabolic pathways: In response to low blood glucose, pancreatic alpha-cells release glucagon. The binding of glucagon to its receptor results in increased cAMP synthesis, and Protein Kinase A (PKA) activation. Pathway 2. PKA mediated phosphorylation:PKA phosphorylates key enzymes, e.g., 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PF2K-Pase) at serine 36, and regulatory proteins, e.g., Carbohydrate Response Element Binding Protein (ChREBP) at serine 196 and threonine 666. Insulin mediated responses to high blood glucose will be annotated in future versions of Reactome. In brief, the binding of insulin to its receptor leads to increased protein phosphatase activity and to hydrolysis of cAMP by cAMP phosphodiesterase. These events counteract the regulatory effects of glucagon. Pathway 3: Insulin stimulates increased synthesis of Xylulose-5-phosphate (Xy-5-P). Activation of the insulin receptor results indirectly in increased Xy-5-P synthesis from Glyceraldehyde-3-phosphate and Fructose-6-phosphate. Xy-5-P, a metabolite of the pentose phosphate pathway, stimulates protein phosphatase PP2A. Pathway 4: AMP Kinase (AMPK) mediated response to high AMP:ATP ratio: In response to diet with high fat content or low energy levels, the cytosolic AMP:ATP ratio is increased. AMP triggers a complicated cascade of events. In this module we have annotated only the phosphorylation of ChREBP by AMPK at serine 568, which inactivates this transcription factor. Pathway 5: Dephosphorylation of key metabolic factors by PP2A: Xy-5-P activated PP2A efficiently dephosphorylates phosphorylated PF2K-Pase resulting in the higher output of F-2,6-P2 that enhances PFK activity in the glycolytic pathway. PP2A also dephosphorylates (and thus activates) cytosolic and nuclear ChREBP. Pathway 6: Transcriptional activation of metabolic genes by ChREBP: Dephosphorylated ChREBP activates the transcription of genes involved in glucose metabolism such as pyruvate kinase, and lipogenic genes such as acetyl-CoA carboxylase, fatty acid synthetase, acyl CoA synthase and glycerol phosphate acyl transferase. The illustration below summarizes this network of events. Black lines are metabolic reactions, red lines are negative regulatory events, and green lines are positive regulatory events (figure reused with permission from Veech (2003) - Copyright (2003) National Academy of Sciences, U.S.A.).
The PKLR gene is transcribed, its mRNA is translated, spliced, and translated to yield the L isoform of PKLR protein. PKLR expression is positively regulated by HNF1A. Mutations in HNF1A are associated with a form of MODY (maturity onset diabetes of the young) (Fanjans et al. 2001) but the molecular details of PKLR expression in intact pancreatic beta cells have not been studied in humans, and are inferred from corresponding ones worked out in the mouse.
At the end of this reaction, 1 molecule of 'Acetyl-CoA carboxylase 2 ' is present. This reaction takes place in the 'nucleus'.
One of the downstream effects of insulin, mediated via protein phosphatase 2A (PP2A), is increased synthesis of Fructose-2,6-bisphosphate, an allosteric activator of phosphofructokinase 1 (PFK1). PFK1 in turn catalyzes the committed step of glycolysis so the net effect of this whole sequence of events set off by insulin is to increase cytosolic concentrations of the small molecules formed in the course of glycolysis. This in turn drives the increased synthesis of Xylulose-5-phosphate, itself a positive regulator of PP2A.
At the end of this reaction, 1 molecule of 'pyruvate kinase, liver and RBC' is present. This reaction takes place in the 'nucleus'.
Interferon induces tryptophanyl-tRNA synthetase expression in human fibroblasts
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Molecular mechanism of the Syk activation switch
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The role of leptin in the control of insulin-glucose axis
Purification and characterization of human phosphatidylserine synthases 1 and 2
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Pyruvate (PYR) and a proton are transported from the cytosol into the mitochondrial matrix, mediated by a complex of MCP1 and MCP2 in the inner mitochondrial membrane. Studies of pyruvate uptake in rat indicate that it is specific, saturable, and competitively inhibitable, indicating a specific role for a membrane transport protein (Papa et al. 1971; Halestrap and Denton 1974), and the stoichiometry of the human reaction is inferred from this work. MCP1 and MCP2 have been identified as essential components of the transporter based on the observation that expression of both proteins (but not either one alone) restored mitochondrial pyruvate uptake in mutant budding yeast. The proteins form a multimeric complex; its stoichiometry is unknown (Bricker et al. 2012).
Cytosolic lactate dehydrogenase catalyzes the freely reversible reaction of lactate and NAD+ to form pyruvate and NADH + H+. In liver parenchymal cells, this reaction allows lactate from red blood cells and exercising muscle to be converted to pyruvate which in turn is typically used for gluconeogenesis which also consumes the NADH from the reaction. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
The mitochondrial pyruvate dehydrogenase complex catalyzes the reaction of pyruvate, CoASH, and NAD+ to form acetylCoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 alpha, E1 beta, E2, and E3, each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of pyruvate catalyzed by E1 alpha and beta (pyruvate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the acetyl group derived from pyruvate is transferred to coenzyme A in two steps catalyzed by E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with pyruvate dehydrogenase complex and subunits purified from bovine tissue and other non-human sources. Direct evidence for the roles of the corresponding human proteins comes from studies of patients expressing mutant forms of E1 alpha (Lissens et al. 2000), E1 beta (Brown et al. 2004), E2 (Head et al. 2005), and E3 (Brautigam et al. 2005).
Tetrahydrobiopterin (BH4) is an essential co-factor for the aromatic amino acid hydroxylases and glycerol ether monooxygenase and it regulates nitric oxide synthase (NOS) activity. Inherited BH4 deficiency leads to hyperphenylalaninemia, and dopamine and neurotransmitter deficiency in the brain. BH4 maintains enzymatic coupling to L-arginine oxidation to produce NO. Oxidation of BH4 to BH2 results in NOS uncoupling, resulting in superoxide (O2.-) formation rather than NO. Superoxide rapidly reacts with NO to produce peroxynitrite which can further uncouple NOS. These reactive oxygen species (superoxide and peroxynitrite) can contribute to increased oxidative stress in the endothelium leading to atherosclerosis and hypertension (Thony et al. 2000, Crabtree and Channon 2011,Schulz et al. 2008, Schmidt and Alp 2007). The synthesis, recycling and effects of BH4 are shown here. Three enzymes are required for the de novo biosynthesis of BH4 and two enzymes for the recycling of BH4.
Originally identified as endothelium-derived relaxing factor, eNOS derived NO is a critical signaling molecule in vascular homeostasis. It regulates blood pressure and vascular tone, and is involved in vascular smooth muscle cell proliferation, platelet aggregation, and leukocyte adhesion. Loss of the bioavailability of endothelium derived NO is a key feature of endothelial dysfunction and is implicated in the pathogenesis of cardiovascular disease such as hypertension and atherosclerosis. The endothelial isoform eNOS is unique among the nitric oxide synthase (NOS) family in that it is co-translationally modified at its amino terminus by myristoylation and is further acylated by palmitoylation (two residues next to the myristoylation site). These modifications target eNOS to the plasma membrane caveolae and lipid rafts. eNOS activation and subsequent nitric oxide (NO) production is stimulated by a variety of stimuli, such as fluid shear stress generated by blood flow, vascular endothelial growth factor (VEGF), bradykinin, estrogen, insulin, and angiopoietin. The activity of eNOS is further regulated by numerous post-translational modifications, including protein-protein interactions, phosphorylation, and subcellular localization. Following activation, eNOS shuttles between caveolae and other subcellular compartments such as the noncaveolar plasma membrane portions, Golgi apparatus, and perinuclear structures. This subcellular distribution is variable depending upon cell type and mode of activation. Subcellular localization of eNOS has a profound effect on its ability to produce NO as the availability of its substrates and cofactors will vary with location. eNOS is primarily particulate, and depending on the cell type, eNOS can be found in several membrane compartments: plasma membrane caveolae, lipid rafts, and intracellular membranes such as the Golgi complex. In addition, it has been reported that eNOS can also be detected in the nucleus, however, the conditions associated with nuclear localization of eNOS and its precise role in this cell compartment remains to be determined. Several stimuli can trigger a transient displacement of eNOS from the plasma membrane to other subcellular locations. This process can be mediated through various protein-protein interactions and/or changes in post-translational modifications. Knowledge of the precise molecular mechanisms governing the intracellular redistribution process is still rather limited.
Nitric oxide (NO), a multifunctional second messenger, is implicated in physiological functions in mammals that range from immune response and potentiation of synaptic transmission to dilation of blood vessels and muscle relaxation. NO is a highly active molecule that diffuses across cell membranes and cannot be stored inside the producing cell. Its signaling capacity must be controlled at the levels of biosynthesis and local availability. Indeed, NO production by NO synthases is under complex and tight control, being regulated at transcriptional and translational levels, through co- and posttranslational modifications, and by subcellular localization. NO is synthesized from L-arginine by a family of nitric oxide synthases (NOS). Three NOS isoforms have been characterized: neuronal NOS (nNOS, NOS1) primarily found in neuronal tissue and skeletal muscle; inducible NOS (iNOS, NOS2) originally isolated from macrophages and later discovered in many other cells types; and endothelial NOS (eNOS, NOS3) present in vascular endothelial cells, cardiac myocytes, and in blood platelets. The enzymatic activity of all three isoforms is dependent on calmodulin, which binds to nNOS and eNOS at elevated intracellular calcium levels, while it is tightly associated with iNOS even at basal calcium levels. As a result, the enzymatic activity of nNOS and eNOS is modulated by changes in intracellular calcium levels, leading to transient NO production, while iNOS continuously releases NO independent of fluctuations in intracellular calcium levels and is mainly regulated at the gene expression level (Pacher et al. 2007). The NOS enzymes share a common basic structural organization and requirement for substrate cofactors for enzymatic activity. A central calmodulin-binding motif separates an oxygenase (NH2-terminal) domain from a reductase (COOH-terminal) domain. Binding sites for cofactors NADPH, FAD, and FMN are located within the reductase domain, while binding sites for tetrahydrobiopterin (BH4) and heme are located within the oxygenase domain. Once calmodulin binds, it facilitates electron transfer from the cofactors in the reductase domain to heme enabling nitric oxide production. Both nNOS and eNOS contain an additional insert (40-50 amino acids) in the middle of the FMN-binding subdomain that serves as autoinhibitory loop, destabilizing calmodulin binding at low calcium levels and inhibiting electron transfer from FMN to the heme in the absence of calmodulin. iNOS does not contain this insert. Because NOS enzymatic activity is modulated by the presence of its substrates and cofactors within the cell, under certain conditions, NOS may generate superoxide instead of NO, a process referred to as uncoupling (uncoupling of NADPH oxidation and NO synthesis). The molecular details of eNOS function are annotated here.
Cytosolic lactate dehydrogenase catalyzes the reversible reaction of pyruvate and NADH + H+ to form lactate and NAD+. In the body under anaerobic conditions such as are found in red blood cells or rapidly exercising skeletal muscle, this reaction regenerates NAD+, allowing the continuation of glycolysis. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
eNOS activity is regulated by numerous post-translational modifications including phosphorylation and acylation, which also modulate its interactions with other proteins and its subcellular localization. In general, following myristoylation and palmitoylation, eNOS localizes to caveolae in the plasma membrane, where in resting cells, it is bound to caveolin and remains inactive. Several agonists that raise intracellular calcium concentrations promote calmodulin binding to eNOS and the dissociation of caveolin from the enzyme, leading to an activated eNOS-calmodulin complex. Phosphorylation plays a significant role in regulating eNOS activity, especially the phosphorylation of Ser1177, located within the reductase domain, which increases enzyme activity by enhancing reductase activity and calcium sensitivity. In unstimulated, cultured endothelial cells, Ser1177 is rapidly phosphorylated following a variety of stimuli: fluid shear stress, insulin, estrogen, VEGF, or bradykinin. The kinases involved in this process depend upon the stimuli applied. For instance, shear stress phosphorylates Ser1177 by activating Akt and PKA; insulin activates both Akt and the AMP-activated protein kinase (AMPK); estrogen and VEGF mainly phosphorylate eNOS via Akt; whereas the bradykinin-induced phosphorylation of Ser1177 is mediated by CaMKII. When Ser1177 is phosphorylated, NO production is increased several-fold above basal levels. The phosphorylation of a threonine residue (Thr 495), located in the CaM binding domain, is associated with a decrease in eNOS activity. When this residue is dephosphorylated, substantially more CaM binds to eNOS and elevates enzyme activity. Stimuli associated with dephosphorylation of Thr495 (e.g., bradykinin, histamine, and Ca2+ ionophores) also increase Ca2+ levels resulting in the phosphorylation of Ser1177. Additional phosphorylation sites, such as Ser114 and Ser633, and tyrosine phosphorylation have all been detected, but their functional relevance remains unclear. It is speculated that the tyrosine phosphorylation of eNOS is unlikely to affect enzyme activity directly, but more likely to impact the protein-protein interactions with associated scaffolding and regulatory proteins.
The first and rate-limiting enzyme in tetrahydrobiopterin de novo biosynthesis is GTP cyclohydrolase I (GCH1, GTPCHI). Three different isoforms are produced but only isoform 1 is functionally active (Gütlich et al. 1994). GCH1 is functional as a homodecamer. First, a monomer of GCH1 forms a dimer. Then five dimers arrange into a ring-like structure to form the homodecamer (Nar et al. 1995).
The oxidation product of BH4, 7,8-dihydrobiopterin (BH2), can compete with BH4 for binding to eNOS. This can lead to the uncoupling of eNOS and can result in the formation of reactive oxygen species (Vasquez-Vivar et al. 2002).
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The reversible conversion of 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) and fumarate is catalyzed by adenylosuccinate lyase. The active form of this enzyme is a cytosolic tetramer (Stone et al. 1993), and fluoresence microscopy of cultured human cells suggests that it may associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The enzyme also catalyzes the conversion of adenylosuccinate to adenosine 5'-monophosphate and fumarate. Humans lacking the enzyme accumulate dephosphorylated forms of both substrates, indicating that the enzyme mediates both reactions in vivo as well (Race et al. 2000).
The metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalents are re-oxidized back to NAD+ in the electron transport chain (ETC), coupling this process with the export of protons across the inner mitochondrial membrane. The chemiosmotic gradient created is used to drive ATP synthesis.
Distribution of the AQP4 water channel in normal human tissues: protein and tissue microarrays reveal expression in several new anatomical locations, including the prostate gland and seminal vesicles
Mitochondrial isocitrate dehydrogenase IDH2 catalyzes the irreversible reaction of isocitrate and NADP+ to form alpha ketoglutarate, CO2, and NADPH + H+ (Hartong et al. 2008). The structure of the active human enzyme has not been determined experimentally, but is inferred to be a homodimer with one Mn++ bound to each subunit based on detailed studies of the homologous pig enzyme (Ceccarelli et al. 2002). NADP-specific IDH2 was the first isocitrate dehydrogenase isoenzyme to be characterized in biochemical studies of the mammalian TCA cycle (Ochoa 1948). Later work with yeast revealed the existence of both NADP-specific (IDH2-homologous) and NAD-specific (IDH3-homologous) enzymes and demonstrated the ADP-dependence of the latter (Kornberg and Pricer 1951), consistent with the now widely accepted view that IDH3 mediates the conversion of isocitrate to alpha-ketoglutarate in the TCA cycle. The physiological function of IDH2 is thus unclear. The recent observation that individuals homozygous for IDH3 mutations that sharply reduce its activity do not show symptoms of deficient energy metabolism in most tissues raises the possibility that the IDH2 reaction may play an accessory role in the TCA cycle (Hartong et al. 2008).
Novel mutant-selective EGFR kinase inhibitors against EGFR T790M
NNT (nicotinamide nucleotide transhydrogenase) associated with the inner mitochondrial membrane catalyzes the reaction of mitochondrial NADPH and NAD+ to form NADP+ and NADH. The reaction is coupled to the translocation of a proton across the inner mitochondrial membrane into the mitochondrial matrix (White et al, 2000). The active form of NNT is inferred to be a homodimer based on the known structure of its bovine homolog (Yamaguchi and Hatefi 1991).
Pyruvate sits at an intersection of key pathways of energy metabolism. It is the end product of glycolysis and the starting point for gluconeogenesis, and can be generated by transamination of alanine. It can be converted by the pyruvate dehydrogenase complex to acetyl CoA (Reed and Hackert 1990) which can enter the TCA cycle or serve as the starting point for the syntheses of long chain fatty acids, steroids, and ketone bodies depending on the tissue and metabolic state in which it is formed. It also plays a central role in balancing the energy needs of various tissues in the body. Under conditions in which oxygen supply is limiting, e.g., in exercising muscle, or in the absence of mitochondria, e.g., in red blood cells, re-oxidation of NADH produced by glycolysis cannot be coupled to generation of ATP. Instead, re-oxidation is coupled to the reduction of pyruvate to lactate. This lactate is released into the blood, and is taken up primarily by the liver, where it is oxidized to pyruvate and can be used for gluconeogenesis (Cori 1981).
Mitochondrial citrate synthase dimer catalyzes the irreversible reaction of acetyl-CoA, water, and oxaloacetate to form citrate and coenzyme A. This reaction is the entry point of two-carbon units into the citric acid cycle. The reaction is subject to allosteric regulation. The gene encoding the human enzyme has been cloned (Goldenthal et al. 1998), but the enzyme has not been characterized in detail - its properties are inferred from those of the well-studied homologous pig enzyme (e.g., Morgunov and Srere 1998).
In the citric acid or tricarboxylic acid (TCA) cycle, the acetyl group of acetyl CoA (derived primarily from oxidative decarboxylation of pyruvate, beta-oxidation of long-chain fatty acids, and catabolism of ketone bodies and several amino acids) can be completely oxidized to CO2 in reactions that also yield one high-energy phosphate bond (as GTP or ATP) and four reducing equivalents (three NADH + H+, and one FADH2). The NADH and FADH2 are then oxidized by the electron transport chain to yield nine more high-energy phosphate bonds (as ATP). All reactions of the citric acid cycle take place in the mitochondrion. Eight canonical reactions mediate the synthesis of citrate from acetyl-CoA and oxaloacetate and the metabolism of citrate to re-form oxaloacetate. Six additional reactions are included here. Three reversible reactions, the interconversions of citrate and isocitrate, of fumarate and malate, and of malate and oxaloacetate are annotated in both their canonical (forward) and reverse directions. The synthesis of succinate from succinyl-CoA can be coupled to the phosphorylation of either GDP (the canonical reaction) or ADP; both reactions are annotated. Two mitochondrial isocitrate dehydrogenase isozymes catalyze the oxidative decarboxylation of isocitrate to form alpha-ketoglutarate (2-oxoglutarate): IDH3 catalyzes the canonical reaction coupled to the reduction of NAD+, while IDH2 catalyzes the same reaction coupled to reduction of NADP+, a reaction whose normal physiological function is unclear. Both reactions are annotated. Finally, a reaction is annotated in which reducing equivalents are transferred from NADPH to NAD+ coupled to proton import across the inner mitochondrial membrane. The cyclical nature of the reactions responsible for the oxidation of acetate was first suggested by Hans Krebs, from biochemical studies of pigeon breast muscle (Krebs et al. 1938; Krebs and Eggleston 1940). Many of the molecular details of individual reactions were worked out by Ochoa and colleagues, largely through studies of enzymes purified from pig heart (Ochoa 1980). While the human homologues of these enzymes have all been identified, their biochemical characterization has in general been limited and many molecular details of the human reactions are inferred from those worked out in studies of the model systems.
Pyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the reversible oxidation of lactate or transamination of alanine, can be converted to acetyl CoA. Other sources of acetyl CoA include breakdown of free fatty acids and ketone bodies in the fasting state. Acetyl CoA can enter the citric acid cycle, a major source of reducing equivalents used to synthesize ATP, or enter biosynthetic pathways. In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
The mitochondrial alpha-ketoglutarate dehydrogenase complex catalyzes the reaction of alpha-ketoglutarate, CoASH, and NAD+ to form succinyl-CoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of alpha ketoglutarate catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the succinyl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998). While all of the human proteins are known as predicted protein products of cloned genes, direct experimental evidence for their functions is available only for E3 (DLD) (Brautigam et al. 2005).
Mitochondrial succinate CoA ligase (ADP-forming) catalyzes the reversible conversion of succinyl CoA to succinate plus Coenzyme A, coupled to the conversion of ADP and orthophosphate to ATP. The enzyme is a heterodimer containing SUCLG1 and SUCLA2 monomers. The enzyme catalyzing the reaction in vertebrates is a heterodimer that occurs in two isoforms. The enzymes have been purified from pigeon and rat tissue and characterized in detail. Both isoforms, an alpha:betaA heterodimer and an alpha:betaG heterodimer, catalyze the reversible conversion of succinyl CoA to succinate plus Coenzyme A. The alpha:betaA heterodimer couples this conversion to the synthesis of ATP from ADP and orthophosphate, while the alpha:betaG heterodimer couples it to the synthesis of GTP from GDP and orthophosphate (Johnson et al. 1998a,b; Lambeth et al. 2004). Consistent with these results in model systems, patients homozygous for a mutant allele of the gene encoding the ADP enzyme beta subunit, SUCLA2, are deficient in succinyl CoA ligase activity (Elpeleg et al. 2005). Both isoforms are found in vivo, and appear to be expressed at different levels in various tissues. Their relative contributions to the flux of carbon atoms through the TCA cycle are unknown. Genetic and biochemical data suggest that the alpha:betaA isoform may be required to catalyze the reverse reaction, conversion of succinate, Coenzyme A, and ATP to succinyl CoA, ADP, and orthophosphate for heme biosynthesis (Furuyama and Sassa 2000).
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GLUT8, a novel member of the sugar transport facilitator family with glucose transport activity
Nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis. Nucleosides and free bases generated by DNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis. Nucleosides and free bases generated by RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of purine biosynthesis. Under normal conditions, DNA turnover is limited and deoxyribonucleotide salvage operates at a correspondingly low level (Watts 1974).
Cytosolic GMP synthase (GMPS) catalyzes the reaction of xanthosine 5'-monophosphate (XMP), ATP, glutamine and water to form guanosine 5'-monophosphate (GMP), AMP, glutamate and pyrophosphate. GMPS is a monomer (Hirst et al. 1994; Nakamura and Lou 1995).
Two isoforms of adenylosuccinate synthetase, ADSS and ADSSL1, catalyze the reaction of IMP, aspartate, and GTP to form adenylosuccinate, GDP, and orthophosphate (Powell et al. 1992; Sun et al. 2005). ADSS is a homotetramer (unpublished crystallographic data - PDB 2V40) and ADSSL1 is inferred to be a tetramer likewise.
The irreversible conversion of adenylosuccinate to adenosine 5'-monophosphate and fumarate is catalyzed by adenylosuccinate lyase. The active form of this enzyme is a cytosolic tetramer (Stone et al. 1993). The enzyme also catalyzes the conversion of 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) and fumarate. Humans lacking the enzyme accumulate dephosphorylated forms of both substrates, indicating that the enzyme mediates both reactions in vivo as well (Race et al. 2000).
Interaction of recombinant human eIF2 subunits with eIF2B and eIF2alpha kinases
The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), with atoms derived from aspartate, glutamine, glycine, N10-formyl-tetrahydrofolate, and carbon dioxide. Although several of the individual reactions in this sequence are reversible, as indicated by the double-headed arrows in the diagram, other irreversible steps drive the pathway in the direction of IMP synthesis in the normal cell. All of these reactions are thus annotated here only in the direction of IMP synthesis. Guanosine 5'-monophosphate (GMP) and adenosine 5'-monophosphate (AMP) are synthesized from IMP.
Cytosolic adenosine deaminase (ADA) catalyzes the hydrolysis of 2'deoxyadenosine and adenosine to yield deoxyinosine and inosine, respectively, plus ammonia (Akeson et al. 1988). Unpublished crystallographic data (PDB 3IAR) indicate that the human enzyme is a monomer.
Cytosolic AMP deaminase (AMPD) catalyzes the hydrolysis of AMP to yield IMP and ammonia. Three isoforms of AMPD, E, L, and M, have been identified that differ in their expression patterns in the body. All occur as tetramers and all have qualitatively the same catalytic activity, however (Bausch-Jurken et al. 1992; Mahnke-Zizelman et al. 1998).
Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of N6-methyl-AMP and water to form IMP and methylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
Cytosolic hypoxanthine-guanine phosphoribosyltransferase (HPRT1) tetramer catalyzes the reactions of guanine or hypoxanthine with PRPP to form GMP ir IMP and pyrophosphate (Holden and Kelley 1978; Jolly et al. 1983).
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Two human isoenzymes, IMP dehydrogenase 1 and 2 (IMPDH1,2) catalyze the irreversible dehydrogenation of inosine 5'-monophosphate (IMP) to form xanthosine 5'-monophosphate (XMP). The active forms of both isoenzymes are homotetramers, and they are nearly identical in their catalytic efficiencies and their susceptibility to inhibition by XMP (Carr et al. 1993; Colby et al. 1999; Hager et al. 1995). Both enzymes occur as homotetramers (Colby et al. 1999 - IMPDH2; unpubliched data in PDB 1JCN IMPDH1). A variety of experiments suggest that IMPDH1 and 2 have distinct functions in vivo. While IMPDH1 is expressed at constant levels, IMPDH2 is expressed at elevated levels in tumor cells and in mitotic normal cells. In humans, heterozygosity for mutant forms of IMPDH1 is associated with a form of retinitis pigmentosa (Bowne et al. 2002). In laboratory mice, mutations that disrupt the homologue of IMPDH1 have no obvious effect at the level of the whole organism, while ones that disrupt IMPDH2 are lethal (Gu et al. 2003). This reaction is the rate limiting step in the synthesis of guanosine 5'-monophosphate (GMP) from IMP, and GMP competitively inhibits the well-characterized bacterial IMP dehydrogenase enzyme. Evidence for an inhibitory effect of GMP on the human isoenzymes has not been reported. Rather, they appear to be inhibited by XMP; in addition, transcription of one or both IMP dehydrogenase mRNAs may be inhibited by high cellular GMP concentrations (Glesne et al. 1991).
PPARalpha controls the intracellular coenzyme A concentration via regulation of PANK1alpha gene expression
Cori Cycle (interconversion of glucose and lactate)
Am. J. Physiol., Cell Physiol. 302:C943-65
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Biosynthesis and metabolism of leukotrienes
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Yin and Yang of hypothalamic insulin and leptin signaling in regulating white adipose tissue metabolism
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STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity
Identification of a mammalian mitochondrial porphyrin transporter
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Humans possess two mitochondrial ferredoxins, Fdx1 and Fdx2, with distinct roles in steroidogenesis, heme, and Fe/S cluster biosynthesis
Evidence that the coproporphyrinogen oxidase activity of rat liver is situated in the intermembrane space of mitochondria
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Mitochondrial energy-linked nicotinamide nucleotide transhydrogenase. Membrane topography of the bovine enzyme
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The mechanism of phospholipase C-gamma1 regulation
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Inositol polyphosphate multikinase regulates inositol 1,4,5,6-tetrakisphosphate
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Isolation and complete sequence of a functional human glyceraldehyde-3-phosphate dehydrogenase gene
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Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin
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1-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:29017]
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Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling
The C-terminal appended domain of human cytosolic leucyl-tRNA synthetase is indispensable in its interaction with arginyl-tRNA synthetase in the multi-tRNA synthetase complex
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Formation of transcription-coupled NER (TC-NER) repair complex
Mercury-sensitive residues and pore site in AQP3 water channel
S-(2,4-Dinitrophenyl)glutathione [ChEBI:8927]
Transient receptor potential 1 regulates capacitative Ca(2+) entry and Ca(2+) release from endoplasmic reticulum in B lymphocytes
Syk protein-tyrosine kinase is regulated by tyrosine-phosphorylated Ig alpha/Ig beta immunoreceptor tyrosine activation motif binding and autophosphorylation
Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers
The sodium/glucose cotransport family SLC5
Catalytic properties of human manganese superoxide dismutase
Phosphoinositide signalling in cancer: beyond PI3K and PTEN
(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
The SLC39 family of metal ion transporters
Cloning and functional expression of the human GlcNAc-1-P transferase, the enzyme for the committed step of the dolichol cycle, by heterologous complementation in Saccharomyces cerevisiae
Reconstitution of 5'-directed human mismatch repair in a purified system
Vasopressin regulates renal water homeostasis via Aquaporins
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HDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and excretion from the body and provided to tissues such as the adrenals and gonads for steroid hormone synthesis (Tall et al. 2008). HDL particles are heterogeneous and can be fractionated into sub-populations based on their electrophoretic mobility, their density, or their content of various apolipoproteins. Sub-populations yielded by any one fractionation strategy, however, remain heterogeneous with respect to the other two parameters (Kontush and Chapman 2006). All HDL particles share two key features: they are assembled on a protein scaffold provided by apolipoprotein A-I (apoA-I), and they are recycled to allow a net flow of lipids from peripheral tissues to the liver and steroidogenic tissues while allowing apoA-I molecules to be re-used. The HDL life cycle annotated here does not capture the full complexity of HDL structure and function but rather is an attempt to outline the key steps by which HDL particles assemble and transfer their lipid content. These steps include the assembly of nascent (discoidal) HDL particles on newly synthesized apoA-I, a process that in the body occurs primarily in the liver, the loading of discoidal HDL with additional lipid through interaction with cells carrying excess cholesterol (transformation to spherical HDL), the conversion of HDL-associated cholesterol to cholesterol esters (remodeling of spherical HDL), the transfer of HDL lipids to target cells with the regeneration of pre-beta HDL (lipid-poor apoA-I), and the conversion of pre-beta HDL to discoidal HDL to complete the cycle. Additional reactions provide houekeeping functions needed for the efficient operation of the cycle: binding and release of CETP, dispersal of byproducts of the CETP reaction, and export and degradation of excess apoA-I protein. Finally, the function of torcetrapib as an inhibitor of CETP function is annotated.
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LCAT activated by apoA-I catalyzes the reaction of cholesterol and phosphatidylcholine to yield cholesterol esterified with a long-chain fatty acid and 2-lysophosphatidylcholine. While this reaction was first studied in vitro using purified proteins in solution, it occurs in vivo on the surfaces of HDL particles where transiently-bound LCAT is activated by HDL-associated apoA-I protein and consumes HDL-associated cholesterol and phosphatidylcholine. The cholesterol ester reaction product is strongly associated with the HDL particle because of its increased hydrophobicity, while the 2-lysophosphatidylcholine product is released from the particle (Fielding et al. 1972 [2 references]; Adimoolam et al. 1998).
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Because of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport dietary lipids to other tissues in the body. Very low density lipoproteins (VLDL) form in the liver and transport triacylglycerol synthesized there to other tissues of the body. As they circulate, VLDL are acted on by lipoprotein lipases on the endothelial surfaces of blood vessels, liberating fatty acids and glycerol to be taken up by tissues and converting the VLDL first to intermediate density lipoproteins (IDL) and then to low density lipoproteins (LDL). IDL and LDL are cleared from the circulation via a specific cell surface receptor, found in the body primarily on the surfaces of liver cells. High density lipoprotein (HDL) particles, initially formed primarily by the liver, shuttle several kinds of lipids between tissues and other lipoproteins. Notably, they are responsible for the so-called reverse transport of cholesterol from peripheral tissues to LDL for return to the liver. Three aspects of lipoprotein function are currently annotated in Reactome: chylomicron-mediated lipid transport, LDL endocytosis and degradation, and HDL-mediated lipid transport.
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Inositol-3-phosphate synthase 1 (ISYNA1) aka hIPS isomerises glucose 6-phosphate (Glc6P) to inositol 3-phosphate (I3P) (Ju et al. 2004).
A group of inositol phosphatases dephosphorylate inositol 1,4,5-trisphosphate (I(1,4,5)P3) to inositol 1,4-bisphosphate (I(1,4)P2). The group of inositol phosphatases involved are: inositol polyphosphate 5-phosphatase OCRL-1 (OCRL), phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J), and synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1). The following lists the above proteins with their corresponding literature references: OCRL (Zhang et al. 1995, Zhang et al. 1998, Schmid et al. 2004); INPP5J (Mochizuki & Thompson 1999); SYNJ1 (Schmid et al. 2004).
Inositol phosphates (IPs) are molecules involves in signalling processes in eukaryotes. myo-Inositol consists of a six-carbon cyclic alcohol with an axial 2-hydroxy and five equatorial hydroxyls. Mono-, di-, and triphosphorylation of the inositol ring generates a wide variety of stereochemically distinct signalling entities. Inositol 1,4,5-trisphosphate (I(1,4,5)P3), is formed when the phosphoinositide phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is hydrolysed by a phospholipase C isozyme. An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol. These species then transport between the cytosol and the nucleus where they are acted on by inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2), to produce IP5, IP6, IP7, and IP8 molecules. Some of these nuclear produced IPs transport back to the cytosol where they are converted to an even wider variety of IPs, by kinases and phosphatases, including the di- and triphospho inositol phosphates aka pyrophosphates (Irvine & Schell 2001, Bunney & Katan 2010, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010).
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Inositol phosphates IP2, IP and the six-carbon cyclic alcohol inositol (Ins) are produced by various phosphatases and the inositol-3-phosphate synthase 1 (ISYNA1) (Ju et al. 2004, Ohnishi et al. 2007, Irvine & Schell 2001, Bunney & Katan 2010).
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1/2 (PPIP5K1) and 2 (PPIP5K2) phosphorylate inositol 1,2,3,4,5,6-hexakisphosphate (IP6) to inositol 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5)) (Fridy et al. 2007, Mulugu et al. 2007, Choi et al. 2007, Lin et al. 2009; Wang et al. 2011).
Molecular cloning and characterization of a novel muscle adenylosuccinate synthetase, AdSSL1, from human bone marrow stromal cells
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1/2 (PPIP5K1) and 2 (PPIP5K2) phosphorylate inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5) to inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) (Fridy et al. 2007, Mulugu et al. 2007, Choi et al. 2007, Lin et al. 2009).
A sequence variation (I148M) in PNPLA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis
Inositol phosphates such as IP4, IP5 and IP6 are converted to an even wider variety of IPs including the di- and triphospho inositol phosphates, also known as pyrophosphates (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Ho et al. 2002, Saiardi et al. 2001, Draskovic et al. 2008, Choi et al. 2007, Caffrey et al. 2000, Leslie et al. 2002).
The human homologue of yeast ArgRIII protein is an inositol phosphate multikinase with predominantly nuclear localization
Metabolism, function and mass spectrometric analysis of bis(monoacylglycero)phosphate and cardiolipin
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Oligomerization of STIM1 couples ER calcium depletion to CRAC channel activation
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Elongation of very long chain fatty acids protein 3 (ELOVL3) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH. Indirect data from studies of transfected cells expressing ELOVL3 are consistent with its localization to the endoplasmic reticulum and activity on palmitoyl-CoA (Kobayashi et al. 2007).
Elongation of very long chain fatty acids protein 2 (ELOVL2) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH. Indirect data from studies of transfected cells expressing ELOVL2 are consistent with its localization to the endoplasmic reticulum and activity on palmitoyl-CoA. It may also catalyze the condensation of arachidonyl-CoA with malonyl-CoA (Kobayashi et al. 2007).
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Elongation of very long chain fatty acids protein 1 (ELOVL1) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH. Limited data are available for human ELOVL1 protein. Its localization to the endoplasmic reticulum membrane and catalytic activity are inferred from the properties of better-studied human ELOVL proteins (Jakobsson et al. 2006; Shimamura et al. 2009).
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Acyl-CoA synthetase long-chain family member 6 (ACSL6) associated with the plasma membrane catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. In the body, ACSL6 is found in red blood cells. It is active on oleic acid as well as palmitic acid (Malhotra et al. 1999).
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Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
Acyl-CoA synthetase long-chain family member 5 (ACSL5) associated with the endoplasmic reticulum membrane catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water (Gassler et al. 2007).
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Acyl-CoA synthetase long-chain family member 4 (ACSL4) associated with the endoplasmic reticulum membrane catalyzes the reaction of arachidonate, CoASH, and ATP to form arachidonyl-CoA, AMP, pyrophosphate, and water (Longo et al. 2003; Meloni et al. 2003).
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Membrane-associated acyl-CoA synthetase long-chain family member 1 (ACSL1) catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. Human ACSL1 has not been characterized in detail, but available data suggest that it is associated specifically with the membrane of the endoplasmic reticulum and that it can act on oleic acid as well as on palmitic acid (Malhotra et al. 1999).
Membrane-associated acyl-CoA synthetase long-chain family member 3 (ACSL3) catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. The enzyme is probably associated specifically with the endoplasmic reticulum membrane, and can also associate with lipid droplets. It is active on oleic acid as well as on palmitic acid (Fujimoto ea 2007).
Processes annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids through the action of hormone-sensitive lipase.
Cytosolic acetyl-CoA carboxylase 1 (ACACA) catalyzes the reaction of bicarbonate, ATP, and acetyl-CoA to form malonyl-CoA, ADP, and orthophosphate. The reaction is positively regulated by citrate. The human ACACA cDNA has been cloned (Abu-Elheiga et al. 1995) and the biochemical properties of the human enzyme have recently been described (Cheng et al. 2007; Locke et al. 2008). Four ACACA isoforms generated by alternative splicing have been identified as mRNAs - the protein product of the first has been characterized experimentally.
Vitamins are essential nutrients, required in small amounts from the diet for the normal growth and development of a multicellular organism. Where there is vitamin deficiency, either by poor diet or a defect in metabolic conversion, diseases called Avitaminoses occur. Currently, cobalamin (Cbl, vitamin B12) metabolic defects are described below (Chapter 155 in The Metabolic and Molecular Bases of Inherited Disease, 8th ed, Scriver et al. 2001)
Biochemical and stability properties of recombinant human MnSOD
Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation
Defects in MUT cause methylmalonic aciduria, mut type (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006).
Defects in MMAA cause methylmalonic aciduria type cblA (cblA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonic aciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
Cobalamin (Cbl, vitamin B12) is a nutrient essential for normal functioning of the brain and nervous system and for the formation of blood. Cbl-dependent methionine synthase (MTR) is required for conversion of 5-methyltetrahydrofolate (metTHF) to tetrahydrofolate (THF), in addition to its role in conversion of homocysteine to methionine. In Cbl deficiency, and in inborn errors of Cbl metabolism that affect function of methionine synthase, inability to regenerate THF from metTHF results in decreased function of folate-dependent reactions that are involved in 2 steps of purine biosynthesis and thymidylate synthesis. Cbl deficiency results in hyperhomocysteinemia (due to defects in the conversion of homocysteine to methionine which requires Cbl as a cofactor) and increased levels of methylmalonic acid (MMA). Methionine is used in myelin production, protein, neurotransmitter, fatty acid and phospholipid production and DNA methylation. Symptoms of Cbl deficiency are bone marrow promegaloblastosis (megaloblastic anemia) due to the inhibition of DNA synthesis (specifically purines and thymidine) and neurological symptoms. The defective genes involved in Cbl deficiencies are described below (Froese & Gravel 2010, Nielsen et al. 2012, Whitehead 2006, Watkins & Rosenblatt 2011, Fowler 1998).
Defects in CD320 cause methylmalonic aciduria type TCblR (MMATC aka methylmalonic aciduria; MIM:613646) resulting in elevated methylmalonic acid (MMA) and homocysteine (HCYS) in newborns (Quadros et al. 2010).
Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five biotin-dependent carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). Patients can present symptoms shortly after birth to up to early childhood and will be prescribed oral biotin supplements, typically 10-20 mg daily. Two classes of HLCS deficiency have been reported depending on whether patients respond to biotin therapy. Most patients respond favourably to treatment and show complete reversal of biochemical and clinical symptoms (Morrone et al. 2002, Dupuis et al. 1999). Here mutations in the HLCS active site cause a reduced affinity for biotin that can be overcome by pharmacological doses of the vitamin (Pendini et al. 2008). Patients who display incomplete responsiveness to biotin therapy have a poor long-term prognosis (Bailey et al. 2008). Here mutations that reside outside of the enzyme's active site have no effect on biotin binding but do compromise the protein-protein interaction between the HLCS and its substrates, resulting in reduced biotinylation of all five carboxylases thus reducing their enzymatic activity (Mayende et al. 2012).
Biotin (Btn) acts as a coenzyme for 5 carboxylases that exist in their inactive apo forms. In the cytosol and mitochondrion, these apo carboxylases (apo-CBXs) are biotinylated to their active holo forms by the activity of biotin protein ligase (HCLS) (Ingaramo & Beckett 2012, Bailey et al. 2010, Hiratsuka et al. 1998). Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early-onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all 5 carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis. Mutations in HCLS associated with HLCS deficiency include the compound heterozygote G261Vfs*20/L237P, D571N, R508W, G581S, V550M and L216R (Suzuki et al. 1994, Yang et al. 2000, Dupuis et al. 1996, Aoki et al, 1999, Yang et al. 2001, Morrone et al. 2002).
Biotin (Btn, vitamin B7, vitamin H, coenzyme R) is an essential cofactor for five biotin-dependent carboxylase enzymes, involved in the synthesis of fatty acids, isoleucine, valine and in gluconeogenesis. Thus, Btn is necessary for cell growth, fatty acid synthesis and the metabolism of fats and amino acids. Inherited metabolic disorders characterized by deficient activities of all five biotin dependent carboxylases are termed multiple carboxylase deficiencies. Two congenital defects in biotin metabolism leading to multiple carboxylase deficiency are known, holocarboxylase synthetase deficiency (MIM 609018) and biotinidase deficiency (MIM 253260). In both scenarios symptoms include ketolactic acidosis, organic aciduria, hyperammonemia, skin rashes, hypotonia, seizures, developmental delay, alopecia, and coma. As humans are auxotrophic for Btn, the micronutrient must be obtained from external soures such as intestinal microflora and dietary forms. Accordingly, severe malnutrition can also give rise to biotin deficiency and multiple carboxylase deficiency. Biotin deficiency can also be induced by the excessive consumption of raw egg white that contains the biotin-binding protein avidin. Holocarboxylase synthetase deficiency arises when all five biotin-dependent enzymes are not biotinylated leading to their reduced activities. The defective genes causing these conditions are described here (Pendini et al. 2008, Suzuki et al. 2005). Biotinidase deficiency is caused by defects in the recycling of Btn. General symptoms include decreased appetite and growth, dermatitis and perosis. The defective genes causing these conditions are described here (Procter et al. 2013).
ChEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate
BTD deficiency is an autosomal recessive disorder in which the body is unable to recycle and reuse biotin (Btn). This results in a secondary Btn deficiency that leads to juvenile-onset multiple carboxylase deficiency (MIM:253260) (Wolf 2012, Wolf et al. 1983). Patients present with neurological and cutaneous symptoms, including seizures, hypotonia, skin rash, and alopecia, usually between the second and fifth months of life (Wolf 2010). Children with profound BTD deficiency are treated with pharmacological doses of biotin (5-20 mg daily). Neonatal screening for BTD deficiency is performed in most states of the United States and many other countries.
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
Defects in MMAB cause methylmalonic aciduria type cblB (cblB aka methylmalonic aciduria type B or vitamin B12 responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and episodes of metabolic ketoacidosis, despite a functional methylmalonyl CoA mutase. In severe cases, newborns become severely acidotic and may die if acidosis is not treated promptly (Dobson et al. 2002).
Gap-filling DNA repair synthesis and ligation in TC-NER
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,4,5-trisphosphate (I(1,4,5)P3) to inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) (Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006).
An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol (Irvine & Schell 2001, Bunney & Katan 2010).
A group of inositol phosphatases and the broad specificity enzyme inositol-tetrakisphosphate 1-kinase (ITPK1) dephosphorylate inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) to inositol 1,3,4-trisphosphate (I(1,3,4)P3). The group of inositol phosphatases involved are: inositol polyphosphate 5-phosphatase OCRL-1 (OCRL), phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 1 (INPP5D) aka SHIP1, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2 (INPPL1) aka SHIP2, phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) aka PIPP, and synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1). The following lists the above proteins with their corresponding literature references: OCRL (Chang et al. 2002, Zhang et al. 1995, Zhang et al. 1998, Schmid et al. 2004); INPP5D (Drayer et al. 1996, Kavanaugh et al. 1996); INPPL1 (Chi et al. 2004); INPP5J (Mochizuki & Thompson 1999); SYNJ1 (Schmid et al. 2004); ITPK1 (Ho et al. 2002).
A group of phospholipase C proteins (PLC(degh)) bind to the plasma membrane via their PH domains. These phospholipases hydrolyse phosphatidylinositol 4,5 bisphosphate (PI(4,5)P2) to inositol 1,4,5 trisphosphate (I(1,4,5)P3) and diacylglycerol (DAG). The C2 domains of the enzymes bind to PI(4,5)P2 at the membrane. The phospholipase C isoforms involved and their corresponding literature references are: phosphoinositide phospholipase C delta-1(PLCD1) (Cheng et al. 1995); epsilon-1 (PLCE1) (Song et al. 2001, Lopez et al. 2001); delta-3 (PLCD3) (Pawelczyk & Matecki 1997); gamma-1 (PLCG1) (Harita et al. 2009, Baldassare et al. 1989); gamma-2 (PLCG2) (Banno et al. 1988); eta-1 (PLCH1) (Hwang et al. 2005); and eta-2 (PLCH2) (Zhou et al 2005).
Within the nucleus, inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) produce IP5, IP6, IP7, and IP8 inositol phosphate molecules (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006, Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008, Mulugu et al. 2007).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,4,5,6-tetrakisphosphate (I(1,4,5,6)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Nalaskowski et al. 2002, Chang & Majerus 2006).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,3,4,6-tetrakisphosphate (I(1,3,4,6)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Chang et al. 2002, Chang & Majerus 2006).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Nalaskowski et al. 2002, Chang & Majerus 2006).
Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes: the inclusion of microbially-expressed proteins, altered functions of human proteins, or changed expression levels of otherwise functionally normal human proteins. The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's. Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.
At the plasma membrane, a group of phospholipase C (PLC(bz)) proteins hydrolyse phosphatidylinositol 4,5 bisphosphate (PI(4,5)P2) to inositol 1,4,5 trisphosphate (I(1,4,5)P3) and diacylglycerol (DAG). This group of phospholipase C proteins lack a PH domain and so are is cytosolic. Their C2 domains bind to PI(4,5)P2 at the membrane. The PLC-beta proteins are thought to be responsible for the majority of PI(4,5)P2 hydrolysis. The phospholipase C isoforms involved and their corresponding literature references are: phosphoinositide phospholipase C beta-1 (PLCB1) (Caricasole et al. 2000, Jhon et al. 1993, Park et al. 1992); beta-2 (PLCB2) (Jhon et al. 1993, Park et al. 1992); beta-3 (PLCB3) (Carozzi et al. 1992, Jhon et al. 1993); beta-4 (PLCB4) (Alvarez et al. 1995, Lee et al. 1993); and zeta-1 (PLCZ1) (Kouchi et al. 2005, Rogers et al. 2004).
Functional characterization of a human aquaporin 0 mutation that leads to a congenital dominant lens cataract
The Nod-like receptor (NLR) family: a tale of similarities and differences
Androgens are the determining factors for male development and behaviour in vertebrates (Miller 2002).
The conversion of testosterone to the most potent androgen, 5-alpha-dihydrotestosterone (DHT), is catalyzed by the microsomal 5alpha-steroid reductase enzymes, of which there are three reported types in humans to date (SRD5A1-3) (Andersson S and Russell DW, 1990; Andersson S et al, 1991; Uemura M et al, 2008 respectively). These enzymes are expressed in the prostate and other androgen target sites. Defects in SRD5A2 are the cause of pseudovaginal perineoscrotal hypospadias, also known as male pseudohermaphroditism (Anwar R et al, 1997). Corticotropin (Adrenocorticotropic hormone, ACTH) acts through the ACTH receptor called melanocortin receptor type 2 (MC2R) to stimulate steroidogenesis, increasing the production of androgens (McKenna et al, 1997).
In the de novo synthesis of phosphatidic acid (PA), lysophosphatidic acid (LPA) is initially formed by the esterification of sn-1 by glycerol 3-phosphate acyltransferase (GPAT) from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT). In addition to this, PA is also formed when phosphatidylcholine (PC) is hydrolyzed by phospholipase D1/2 (PLD1/2). PA is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by acyltransferases (Ghomashchi et al. 2010, Singer et al. 2002, Prasad et al. 2011, Shindou & Shimizu 2009, Cao et al. 2006).
Steroid hormones are synthesized primarily in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). All steroids are synthesized from cholesterol. Steroid hormone synthesis is largely regulated at the initial steps of cholesterol mobilization and transport into the mitochondrial matrix for conversion to pregnenolone. In the body, the fate of pregnenolone is tissue-specific: in the zona fasciculata of the adrenal cortex it is converted to cortisol, in the zona glomerulosa to aldosterone, and in the gonads to testosterone and then to estrone and estradiol. These pathways are outlined in the figure below, which also details the sites on the cholesterol molecule that undergo modification in the course of these reactions. Vitamin D3 (cholecalciferol) is a steroid hormone that plays a role in regulating calcium and bone metabolism. The processes by which it is synthesized, modified, and transported in the body are annotated here.
At the endoplasmic reticulum (ER) membrane, diacylglycerol (DAG) is acylated and forms triacylglycerol (TAG) by the action of diacylglycerol O-acyltransferase 1 (DGAT1) tetramer or by diacylglycerol O-acyltransferase 2 (DGAT2) (Wakimoto et al. 2003, Oelkers et al. 1998, Cases et al. 2001).
At the endoplasmic reticulum (ER) membrane, triacylglycerol (TAG) is hydrolyzed, removing one of its acyl groups to form diacylglycerol (DAG) by patatin-like phospholipase domain-containing protein 2/3 (PNPLA2/3) (He et al. 2010, Jenkins et al. 2004, Basantani et al. 2011).
At the endoplasmic reticulum (ER) membrane, two 2-monoacylglycerol (2-MAG) molecules are transacylated by patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3) to form diacylglycerol (DAG) and glycerol (Jenkins et al. 2004).
At the endoplasmic reticulum (ER) membrane, patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3) hydrolyze diacylglycerol (DAG), removing an acyl group to form 2-monoacylglycerol (2-MAG) (He et al. 2010, Jenkins et al. 2004, Basantani et al. 2011).
At the endoplasmic reticulum (ER) membrane, a 2-monoacylglycerol (2-MAG) molecule and a diacylglycerol (DAG) molecule are transacylated by patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3). This forms triacylglycerol (TAG) and glycerol (Jenkins et al. 2004).
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Acyl chain remodeling of triacylglycerol (TAG) and diacylglycerol (DAG) progresses through their hydrolysis by patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3). DAG is reacylated back to TAG by acylglycerol O-acyltransferase 1/2 (DGAT1/2), while DAG and its hydrolysis product 2-monoacylglycerol (2-MAG) are transacylated back to TAG by PNPLA2/3. In addition, the DAG hydrolysis product 2-MAG is subsequently hydrolyzed to fatty acid and glycerol by monoglyceride lipase (MGLL) (Jenkins et al. 2004).
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Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
Human liver type pyruvate kinase: complete amino acid sequence and the expression in mammalian cells
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The TXNRD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ACSL1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
FAD-linked mitochondrial glycerol 3-phosphate dehydrogenase (GPD2, alias: mGPDH) and its NAD-linked cytosolic isoform (GPD1, alias:cGPDH) constitute glycerol phosphate shuttle. GPD2 catalyzes the unidirectional conversion of glycerol-3-phosphate (G-3-P) to dihydroxyacetone phosphate (DHAP) with concomitant reduction of the enzyme-bound FAD. Impaired activity of GPD2 has been suggested to be one of the primary causes of insulin secretory defects in beta-cells and thus it is a candidate gene for type 2 diabetes.
The family of enzymes called prenyltransferases is involved in the biosynthesis of isoprenoids. Two members of this family are known to catalyse the sequential condensation of isopentenyl pyrophosphate to DMAPP: farnesyl pyrophosphate synthase (FPPS) and geranylgeranyl pyrophosphate synthetase (GGPPS) (Kavanaugh et al, 2006).
The reactions involved in the metabolism of fatty acids and of the triacylglycerols and ketone bodies derived from them form a closely interrelated, coordinately regulated module that plays a central role in human energy metabolism.
Peroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma lipid levels. PPAR-alpha is a type II nuclear receptor (its subcellular location does not depend on ligand binding). PPAR-alpha forms heterodimers with Retinoid X receptor alpha (RXR-alpha), another type II nuclear receptor. PPAR-alpha is activated by binding fatty acid ligands, especially polyunsaturated fatty acids having 18-22 carbon groups and 2-6 double bonds. The PPAR-alpha:RXR-alpha heterodimer binds peroxisome proliferator receptor elements (PPREs) in and around target genes. Binding of fatty acids and synthetic ligands causes a conformational change in PPAR-alpha such that it releases the corepressors and binds coactivators (CBP-SRC-HAT complex, ASC complex, and TRAP-Mediator complex) which initiate transcription of the target genes. Target genes of PPAR-alpha participate in fatty acid transport, fatty acid oxidation, triglyceride clearance, lipoprotein production, and cholesterol homeostasis.
The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: 1) genes involved in fatty acid oxidation and ketogenesis (Acox1, Cyp4a, Acadm, Hmgcs2); 2) genes involved in fatty acid transport (Cd36, , Slc27a1, Fabp1, Cpt1a, Cpt2); 3) genes involved in producing fatty acids and very low density lipoproteins (Me1, Scd1); 4) genes encoding apolipoproteins (Apoa1, Apoa2, Apoa5); 5) genes involved in triglyceride clearance ( Angptl4); 6) genes involved in glycerol metabolism (Gpd1 in mouse); 7) genes involved in glucose metabolism (Pdk4); 8) genes involved in peroxisome proliferation (Pex11a); 9) genes involved in lipid storage (Plin, Adfp). Many other genes are known to be regulated by PPAR-alpha but whether their regulation is direct or indirect remains to be found. These genes include: ACACA, FAS, SREBP1, FADS1, DGAT1, ABCA1, PLTP, ABCB4, UGT2B4, SULT2A1, Pnpla2, Acsl1, Slc27a4, many Acot genes, and others (reviewed in Rakhshandehroo et al. 2010).
The 17HSD family of enzymes catalyze the final step in the synthesis of estradiol and testosterone. They convert inactive 17-ketosteroids to their active 17beta-hydroxy forms. Androstenedione, a ketosteroid, is reduced to testosterone, a highly potent androgen, by the enzyme 17beta-hydroxysteroid dehydrogenase isoform III (17HSD3). The other human isoforms of 17HSDs to take part in the final steps of active steroid biosynthesis are types 1 and VII, which reduce estrone to estradiol. Corticotropin (Adrenocorticotropic hormone, ACTH) acts through the ACTH receptor called melanocortin receptor type 2 (MC2R) to stimulate steroidogenesis, increasing the production of androgens (McKenna et al, 1997). In males, Lutropin (LH) stimulates testosterone production.
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Further condensation of an isopentenyl pyrophosphate with geranyl pyrophosphate to form farnesyl pyrophosphate is catalyzed by the prenyltransferases FPP synthase and GGPP synthase. (Kavanagh et al, 2006)
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Cholesterol is synthesized de novo from from acetyl CoA. The overall synthetic process is outlined in the figure below. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of lanosterol into cholesterol requires multiple steps, including the removal of three methyl groups, the reduction of one double bond and the migration of another. These reactions may not occur in a single fixed order in the body, so the linear pathway laid out here following the work of Gaylor and colleagues (Gaylor 2002) is an oversimplification of the process that occurs in vivo. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Herman 2003; Song et al. 2005).
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Isolation of MutSbeta from human cells and comparison of the mismatch repair specificities of MutSbeta and MutSalpha
The overall process of triglyceride (triacylglycerol) biosynthesis consists of four biochemical pathways: fatty acyl-CoA biosynthesis, conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion fo diacylglycerol to triacylglycerol.
Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of two molecules of acetyl-CoA to form acetoacetyl-CoA and CoA (Middleton et al. 1986).
Antigenic analysis of the major human phosphoglucomutase isozymes: PGM1, PGM2, PGM3 and PGM4
The mitochondrial carnitine system catalyzes the transport of long-chain fatty acids into the mitochondrial matrix where they undergo beta oxidation. This transport system consists of the malonyl-CoA sensitive carnitine palmitoyltransferase I (CPT-I) localized in the mitochondrial outer membrane, the carnitine:acylcarnitine translocase, an integral inner membrane protein, and carnitine palmitoyltransferase II localized on the matrix side of the inner membrane. (Kerner and Hoppel, 2000).
Tetrameric diacylglycerol O-acyltransferase 1 (DGAT1) associated with the endoplasmic reticulum membrane catalyzes the reaction of 1,2-diacyl-glycerol and acyl-CoA to form triacylglycerol + CoASH (Cheng et al. 2001).
Predominant expression and activation-induced tyrosine phosphorylation of phospholipase C-gamma 2 in B lymphocytes
Lipin proteins LPIN1, 2, and 3, associated with the endoplasmic reticulum membrane, can each catalyze the hydrolysis of phosphatidate to yield 1,2-diacyl-glycerol and orthophosphate. The activities of LPIN1 and LPIN2 have been established experimentally (Grimsey et al. 2008); that of LPIN3 is inferred from its structural similarities both to its human paralogues and to its mouse ortholog (Donkor et al. 2007). Only LPIN1 has been shown to be stably associated with the endoplasmic reticulum, but all three enzymes appear to be catalytically active at that location (Grimsey et al. 2008; Donkor et al. 2007).
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In a healthy, well-nourished individual, the production of ketone bodies occurs at a relatively low rate. During periods of normal physiological responses to carbohydrate shortages, the liver increases the production of ketone bodies from acetyl-CoA generated from fatty acid oxidation. This allows heart and skeletal muscle to use ketone bodies as the primary source of energy, thereby preserving the limited glucose supply for use in brain tissue. In untreated diabetes mellitus, a huge buildup of ketone bodies occurs due to an increase in fatty acid oxidation. The production of ketone bodies exceeds the ability of peripheral tissues to oxidize them, and results in lowering the pH of blood. Blood acidification is dangerous, chiefly as it impairs the ability of hemoglobin to bind oxygen. Ketone body synthesis proceeds via the synthesis of ccetoacetic acid in three steps from acetyl CoA, followed by the reduction of acetoacetic acid to beta-hydroxybutyrate. In the body, these reactions occur in the mitochondria of liver cells (Sass 2011).
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Phosphorylation by p34cdc2 regulates spindle association of human Eg5, a kinesin-related motor essential for bipolar spindle formation in vivo
Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of acetoacetyl-CoA and CoA to form two molecules of acetyl-CoA (Middleton et al. 1986).
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The levels of acetone in ketone bodies are much lower than those of acetoacetic acid and beta-hydroxybutyric acid. Acetone cannot be converted back to acetyl-CoA, and is excreted in urine, or breathed out through the lungs. Extrahepatic tissues utilize ketone bodies by converting the beta-hydroxybutyrate successively to acetoacetate, acetoacetatyl-CoA, finally to acetyl-CoA (Sass 2011).
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Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells. Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. There, they are broken down to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose (Sass 2011).
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Hydroxysteroid (17-beta) dehydrogenase 12 (HSD17B12) catalyzes the reaction of 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) and NADPH + H+ to form 3-hydroxyoctadecanoyl-CoA and NADP+. This activity of HSD17B12 protein and its localization to the endoplasmic reticulum membrane was established in studies of transfected cells expressing the protein (Moon and Horton 2003).
Elongation of very long chain fatty acids protein 7 (ELOVL7) catalyzes the reaction of arachidoyl-CoA (C20:0) and malonyl-CoA to form 3-oxobehenoyl-CoA, CO2, and CoASH. ELOVL7 is localized to the endoplasmic reticulum in transfected cells expressing the cloned cDNA (Tamura et al. 2009).
Elongation of very long chain fatty acids protein 6 (ELOVL6) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH (Shimamura et al. 2009). The localization of ELOVL6 to the endoplasmic reticulum membrane is inferred from that experimentally determined for the homologous mouse protein (Moon et al. 2001; Matsuzaka et al. 2002).
Elongation of very long chain fatty acids protein 5 (ELOVL5) catalyzes the reaction of arachidonyl-CoA and malonyl-CoA to form 3-oxo-(7,10,13,16)-docosatetraenoyl-CoA, CO2, and CoASH. Localization of ELOVL5 to the endoplasmic reticulum membrane is inferred from that of other human ELOVL proteins; its catalytic activity has been studied in ELO- yeast cells expressing human ELOVL5 protein (Leonard et al. 2000).
Elongation of very long chain fatty acids protein 4 (ELOVL4) catalyzes the reaction of lignoceroyl-CoA and malonyl-CoA to form 3-oxocerotoyl-CoA, CO2, and CoASH. ELOVL4 is abundant in retinal cells, where it is localized to the endoplasmic reticulum membrane (Grayson and Molday 2005). The catalytic activity of ELOVL4 has not been examined directly but is inferred from that of the homologous mouse protein, which is also active on polyunsaturated fatty acids (PUFAs) (Agbada et al. 2008).
Glycerol can be a source for glycerol-3-phosphate, in which case, a phosphate form ATP is transferred to glycerol by glycerol kinase forming glycerol-3-phosphate and ADP.
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Fatty acyl-CoA biosynthesis involves following steps: -Palmitate synthesis catalyzed by Acetyl-CoA carboxylase and Fatty acid synthase -Conversion of palmitic acid to long chain fatty acids and -Conversion of long chain fatty acids to fatty acyl-CoA by acyl-CoA synthases.
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Dihydroxyacetone phosphate (DHAP) is converted to glycerol-3-phosphate (G3P) by glycerol-3-phosphate dehydrogenase (GPD1) or by glycerol-3-phosphate dehydrogenase-like (GPD1L) enzymes (Ou et al. 2006, Valdivia et al. 2009). The active forms of both enzymes are homodimers. This reaction may be found in white adipose tissues where glycerol-3-kinase activity is not observed in sufficient levels. GPD1/GPD1L reduces dihydroxyacetone phosphate with NADH donating electrons to this reduction.
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Trans-2,3-enoyl-CoA reductase (TECR) catalyzes the reaction of trans-octadec-2-enoyl-CoA and NADPH + H+ to form stearoyl-CoA and NADP+. This activity of TECR protein and its localization to the endoplasmic reticulum membrane was established in studies of transfected cells expressing the protein (Moon and Horton 2003).
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Very long-chain fatty acyl-CoA molecules are synthesized from palmitic acid (C16) or other fatty acids that are synthesized de novo or obtained from the diet. Before they can be elongated, these fatty acids are activated by conversion to fatty acyl-CoAs in reactions catalyzed by the five members of the ACSL (acyl-CoA synthetase long-chain) enzyme family. Elongation proceeds by a four-step reaction sequence parallel to that responsible for the synthesis of palmitate (C16) from acetyl-CoA and malonyl-CoA: a molecule of malonyl-CoA condenses with the long chain fatty acyl-CoA forming a 3-oxoacyl-CoA containing two more carbon atoms than the starting long chain fatty acyl-CoA and CO2. This reaction is catalyzed by one of the seven members of the ELOVL (Elongation of very long chain fatty acids protein) enzyme family. The 3-oxoacyl-CoA is reduced to a 3-hydroxyacyl-CoA by HSD17B12 (hydroxysteroid (17-beta) dehydrogenase 12), 3-hydroxyacyl-CoA is dehydrated to a trans-2,3-enoyl-CoA, and the trans-2,3-enoyl-CoA is reduced to a fatty acid two carbon atoms longer than the input one by TECR (trans-2,3-enoyl-CoA reductase) enzyme. All of these enzyme activities are associated with separate polypeptides associated with the endoplasmic reticulum membrane, unlike the multifunctional and cytosolic FAS complex responsible for synthesis of palmitic acid (Jakobsson ea 2006; Nugteren 1965). The specific reactions annotated here mediate the synthesis of stearoyl-CoA (3-hydroxyoctadecanoyl-CoA) from palmitate, as well as the activation and condensation with malonyl-CoA of arachidonic acid, a 20-carbon unsaturated fatty acid that plays a central role in the synthesis of prostaglandins and related hormones. Human cells contain a wide range of very long chain fatty acids, and the enzymes involved in these reactions are believed to have broader substrate specificities than are shown in these annotations, but few direct experimental data are available to support more extensive annotations.
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Wnt/beta-catenin signaling: components, mechanisms, and diseases
3-decaprenyl-4-hydroxybenzoic acid [ChEBI:64136]
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Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes
Resistance to thromboembolism in PI3Kgamma-deficient mice
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In the acyl chain remodelling pathway (Lands cycle), phosphatidylcholine (PC) is hydrolysed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Zhao et al. 2008).
At the endoplasmic reticulum (ER) membrane, phosphatidylserine synthase 1 (PTDSS1) converts phosphatidylcholine (PC) into phosphatidylserine (PS) by facilitating the exchange of L-Serine (L-Ser) with the choline (Cho) head group (Saito et al. 1998, Tomohiro et al. 2009).
Molecular cloning of cDNA for nonhepatic mitochondrial arginase (arginase II) and comparison of its induction with nitric oxide synthase in a murine macrophage-like cell line
At the endoplasmic reticulum (ER) membrane, phosphatidylserine synthase 2 (PTDSS2) converts phosphatidylethanolamine (PE) into phosphatidylserine (PS) by facilitating the exchange of L-Serine (L-Ser) with the ethanolamine (ETA) head group (Saito et al. 1998, Tomohiro et al. 2009).
Phosphatidylserine (PS) is synthesized by facilitating the exchange of L-Serine (L-Ser) with the choline (Cho) head group in phosphatidylcholine (PC) and with the ethanolamine (ETA) head group in phosphatidylethanolamine (PE) (Saito et al. 1998, Tomohiro et al. 2009).
At the Golgi membrane, cholinephosphotransferase 1 (CHPT1) converts CDP-choline (CDP-Cho) and diacylglycerol (DAG) to phosphatidylcholine (PC) and cytidine monophosphate (CMP) (Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
De novo (Kennedy pathway) synthesis of phosphatidylcholine (PC) involves phosphorylation of choline (Cho) to phosphocholine (PCho) followed by condensing with cytidine triphosphate (CTP) to form CDP-choline (CDP-Cho). Diacylglycerol (DAG) and CDP-ETA together then form PC. Alternatively, PC is formed when phosphatidylethanolamine (PE) is methylated by phosphatidylethanolamine N-methyltransferase (PEMT) (Henneberry et al. 2002; Wright & McMaster 2002).
At the endoplasmic reticulum (ER) membrane, phosphatidylcholine (PC) is hydrolyzed and has one of its acyl chains cleaved off by a phospholipase A2 to form 1-acyl lysophosphatidylcholine (LPC). The phospholipases are either cytosolic phospholipase A2 alpha/beta/delta/zeta (PLA2G4A/B/D/F) (Ghomashchi et al. 2010, Clarke et al. 1991, Sharp et al. 1994, Song et al. 1999, Chiba et al. 2004), 85 kDa calcium-independent phospholipase A2 (PLA2G6) (Larsson et al. 1998, Ma et al. 1999, Larsson Forsell et al. 1999), group XVI phospholipase A2 (PLA2G16) (Duncan et al. 2008), or Phospholipase B-like 1 (PLBD1) (Xu et al. 2009). PLBD1 acts as a phospholipase A2 but in addition has the propensity to hydrolyze the lysophospholipid formed in its initial reaction.
At the endoplasmic reticulum (ER) membrane, phosphatidylcholine (PC) is hydrolyzed, and has one of its acyl chains cleaved off, by a membrane-associated phospholipase A2 to form 1-acyl lysophosphatidylcholine (LPC). The phospholipases are either phospholipase A2 group II alpha (PLA2G2A) (Seihamer et al. 1989, Singer et al. 2002), cytosolic phospholipase A2 group IV gamma (PLA2G4C) (Yamashita et al. 2005, Pickard et al. 1999, Ghomashchi et al. 2010, Yamashita et al. 2009), or calcium-independent phospholipase A2-gamma (PNPLA8) (Murakami et al. 2005, Underwood et al. 1998).
At the endoplasmic reticulum (ER) membrane, active membrane-bound choline-phosphate cytidylyltransferase A (PCYT1A) or B (PCYT1B) homodimer condenses phosphocholine (PCho) and cytidine triphosphate (CTP) to produce CDP-choline (CDP-Cho) (Lykidis et al. 1998).
At the endoplasmic reticulum (ER) membrane, choline/ethanolaminephosphotransferase (CEPT1) converts CDP-choline (CDP-Cho) and diacylglycerol (DAG) to phosphatidylcholine (PC) and cytidine monophosphate (CMP) (Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
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At the endoplasmic reticulum (ER) membrane, phosphatidylethanolamine (PE) is hydrolyzed, and has one of its acyl chains cleaved off, by membrane-associated phospholipase A2 gamma 2A, (PLA2G2A) or by calcium-independent phospholipase A2-gamma (PNPLA8), to form 1-acyl lysophosphatidylethanolamine (LPE) (Murakami et al. 2005, Kramer et al. 1989, Singer et al. 2002).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylethanolamine (PE) is hydrolyzed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Zhao et al. 2008, Hishikawa et al. 2008).
De novo (Kennedy pathway) synthesis of phosphatidylethanolamine (PE) involves phosphorylation of ethanolamine (ETA) to phosphoethanolamine (PETA) followed by condensing with cytidine triphosphate (CTP) to form CDP-ethanolamine (CDP-ETA). Diacylglycerol (DAG) and CDP-ETA together then form PE. Alternatively, PE is formed when phosphatidylserine (PS) is decarboxylated by phosphatidylserine decarboxylase proenzyme (PISD) (Henneberry et al. 2002, Vance 1991, Vance 1990).
At the endoplasmic reticulum (ER) membrane, phosphatidylethanolamine (PE) is hydrolyzed, and has one of its acyl chains cleaved off, by phospholipase A2 to form 1-acyl lysophosphatidylethanolamine (LPE). The phospholipases are either cytosolic phospholipase A2 alpha/beta/delta/epsilon/zeta (PLA2G(4A/B/D/E/F) (Ghosh et al. 2006, Yamashita et al. 2009, Yamashita et al. 1999, Ghomashchi et al. 2010), 85 kDa calcium-independent phospholipase A2 (PLA2G6) (Larsson et al. 1998, Ma et al. 1999, Larsson Forsell et al. 1999), group XVI phospholipase A2 (PLA2G16) (Duncan et al. 2008), or Phospholipase B-like 1 (PLBD1) (Xu et al. 2009). PLBD1 acts as a phospholipase A2 but in addition has the propensity to hydrolyze the lysophospholipid formed in its initial reaction.
Sulfation in high endothelial venules: cloning and expression of the human PAPS synthetase
At the endoplasmic reticulum (ER) membrane, choline/ethanolaminephosphotransferase 1 (CEPT1) or ethanolaminephosphotransferase 1 (EPT1) converts CDP- ethanolamine (CDP-ETA) and diacylglycerol (DAG) to phosphatidylethanolamine (PE) and cytidine monophosphate (CMP) (Horibata et al. 2007, Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
At the inner mitochondrial (IM) membrane, phosphatidylserine decarboxylase proenzyme (heterodimer of two chains from the same protein) (PISD) decarboxylates phosphatidylserine (PS) to phosphatidylethanolamine (PE). This event has been inferred from rats and limited data for a human PISD (Forbes et al. 2007).
At the endoplasmic reticulum (ER) membrane, active membrane-bound ethanolamine-phosphate cytidylyltransferase (PCY2) dimer condenses phosphoethanolamine (PETA) and cytidine triphosphate (CTP) to produce CDP-ethanolamine (CDP-ETA) (Zhu et al. 2008, Nakashima et al. 1997).
At the endoplasmic reticulum (ER) membrane, phosphatidate phosphatase 1-3 (LPIN) dephosphorylates phosphatidic acid (PA) to form diacylglycerol (DAG) (Grimsey et al. 2008, Donkor et al. 2007).
In the cytosol, ethanolamine (ETA) is phosphorylated to phosphoethanolamine (PETA) by choline kinase (CHK) dimer or by ethanolamine kinase 1/2 (ETNK1/2) (Lykidis et al. 2001, Gallego-Ortega et al. 2009). CHK dimer consists of either choline kinase alpha subunit (CHKA) or beta subunit (CHKB) homodimer, or of CHKA:CHKB heterodimer.
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Methionine regeneration and aspartate aminotransferase in parasitic protozoa
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Function and dysfunction of the PI system in membrane trafficking
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
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In the cytosol, choline kinase alpha subunit (CHKA) homodimer, choline kinase beta subunit (CHKB) dimer, or CHKA:CHKB heterodimer phosphorylates choline (Cho) to produce phosphocholine (PCho) (Malito et al. 2006, Gallego-Ortega et al. 2009).
Rat liver adenosine triphosphate:adenosine monophosphate phosphotransferase activity. II. Subcellular localization of adenylate kinase isozymes
Telomerase catalytic subunit homologs from fission yeast and human
Identification of a target RNA motif for RNA-binding protein HuR
The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
Growth factors and insulin stimulate tyrosine phosphorylation of the 51C/SHIP2 protein
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Male pseudohermaphroditism caused by mutations of testicular 17 beta-hydroxysteroid dehydrogenase 3
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Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase.
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ELOVL2 overexpression enhances triacylglycerol synthesis in 3T3-L1 and F442A cells
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Review of epidermal growth factor receptor biology
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Isolation and characterization of cDNAs corresponding to two human calcium, calmodulin-regulated, 3',5'-cyclic nucleotide phosphodiesterases
Platelet hyperaggregability: impaired responsiveness to nitric oxide ("platelet NO resistance") as a therapeutic target
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De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics
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Regulation of Ca2+ signaling in mast cells by tyrosine-phosphorylated and unphosphorylated non-T cell activation linker
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2-methoxy-6-decaprenyl-1,4-benzoquinol [ChEBI:64180]
6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol [ChEBI:64181]
Mutations in NHLRC1 cause progressive myoclonus epilepsy
The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity.
phosphoribosyl pyrophosphate synthetase holoenzyme
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phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens)
transketolase dimer (name copied from entity in Homo sapiens)
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RPE dimer (name copied from entity in Homo sapiens)
PGD dimer (name copied from entity in Homo sapiens)
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G6PD tetramer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
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PGM2:Mg++ (name copied from entity in Homo sapiens)
2xTPK1:Mg2+ (name copied from entity in Homo sapiens)
RFK:Mg2+ (name copied from entity in Homo sapiens)
Expression of human aspartyl-tRNA synthetase in Escherichia coli. Functional analysis of the N-terminal putative amphiphilic helix
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SLC25A11 homodimer (name copied from entity in Homo sapiens)
GOT2 dimer (name copied from entity in Homo sapiens)
enolase 2 dimer, (gamma, neuronal) (name copied from entity in Homo sapiens)
pyruvate kinase complex, liver and RBC (name copied from entity in Homo sapiens)
pyruvate kinase M1 complex (name copied from entity in Homo sapiens)
phosphoglycerate mutase 2 dimer (name copied from entity in Homo sapiens)
phosphoglycerate mutase 1 dimer (name copied from entity in Homo sapiens)
Pathways of chaperone-mediated protein folding in the cytosol
enolase 1 dimer, (alpha) (name copied from entity in Homo sapiens)
GOT1 dimer (name copied from entity in Homo sapiens)
Molecular mechanisms of translational control
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phosphoglycerate kinase 1 complex (name copied from entity in Homo sapiens)
glyceraldehyde-3-phosphate dehydrogenase, testis-specific, tetramer (name copied from entity in Homo sapiens)
Identification and characterization of eukaryotic initiation factor 5A-2
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glucose 6-phosphate isomerase dimer (name copied from entity in Homo sapiens)
AKT inhibitors:AKT (name copied from entity in Homo sapiens)
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AKT1 E17K mutant:PIP2 (name copied from entity in Homo sapiens)
The mucopolysaccharidoses: inborn errors of glycosaminoglycan catabolism
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glyceraldehyde-3-phosphate dehydrogenase tetramer (name copied from entity in Homo sapiens)
glyceraldehyde-3-phosphate dehydrogenase tetramer
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triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
ALDOB tetramer (name copied from entity in Homo sapiens)
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HSP90 (name copied from entity in Homo sapiens)
AKT:PIP3 (name copied from entity in Homo sapiens)
lactate dehydrogenase B4 complex (name copied from entity in Homo sapiens)
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HSP90:Benzoquinoid ansamycins (name copied from entity in Homo sapiens)
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ATP6V0C hexamer (name copied from entity in Homo sapiens)
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ATP6V0A (name copied from entity in Homo sapiens)
ATP6V0D (name copied from entity in Homo sapiens)
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ATP6V0E (name copied from entity in Homo sapiens)
p-Raf1(S259,S621):14-3-3 protein beta/alpha (name copied from entity in Homo sapiens)
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4xCa2+:CaM (name copied from entity in Homo sapiens)
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Concerted dephosphorylation of the transcription factor NFAT1 induces a conformational switch that regulates transcriptional activity
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ATP6V1 (name copied from entity in Homo sapiens)
ATP6V1A trimer (name copied from entity in Homo sapiens)
ATP6V0 (name copied from entity in Homo sapiens)
Differential role of human choline kinase alpha and beta enzymes in lipid metabolism: implications in cancer onset and treatment
V-ATPase:ATP6AP1 (name copied from entity in Homo sapiens)
ATP2C1/2:Mg2+ (name copied from entity in Homo sapiens)
V-ATPase (name copied from entity in Homo sapiens)
ATP6V1B trimer (name copied from entity in Homo sapiens)
ATP6V1G dimer (name copied from entity in Homo sapiens)
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Thrombopoietin: a tool for understanding thrombopoiesis
Functional and genetic studies demonstrate that mutation in the COX15 gene can cause Leigh syndrome
Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
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Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
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Human liver glucokinase gene: cloning and sequence determination of two alternatively spliced cDNAs
6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species
A comparison of the enzymatic and physicochemical properties of human glutathione transferase M4-4 and three other human Mu class enzymes
Enzymes of the SUMO modification pathway localize to filaments of the nuclear pore complex
The nature of the phagosomal membrane: endoplasmic reticulum versus plasmalemma
Knockdown of hepatocyte aquaporin-8 by RNA interference induces defective bile canalicular water transport
Am J Physiol Gastrointest Liver Physiol 296:G93-100
A new sperm-specific Na+/H+ exchanger required for sperm motility and fertility
Defects in vitamin and cofactor metabolism
Identification of human phosphoglucomutase 3 (PGM3) as N-acetylglucosamine-phosphate mutase (AGM1)
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
On the mechanism of sensing unfolded protein in the endoplasmic reticulum
Subcellular targeting and trafficking of nitric oxide synthases
Phosphorylation of Mcm4 at specific sites by cyclin-dependent kinase leads to loss of Mcm4,6,7 helicase activity.
Requirement of human renal water channel aquaporin-2 for vasopressin-dependent concentration of urine
Leptin in human physiology and therapeutics
A dityrosyl-diiron radical cofactor center is essential for human ribonucleotide reductases
The Bcl-2 family: roles in cell survival and oncogenesis.
Role of immunoproteasomes in cross-presentation
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration. A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
The outer segment of photoreceptor cells is shed every 10-14 days to be completely replaced. The shed material is phagocytosed and transferred to the retinal pigment epithelium (RPE). Diretinoid-pyridinium-phosphatidylethanolamine (A2PE) can be hydrolysed to diretinoid-pyridinium-ethanolamine (A2E), a prominent constituent of lipofuscin (the material deposited in retinal tissue which accumulates over time and is implicated in macular degeneration). Evidence suggests this happens before transfer to RPE cells as part of the phagocytosed outer segment. A2E has been detected in outer segments (Ben-Shabat et al. 2002) and an N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (NAPEPLD) activity detected in rat, mouse and human proteins (Okamoto et al. 2004, Ueda et al. 2005, Wang et al. 2006). This activity has been shown to hydrolyse A2PE to A2E in bovine outer segments before phagocytosis and transfer to RPE cells, suggesting A2PE is hydrolysed to A2E in photoreceptor outer segment membranes (Sparrow et al. 2003, Salvador & Giusto 1998).
The retinoid cycle (also referred to as the visual cycle) is the process by which the visual chromophore 11-cis-retinal (11cRAL) is released from light-activated opsins in the form all-trans-retinal and isomerized back to its 11-cis isomer ready for another photoisomerization reaction. This process involves oxidation, reduction and isomerization reactions and take place in the retinal pigment epithelium (RPE) and photoreceptor segments of the eye (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011). This section describes the retinoid cycle in rods during dark/twilight conditions.
The gene defects which cause diseases related to the retinoid cycle are described here (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
Mucopolysaccharidosis type VII (MPS VII, Sly syndrome, beta-glucuronidase deficiency; MIM:253220) is an autosomal recessive lysosomal storage disease characterized by a deficiency of the enzyme beta-glucuronidase (GUSB; MIM:611499) which would normally cleave glucuronide residues from dematan sulphate, keratan sulphate and chondroitin sulphate, resulting in build up of these GAGs in cells and tissues (Sly et al. 1973). The gene encoding GUSB is 21 kb long, contains 12 exons and gives rise to two different types of cDNAs, through an alternate splicing mechanism (Miller et al. 1990). It maps to 7q11.21-q11.22 (Speleman et al. 1996). The phenotype is highly variable, ranging from severe causing death, non-immune hydrops fetalis (Vervoort et al. 1996) to mild forms with survival into adulthood (Storch et al. 2003). Most patients with the intermediate phenotype show hepatomegaly, skeletal anomalies, coarse facies, and variable degrees of mental impairment (Shipley et al. 1993, Tomatsu et al. 2009).
Mucopolysaccharidosis type VI (MPS VI, Maroteaux-Lamy syndrome, polydystrophic dwarfism; MIM:253200) is an autosomal recessive lysosomal storage disorder caused by a deficiency in arylsulfatase B (ARSB, N-acetyl-galactosamine 4-sulfatase; MIM:611542). It is named after two French physicians, Pierre Maroteaux and Maurice Emil Joseph Lamy. Maroteaux first described this disorder as a novel dysostosis associated with increased urinary excretion of chondroitin sulfate (CS; Maroteaux et al. 1963). The gene encoding ARSB is mapped to chromosome 5q11-q13 (Fidzianska et al. 1984) and contains 8 exons spanning about 206 kb (Karangeorgos et al. 2007). Defective ARSB results in build up of dermatan sulfate (DS) and chondroitin sulfate (CS) in soft tissues causing compression and blockages in blood vessels, nerves, trachea, corneal clouding and disrupting normal bone development. Symptoms are similar to MPS I but with normal intelligence generally (Rapini et al. 2007, Valayannopoulos et al. 2010).
The mucopolysaccharidoses (MPS) are a group of rare, inherited lysosomal storage disorders caused by deficiencies of enzymes catalyzing the stepwise degradation of glycosaminoglycans (GAGs, originally called mucopolysaccharides) (Neufeld & Muenzer in Scriver et al. 2001). Catabolism of the GAGs dermatan sulfate, heparan sulfate, heparin, keratan sulfate, chondroitin sulfate or hyaluronan may be blocked at one or more steps, resulting in lysosomal accumulation of GAG fragments of varying size. Over time these collect in the cells, blood and connective tissues ultimately resulting in progressive irreversible cellular damage which affects appearance, physical abilities, organ and system function, vision, and usually mental development (Lehman et al. 2011, Ashworth et al. 2006). Life expectancy is also reduced. There are 11 known enzyme deficiencies that give rise to 7 distinct MPS. These disorders are biochemically characterized by elevated levels of partially or undegraded GAGs in lysosomes, blood, urine and cerebro-spinal fluid (Muenzer 2011, Coutinho et al. 2012). The MPS are part of the lysosomal storage disease family, a group of about 50 genetic disorders caused by deficient lysosomal proteins (Ballabio & Gieselmann 2009).
Mucopolysaccharidosis type IX (MPS IX, Natowicz syndrome, Hyaluronidase deficiency, MIM:601492) is a rare lysosomal storage disease characterized by high hyaluronan (HA) concentration in the serum resulting from deficiency in hyaluronidase 1 (HYAL1, MIM:607071) which normally hydrolyses 1-4 linkages between N-acetylglucosamine (GlcNAc) and D-glucuronate (GlcA) residues. Symptoms of MPS IX are periodically painful soft tissue masses around the joints, acquired short stature and erosion of the hip joint, although joint movement and intelligence are normal (Natowicz et al. 1996, Triggs-Raine et al. 1999).
A missense mutation in SLC33A1, which encodes the acetyl-CoA transporter, causes autosomal-dominant spastic paraplegia (SPG42)
Mucopolysaccharidosis IV A (MPS IVA, MPS4A, Morquio's syndrome, Morquio's; MIM:253000) is a rare, autosomal recessive mucopolysaccharide storage disease, first described simultaneously in 1929 by L Morquio (Morquio L, Sur une forme de distrophie familiale, Bull Soc Pediat, Paris, 27, 1929, 145-152) and JF Brailsford (Brailsford, JF, Chondro-osteo-dystrophy: roentgenographic and clinical features of child with dislocation of vertebrae, Am j Surg, 7, 1929, 404-410). MPSIVA is caused by a deficiency in N-acetylgalactosamine 6-sulfatase (GALNS; MIM:612222) which normally hydrolyses 6-sulfate groups of N-acetylgalactosamine 6-sulfate units of chondroitin sulfate (CS) and of galactose 6-sulfate units of keratan sulfate (KS) (Matalon et al. 1974). The result is accumulation of KS/DS in cells and overexcretion in urine. Severe osteochondrodysplasia is a commonly seen phenotype for this disease. The severity of the disease is variable but severe cases limits lifespan to their 20's or 30's (Prat et al. 2008, Tomatsu et al. 2011). The gene coding for human GALNS was mapped to chromosome 16q24.3 (Masuno et al. 1993) and its structure described at the same time by two independent groups as comprising 14 exons and spanning approximately 40-50 kb (Nakashima et al.1994, Morris et al.1994).
Defects in beta-galactosidase (GLB1; MIM:611458) can result in GM1 gangliosidosis (GM1; MIM:230500) (Nishimoto et al. 1991) (not described here), with several phenotypes indicating mental deterioration, as well as in mucopolysaccharidosis IVB, a characteristic mucopolysaccharidosis with no neurological symptoms (Callahan 1999). Mucopolysaccharidosis IVB (MPS IVB, Morquio's syndrome B; MIM:253010) is a rare, autosomal recessive mucopolysaccharide storage disease characterized by intracellular accumulation of keratan sulfate (KS), skeletal dysplasia and corneal clouding. There is no central nervous system involvement, intelligence is normal and there is increased KS excretion in urine (Suzuki et al. "Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease", p3775-3809 in Stryer et al. 2001). MPSIVB is caused by a defect in betagalactosidase (GLB1), which normally cleaves terminal galactosyl residues from glycosaminoglycans, gangliosides and glycoproteins. The GLB1 gene spans 62.5 kb and contains 16 exons (Oshima et al.1988, Santamaria et al. 2007) and maps to chromosome 3p21.33 (Takano & Yamanouchi 1993).
Induction of ceruloplasmin synthesis by IFN-gamma in human monocytic cells
Cytosolic aldolase catalyzes the cleavage of D-fructose 1,6-bisphosphate to yield dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate. The active form of aldolase is a homotetramer. Three aldolase isozymes have been identified which differ in their patterns of expression in various adult tissues and during development but are otherwise functionally indistinguishable (Ali and Cox 1995; Freemont et al. 1984, 1988).
Structural and functional modules in RNA interference
Cytosolic phosphoglucose isomerase catalyzes the reversible interconversion of glucose 6-phosphate and fructose 6-phosphate (Tsuboi et al. 1958; Noltmann 1972; Bloxham and Lardy 1973). The active form of the enzyme is a homodimer (Read et al. 2001). Mutations in the enzyme are associated with hemolytic anemia (Xu and Beutler 1994).
This pathway describes how normal signaling by PI3K/AKT, presented in the contained module 'PIP3 Activates AKT Signaling' and recently reviewed by Manning and Cantley in 2007, is perturbed in cancer, as described in the contained module 'Constitutive Signaling by PI3K/AKT'. Please refer to Liu et al. 2009 and Hollander et al. 2011 for recent reviews.
Class IA PI3K is a heterodimer of a p85 regulatory subunit (encoded by PIK3R1, PIK3R2 or PIK3R3) and a p110 catalytic subunit (encoded by PIK3CA, PIK3CB or PIK3CD). In the absence of activating signals, the regulatory subunit stabilizes the catalytic subunit while inhibiting its activity. The complex becomes activated when extracellular signals stimulate the phosphorylation of the cytoplasmic domains of transmembrane receptors or receptor-associated proteins. The p85 regulatory subunit binds phosphorylated motifs of activator proteins, which induces a conformational change that relieves p85-mediated inhibition of the p110 catalytic subunit and enables PI3K to phosphorylate PIP2 to form PIP3. The phosphoinositide kinase activity of PI3K is opposed by the phosphoinositide phosphatase activity of PTEN. PIP3 acts as a messenger that recruits PDPK1 (PDK1) and AKT (AKT1, AKT2 or AKT3) to the plasma membrane. PDPK1 also possesses a low affinity for PIP2, so small amounts of PDPK1 are always present at the membrane. Binding of AKT to PIP3 induces a conformational change that enables TORC2 complex to phosphorylate AKT at a conserved serine residue (S473 in AKT1). Phosphorylation at the serine residue enables AKT to bind to PDPK1 and exposes a conserved threonine residue (T308) that is phosphorylated by PDPK1. AKT phosphorylated at both serine and threonine residues dissociates from the plasma membrane and acts as a serine/threonine kinase that phosphorylates a number of cytosolic and nuclear targets involved in regulation of cell metabolism, survival and gene expression. For a recent review, please refer to Manning and Cantley, 2007. Signaling by PI3K/AKT is frequently constitutively activated in cancer. This activation can be via gain-of-function mutations in PI3KCA (encoding catalytic subunit p110alpha), PIK3R1 (encoding regulatory subunit p85alpha) and AKT1. The PI3K/AKT pathway can also be constitutively activated by loss-of-function mutations in tumor suppressor genes such as PTEN. Gain-of-function mutations activate PI3K signaling by diverse mechanisms. Mutations affecting the helical domain of PIK3CA and mutations affecting nSH2 and iSH2 domains of PIK3R1 impair inhibitory interactions between these two subunits while preserving their association. Mutations in the catalytic domain of PIK3CA enable the kinase to achieve an active conformation. PI3K complexes with gain-of-function mutations therefore produce PIP3 and activate downstream AKT in the absence of growth factors (Huang et al. 2007, Zhao et al. 2005, Miled et al. 2007, Horn et al. 2008, Sun et al. 2010, Jaiswal et al. 2009, Zhao and Vogt 2010, Urick et al. 2011). While AKT1 gene copy number, expression level and phosphorylation are often increased in cancer, only one low frequency point mutation has been repeatedly reported in cancer and functionally studied. This mutation represents a substitution of a glutamic acid residue with lysine at position 17 of AKT1, and acts by enabling AKT1 to bind PIP2. PIP2-bound AKT1 is phosphorylated by TORC2 complex and by PDPK1 that is always present at the plasma membrane, due to low affinity for PIP2. Therefore, E17K substitution abrogates the need for PI3K in AKT1 activation (Carpten et al. 2007, Landgraf et al. 2008). Loss-of-function mutations affecting the phosphatase domain of PTEN are frequently found in sporadic cancers (Kong et al. 1997, Lee et al. 1999, Han et al. 2000), as well as in PTEN hamartoma tumor syndromes (PHTS) (Marsh et al. 1998). PTEN can also be inactivated by gene deletion or epigenetic silencing, or indirectly by overexpression of microRNAs that target PTEN mRNA (Huse et al. 2009). Cells with deficient PTEN function have increased levels of PIP3, and therefore increased AKT activity. For a recent review, please refer to Hollander et al. 2011. Because of their clear involvement in human cancers, PI3K and AKT are targets of considerable interest in the development of small molecule inhibitors. Although none of the currently available inhibitors display preference for mutant variants of PIK3CA or AKT, several inhibitors targeting the wild-type kinases are undergoing clinical trials. These include dual PI3K/mTOR inhibitors, class I PI3K inhibitors, pan-PI3K inhibitors, and pan-AKT inhibitors. While none have yet been approved for clinical use, these agents show promise for future therapeutics. In addition, isoform-specific PI3K and AKT inhibitors are currently being developed, and may provide more specific treatments along with reduced side-effects. For a recent review, please refer to Liu et al. 2009.
AKT inhibitors bind AKT and prevent its association with the membrane, thereby blocking AKT activation (Kondapaka et al. 2003, Yap et al. 2011, Berndt et al. 2010). AKT inhibitors annotated here target all AKT isoforms (AKT1, AKT2 and AKT3). None of the annotated inhibitors are AKT E17K mutant specific and none of them have been approved for clinical use. For a recent review, please refer to Liu et al. 2009.
AKT1 E17K gain-of-function mutant is expected to translocate to the nucleus, like the wild-type AKT (Borgatti et al. 2003), but this has not been directly experimentally tested.
AKT1 E17K gain-of-function mutant preserves the ability to phosphorylate GSK3 (Malanga et al. 2008). AKT-mediated phosphorylation inactivates GSK3 and enables WNT-independent stabilization of beta-catenin (CTNNB1) (Haq et al. 2003). AKT-mediated inactivation of GSK3 also triggers changes in glucose metabolism (Ueki et al. 1997).
The process of vision involves two stages; the retinoid cycle which supplies and regenerates the visual chromophore required for vision and phototransduction which propagates the light signal. Defects in the genes involved in the retinoid cycle cause degenerative retinal diseases. These defective genes are described here (for reviews see Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
Substitution of glutamic acid with lysine at position 17 of AKT1 results in constitutive plasma membrane localization of AKT1, independent of PI3K activity and PIP3 generation (Carpten et al. 2007). This constitutive plasma membrane targeting of AKT1 E17K mutant is due to an increased affinity for PIP2 (Landgraf et al. 2008).
Visual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are photochemical, biochemical and electrophysiological and are highly conserved across many species. This process occurs in two types of photoreceptors in the retina, rods and cones. Each type consists of two parts, the outer segment which detects a photon signal and the inner segment which contains the necessary machinery for cell metabolism. Each type of cell functions differently. Rods are very light sensitive but their flash response is slow so they work best in twilight conditions but are not good at detecting objects moving quickly. Cones are less light-sensitive and have a fast flash response so they work best in daylight conditions and are better at detecting fast moving objects than rods. The visual pigment consists of a chromophore (11-cis-retinal, 11cRAL, A1) covalently attached to a GPCR opsin family member. The linkage is via a Schiff base forming retinylidene protein. Upon photon absorption, 11cRAL isomerises to all-trans retinal (atRAL), changing the conformation of opsin to an activated form which can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. As high level of cGMP keep cGMP-gated sodium channels open, the lowering of cGMP levels closes these channels which causes hyperpolarization of the cell and subsequently, closure of voltage-gated calcium channels. As calcium levels drop, the level of the neurotransmitter glutamate also drops causing depolarization of the cell. This effectively relays the light signal to postsynaptic neurons as electrical signal (Burns & Pugh 2010, Korenbrot 2012, Pugh & Lamb 1993). 11cRAL cannot be synthesised in vertebrates. Vitamin A from many dietary sources is the precursor for 11cRAL. It is taken from food in the form of esters such as retinyl acetate or palmitate or one of four caretenoids (alpha-carotene, beta-carotene, gamma-carotene and beta-cryptoxanthin). Retinoids are transported from the gut to be stored in liver, until required by target organs such as the eye (Harrison & Hussain 2001, Harrison 2005). In the eye, in the form 11cRAL, it is used in the retinoid (visual) cycle to initiate phototransduction and for visual pigment regeneration to ready the photoreceptor for the next phototransduction event (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
Cytosolic phosphoglycerate kinase complexed with magnesium catalyzes the reversible phosphorylation of 3-phosphoglycerate to form 1,3-bisphosphoglycerate (Huang et al. 1980a, 1980b).
Cytosolic phosphoglycerate mutase dimer catalyzes the reversible isomerisation of 2- and 3-phosphoglycerate. There are two isoforms of this enzyme, PGAM1 (isoform B) and PGAM2 (isoform M). In the body, erythrocytes express only PGAM1, while skeletal muscle expresses only PGAM2. Other tissues express both isoforms (Repiso et al. 2005; Tsujino et al. 1993).
The reversible conversion of glyceraldehyde-3-phosphate to dihydroxyacetone phosphate is catalyzed by cytosolic triose phosphate isomerase (Watanabe et al. 1996; Lu et al. 1984).
The reversible reduction of 1,3-bisphosphoglycerate to form glyceraldehyde-3-phosphate is catalyzed by cytosolic glyceraldehyde-3-phosphate dehydrogenase tetramer. There are multiple human glyceraldehyde 3-phosphate dehydrogenase-like pseudogenes, but only one glyceraldehyde 3-phosphate dehydrogenase gene expressed in somatic tissue (Benham and Povey 1989). Consistent with this conclusion, the homogeneous enzymes purified from various human tissues had indistinguishable physical and immunochemical properties (Heinz and Freimuller 1982), and studies of human erythrocytes of various ages suggested that variant forms of the enzyme arise as a result of post-translational modifications (Edwards et al. 1976). There is, however, an authentic second isoform of glyceraldehyde 3-phosphate dehydrogenase whose expression is confined to spermatogenic cells of the testis (Welch et al. 2000).
Studies on human erythrocyte inorganic pyrophosphatase.
Cytosolic enolase dimer catalyzes the reversible reaction of phosphoenolpyruvate and water to form 2-phosphoglycerate. Three enolase isozymes have been purified and biochemically characterized. The alpha isoform is widely expressed (Giallongo et al. 1986). The beta isoform is expressed in muscle. Evidence for its function in vivo in humans comes from studies of a patient in whom a point mutation in the gene encoding the enzyme was associated specifically with reduced enolase activity in muscle extracts, and with other symptoms consistent with a defect in glycolysis (Comi et al. 2001). The gamma isoform of human enolase is normally expressed in neural tissue. It is not known to have distinctive biochemical functions, but is of possible clinical interest as a marker of some types of neuroendocrine and lung tumors (McAleese et al. 1988). Verma and Kurl (1993) identifed a possible fourth isoform, a "lung-specific" enolase whose expression is increased in response to dexamethasone treatment. The protein has not been biochemically characterized, however, nor have the levels of mRNA and protein in other tissues been examined. Thus, the observation that this protein is particularly similar in its predicted amino acid sequence to a duck crystallin (Wistow et al. 1988) raises the possibility that its normal function is unrelated to glycolysis.
Phosphoinositide 3-kinase: the key switch mechanism in insulin signalling.
Defective TCN2 causes hereditary megaloblastic anemia
Glycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has been studied in most detail in muscle, although considerable experimental data are available concerning these reactions in liver as well. Glycogen metabolism in other tissues has not been studied as extensively, and is thought to resemble the muscle process. Glycogen synthesis involves five reactions. The first two, conversion of glucose 6-phosphate to glucose 1-phosphate and synthesis of UDP-glucose from glucose 1-phosphate and UTP, are shared with several other pathways. The next three reactions, the auto-catalyzed synthesis of a glucose oligomer on glycogenin, the linear extension of the glucose oligomer catalyzed by glycogen synthase, and the formation of branches catalyzed by glycogen branching enzyme, are unique to glycogen synthesis. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of glycogenin glucosylation and oligoglucose chain extension by distinct isozymes in liver and nonhepatic tissues allows them to be regulated independently (Agius 2008; Bollen et al. 1998; Roach et al. 2012).
In this freely reversible cytosolic reaction, dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate react to form D-fructose 1,6-bisphosphate. The active form of aldolase, the enzyme that catalyzes the reaction, is a homotetramer. Three aldolase isozymes have been identified which differ in their patterns of expression in various adult tissues and during development but are otherwise functionally indistinguishable (Ali and Cox 1995; Dunbar and Fothergill-Gilmore 1988).
The reversible isomerization of fructose-6-phosphate to form glucose-6-phosphate is catalyzed by cytosolic phosphoglucose isomerase (Noltman 1972; Xu and Beutler 1994; Tsuboi et al. 1958).
The reactions of gluconeogenesis convert mitochondrial pyruvate to cytosolic glucose 6-phosphate which in turn can be hydrolyzed to glucose and exported from the cell. Gluconeogenesis is confined to cells of the liver and kidney and enables glucose synthesis from molecules such as lactate and alanine and other amino acids when exogenous glucose is not available (reviewed, e.g., by Gerich 1993). The process of gluconeogenesis as diagrammed below occurs in two parts: a network of reactions converts mitochondrial pyruvate to cytosolic phosphoenolpyruvate; then phosphoenolpyruvate is converted to glucose 6-phosphate in a single sequence of cytosolic reactions. Three variants of the first part of the process are physiologically important. 1) A series of transport and transamination reactions convert mitochondrial oxaloacetate to cytosolic oxaloacetate which is converted to phosphoenolpyruvate by a hormonally regulated, cytosolic isoform of phosphoenolpyruvate carboxykinase. This variant allows regulated glucose synthesis from lactate. 2) Mitochondrial oxaloacetate is reduced to malate, which is exported to the cytosol and re-oxidized to oxaloacetate. This variant provides reducing equivalents to the cytosol, needed for glucose synthesis from amino acids such as alanine and glutamine. 3) Constitutively expressed mitochondrial phosphoenolpyruvate carboxykinase catalyzes the conversion of mitochondrial oxaloacetate to phosphoenolpyruvate which is then transported to the cytosol. The exact path followed by any one molecule of pyruvate through this reaction network is determined by the tissue in which the reactions are occurring, the source of the pyruvate, and the physiological stress that triggered gluconeogenesis. In all cases, the synthesis of glucose from two molecules of pyruvate requires the generation and consumption of two reducing equivalents as cytosolic NADH + H+. For pyruvate derived from lactate (variants 1 and 3), NADH + H+ is generated with the oxidation of lactate to pyruvate in the cytosol (a reaction of pyruvate metabolism not shown in the diagram). For pyruvate derived from amino acids (variant 2), mitochondrial NADH + H+ generated by glutamate dehydrogenase (a reaction of amino acid metabolism, not shown) is used to reduce oxaloacetate to malate, which is transported to the cytosol and re-oxidized, generating cytosolic NADH + H+. The synthesis of glucose from pyruvate also requires the consumption of six high-energy phosphates, four from ATP and two from GTP. In the second part of gluconeogenesis, cytosolic phosphoenolpyruvate, however derived, is converted to fructose 1,6-bisphosphate by reactions that are the reverse of steps of glycolysis. Hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate is catalyzed by fructose 1,6-bisphosphatase, and fructose 6-phosphate is reversibly isomerized to glucose 6-phosphate.
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 6-phosphate to glucose 1-phosphate (Drago et al. 1991). Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
Cytosolic phosphoglycerate mutase catalyzes the reversible isomerisation of 3- and 2-phosphoglycerate. The active form of the enzyme is a dimer. There are two isoforms of this enzyme, PGAM1 (isoform B, widely expressed in non-muscle tissue) and PGAM2 (isoform M, expressed in muscle) (Blouquit et al. 1988; Omenn and Cheung 1974; Repiso et al. 2005; Tsujino et al. 1993).
Cytosolic phosphoglycerate kinase catalyzes the reaction of ADP and 1,3-bisphosphoglycerate to form D glyceraldehyde 3-phosphate and ATP. The active form of the enzyme is a monomer and requires Mg++ (Yoshida and Watanabe 1972; Huang et al. 1980a,b). This is the first substrate level phosphorylation reaction in glycolysis.
ArPIKfyve homomeric and heteromeric interactions scaffold PIKfyve and Sac3 in a complex to promote PIKfyve activity and functionality
Cytosolic glyceraldehyde 3-phosphate dehydrogenase catalyzes the reversible reaction of glyceraldehyde 3-phosphate, orthophosphate, and NAD+ to form NADH + H+ and 1,3-bisphosphoglycerate, the first energy rich intermediate of glycolysis. The biochemical details of this reaction were worked out by C and G Cori and their colleagues (Taylor et al. 1948; Cori et al. 1948). While there are multiple human glyceraldehyde 3-phosphate dehydrogenase-like pseudogenes, there is only one glyceraldehyde 3-phosphate dehydrogenase gene expressed in somatic tissue (Benham and Povey 1989; Heinz and Freimuller 1982; Ercolani et al. 1988), and studies of aged human erythrocytes suggest that variant forms of the enzyme arise as a result of post-translational modifications (Edwards et al. 1976). There is, however, an authentic second isoform of glyceraldehyde 3-phosphate dehydrogenase whose expression is confined to spermatogenic cells of the testis (Welch et al. 2000).
Cytosolic triose phosphate isomerase catalyzes the freely reversible interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate (Lu et al. 1984). The active form of the enzyme is a homodimer (Kinoshita et al. 2005).
G(1) to S transition: more than a cell cycle engine switch.
Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders
Defects in human methionine synthase in cblG patients
The SLC25A11 transport protein in the inner mitochondrial membrane mediates the reversible exchange of mitochondrial malate and cytosolic alpha-ketoglutarate (2-oxoglutarate). Qualitative evidence for this process comes from studies of the human protein (Kabe et al. 2006); kinetic details are inferred from stdies of rat mitochondria under conditions in which only the one transport protein appears to be active (Sluse et al. 1973). The dimeric state of the transport protein is inferred from studies of its bovine homologue (Bisaccia et al. 1996).
Cytosolic aspartate aminotransferase (glutamate oxaloacetate transaminase 1 - GOT1) catalyzes the reversible reaction of aspartate and 2-oxoglutarate (alpha-ketoglutarate) to form oxaloacetate and glutamate (Doyle et al. 1990). Unpublished crystallographic data (PBD 3IIO) suggest the enzyme is a homodimer).
The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate.
Mitochondrial aspartate aminotransferase catalyzes the reversible reaction of oxaloacetate and glutamate to form aspartate and 2-oxoglutarate (alpha-ketoglutarate) (Martini et al. 1985). The active form of the enzyme is inferred to be a dimer with one molecule of pyridoxal phosphate associated with each monomer.
NLR proteins: integral members of innate immunity and mediators of inflammatory diseases
Cytosolic enolase catalyzes the reversible reaction of 2 phosphoglycerate to form phosphoenolpyruvate and water, elevating the transfer potential of the phosphoryl group. Enolase is a homodimer and requires Mg++ for activity. Three isozymes have been purified and biochemically characterized. The alpha isoform is expressed in many normal human tissues (Giallongo et al. 1986). The beta isoform is expressed in muscle. Evidence for its function in vivo in humans comes from studies of a patient in whom a point mutation in the gene encoding the enzyme was associated specifically with reduced enolase activity in muscle extracts and with other symptoms consistent with a defect in glycolysis (Comi et al. 2001). The gamma isoform of human enolase is normally expressed in neural tissue and is of possible clinical interest as a marker of some types of neuroendocrine and lung tumors (McAleese et al. 1988). Biochemical studies of the homologous rat proteins indicate that both homo- and heterodimers of enolase form and are enzymatically active (Rider and Taylor 1974).
Cytosolic pyruvate kinase catalyzes the transfer of a high-energy phosphate from phosphoenolpyruvate to ADP, forming pyruvate and ATP. This reaction, an instance of substrate-level phosphorylation, is essentially irreversible under physiological conditions. Four isozymes of human pyruvate kinase have been described, L, R, M1 and M2. Isozymes L and R are encoded by alternatively spliced transcripts of the PKLR gene; isozymes M1 and M2 are encoded by alternatively spliced transcripts of PKM2. In the body, L pyruvate kinase is found in liver (Tani et al. 1988), R in red blood cells (Kanno et al. 1991), M1 in muscle, heart and brain (Takenaka et al. 1991), and M2 in early fetal tissues and tumors (e.g., Lee et al. 2008). In all cases, the active form of the enzyme is a homotetramer, activated by fructose 1,6-bisphosphate (Valentini et al. 2002; Dombrauckas et al. 2005). Mutations in PKLR have been associated with hemolytic anemias (e.g., Zanella et al. 2005).
Cytosolic transketolase catalyzes the reversible reaction of D-xylulose 5-phosphate and D-ribose 5-phosphate to form D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
Cytosolic transketolase catalyzes the reaction of D-erythrose 4-phosphate and D-xylulose 5-phosphate to form D-glyceraldehyde 3-phosphate and D-fructose 6-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
Lipid digestion, mobilization, and transport
Cytosolic transketolase catalyzes the reversible reaction of D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate to form D-xylulose 5-phosphate and D-ribose 5-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
The reversible interconversion of ribulose 5-phosphate and ribose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
Cytosolic transketolase catalyzes the reaction of D-glyceraldehyde 3-phosphate and D-fructose 6-phosphate to form D-erythrose 4-phosphate and D-xylulose 5-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
The pentose phosphate pathway is responsible for the generation of a substantial fraction of the cytoplasmic NADPH required for biosynthetic reactions, and for the generation of ribose 5-phosphate for nucleotide synthesis. Although the pentose phosphate pathway and glycolysis are distinct, they involve three common intermediates, glucose 6-phosphate, glyceraldehyde 3-phosphate, and fructose 6-phosphate, so the two pathways are interconnected. The pentose phosphate pathway consists of eight reactions:1. Conversion glucose 6-phosphate to D-glucono-1,5-lactone 6-phosphate, with the formation of NADPH; 2. Conversion of D-glucono-1,5-lactone 6-phosphate to 6-phospho-D-gluconate; 3. Conversion of 6-phospho-D-gluconate to ribulose 5-phosphate, with the formation of NADPH; 4. Conversion of ribulose 5-phosphate to xylulose 5-phosphate; 5. Conversion of ribulose 5-phosphate to ribose 5-phosphate; 6. Rearrangement of ribose 5-phosphate and xylulose 5-phosphate to form sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; 7. Rearrangement of sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate; and 8. Rearrangement of xylulose 5-phosphate and erythrose 4-phosphate to form glyceraldehyde 3-phosphate and fructose-6-phosphate. The oxidative branch of the pentose phosphate pathway, reactions 1-3, generates NADPH and pentose 5-phosphate. The non-oxidative branch of the pathway, reactions 4-8, converts pentose 5-phosphate to other sugars. The overall pathway can operate to generate only NADPH (glucose 6-phosphate is converted to pentose 5-phosphates, which are directed to the synthesis of fructose 6-phosphate and glyceraldehyde 3-phosphate, which in turn are converted back to glucose 6-phosphate). The reactions of the non-oxidative branch can operate to generate net amounts of ribose 5-phosphate with no production of NADPH. Net flux through this network of reactions appears to depend on the metabolic state of the cell and the nature of the biosynthetic reactions underway (Casazza and Veech 1987). G6PD, the enzyme that catalyzes the first reaction of the pathway, is more extensively mutated in human populations than any other enzyme, pehaps because these mutant alleles confer malaria resistance (Luzzatto and Afolayan 1968). Mutations affecting other parts of the pathway are rare, though several have been described and studies of their effects have contributed to our understanding of the normal flux of metabolites through this network of reactions (Wamelink et al. 2008).
The reversible interconversion of ribose 5-phosphate and ribulose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
Unspecific permeation and specific exchange of adenine nucleotides in
Functional and molecular characterization of the human neutral solute channel aquaporin-9
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Polymerase switching on the C-strand of the telomere
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Cytosolic phosphoribosyl pyrophosphate synthetase 1 catalyzes the reaction of D-ribose 5-phosphate and dATP to form 5-phospho-alpha-D-ribose 1-diphosphate and 2'-deoxyadenosine 5'-monophosphate. While phosphoribosyl pyrophosphate synthetase 1 works well with either ATP or dATP as a substrate in vitro, the extent of the dATP reaction in vivo is unclear, as cellular dATP concentrations are normally very low (Fox and Kelley 1971).
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Cytosolic phophoribosyl pyrophosphate synthetase catalyzes the reaction of D-ribose 5-phosphate and ATP to form 5-phospho-alpha-D-ribose and AMP. Three isoforms of the enzyme have been described. The first has been purified and characterized biochemically (Fox and Kelley 1971). The others are known only as inferred protein products of cloned genes; their catalytic properties have not been determined.
5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) is a key intermediate in both the de novo and salvage pathways of purine and pyrimidine synthesis. PRPP and the enzymatic activity responsible for its synthesis were first described by Kornberg et al. (1955). The enzyme, phosphoribosyl pyrophosphate synthetase 1, has been purified from human erythrocytes and characterized biochemically. The purified enzyme readily forms multimers; its smallest active form appears to be a dimer and for simplicity it is annotated as a dimer here. It specifically catalyzes the transfer of pyrophosphate from ATP or dATP to D-ribose 5-phosphate, and has an absolute requirement for Mg++ and orthophosphate (Fox and Kelley 1971; Roth et al. 1974). The significance of the reaction with dATP in vivo is unclear, as the concentration of cytosolic dATP is normally much lower than that of ATP. The importance of this enzyme for purine synthesis in vivo has been established by demonstrating excess phosphoribosyl pyrophosphate synthetase activity, correlated with elevated enzyme levels or altered enzyme properties, in individuals whose rates of uric acid production are constitutively abnormally high (Becker and Kim 1987; Roessler et al. 1993). Molecular cloning studies have revealed the existence of two additional genes that encode phosphoribosyl pyrophosphate synthetase-like proteins, one widely expressed (phosphoribosyl pyrophosphate synthetase 2) and one whose expression appears to be confined to the testis (phosphoribosyl pyrophosphate synthetase 1-like 1) (Taira et al. 1989; 1991). Neither of these proteins has been purified and characterized enzymatically, nor have variations in the abundance or sequence of either protein been associated with alterations in human nucleotide metabolism (Roessler et al. 1993; Becker et al. 1996), so their dimerization and ability to catalyze the synthesis of PRPP from D-ribose 5-phosphate are inferred here on the basis of their predicted amino acid sequence similarity to phosphoribosyl pyrophosphate synthetase 1.
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Cytosolic glycogen breakdown occurs via the same chemical steps in all tissues but is separately regulated via tissue specific isozymes and signaling pathways that enable distinct physiological fates for liver glycogen and that in other tissues. Glycogen phosphorylase, which can be activated by phosphorylase kinase, catalyzes the removal of glucose residues as glucose 1-phosphate from the ends of glycogen branches. The final four residues of each branch are removed in two steps catalyzed by debranching enzyme, and further glycogen phosphorylase activity completes the process of glycogen breakdown. The figure shows the actions of phosphorylase and debranching enzyme. The first glucose residue in each branch is released as free glucose; all other residues are released as glucose 1-phosphate. The latter molecule can be converted to glucose 6-phosphate in a step shared with other pathways (Villar-Palasi and Larner 1970; Hers 1976). Glycogen can also be taken up into lysosomes, where it is normally broken done by the action of a single enzyme, lysosomal alpha-glucosidase (GAA).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 1-phosphate to glucose 6-phosphate. Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
Fructose occurs naturally in foods as a free monosaccharide and as a component of the disaccharide sucrose. It is also widely used as a sweetener. In the body, fructose is converted to dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, two intermediates in the glycolytic pathway, in a sequence of three reactions: fructose is phosphorylated, then cleaved by aldolase to yield dihydroxyacetone phosphate and D-glyceraldehyde, and the latter compound is phosphorylated to yield D-glyceraldehyde 3-phosphate. Other pathways exist for the conversion of D-glyceraldehyde to intermediates of glycolysis, but these appear to play only a minor role in normal fructose metabolism. The cleavage of fructose 1-phosphate is catalyzed by the same enzyme that catalyzes the reversible cleavage of fructose 1,6-bisphosphate in glycolysis. The isoform of this enzyme found in liver, kidney, and intestine (B) is approximately equally active with fructose 1-phosphate and fructose 1,6-bisphosphate as substrates, while the muscle and brain isoforms (A and C, respectively), have little activity with fructose 1-phosphate. Fructose metabolism thus occurs mainly in tissues expressing the B isoform, and mutations that affect the catalytic activity of this isoform are associated with hereditary fructose intolerance (Steinmann et al. 2001).
Cytosolic aldolase B (ALDOB) catalyzes the reaction of D-fructose 1-phosphate to form dihydroxyacetone phosphate and D-glyceraldehyde (Sakakibara et al. 1989). The active form of the enzyme is a tetramer (Dalby et al. 2001). Deficiencies in the enzyme are associated with hereditary fructose intolerance in vivo (e.g., Tolan 1995).
Glucose is the major form in which dietary sugars are made available to cells of the human body. Its breakdown is a major source of energy for all cells, and is essential for the brain and red blood cells. Glucose utilization begins with its uptake by cells and conversion to glucose 6-phosphate, which cannot traverse the cell membrane. Fates open to cytosolic glucose 6-phosphate include glycolysis to yield pyruvate, glycogen synthesis, and the pentose phosphate pathway. In some tissues, notably the liver and kidney, glucose 6-phosphate can be synthesized from pyruvate by the pathway of gluconeogenesis.
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Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
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Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-xylulose 5-phosphate and D-ribulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
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Cytosolic glucose-6-phosphate dehydrogenase (G6PD) catalyzes the reaction of glucose 6-phosphate and NADP+ to form D-glucono-1,5-lactone 6-phosphate and , and NADPH + H+. Biochemical studies indicate that both G6PD dimers and tetramers are catalytically active and capable or forming under physiological conditions in vivo (Au et al. 2000). Mutations that reduce the catalytic efficientcy of G6PD are remarkably common in human populations; these appear to have a protective effect against malaria (e.g., Luzzatto and Afolayan 1968).
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Cytosolic phosphogluconate dehydrogenase (PGD) catalyzes the reaction of 6-phospho-D-gluconate and NADP+ to form D-ribulose 5-phosphate, CO2, and NADPH + H+ (Beutler and Kuhl 1985; Rippa et al. 1998). The PGD enzyme is dimeric (Dallocchio et al. 1985).
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The conjugation of cysteine (Cys) and 4'- phosphopantothenate (PPanK) to form 4-phosphopantothenoylcysteine (PPC) , coupled to the conversion of ATP to AMP and pyrophosphate, is catalyzed by cytosolic phosphopantothenate-cysteine ligase (PPCS aka Phosphopantothenoylcysteine synthase or PPC synthase). Mammalian PPCS prefers ATP to CTP, unlike the E. coli ortholog (Daughtery et al. 2002; Manoj et al. 2003).
In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2
Biochem. Biophys. Res. Commun. 254:693-8
Panthothenate (vitamin B5) is the precursor of coenzyme A (Robishaw and Neely 1985) and is the prosthetic group of acyl carrier protein (ACP) (Joshi et al. 2003). Its name is derived from the Greek pantothen meaning "from everywhere" and small quantities of pantothenic acid are found in nearly every foodstuff.
The probable lysosomal cobalamin transporter (LMBD1) is the most likely candidate to transport cobalamin (Cbl) from inside the lysosome to the cytosol (Rutsch et al. 2009). From here, Cbl can either be used to synthesise the essential cofactors for methionine synthase in the cytosol or methylmalonyl-CoA mutase in the mitochondria or, it can transported out of the cell to tissues that require Cbl. Defects in LMBRD1 (the gene that produces LMBD1) cause methylmalonic aciduria and homocystinuria type cblF (MMAHCF; MIM:277380), characterised biochemically by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) (Rutsch et al. 2009, Gailus et al. 2010).
Vitamin B12 (cobalamin, Cbl) is a water-soluble vitamin with a key role in blood formation and normal functioning of the brain and nervous system. Cbl consists of a planar corrin ring coordinating with a cobalt atom through four nitrogen atoms. A 5,6-dimethylbenzamidizole base coordinates with the cobalt atom in the lower axial position while a number of different species can coordinate with the cobalt atom in the upper axial position. It is the cobalt-corrin ring complex that gives all Cbls a deep red colour. Only bacteria and archaea are able to synthesize Cbl thus humans need a dietary intake to prevent deficiency (Green 2010, Quadros 2010, Watkins & Rosenblatt 2011). A common semi-synthetic form of the vitamin, cyanocobalamin (CNCbl, where a cyanide group is in the upper axial position), is produced from bacterial hydroxocobalamin and used in many pharmaceuticals, supplements and as a food additive. In mammalian cells, Cbl or CNCbl is converted to two active coenzyme derivatives; methylcobalamin (MetCbl) and adenosylcobalamin (AdoCbl). MetCbl is required for activity of the cytoplasmic enzyme methionine synthase, which converts homocysteine to methionine. AdoCbl is required for activity of the mitochondrial enzyme methylmalonyl CoA mutase, which converts L-methylmalonyl-CoA to succinyl-CoA (Seetharam 1999). This pathway outlines the intake, transport and metabolism of Cbl and is assumed to be equally applicable to CNCbl.
NAD synthase catalyzes the final step in the biosynthesis of NAD+, both in the de novo synthesis and in the salvage pathways. The enzyme makes use of glutamine as an amide donor in the reaction. NAD synthase exists as a homohexamer in the cytosol. There are two forms of NAD synthase in humans, NADsyn1 and NADsyn2. The major difference between the two forms is that NADsyn1 appears to be glutamine-dependent whereas NADsyn2 is strictly ammonia-dependent.
The decarboxylation of phosphopantothenoylcysteine (PPC) to 4'-phosphopantetheine (PPANT) is carried out by phosphopantothenoylcysteine decarboxylase (PPCDC). PPCDC is cytosolic and exists as a homotrimer, binding one FMN cofactor per subunit. While a second isoform has been inferred from large-scale sequnceing studies, it lacks the protein's FMN-binding domain and would thus appear to be nonfunctional if it is expressed.
The adenylyl transferase activity of bifunctional coenzyme A synthase (COASY) catalyzes the transfer of an adenylyl group from ATP to pantetheinephosphate (PPANT) to form dephospho-Coenzyme A (DP-CoA) (Daugherty et al. 2002). The enzyme is associated with the mitochondrial outer membrane (Zhyvoloup et al. 2003).
The kinase activity of CoA synthase (COASY) catalyzes the phosphorylation of dephospho-CoA to form Coenzyme A (CoA-SH). The enzyme is located in the mitochondrial outer membrane (Daugherty et al. 2002; Zhyvoloup et al. 2003).
Coenzyme A (CoA) is a ubiquitous cofactor that functions as an acyl group carrier in diverse processes including fatty acid metabolism and the TCA cycle (Lipmann 1953). It is synthesized from the vitamin pantothenate in a sequence of five reactions (Daugherty et al. 2002; Leonardi et al. 2005; Robishaw and Neely 1985). These reactions all occur in the cytosol or the mitochondrial intermembrane space (Leonardi et al. 2005). A recently described transport protein appears to mediate the uptake of Coenzyme A into the mitochondrial matrix (Prohl et al. 2001).
Type I phosphatidylinositol-4-phosphate 5-kinases synthesize the novel lipids phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 5-phosphate
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Cytosolic nicotinate phosphoribosyltransferase (NaPRT) catalyzes the Mg++-dependent reaction of nicotinate and phosphoribosyl pyrophosphate to form nicotinate mononucleotide (NaMN, nicotinate D-ribonucleotide) and pyrophosphate. The active form of the enzyme is a homodimer (Preiss and Handler 1958; Niedel and Dietrich 1973; Hara et al. 2007).
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Regulation of Ras in lymphocytes: get a GRP
FMN can be phosphorylated and adenylated to produce the second cofactor from riboflavin origins, flavin adenine dinucleotide (FAD). The enzyme responsible , FMN adenylyltransferase (FLAD1 aka FAD synthase), is cytosolic and transfers a phosphate and an adenyl group from ATP to form FAD.
Riboflavin (vitamin B2, E101) is an essential component for the cofactors FAD (flavin-adenine dinucleotide) and FMN (flavin mononucleotide). Together with NAD+ and NADP+, FAD and FMN are important hydrogen carriers and take part in more than 100 redox reactions involved in energy metabolism. Riboflavin is present in many vegetables and meat and during digestion, various flavoproteins from food are degraded and riboflavin is resorbed. The major degradation and excretion product in humans is riboflavin (Rivlin 1970).
Vitamin B1 (thiamin) is found naturally in certain foodstuffs such as green peas, spinach, liver, bananas, whole grains and legumes. Human diseases associated with thiamin deficiency include beriberi, due to a thiamin-deficient diet, TMRA, due to defects in the SLC19A2 transport protein, and Wernicke-Korsakoff Syndrome, associated with thiamin deficiency in alcoholism (Haas 1988). Thiamin is water-soluble so is not stored in the body. When pyrophosphorylated, thiamin is converted into the coenzyme thiamin pyrophosphate (ThPP, codecarboxylase) which plays an essential role in oxidative decarboxylation and group transfer reactions.
Phosphorylation of riboflavin (RIB) results in the formation of the first cofactor, flavin mononucleotide (FMN). This reaction is catalyzed by riboflavin kinase (RFK), a cytosolic enzyme existing as a monomer. It utilizes either zinc or magnesium ions in the reaction.
The regulated turnover of glycogen plays a central, tissue-specific role in the maintenance of blood glucose levels and in the provision of glucose to tissues such as muscle and brain in response to stress. Defects in the enzymes involved in glycogen turnover are associated with abnormal responses to fasting and exercise that can differ widely in their presentation and severity. Additional symptoms can be the result of accumulation of abnormal products of glycogen metabolism (www.ommbid.com). In this initial release, we have annotated two forms of myoclonic epilepsy of Lafora that are due to defects in proteins required for the turnover of the low levels of phosphoglycogen that accumulate in many tissues of the body. This module will be extended in future releases to cover diseases due to deficiencies in GYG1, the ubiquitously expressed form of glycogenin (GSD type XV), GYS2 and GYS1, the liver-specific and ubiquitously expressed forms of glycogen synthase (GSD type 0), GBE1, the single form of branching enzyme (GSD type IV), and in the endoplasmic reticulum-associated phosphatase (G6PC) and transporter (SLC37A4) required for export of glucose geneated by glycogen breakdown in liver (GSD type 1a and 1b, respectively). Severe congenital neutropenia type 4 (SCN4) is included in this group because its molecular basis is loss of glucose 6-phosphatase 3 (G6PC3) activity (Boztug et al. 2009). G6PC3 is a ubiquitously expressed isozyme of G6PC, the enzyme whose deficiency is the cause of glycogen storage disease type 1a (GSD 1a).
Cytosolic thiamin pyrophosphokinase (TPK1) catalyzes the reaction of thiamin (THMN) and ATP to form thiamin diphosphate (ThDP aka thiamin pyrophosphate) and ADP. ThDP is an active cofactor for transketolase, pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, enzymes involved in glycolysis and energy production. The gene encoding the human enzyme has been cloned and its protein product has been shown to have TPK1 activity (Nosaka et al. 2001; Zhao et al. 2001). Its homodomeric structure and association with Mg2+ are inferred from properties of the homologous yeast enzyme (Baker et al. 2001).
These pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the body (as glycogen) and its mobilization during a short fast; and 3) the synthesis of glucose from pyruvate during extended fasts.
Lafora disease is a progressive neurodegenerative disorder with onset typically late in childhood, characterized by seizures and progressive neurological deterioration and death within ten years of onset. Recessive mutations in EPM2A (laforin) and NHLRC1 (malin) have been identified as causes of the disease. The disease is classified here as one of glycogen storage as EPM2A (laforin) and NHLRC1 (malin) regulate normal glycogen turnover and defects in either protein are associated with the formation of Lafora bodies, accumulations of abnormal, insoluble glycogen molecules in tissues including brain, muscle, liver, and heart (Ramachandran et al. 2009; Roach et al. 2012). Consistent with a central role for glycogen accumulation in the disease, reduced (Turnbull et al. 2011) or absent (Pederson et al. 2013) glycogen synthase activity prevents Lafora Disease in mouse models. Type 2A disease. EPM2A (laforin) associated with cytosolic glycogen granules, normally catalyzes the removal of the phosphate groups added rarely but consistently to growing glycogen molecules (Tagliabracci et al. 2011). Defects in this catalytic activity lead to the formation of phosphorylated glycogen molecules that are insoluble and that show abnormal branching patterns (Minassian et al. 1998, Serratosa et al. 1999, Tagliabracci et al. 2011). Type 2B disease. NHLRC1 (malin) normally mediates polyubiquitination of EPM2A (laforin) and PPP1R3C (PTG). The two polyubiquitinated proteins are targeted for proteasome-mediated degradation, leaving a glycogen-glycogenin particle associated with glycogen synthase. In the absence of NHLRC1 activity, EPM2A and PPP1R3C proteins appear to persist, associated with the formation of abnormal, stable glycogen granules (Lafora bodies) (Chan et al. 2003; Gentry et al. 2005). In NHLRC1 knockout mice PPP1R3C levels are unchanged rather than increased, suggesting that NHLRC1 does not target PPP1R3C for degradation. However, EPM2A protein levels are increased in this knockout consistent with NHLRC1's proposed role (DePaoli-Roach et al. 2010).
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Cytosolic pantothenate kinases catalyze the reaction of ATP and pantothenate to form ADP and phosphopantothenate. This enzymatic activity has been demonstrated in crude cell extracts for two isoforms of mouse pantothenate kinase 1 (Rock et al. 2002) and for their human homologues (Ramaswamy and 2004). Two additional human genes, PANK3 and PANK4, encode closely related proteins but pantothenate kinase activity has not been demonstrated experimentally for them (Leonardi et al. 2005; Zhou et al. 2001).
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Pantothenate kinase 2 catalyzes the reaction of ATP and pantothenate to form ADP and phosphopantothenate. While pantothenate kinase 2 co-purifies with mitocondria, its precise location within the mitochondrion has not been established (Hortnagel et al. 2003; Johnson et al. 2004). Recent work by Leonardi et al. (2007) supports a model in which the enzyme is located in the intermembrane space, hence freely accessible to small molecules from the cytosol.Pantothenate is phosphorylated by pantothenate kinase (PANK). Deficiencies in PANK2 cause a progressive neurodegenerative disorder associated with iron accumulation in the brain, but the relationship between disease symptoms and pantothenate metabolism remains unclear (Zhou et al. 2001; Zhang et al. 2006).
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Leptin and the central nervous system control of glucose metabolism
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Vitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only in limited amounts by human cells. Vitamins are classified according to their solubility, either fat-soluble or water-soluble. The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases. Water-soluble vitamins include ascorbate (vitamin C) and the members of the B group: thiamin (vitamin B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), and cobalamin (B12). Metabolic processes annotated here include the synthesis of thiamin pyrophosphate (TPP) from thiamin (B1), the synthesis of FMN and FAD from riboflavin (B2), the synthesis of nicotinic acid (niacin - B3) from tryptophan, the synthesis of Coenzyme A from pantothenate (B5), and features of the metabolism of folate (B9).
Defects in AMN cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Norwegian type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Norwegian cases described by Imerslund were due to defects in AMN (Imerslund 1960). The resultant malabsorption of Cbl (vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
Defects in the CUBN gene cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Finnish type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Finnish cases described by Grasbeck et al. were caused by defects in CUBN (Grasbeck et al. 1960). The resultant malabsorption of Cbl (cobalamin, vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
Defective transcobalamin II (produced by the TCN2 gene) results in TCN2 deficiency (MIM:275350), an autosomal recessive disorder with early-onset in infancy characterized by failure to thrive, megaloblastic anemia, and pancytopenia. If left untreated, the disorder can result in mental retardation and neurologic abnormalities (Haberle et al. 2009).
Defects in LMBRD1 cause methylmalonic aciduria and homocystinuria type cblF (MMAHCF; MIM:277380), characterised biochemically by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MetCbl) (Rutsch et al. 2009, Gailus et al. 2010).
The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
Defects in GIF cause hereditary intrinsic factor deficiency (IFD, aka congenital pernicious anemia; MIM:261000). IFD is an autosomal recessive disorder characterized by megaloblastic anemia (Tanner et al. 2005).
Defects in MMACHC cause methylmalonic aciduria and homocystinuria type cblC (MMAHCC; MIM:277400). MMAHCC is the most common disorder of cobalamin metabolism and is characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Affected individuals may have developmental, haematologic, neurologic, metabolic, ophthalmologic, and dermatologic clinical findings (Lerner-Ellis et al. 2006).
Defects in MMADHC cause methylmalonic aciduria and homocystinuria type cblD (MMAHCD; MIM:277410), a disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) (Coelho et al. 2008).
Defects in MTRR cause methylcobalamin deficiency type E (cblE; methionine synthase reductase deficiency; MIM:236270) (Wilson et al. 1999). Patients with cblE exhibit megaloblastic anemia and hyperhomocysteinemia. SAM is used as a methyl donor in many biological reactions and demethylation of SAM produces S-adenosylhomocysteine, which is deadenosylated to form homocysteine. Homocysteine remethylation is carried out by MTR, which requires MTRR to maintain enzyme-bound cobalamin (Cbl) in its active form; but in cblE patients, MTR becomes inactivated and thus homocysteine accumulates.
Defects in MTR cause methylcobalamin deficiency type G (cblG; MIM:250940), an autosomal recessive inherited disease that causes mental retardation, macrocytic anemia, and homocystinuria (Leclerc et al. 1996, Gulati et al. 1996, Watkins et al. 2002).
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Transcriptional networks controlling pancreatic development and beta cell function
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Nicotinamide (NAM) levels are modulated by the action of three enzymes involved in nicotinamide salvaging. They are nicotinamide deaminase, nicotinamide phosphoribosyltransferase and nicotinate phosphoribosyltransferase. These enzymes are poorly characterized in humans, depsite their importance in NAM utilization (Magni et al. 2004). Although not a salvage reaction, NAM levels can also be regulated by nicotinamide N-methyltransferase (NNMT), a potential regulator of diet-induced obesity (Kraus et al. 2014).
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Nicotinate (niacin) and nicotinamide are precursors of the coenzymes nicotinamide-adenine dinucleotide (NAD+) and nicotinamide-adenine dinucleotide phosphate (NADP+). When NAD+ and NADP+ are interchanged in a reaction with their reduced forms, NADH and NADPH respectively, they are important cofactors in several hundred redox reactions. Nicotinate is synthesized from 2-amino-3-carboxymuconate semialdehyde, an intermediate in the catabolism of the essential amino acid tryptophan.
The quality control of MHC class I peptide loading
Molecular cloning of a novel member of the GLUT family of transporters, SLC2a10 (GLUT10), localized on chromosome 20q13.1: a candidate gene for NIDDM susceptibility
Mitochondrial folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest mitochondrial form of THF has six added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the mitochondrial matrix so this reaction is needed for normal THF function under physiological conditions. The mitochondrial and cytosolic forms of folylpolyglutamate synthase are encoded by the same gene - alternative splicing generates mRNA with or without an initial exon encoding a mitochondrial targeting sequence (Garrow et al. 1992; Chen et al. 1996).
Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of tetrahydrofolate polyglutamate (THF polyglutamate) and serine to form 5,10-methyleneTHF polyglutamate and glycine. The active form of the enzyme is a tetramer (Renwick et al. 1998). In the body, this reaction is a major source of 5,10-methyleneTHF, which in turn is a critical precursor in the synthesis of dTMP.
Cytosolic folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of THF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal THF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
Cytosolic folylpolyglutamate synthase catalyzes the reaction of 5-methylTHF-glutamate(n), L-glutamate, and ATP to form 5-methylTHF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of 5-methylTHF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of 5-methylTHF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, 5-methylTHF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal 5-methylTHF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
In order to get a sulfur atom for subsequent sulfuration reactions, cysteine is first desulfurated by NFS1 which transfers it onto a cysteine of MOCS3, yielding a protein persulfide (Marelja et al, 2008).
Molybdenum cofactor (MoCo) is needed by three enzymes in humans: sulfite oxidase, xanthine oxidase and aldehyde oxidase. The pathway of its synthesis is so conserved that plants and bacteria can readily use human enzymes. Bacteria, however, diverge after the first three steps from this path and their final MoCo differs from that of the eukaryotes. Plants and animals have also developed a refinement of their MoCo which is needed for the function of their xanthine and aldehyde oxidases. This means, in humans we find sulfurated instead of desulfurated molybdenum cofactor on these two enzymes (Schwarz 2005; Schwarz, Mendel, Ribbe 2009).
Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of 5,10-methyleneTHF polyglutamate and glycine to form tetrahydrofolate polyglutamate (THF polyglutamate) and serine. The active form of the enzyme is a tetramer (Renwick et al. 1998).
Folates are essential cofactors that provide one-carbon moieties in various states of reduction for biosynthetic reactions. Processes annotated here include transport reactions by which folates are taken up by cells and moved intracellularly, folate conjugation with glutamate (required for folate retention within a cell), and some of the key reactions in the generation of reduced folates and one-carbon derivatives of folate.
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Quantitative studies on the release of platelet fibrinogen by thrombin
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The Biotinidase Gene Variants Registry: A Paradigm Public Database
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The phosphatidylinositol polyphosphate 5-phosphatase SHIP1 associates with the dok1 phosphoprotein in bcr-Abl transformed cells
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Cloning, genomic organization, and characterization of a human cholinephosphotransferase
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Mutational analysis of 105 mucopolysaccharidosis type VI patients
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594311
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3541.2
Di- and triphosphopyridine nucleotide isocitric dehydrogenases in yeast
Signal transduction via platelet-derived growth factor receptors
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110668
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3368.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110720
GPD1L dimer (name copied from entity in Homo sapiens)
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Novel lipogenic enzyme ELOVL7 is involved in prostate cancer growth through saturated long-chain fatty acid metabolism
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2(FDPS:3Mg2+) (name copied from entity in Homo sapiens)
ACAT1 tetramer (name copied from entity in Homo sapiens)
Btn-ACACA:2Mn2+ (name copied from entity in Homo sapiens)
DGAT1 tetramer (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110732
PLCH2:Ca2+ (name copied from entity in Homo sapiens)
Bleeding due to disruption of a cargo-specific ER-to-Golgi transport complex
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ISYNA1:NAD+ (name copied from entity in Homo sapiens)
Inflammasomes: guardians of cytosolic sanctity
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PLCG2:Ca2+ (name copied from entity in Homo sapiens)
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PLCH1:Ca2+ (name copied from entity in Homo sapiens)
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595187
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595190
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GPD1 dimer (name copied from entity in Homo sapiens)
Dimerization and release of molecular chaperone inhibition facilitate activation of eukaryotic initiation factor-2 kinase in response to endoplasmic reticulum stress
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Adrenodoxin: structure, stability, and electron transfer properties
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4564.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110653
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4430.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110731
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595579
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113573
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110693
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4471.2
Morquio A syndrome: cloning, sequence, and structure of the human N-acetylgalactosamine 6-sulfatase (GALNS) gene
FDPS:3Mg2+ (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595507
CHKA:CHKA (name copied from entity in Homo sapiens)
CHKB:CHKB (name copied from entity in Homo sapiens)
CHKA:CHKB (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595162
PCYT2 dimer (name copied from entity in Homo sapiens)
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595143
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595133
DAP10- and DAP12-associated receptors in innate immunity
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Function of Nod-like receptors in microbial recognition and host defense
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595580
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An asparagine-phenylalanine substitution accounts for catalytic differences between hGSTM3-3 and other human class mu glutathione S-transferases
Isolation and characterization of human Nramp cDNA
ACACB:2Mn2+ (name copied from entity in Homo sapiens)
ACACA:2Mn2+ (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3210.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110669
Identification of the gene encoding the enzyme deficient in mucopolysaccharidosis IIIC (Sanfilippo disease type C)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3930.1
Traffic control: regulation of kinesin motors
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5560.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110694
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5573.1
MOCS3-S-S(1-):Zn2+ (name copied from entity in Homo sapiens)
2xNFS1:2xPXLP (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596521
4xSHMT1 (name copied from entity in Homo sapiens)
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MOCS3:Zn2+ (red.) (name copied from entity in Homo sapiens)
NADSYN1 hexamer (name copied from entity in Homo sapiens)
2xNAPRT1 (name copied from entity in Homo sapiens)
2xPPCS (name copied from entity in Homo sapiens)
3xPPCDC:3xFMN (name copied from entity in Homo sapiens)
SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596490
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_151581.1
PLCE1:Ca2+ (name copied from entity in Homo sapiens)
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PLCD1:Ca2+ (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_206154.2
PLCG1:Ca2+ (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595584
PLCD3:Ca2+ (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_224567.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2509836
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596702
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_242037.1
PLCB4:Ca2+ (name copied from entity in Homo sapiens)
PLCZ1:Ca2+ (name copied from entity in Homo sapiens)
PLCB1:Ca2+ (name copied from entity in Homo sapiens)
PLCB2:Ca2+ (name copied from entity in Homo sapiens)
PLCB3:Ca2+ (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594797
Ded1p, a DEAD-box protein required for translation initiation in Saccharomyces cerevisiae, is an RNA helicase.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594301
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113518
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3468.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594302
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111793
Characterization of a mutant pancreatic eIF-2alpha kinase, PEK, and co-localization with somatostatin in islet delta cells
ErbB-3 and ErbB-4 function as the respective low and high affinity receptors of all Neu differentiation factor/heregulin isoforms
N(epsilon)-(carboxymethyl)lysine adducts of proteins are ligands for receptor for advanced glycation end products that activate cell signaling pathways and modulate gene expression
Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
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Aquaporins: highways for cells to recycle water with the outside world
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3998.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113525
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595566
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595565
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_212589.2
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Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4768.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110685
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2310.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110711
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2857.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110660
Comparison of the intracellular signaling responses by three chimeric fibroblast growth factor receptors in PC12 cells
PIG-W is critical for inositol acylation but not for flipping of glycosylphosphatidylinositol-anchor
The Wnt/calcium pathway activates NF-AT and promotes ventral cell fate in Xenopus embryos
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_232841.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5595562
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241213.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110672
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2490.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593889
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593887
Selective active site inhibitors of human lactate dehydrogenases A4, B4, and C4
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_250348.1
Identification of a cDNA encoding an isoform of human CTP synthetase
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_187031.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594290
'Mg2+ [cytosol]' is required for 'pyrophosphate + H2O => 2 orthophosphate [cytosolic]'
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'Mg2+ [mitochondrial matrix]' is required for 'pyrophosphate + H2O => 2 orthophosphate [mitochondrial]'
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_248405.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593577
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5593575
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_246877.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594304
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594306
'GSH [cytosol]' negatively regulates 'gamma-glutamylcysteine combines with glycine to form glutathione'
'GTP [cytosol]' is required for 'Met-tRNAi binds to eIF2:GTP to form the ternary complex'
'heme [mitochondrial matrix]' negatively regulates 'ALAS condenses SUCC-CoA and Gly to form dALA'
'Pb2+ [mitochondrial matrix]' negatively regulates 'FECH binds Fe2+ to PRIN9 to form heme'
'GTP [mitochondrial matrix]' negatively regulates 'glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]'
'ADP [mitochondrial matrix]' positively regulates 'glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]'
'GTP [mitochondrial matrix]' negatively regulates 'alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]'
'ADP [mitochondrial matrix]' positively regulates 'alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]'
Proteasome and peptidase function in MHC-class-I-mediated antigen presentation
'ATP [cytosol]' is required for 'Ribosomal scanning '
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_249953.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10325.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193079
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5596883
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594666
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193057
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594665
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10360.2
'ATP [cytosol]' positively regulates 'NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O'
'dATP [cytosol]' negatively regulates 'NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O'
'ATP [cytosol]' positively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
'dATP [cytosol]' negatively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
'D-Fructose 1,6-bisphosphate [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'GDP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'ADS [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'GMP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
Signal transduction by the neurotrophin receptors
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses ITP to IMP'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses dITP to dIMP'
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5594654
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Defective MMADHC causes methylmalonic aciduria and homocystinuria type cblD
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(GlcN)1 (Ino(acyl)-P)1 (Man)2 (EtN)1 (P)1
6-O-{alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [ChEBI:53059]
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Phagocytosis of retinal rod and cone photoreceptors
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Diversification of Neu differentiation factor and epidermal growth factor signaling by combinatorial receptor interactions
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Hydrogen peroxide as a signaling molecule
D-Fructose 1,6-bisphosphate [ChEBI:16905]
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Nucleotide receptor signaling in platelets
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Tuberculosis - metabolism and respiration in the absence of growth
Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 gene
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High protonic potential actuates a mechanism of production of reactive oxygen species in mitochondria
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A microRNA polycistron as a potential human oncogene
Reconstitution of proliferating cell nuclear antigen-dependent repair of apurinic/apyrimidinic sites with purified human proteins.
Red cell pyruvate kinase deficiency: molecular and clinical aspects
Steroidogenic electron transport in adrenal cortex mitochondria
Acyl-CoA:lysophospholipid acyltransferases
Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Cobalamin (Cbl, vitamin B12) transport and metabolism
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3' -UTR-mediated translational regulation
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Newly made phosphatidylserine and phosphatidylethanolamine are preferentially translocated between rat liver mitochondria and endoplasmic reticulum
D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
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Synthesis of glycosylphosphatidylinositol (GPI)
Cloning and expression of human deoxyhypusine synthase cDNA. Structure-function studies with the recombinant enzyme and mutant proteins.
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Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex
Discovery of an arachidonoyl coenzyme A synthetase in human platelets
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The structure of apo human glutamate dehydrogenase details subunit communication and allostery
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Shelterin: the protein complex that shapes and safeguards human telomeres
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Class II MHC peptide loading by the professionals
FACL4, encoding fatty acid-CoA ligase 4, is mutated in nonspecific X-linked mental retardation
Leptin therapy, insulin sensitivity, and glucose homeostasis
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Novel interleukin-2 receptor subunit detected by cross-linking under high-affinity conditions
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Comprehensive proteomic analysis of the human spliceosome.
Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways
The ERBB4/HER4 intracellular domain 4ICD is a BH3-only protein promoting apoptosis of breast cancer cells
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
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Gene identification for the cblD defect of vitamin B12 metabolism
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Zinc transporters and the cellular trafficking of zinc
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
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The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals
Association with HSP90 inhibits Cbl-mediated down-regulation of mutant epidermal growth factor receptors
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The sodium/calcium exchanger family-SLC8
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Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
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A minus-end-directed kinesin with plus-end tracking protein activity is involved in spindle morphogenesis
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P110delta, a novel phosphoinositide 3-kinase in leukocytes
Translation of the phosphoinositide code by PI effectors
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Intracellular signaling pathways in IgE-dependent mast cell activation
Arch. Immunol. Ther. Exp. (Warsz.) 54:393-401
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Wnt and calcium signaling: beta-catenin-independent pathways
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Isolation of the human phosphomannomutase gene (PMM1) and assignment to chromosome 22q13
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Adaptors and molecular scaffolds in immune cell signaling
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Advanced glycation endproduct (AGE) receptor 1 is a negative regulator of the inflammatory response to AGE in mesangial cells
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Molecular cloning, expression, and characterization of human bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase and its functional domains
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Phosphorylation of Nephrin Triggers Ca2+ Signaling by Recruitment and Activation of Phospholipase C-{gamma}1
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Roles of aquaporin-3 water channels in volume-regulatory water flow in a human epithelial cell line
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Acidosis, acid-sensing ion channels, and neuronal cell death
Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein
Characterization of human type I and type II IMP dehydrogenases
Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.
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Apoptosis-inducing factor (AIF): a ubiquitous mitochondrial oxidoreductase involved in apoptosis.
Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes
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Minireview: implication of mitochondria in insulin secretion and action
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans
Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling
Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex.
The mitochondrial ABC transporter Atm1p functions as a homodimer
Vascular endothelial growth factor signaling to endothelial nitric oxide synthase: more than a FLeeTing moment
Isolation and characterization of one soluble and two membrane-associated forms of phosphoinositide-specific phospholipase C from human platelets
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A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair.
DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts.
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ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1
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SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder
Fibroblast growth factors and their receptors in cancer
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The Hsp70 and TRiC/CCT chaperone systems cooperate in vivo to assemble the von Hippel-Lindau tumor suppressor complex
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Biotinidase deficiency: the enzymatic defect in late-onset multiple carboxylase deficiency
Crystal structure of human recombinant ornithine aminotransferase.
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Crystal structure of maleylacetoacetate isomerase/glutathione transferase zeta reveals the molecular basis for its remarkable catalytic promiscuity.
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LAB/NTAL/Lat2: a force to be reckoned with in all leukocytes?
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Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function
Human cytoplasmic isoleucyl-tRNA synthetase: selective divergence of the anticodon-binding domain and acquisition of a new structural unit
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Mucopolysaccharidosis type II (Hunter syndrome): a clinical review and recommendations for treatment in the era of enzyme replacement therapy
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Inositol phosphate synthesis and the nuclear processes they affect
Type II chaperonins, prefoldin, and the tubulin-specific chaperones
Global gene expression profiling and histochemical analysis of the developing human fetal pancreas
ZnT-8, a pancreatic beta-cell-specific zinc transporter
A current view of the mammalian aquaglyceroporins
Diversity of the mammalian sodium/proton exchanger SLC9 gene family
Angiogenesis is regulated by a novel mechanism: pro- and antiangiogenic proteins are organized into separate platelet alpha granules and differentially released
On the discovery of precursor processing
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
Plasma concentrations of phenyllactic acid in phenylketonuria
Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins
Identification of a novel glucose transporter-like protein-GLUT-12
Am J Physiol Endocrinol Metab 282:E733-8
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Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways
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A review of the pharmacokinetics of abacavir
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Glyceraldehyde-3-phosphate dehydrogenase from human tissues.
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On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
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Molecular cloning and characterization of PLC-eta2
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1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate [ChEBI:16851]
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Sequencing and expression of a cDNA for human glutathione synthetase
Secretory protein trafficking and organelle dynamics in living cells
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Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
Segregation of MHC class II molecules from MHC class I molecules in the Golgi complex for transport to lysosomal compartments
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Carbohydrate responsive element-binding protein (ChREBP): a key regulator of glucose metabolism and fat storage
The unfolded protein response is an important regulator of inflammatory genes in endothelial cells
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The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism
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Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes
miRNAs on the move: miRNA biogenesis and the RNAi machinery
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TRF1 inhibits telomere C-strand DNA synthesis in vitro
Planar cell polarity signaling: from fly development to human disease
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
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The oncogenic properties of mutant p110alpha and p110beta phosphatidylinositol 3-kinases in human mammary epithelial cells
Proc. Natl. Acad. Sci. U.S.A. 102:18443-8
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Focal adhesions - the cytoskeletal connection
Identification of arylsulfonamides as Aquaporin 4 inhibitors
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Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons.
Fcgamma RI-triggered generation of arachidonic acid and eicosanoids requires iPLA2 but not cPLA2 in human monocytic cells
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Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation
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Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases
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gene ontology term for cellular function
Central leptin and ghrelin signalling: comparing and contrasting their mechanisms of action in the brain
Diseases caused by defects in the visual cycle: retinoids as potential therapeutic agents
Annu. Rev. Pharmacol. Toxicol. 47:469-512
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Human Smp3p adds a fourth mannose to yeast and human glycosylphosphatidylinositol precursors in vivo
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Primary structure and tissue-specific expression of human beta-hydroxyisobutyryl-coenzyme A hydrolase.
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STING mediated induction of host immune responses
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Purification, cDNA-cloning and expression of human diacylglycerol kinase
Identification and characterization of mutations in patients with holocarboxylase synthetase deficiency
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Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase.
Human acetyl-CoA carboxylase 2. Molecular cloning, characterization, chromosomal mapping, and evidence for two isoforms.
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