Protein which contains at least one 2Fe-2S iron-sulfur cluster: 2 iron atoms complexed to 2 inorganic sulfides and 4 sulfur atoms of cysteines from the protein.
Protein, or part of a protein, whose three-dimensional structure has been resolved experimentally (for example by X-ray crystallography or NMR spectroscopy) and whose coordinates are available in the PDB database. Can also be used for theoretical models.
Protein which contains at least one 3Fe-4S iron-sulfur cluster: 3 iron atoms complexed to 4 inorganic sulfides and 3 sulfur atoms of cysteines from the protein. In a number of iron-sulfur proteins, the 4Fe-4S cluster can be reversibly converted by oxidation and loss of one iron ion to a 3Fe-4S cluster.
Protein which contains at least one 4Fe-4S iron-sulfur cluster: 4 iron atoms complexed to 4 inorganic sulfides and 4 sulfur atoms of cysteines from the protein. In a number of iron-sulfur proteins, the 4Fe-4S cluster can be reversibly converted by oxidation and loss of one iron ion to a 3Fe-4S cluster.
Protein involved in the synthesis of abscisic acid (ABA) (5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid). ABA is a plant hormone which play a role in many aspects of plant growth, development and cellular signaling (e.g. seed dormancy, seed maturation, vegetative growth and responses to various environmental stimuli such as stomatal closure during drought). This phytohormone can be synthesized from farnesyl diphosphate (direct C15 pathway) or from 9-cis-violaxanthine (indirect C40 pathway).
Protein involved in the abscisic acid (ABA) (5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth, development and cellular signaling (e.g. seed dormancy, seed maturation, vegetative growth and responses to various environmental stimuli such as stomatal closure during drought). This phytohormone can be synthesized from farnesyl diphosphate (direct C15 pathway) or from 9-cis-violaxanthine (indirect C40 pathway).
abscisic acid-activated signaling pathway
3-hydroxy-2-butanone biosynthetic process
Protein involved in the synthesis of acetoin (3-hydroxy-2-butanone). Acetoin is a component of the butanediol cycle (butanediol fermentation) in microorganisms.
Protein involved in the degradation of acetoin (3-hydroxy-2-butanone). Acetoin is a component of the butanediol cycle (butanediol fermentation) in microorganisms.
Protein which is posttranslationally modified by the attachment of at least one acetyl group; generally at the N-terminus.
Toxin which interferes with the function of the nicotinic acetylcholine receptor (nAChR). The nAChR is a postsynaptic membrane protein that undergoes an extensive conformational change upon binding to acetylcholine, leading to opening of an ion-conducting channel across the plasma membrane. These toxins are mostly found in snake and cone snail venoms.
acetylcholine receptor inhibitor activity
Protein that binds to the free end of the actin filament and thereby blocks further addition of subunits.
Protein which binds to actin, and thereby can modulate the properties and/or functions of the actin filament.
Viral protein that allows the active transport of viral material along actin filaments toward the intracellular replication sites during virus entry. This transport probably involves motor proteins like myosins or polymerization/depolymerization reactions as a driving force. Viruses such as poliovirus may utilize this type of intracellular transport.
actin-dependent intracellular transport of virus towards nucleus
Viral protein involved in the activation of host autophagy. Autophagy is a major intracellular pathway in the delivery of cytoplasmic material to lysosomes for degradation. It is also essential for the removal of pathogenic protein aggregates from the cell during infection. Although autophagy is clearly important for antiviral immune response, it can also be activated by viruses and serves as platform for viral replication. Some viruses such as poliovirus, use the autophagic pathway as a nonlytic mechanism for viral release.
Viral protein involved in the activation of host cell apoptosis by acting on host caspases. While many viruses encode protein that inhibit apoptosis, viruses can also use apoptosis to their advantage to suppress immune response or to disseminate. Therefore, some viral proteins are able to cleave or activate caspases in order to promote apoptosis.
induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
Viral protein involved in the activation of host NF-kappa-B. This protein is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. Several viruses have developed strategies to activate the NF-kappa-B pathway in order to promote viral replication and prevent virus-induced apoptosis.
induction by virus of host NF-kappaB cascade
Protein that positively regulates either the transcription of one or more genes, or the translation of mRNA.
Protein involved in acute phase, a response of the vertebrate body to insults, infections, immunological reactions or inflammatory processes; characterised by redness (rubor), heat (calor), swelling (tumor), pain (dolor) and sometimes loss of function.
Enzyme catalyzing the transfer of acyl- (RCO-) groups.
Protein involved in adaptive immunity. Vertebrates can develop a broad and almost infinite repertoire of antigen-specific receptors, which allows vertebrates to recognize almost any potential pathogen or toxin and to mount antigen-specific responses to it. Two types of adaptive immunity systems have evolved in vertebrates in order to generate immune receptor diversity. The jawed vertebrates strategy uses the V(D)JC recombination to achieve combinatorial diversity of immunoglobulin-based B cell receptors and T cell receptors. The jawless vertebrate strategy uses the somatic rearrangements of variable leucine-rich cassettes in the variable lymphocyte receptors (VLRs). The hallmarks of an adaptive immune system is the production of antigen-specific recognition receptor by somatic gene rearrangement. The long life of some antigen-primed cytotoxic lymphocytes and plasma cells provide protective memory to prevent reinvasion.
Protein which is posttranslationally modified by the attachment of at least one ADP-ribosyl group.
Protein which, if defective, causes age-related macular degeneration (ARMD), the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid (known as drusen) that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch's membrane. ARMD is likely to be a mechanistically heterogeneous group of disorders, and the specific disease mechanisms that underlie the vast majority of cases are currently unknown. However, a number of studies have suggested that both genetic and environmental factors are likely to play a role.
Protein which, if defective, causes Aicardi-Goutieres syndrome, a genetic disorder that is phenotypically similar to in utero viral infection. The disease is characterized by severe neurological dysfunction in infancy, leading to progressive microcephaly, spasticity, dystonic posturing, profound psychomotor retardation and often death in early childhood.
Protein encoded by the human immunodeficiency viruses HIV-1 or HIV-2, which are the cause of acquired immunodeficiency syndrome (AIDS). This disease is characterized by a severe defect of cell-mediated immunity which is often accompanied by cancers such as Kaposi's sarcoma, as well as secondary infections such as tuberculosis.
Protein which, if defective, causes albinism, a genetically determined or environmentally induced absence of pigmentation in animals normally pigmented. This can lead for example to lack of pigmentation in hair, skin and eyes.
Protein involved in the synthesis of alginate. Alginate is an exopolysaccharide in the cell walls of brown algae and in the capsular material of certain strains of Pseudomonas and Azotobacter, in which it provides a protective barrier against host immune defenses and antibiotics.
Protein involved in a biochemical reaction with alkaloids, a group of nitrogenous organic molecules (mostly heterocyclic) usually found in plants. Various alkaloids have toxic or medical properties, such as caffeine, morphine and nicotine.
Protein involved in alkylphosphonate uptake. Certain bacteria such as Escherichia coli can use alkylphosphonates as a phosphorus source.
Protein that stimulates the production of, and reacts with, antibodies (IgE) thus creating an allergic reaction (immediate-type hypersensitivity). Examples are pollen allergens from plants, venom allergens from insects, dust-mite allergens, and animal hair allergens.
Enzyme whose activity is modified by the noncovalent binding of an allosteric effector at a site other than the active site. This binding mediates conformational changes, altering its catalytic or binding properties.
Protein that inhibits alpha-amylase, an enzyme that catalyzes the endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
Protein which, if defective, causes Alport syndrome, an hereditary disorder characterized by a progressive glomerulonephritis leading to end-stage renal disease, often associated with sensorineural hearing loss and ocular abnormalities.
Protein for which at least two isoforms exist due to the usage of alternative initiation codons in the same mRNA (the resulting isoforms differ in their N-terminus if they are in frame).
Protein for which at least two isoforms exist due to the alternative usage of promoters.
Protein for which at least two isoforms exist due to distinct pre-mRNA splicing events.
Protein which, if defective, causes Alzheimer disease, a neurodegenerative disorder characterized by progressive dementia and global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy, senile plaques, neurofibrillary tangles, and neuropil threads. Early-onset forms also occurr.
Protein which, if defective, causes amelogenesis imperfecta, a clinically and genetically heterogeneous group of disorders affecting the dental enamel. The enamel may be hypoplastic, hypomineralized or both, and affected teeth may be discoloured, sensitive or prone to disintegration either pre-eruption or post-eruption. In the hypoplastic type of amelogenesis imperfecta, the enamel is of normal hardness but does not develop to normal thickness. In the hypomineralized type, the enamel is of normal thickness but opaque or yellowish white without lustre on newly erupted teeth; it is so soft that it is lost soon after eruption. Amelogenesis imperfecta occasionally occurs in conjunction with other dental, oral and extra-oral features.
Peptide which is posttranslationally modified by C-terminal amidation. The amino acid to be modified is almost always followed by a glycine, which provides the amide group. In a first reaction step the glycine is oxidized to form alpha-hydroxy-glycine. The oxidized glycine cleaves into the C-terminally amidated peptide and an N-glyoxylated peptide. C-terminal amidation is essential to the biological activity of many neuropeptides and hormones. In a few cases alpha-oxidative cleavage of an amino acid other than glycine has been observed. All such cases are additionally annotated with the word "atypical" in the feature description.
Protein involved in the synthesis of naturally-occuring amino acids. In addition to their use for protein biosynthesis, they are the precursors of many molecules such as purines, pyrimidines, histamines, adrenaline and melanin.
cellular amino acid biosynthetic process
Protein involved in the transport of amino acids.
Enzyme that activates an amino acid for translation by forming an aminoacyladenylate intermediate and then links this activated amino acid to the corresponding tRNA molecule (amino acid-tRNA, aminoacyl-tRNA). In general, a specific aminoacyl-tRNA synthase is available for each amino acid.
Enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins.
Enzyme that catalyzes the transfer of an alpha-amino group from an amino acid to an alpha-keto acid. The amino group is usually covalently bound by the prosthetic group pyridoxal phosphate.
Protein involved in the transport of ammonia/ammonium. Ammonia is an excellent nitrogen source for many bacteria, fungi, and plants, but it can be cytotoxic, especially for animal cells at high concentration. Its transport across cellular membranes is thus of high biological relevance. Ammonia (NH3) is a weak base and exists predominantly as the ammonium ion (NH4+) in biological fluids.
Protein specifically found in the skin of animals belonging to the vertebrate class amphibia, that includes frogs, toads, newts, salamanders and worm-like apoda. The skins of anuran amphibians, in addition to mucous glands, contain highly specialized poison glands, which, in reaction to stress or attack, exude a complex noxious species-specific cocktail of biologically active molecules. These secretions often contain a plethora of peptides such as neuropeptides and hormones. The frog dermatous glands also synthesize and store an extraordinarily rich variety of wide-spectrum antimicrobial peptides that are released onto the outer layer of the skin to provide an effective and fast-acting defense against harmful microorganisms.
Proteins which may form wide, insoluble, unbranched filaments possessing a cross-beta sheet quaternary structure, where the beta sheets are oriented perpendicular to the fibre axis. Amyloid fibrils may be involved in abnormal protein depositions, or amyloidosis, such as Alzheimer's or Parkinson's diseases. Functional amyloids, found in a wide range of organism, from bacteria to mammals are involved in diverse functions such as biofilm formation, formation of aerial hyphae, long-term memory or regulation of melanin biosynthesis.
Protein which, if defective, causes amyloidosis, a vast group of diseases defined by the accumulation of amyloid in tissues. Amyloidoses are classified according to clinical signs, biochemical type of amyloid protein involved, and the extent of amyloid deposition (generalized or localized). Most amyloidoses are multisystemic diseases affecting several organs or systems. Mainly affected organs are the kidneys, heart, gastrointestinal tract, liver, skin, peripheral nerves and eyes, but any organ can be affected. The most frequent forms are primary amyloidosis, also known as light-chain immunoglobulin amyloidosis (AL), reactive or inflammatory amyloidosis, also known as acquired amyloidosis (AA), and transthyretin amyloidosis (ATTR). Localized amyloidosis affecting the brain is characteristic of Alzheimer's disease, trisomy 21, and prion diseases (transmissible spongiform encephalitis, Creutzfeldt-Jakob disease, Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia). In prion diseases the amyloid precursor is the prion protein.
Protein found in the amyloplast, a colorless plant plastid that forms and stores starch. Amyloplasts are found in many tissues, particularly in storage tissues.
Protein which, if defective, causes amyotrophic lateral sclerosis (ALS), a degenerative disorder of motor neurons in the cortex, brain stem and spinal cord. ALS is characterized by muscular weakness and atrophy.
Protein involved in angiogenesis, the sprouting or splitting of capillaries from pre-existing vasculature. Angiogenesis plays an important role for example during embryonic development, normal growth of tissues and maintenance of the normal vasculature, wound healing, tumor growth and metastasis.
Protein involved in the exchange of anions across a membrane. Anion exchange is a cellular transport function which contributes to the regulation of cell pH and volume by a functionally related anion exchanger protein family.
Protein containing at least one ANK repeat, a conserved domain of approximately 33 amino acids, that was originally identified in ankyrin. It has been described as an L-shaped structure consisting of a beta-hairpin and two alpha-helices. Many ankyrin repeat regions are known to function as protein-protein interaction domains.
Protein containing at least one annexin repeat, a conserved domain of 61 residues, which is present in proteins of the annexin family in either four or eight copies. The annexin calcium binding sites are found within the repeated domains.
Component of an antenna complex or protein regulating the expression of such components. Antenna complexes are light-harvesting systems (LHC) which are protein-pigment complexes in or on photosynthetic membranes. LHCs receive radiant energy and transfer it to the reaction centers; an array of LHCs is often referred to as an "antenna". LHCs typically include one or more associated pigments (phycobilins, chlorophylls, bacteriochlorophylls and carotenoids).
Protein involved in the synthesis of antibiotics. Antibiotics are organic compounds produced by living organims that can selectively inhibit the growth of, or kill bacteria.
Protein that confers, on bacteria, the ability to withstand antibiotics. The resistance is often due either to mutations that prevent antibiotic binding to the protein or to amplification of the gene encoding the protein.
Protein that lowers the freezing point of blood or other biological fluids by inhibiting the formation of water ice crystals.
Protein which has deleterious effects on any type of microbe. Microbe is a general term for microscopic unicellular organisms, such as bacteria, archaea, fungi and protista. While the term microbe is often also used for viruses, we do not apply the keyword antimicrobial to antiviral proteins.
Protein capable of counteracting the damaging effects of oxidation, e.g. by trapping free radicals generated during the metabolic burst and possibly inhibiting ageing. Scavengers of highly reactive and harmful oxygen species.
Protein involved in the transport of a solute across a biological membrane coupled, directly, to the transport of a different solute in the opposite direction.
Protein synthesized or activated in the cell in response to viral infection, or protein with specific antiviral activity within the cell. Eukaryotic cells have an innate immune mechanism to fight viral infection, which is activated through the interferon signaling pathway or through dsRNA detection in the cytoplasm. It leads to the establishment of an antiviral cell state, which prevents virus replication or induces apoptosis. Most viruses have developed specific proteins to prevent the establishment of an antiviral state. About half of all bacteria and most archaea have a CRISPR (clustered regularly interspersed short plaindromic repeats) system of adaptive immunity to exogenous DNA. CRISPRs clusters are tandem arrays of alternating repeats and spacers, where the spacers in some cases are homologous to sequences from virus and plasmid genomes. The CRISPR arrays are transcribed, processed and in some way aid in detection and resistance to foreign DNA. In at least a few bacteria (E.coli, S.epidermidis) it seems DNA is the target, whereas in Pyrococcus furiosis it seems the CRISPR system targets RNA.
Protein with antiviral activity. Often this activity is fortuitous (e.g. a bacterial protein displaying anti-HIV activity).
Protein which, if defective, causes aortic aneurysm. Aortic aneurysm is the dilation of the wall of the aorta. It forms a sac that is filled with fluid or clotted blood, often resulting in a pulsating tumor. Aortic aneurysms are classified by their location on the aorta.
Protein encoded by the apicoplast genome or protein located in the apicoplast, a plastid found in some apicomplexan parasites which is a non-photosynthetic plastid relict. This organelle contains ring-like DNA of about 35 Kb as a third type of cell genome. Apicoplasts do not contain thylakoids; it is not yet clear if they contain internal membranes.
Protein which is found in the part of the plant which is external to the living protoplast, ie the cell wall, the intercellular space and the lumina of dead cells such as xylem vessels and tracheids.
Protein involved in apoptotic programmed cell death. Apoptosis is characterized by cell morphological changes, including blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation and chromosomal DNA fragmentation, and eventually death. Unlike necrosis, apoptosis produces cell fragments, called apoptotic bodies, that phagocytic cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage. In general, apoptosis confers advantages during an organism's life cycle.
Protein involved in arabinose breakdown. Arabinose is a 5-carbon aldose sugar found in plant gums, pectins and bacterial cell wall polysaccharides.
The archaellum (archaeal flagellum) is the motility apparatus of archaea which propels the cell through liquid medium. The archaellum is the functional equivalent of the bacterial flagellum but its architecture, composition and mode of assembly is completely unrelated. The archaellum is thinner (10-15 nm) compared to the bacterial flagellum (18-24 nm). Its filament is assembled from archaellin subunits, which are N-glycosylated proteins. The archaellum is considered to be a type IV pilus-like structure and accordingly is assembled from the base into a 3-start helix. Archaellins have a type III signal sequence which is removed by the pre-archaellin peptidase. Core components of the assembly machinery are ArlI and ArlJ (previously FlaI, FlaJ) which are distantly related to PilB and PilC from type II secretion systems and type IV pills assembly systems. ArlI is a dual function ATPase which first assembles the filament and then rotates it by using the energy from ATP hydrolysis. Ion gradients are not used for archaellum rotation.
Protein which is involved in the formation, organization or maintenance of the archaellum (archaeal flagellum) the motility apparatus of archaea which propels the cell through liquid medium. The archaellum is the functional equivalent of the bacterial flagellum but its architecture, composition and mode of assembly is completely unrelated. The archaellum is thinner (10-15 nm) compared to the bacterial flagellum (18-24 nm). Its filament is assembled from archaellin subunits (archaeal flagellin), N-glycosylated proteins. The archaellum is considered to be a type IV pilus-like structure and accordingly is assembled from the base into a 3-start helix. Archaellins have a type III signal sequence which is removed by the pre-archaellin peptidase. Core components of the assembly machinery are ArlI and ArlJ (previously FlaI, FlaJ) which are distantly related to PilB and PilC from type II secretion systems and type IV pills assembly systems. ArlI is a dual function ATPase which first assembles the filament and then rotates it by using the energy from ATP hydrolysis.
Protein involved in the synthesis of the basic amino acid arginine (Arg).
Protein involved in biochemical reactions with the basic amino acid arginine (Arg).
Aromatic amino acid family biosynthetic process
Protein involved in the synthesis of an amino acid with an aromatic side-chain: phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp).
Protein involved in the breakdown of aromatic hydrocarbons. Aromatic hydrocarbons are compounds which only contain carbon and hydrogen, examples include the common pollutants benzene and naphthalene.
Protein that confers, on bacteria and other microorganisms, the ability to withstand aromatic compounds of arsenic.
response to arsenic-containing substance
Protein involved in the synthesis of ascorbate, the ionized form of ascorbic acid (vitamin C). Ascorbic acid is derived from glucose via the uronic acid pathway. This water-soluble vitamin is essential for the synthesis of bone, cartilage and dentine. It is required in the diet of primates and some other species that cannot synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, a key enzyme for the biosynthesis of this vitamin.
Protein involved in the synthesis of the polar amino acid asparagine (Asn).
Protein which inhibits the catalytic activity of an aspartyl protease, a class of proteases that contains an active site aspartate residue (Asp), e.g. pepsin, HIV retropepsin, renin, etc.
aspartic-type endopeptidase inhibitor activity
Enzyme which catalyzes the hydrolysis of esters and is characterized by a catalytically active aspartic acid residue in its active site.
Proteolytic enzyme with an aspartate residue (Asp) in its active site. There are many families of aspartyl proteases. The most well known one is the pepsin family (A1 in MEROPS classification) which is known to exist in vertebrates, fungi, plants, retroviruses and some plant viruses.
Protein which, if defective, is involved in Asperger syndrome, a complex, multifactorial disorder. It is characterized by clinically significant impairment of social interaction, and restricted repetitive and stereotyped patterns of behavior. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases.
Protein which, if defective, is associated with asthma, a bronchial disorder associated with airway inflammation, swelling and obstruction. It is marked by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi.
Protein which, if defective, causes atherosclerosis, which is characterized by deposits of plaques (atheromas) in the blood vessels, thus narrowing the vessel lumen and restricting blood flow. Atheromas consist of lipids (cholesterol), carbohydrates, blood products, fibrous tissue and calcium deposits.
Adenosine 5'-triphosphate biosynthetic process
Adenosine triphosphate biosynthetic process
Protein involved in the synthesis of adenosine 5'-triphosphate (ATP). ATP is a ribonucleotide adenosine (a purine base adenine linked to the sugar D-ribofuranose) which carries 3 phosphate groups esterified to the sugar moiety. It is the cell's source for energy and phosphate.
Protein which binds adenosine 5'-triphosphate (ATP), a ribonucleotide adenosine (a purine base adenine linked to the sugar D-ribofuranose) that carries three phosphate groups esterified to the sugar moiety. It is the cell's source for energy and phosphate.
Protein which, if defective, causes atrial fibrillation, a common cardiac arrhythmia marked by disorganized atrial electrical activity and rapid randomized contractions of small areas of the atrial myocardium, causing a totally irregular, and rapid, ventricular rate.
Protein which, if defective, causes atrial septal defect, a congenital cardiac anomaly characterized by persistent patency of the atrial septum that results in blood flow between the atria. It is due to failure of fusion between either the septum secundum or the septum primum and the endocardial cushions.
Protein which, if defective, is involved in autism, a pervasive developmental disorder. It is a complex, multifactorial disease characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism manifest moderate mental retardation.
Protein which, if defective, is involved in autism spectrum disorder, a clinically heterogeneous group of disorders that share common features of impaired social relationships, impaired language and communication, repetitive behaviors, and a restricted range of interests. The spectrum includes diverse phenotypic manifestations, such as classic autism, Asperger syndrome, childhood disintegrative disorder, Rett syndrome, and pervasive developmental disorder not otherwise specified.
Protein which, if defective, causes autoimmune encephalomyelitis. This form of autoimmune inflammation of the brain and spinal cord causes demyelination.
Protein which, if defective, causes autoimmune inflammation of the uvea, which is the vascular middle coat of the eye, comprising the iris, ciliary body and choroid.
Protein involved in the synthesis of an autoinducer, a molecule which triggers the regulators of biosynthetic genes.
Protein participating in autophagy, a process of intracellular bulk degradation in which cytoplasmic components including organelles are sequestered within double-membrane vesicles that deliver the contents to the lysosome/vacuole for degradation. There are three primary forms of autophagy: chaperone-mediated autophagy, microautophagy and macroautophagy. During macroautophagy, the sequestering vesicles, termed autophagosomes, fuse with the lysosome or vacuole resulting in the delivery of an inner vesicle (autophagic body) into the lumen of the degradative compartment.
Protein involved in the synthesis of auxins. Auxins are plant hormones which play a role in many aspects of plant growth and development.
Protein involved in the auxin signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development (e.g. caulogenesis, rhizogenesis, tropisms, nodulation). The major form of this phytohormone is indole-3-acetic acid (IAA) that can be synthesized both from tryptophan (Trp) using Trp-dependent pathways and from an indolic Trp precursor via Trp-independent pathways. Plants can also obtain IAA by b-oxidation of indole-3-butyric acid (IBA), a second endogenous auxin, or by hydrolysing IAA conjugates, in which IAA is linked to amino acids, sugars or peptides.
Protein involved in the activation and proliferation of B-cells. B-cells are activated by the binding of antigen to receptors on its cell surface which causes the cell to divide and proliferate. Some stimulated B-cells become plasma cells, which secrete antibodies. Others become long-lived memory B-cells which can be stimulated at a later time to differentiate into plasma cells.
Bacterial protein present in a flagellum, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure with switches propels the cell through a liquid medium.
Bacterial flagellar apparatus biogenesis
Protein which is involved in the formation, organization or maintenance of the bacterial flagellum, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure whose switches propels the cell through a liquid medium.
Bacterial flagellar apparatus protein export
Protein which is involved in the export of bacterial flagellar proteins. The bacterial flagellum export apparatus consists of six integral membrane proteins (FlhA, FlhB, FliO, FliP, FliQ and FliR) and three soluble proteins (FliH, FliI and FliJ), and is located at the base of the flagellum. This system is characterized by ATP hydrolysis and a lack of substrate signal peptide cleavage.
Bacterial host gene expression shutoff by virus
Viral protein which prevents host gene expression by blocking host transcription or inducing the degradation of the bacterial chromosome. This gives viral transcripts a competitive edge to use the hijacked host translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
Bacterial host transcription shutoff by virus
Viral protein involved in inhibiting transcription of bacterial genes to ensure the shutoff of host proteins expression and give viral transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Some bacterial viruses inhibit the host RNAP: bacteriophage SPO1 for example is known to shut off host RNA synthesis.
Protein located in or on a bacterial microcompartment (BMC), proteinaceous polyhedral shells that encapsulate enzymes. The selectively permeable organelles protect their contents from the cytoplasm and/or the cytoplasm from reactants in their interior. Examples of BMCs include carboxysomes, which enhance autotrophic CO(2) fixation by encapsulating RuBisCO and carbonic anhydrase, as well as BMCs involved in ethanolamine or propanediol degradation; both pathways make toxic intermediates. Artifical BMCs can be expressed and filled with cargo proteins for biotechnological uses. BMCs are found in many bacterial phyla; in most cases their cargo is unknown.
Protein interacting with bacteriochlorophyll, a photosynthetic pigment found in non-oxygenic photosynthetic bacteria. It is a magnesium-porphyrin complex esterified to a long hydrophobic terpenoid side chain (the alcohol phytol). It differs from chlorophyll of oxygenic organisms in the substituents around the tetrapyrrole nucleus of the molecule, and in the absorption spectra. Different bacteria have different species of bacteriochlorophyll.
Bacteriochlorophyll biosynthetic process
Protein involved in the synthesis of bacteriochlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol). Biosynthesis of bacteriochlorophyll is a light-independent reaction.
Peptidic antibiotic, often plasmid encoded, produced by specific strains of bacteria that is lethal against other strains of the same or related species. E.g. bacteriocin, colicin, lantibiotic.
Protein involved in the synthesis of a bacteriocin.
Protein that confers to a bacteria immunity against a specific bacteriocin that it synthesizes.
Protein involved in the export of a bacteriocin (bacterial antibiotic).
Enzyme, e.g. lysozyme or endopeptidase, essential for lysis of bacterial cell walls.
Protein having a peptide stretch which contains specific cleavage sites for different proteinases, and which enables inhibition of all four classes of proteinases.
negative regulation of peptidase activity
Protein which, if defective, causes Bardet-Biedl syndrome (BBS), a genetically heterogeneous, autosomal recessive disorder. It is characterized by pigmentary retinopathy, obesity, polydactyly, hypogenitalism, renal malformation and intellectual disability. Secondary features include diabetes mellitus, hypertension and congenital heart disease.
Protein which, if defective, causes Bartter syndrome (BS). In general, Bartter syndrome refers to a group of autosomal recessive disorders characterized by often severe intravascular volume depletion due to renal salt-wasting associated with low blood pressure, hypokalemic alkalosis, hypercalciuria, and normal serum magnesium levels. Patients with Bartter syndrome are often critically ill from birth onwards, and their long-term clinical course may be complicated by nephrocalcinosis, leading to renal failure. Clinical disease results from defective renal reabsorption of sodium chloride in the thick ascending limb (TAL) of the Henle loop, where only 30% of filtered salt is normally reabsorbed.
Protein which is a component of the basement membrane, an extracellular matrix found under epithelial cells and around smooth and striated muscle cells. This matrix contains intrinsic macromolecular components such as collagen, laminin, and sulfated proteoglycans.
Protein which affects the behavior, the action or reaction, of an organism to a stimulus or situation.
Protein which is a dimer of immunoglobulin light chains synthesized in large amounts by patients who have myeloma or bone marrow tumor. Bence-Jones protein is sufficiently small to be excreted by the kidney into urine.
Protein which, if defective, causes Bernard Soulier syndrome (BSS), a familial coagulation disorder characterized by a prolonged bleeding time, unusually large platelets, and impaired prothrombin consumption. BSS is caused by a genetic deficiency in platelet membrane glycoprotein Ib alpha chain and platelet glycoprotein IX, where platelets aggregate normally but do not stick to collagen of the sub-endothelial membrane.
Protein involved in degradation of bile acids. Bile acids, which exist mainly as bile salts, are a family of carboxylic acid derivatives of cholesterol which play an important role in the digestion and absorption of fat. They are made in the liver, stored in the gallblader, and secreted as needed into the intestines.
Protein binding covalently at least one linear tetrapyrrole chromophore, e.g. bilirubin, biliverdin, bilifuscin, biliprasin, choleprasin, bilihumin, and bilicyanin. Bile pigments are produced by breaking down protoporphyrin IX derived from hemoglobin and other heme proteins.
Keywords assigned to proteins because they are involved in a particular biological process.
Protein involved in the generation of rhythmic pattern of behaviors or activities, e.g. circadian rhythm which is a metabolic or behavioural rhythm within a cycle of 24 hours.
Protein involved in the process by which mineral crystals are deposited in an organized fashion in the matrix (either cellular or extracellular) of living organisms. Such process give rise to inorganic-based structures such as bone, tooth, ivory, shells, cuticles, corals or bacterial magnetosomes.
Protein which contains at least one biotin as prosthetic group or cofactor (e.g. some carboxylases and decarboxylases, and biotin carboxyl carrier protein) or which binds biotin, like avidin. Biotin is a water-soluble vitamin (member of the B complex vitamins) essential for fatty acid biosynthesis, catabolism, and it acts as a growth factor for many cells.
Protein involved in the synthesis of biotin, a prosthetic group for some carboxylase and decarboxylase enzymes. This water-soluble vitamin is essential for fatty acid biosynthesis, catabolism, and it acts as a growth factor for many cells.
Protein involved in blood clotting, a complex enzymatic cascade, in which the activated form of one factor catalyzes the activation of the next factor. Both, the extrinsic clotting pathway, induced by a damaged surface, and the intrinsic pathway, induced by a trauma, converge in a final common pathway to form cross-linked fibrin clots.
Blood coagulation cascade activating toxin
Toxin which activates the blood coagulation cascade, which leads to the production of fibrin clots. Blood coagulation activating toxins include a variety of snake venom proteases.
Blood coagulation cascade inhibiting toxin
Toxin which inhibits the blood coagulation cascade, which leads to the production of fibrin clots. Blood coagulation inhibiting toxins include a variety of snake venom proteases.
Protein belonging to the set of cell surface antigens found chiefly, but not solely, on blood cells. More than fifteen different blood group systems are recognised in humans. In most cases the antigenic determinant resides in the carbohydrate chains of membrane glycoproteins or glycolipids.
Toxin which interferes with the function of the bradykinin receptor (BDKR). BDKRs are G-protein coupled receptors whose principal ligand is the 9-amino acid peptide bradykinin.
Protein expressed in the bradyzoite stage, a latent, slowly growing and cyst-forming stage in the life cycle of coccidians (e.g. Toxoplasmy). Encysted bradyzoites promote chronic infection and widespread dissemination of the parasite.
Branched-chain amino acid biosynthetic process
Protein involved in the synthesis of the essential aliphatic branched-chain amino acids leucine (Leu), isoleucine (Ile) and valine (Val).
Branched-chain amino acid catabolic process
Protein involved in the degradation of the branched-chain amino acids leucine (Leu), isoleucine (Ile) and valine (Val).
Protein involved in the synthesis of brassinosteroids, a class of steroid plant hormones. Brassinosteroids are involved in numerous plant processes, such as cell expansion and elongation (in association with auxin), vascular differentiation, pollen elongation and pollen tube formation and protection to plants during chilling and drought stress. Brassinolide is the first isolated brassinosteroid.
Protein involved in the brassinosteroid (BR) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development including cell expansion and elongation (in association with auxin), vascular differentiation and pollen elongation and pollen tube formation. Also involved in plants protection during chilling and drought stress. BRs are polyhydroxysteroid phytohormones and over 70 BR compounds have been isolated in plants. Brassinolide was the first BR isolated from Brassica napus and remains one of the most active BR.
brassinosteroid mediated signaling pathway
Protein which is posttranslationally modified by the attachment of at least one bromine.
Protein containing at least one bromodomain. The bromodomain is a conserved region, approximately 70 amino acids, characteristic for a class of regulatory proteins. It mediates interactions with proteins that are necessary for transcriptional activation.
Protein which, if defective, causes Brugada syndrome, a heart disease characterized by an electrocardiogram pattern showing ST segment elevation in right precordial leads (V1 to V3), incomplete or complete right bundle branch block, and ventricular tachyarrhythmia. In some cases, tachycardia does not terminate spontaneously and it may degenerate into ventricular fibrillation and lead to sudden death.
Bis-(3'-5')-cyclic dimeric guanosine monophosphate
Protein whose function is c-di-GMP-dependent or which catalyzes its hydrolysis. c-di-GMP is the abbreviation for cyclic di-GMP, bis-(3'-5') cyclic diguanylic acid. It acts as a bacterial second messenger.
Protein which binds at least one cadmium atom, or protein whose function is cadmium-dependent. Cadmium is a heavy metal, chemical symbol Cd.
Protein that confers, on bacteria and other microorganisms, the ability to withstand the transition metal cadmium (Cd).
Protein which binds at least one calcium atom, or protein whose function is calcium-dependent. Calcium is a metal, chemical symbol Ca. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
Cell membrane glycoprotein forming a channel in a biological membrane selectively permeable to calcium ions. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
Protein which interferes with the function of calcium channels which are membrane proteins forming a channel in a biological membrane selectively permeable to calcium ions. They are found in various venoms from snakes, scorpions and spiders.
Protein involved in the transport of calcium ions. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
Calcium-activated potassium channel impairing toxin
Protein which interferes with the function of calcium-activated potassium channels (KCa) which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions and gated by intracellular calcium. They are mostly found in snake and scorpion venoms.
Protein which contains at least one binding site for calcium and phospholipid. For example, proteins with annexin repeats, of which a pair may form one binding site for calcium and phospholipid, or some proteins with C2 domains.
Protein which binds at least one calmodulin, an ubiquitous small calcium-binding protein. Its binding to proteins may cause a conformational change which either activates or inactivates their function.
Protein involved in the cycle of biochemical reactions responsible for photosynthetic CO(2) fixation in many photosynthetic bacteria and in the stroma of plant chloroplasts. The energy and reducing power for this reaction are provided by the ATP and NADPH produced during the light reactions of photosynthesis. The Calvin cycle is the only photosynthetic pathway in C3 plants. In C4 and CAM plants CO(2) is initially fixed into other organic acids that are subsequently decarboxylated to release CO(2) to the Calvin cycle. Non-photosynthetic organism (e.g. Rhizobium) also use the cycle to fix CO(2).
Protein whose function is cAMP-dependent or which catalyzes its hydrolysis. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate, the first second messenger hormone signaling system to be characterised. It is generated from ATP by the action of adenyl cyclase that is coupled to hormone receptors by G proteins. cAMP activates a specific protein kinase and is inactivated by phosphodiesterase action giving 5'AMP.
Adenosine-3',5'-cyclic-monophosphate anabolism
Adenosine-3',5'-cyclic-monophosphate biosynthesis
Adenosine-3',5'-cyclic-monophosphate biosynthetic process
Adenosine-3',5'-cyclic-monophosphate formation
Adenosine-3',5'-cyclic-monophosphate synthesis
Adenosine 3',5'-phosphate biosynthetic process
Cyclic adenylic acid biosynthetic process
Protein involved in the synthesis of cAMP. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate.
Protein which binds at least one cAMP. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate.
Protein involved in cap snatching, a process in which a cellular mRNA is cleaved few nucleotides after the 5'cap. The resulting 10- to 13-nucleotides long capped fragment serve as primer for the initiation of viral mRNA synthesis. Cap snatching is used by negative stranded RNA virus which do not encode a guanylyl transferase, like influenza or hantaviruses.
Viral decoration protein attached to the capsid of some prokaryotic viruses. Decoration proteins are located on the outermost surface of the capsid and are involved in stabilizing the head structure.
Viral protein part of the inner membrane of the capsid, a lipid bilayer contained inside the virion capsid.
Structural protein which is part of the complex forming the protective shell around the nucleic acids of the virus. In prokaryotic viruses, this closed shell is also referred to as the head.
Protein which is part of a capsule, the protective structure surrounding some bacteria or fungi. The bacterial capsule is a layer of material, usually polysaccharide, attached to the cell wall possibly via covalent attachments to either phospholipid or lipid-A molecules. It has several functions: promote bacterial adhesion to surfaces or interaction with other organisms; act as a permeability barrier, as a defense mechanism against phagocytosis and/or as a nutrient reserve. Among pathogens, capsule formation often correlates with pathogenicity. The fungal capsule is an extracellular layer which lies outside the cell wall and it is usually composed of polysaccharides. It protects the cell from different environmental dangers such as phagocytosis, dessication, etc.
Protein which is involved in the formation, organization, maintenance or degradation of the capsule. The capsule is a protective structure surrounding some bacteria or fungi. The bacterial capsule is a layer of material, usually polysaccharide, attached to the cell wall possibly via covalent attachments to either phospholipid or lipid-A molecules. The fungal capsule is an extracellular layer which lies outside the cell wall and it is usually composed of polysaccharides.
Protein participating in biochemical reactions in which carbohydrates are involved. Carbohydrate is a general term for sugars and related compounds with the general formula Cn(H2O)n. The smallest are monosaccharides (e.g. glucose); polysaccharides (e.g. starch, cellulose, glycogen) can be large and vary in length.
Carbon utilization by fixation of carbon dioxide
Protein involved in the process of carbon dioxide fixation, e.g. incorporation of carbon dioxide into carbohydrates by photosynthetic organisms or formation of oxaloacetate from pyruvate.
Protein that hydrolyzes a C-terminal peptide bond in polypeptide chains.
Protein located in or on the carboxysome, bacterial microcompartments in which ribulose bisphosphate carboxylase (RuBisCO)-mediated CO(2) fixation occurs. The cytoplasmic polyhedral inclusion bodies are surrounded by a thin protein coat. Found in cyanobacteria and some chemoautotrophs, they enhance autotrophic CO(2) fixation in air by increasing the CO(2) concentration around RuBisCO, thus reducing its reaction with O(2), a competing substrate. They contain carbonic anhydrase as part of the CO(2) concentration mechanism.
Protein which, if defective, causes cardiomyopathy, a chronic disorder which affects the heart muscle causing a reduced pumping function. It is a major cause of morbidity and mortality.
Protein which has a poisonous or deleterious effect upon the heart or other parts of the cardiovascular system.
3-hydroxy-4-(trimethylammonio)butanoate anabolism
3-hydroxy-4-(trimethylammonio)butanoate biosynthesis
3-hydroxy-4-(trimethylammonio)butanoate biosynthetic process
3-hydroxy-4-(trimethylammonio)butanoate formation
3-hydroxy-4-(trimethylammonio)butanoate synthesis
Gamma-trimethyl-hydroxybutyrobetaine anabolism
Gamma-trimethyl-hydroxybutyrobetaine biosynthesis
Gamma-trimethyl-hydroxybutyrobetaine biosynthetic process
Gamma-trimethyl-hydroxybutyrobetaine formation
Gamma-trimethyl-hydroxybutyrobetaine synthesis
Protein involved in the biosynthesis of carnitine (L-3-hydroxy-4, N,N,N-trimethylaminobutyrate), an essential metabolite with a number of indispensable roles in intermediary metabolism.
Protein involved in the synthesis of carotenoids, a group of orange, yellow, red, purple or brown pigments in plants, bacteria and some fungi. Carotenoids, which comprise the carotenes and the xanthophylls, are long polyisoprenoid molecules having conjugated double bonds enabling light absorbtion.
Protein which, if defective, causes cataract, a partial or complete ocular opacity that affects the crystalline lens or its capsule, leading to impaired vision or blindness. The many types of cataract are classified by their morphology (size, shape, location) or etiology (cause and time of occurrence). Cataracts may occur as an isolated anomaly, as part of generalized ocular developmental defects, or as a component of a multisystem disorder.
Protein involved in the synthesis of catecholamines, which are amine derivatives of catechol (2-hydroxyphenol). They are synthesized from the amino acid tyrosine (Tyr) in sympathetic-nerve terminals and in the adrenal gland. Catecholamines act as hormones or neuro-transmitters, e.g. adrenaline, noradrenaline and dopamine.
Protein participating the biochemical reactions in which catecholamines are involved. Catecholamines are amine derivatives of catechol (2-hydroxyphenol). They are synthesized from the amino acid tyrosine (Tyr) in sympathetic-nerve terminals and in the adrenal gland. Catecholamines act as hormones or neuro-transmitters, e.g. adrenaline, noradrenaline and dopamine.
Caveolin-mediated endocytosis of virus by host
Virion endocytosis by caveolin-coated vesicle
Viral protein involved in virus internalization by the host cell via caveolae, which are specialized lipid rafts that form 50-70 nm flask-shaped invaginations of the cell membrane. Caveolins form the structural backbone of caveolae. Internalization via caveolae is not a constitutive process but only occurs upon cell stimulation.Endocytic caveolae deliver their viral content to early endosomes. Caveolae represent a low capacity but highly regulated pathway. This pathway is used by viruses including HPV-31, BK virus, NDV, RSV, Coxsackie B virus, SV40, murine polyomavirus, and Echovirus 1.
caveolin-mediated endocytosis of virus by host cell
Protein containing at least one CBS domain, a conserved domain found in a wide range of proteins, which is named after cystathionine beta-synthase (CBS), an enzyme that contains 2 copies of this domain.
Protein involved in the adherence of cells to other cells or to a matrix. Cell adhesion is mediated by cell surface proteins.
Toxin which interferes with the adherence of cells to other cells or to a matrix. Cell adhesion impairing toxins are mostly found in venom of snakes.
Protein involved in the complex series of events by which the cell duplicates its contents and divides into two. The eukaryotic cell cycle can be divided in four phases termed G1 (first gap period), S (synthesis, phase during which the DNA is replicated), G2 (second gap period) and M (mitosis). The prokaryotic cell cycle typically involves a period of growth followed by DNA replication, partition of chromosomes, formation of septum and division into two similar or identical daughter cells.
Protein involved in the separation of one cell into two daughter cells. In eukaryotic cells, cell division includes the nuclear division (mitosis) and the subsequent cytoplasmic division (cytokinesis).
Protein found in or associated with the prokaryotic cell inner membrane, a selectively permeable membrane which separates the cytoplasm from the periplasm in prokaryotes with 2 membranes.
Protein found in or associated with a cell junction, a cell-cell or cell-extracellular matrix contact within a tissue of a multicellular organism, especially abundant in epithelia. In vertebrates, there are three major types of cell junctions: anchoring junctions (e.g. adherens junctions), communicating junctions (e.g. gap junctions) and occluding junctions (e.g. tight junctions).
Protein found in or associated with the cytoplasmic membrane, a selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.
Protein found in or associated with the prokaryotic cell outer membrane, a selectively permeable membrane which separates the prokaryotic periplasm from its surroundings. Traditionally only Gram-negative bacteria were thought of as having an outer membrane, but recent work has shown some Actinobacteria, including Mycobacterium tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.
Protein found in or associated with a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome or axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.
Protein involved in the formation and maintenance of the cell shape, the physical dimensions of a cell. In most plants, algae, bacteria and fungi the cell wall is responsible for the shape of the cells.
Protein found in or associated with a complex and rigid layer surrounding the cell. Cell walls are found in bacteria, archaea, fungi, plants, and algae. The cell wall envelopes the inner or plasma membrane in all bacteria and is surrounded by the outer membrane in bacteria with 2 membranes (Gram-negative). Bacterial cell walls contain peptidoglycan whereas those of archaea do not. Some archaea may contain pseudopeptidoglycan, which is composed of N-acetyltalosaminuronic acid, instead of N-acetyl muramic acid in peptidoglycan. The plant cell wall is made of fibrils of cellulose embedded in a matrix of several other kinds of polymers such as pectin and lignin. Algal cell walls are usually composed of cellulose, glycoproteins, sporopollenin, calcium and various polysaccharides such as manosyl, xylanes, alginic acid. Diatom cell walls (or frustules) contain silica. The cell wall plays a role in cell shape, cell stability and development, and protection against environmental dangers.
Protein which is involved in the formation, organization, maintenance or degradation of the cell wall. The cell wall is an extracellular layer outside the cell membrane which protects the cell against mechanical damage, osmotic strength and which determines the cell shape. It is prominent in most plants, algae, bacteria and fungi.
Keywords assigned to proteins because they are found in a specific cellular or extracellular component.
Protein involved in the synthesis of cellulose, a linear polymer of (1-4)-beta-linked D-glucose subunits. It is the most abundant cell-wall and structural polysaccharide in plants and it is also found in some lower invertebrates. Cellulose is the major component of wood and thus of paper. Cotton is the purest natural form of cellulose. As a raw material, it forms the basis for many derivatives used in chromatography, ion exchange materials, explosives manufacturing and pharmaceutical preparations.
Protein involved in the conversion of cellulose into D-glucose. Cellulose is the most abundant cell-wall and structural polysaccharide in plants and it is also found in some lower invertebrates. Cellulose is the major component of wood and thus of paper. Cotton is the purest natural form of cellulose. As a raw material, it forms the basis for many derivatives used in chromatography, ion exchange materials, explosives manufacturing and pharmaceutical preparations.
Protein which binds centromeres or which is required for the assembly and movement of centromeres. Centromeres are the regions of replicated eukaryotic chromosomes where the two chromatids are joined together.
Proton-transporting ATP synthase complex coupling factor F(0)
Protein component of the F-type ATP synthase complex CF(0) or protein involved in its assembly. F-type ATPases consist of the two complex components CF(0), the membrane proton channel, and CF(1), the catalytic core.
proton-transporting ATP synthase complex, coupling factor F(o)
Proton-transporting ATP synthase complex catalytic core F(1)
Protein component of the F-type ATP synthase complex CF(1) or protein involved in its assembly. F-type ATPases consist of the two complex components CF(0), the membrane proton channel, and CF(1), the catalytic core.
proton-transporting ATP synthase complex, catalytic core F(1)
Protein whose function is cGMP-dependent or which catalyzes its hydrolysis. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate. It acts as a second messenger.
Cyclic guanylic acid biosynthetic process
Guanosine-3',5'-cyclic-monophosphate anabolism
Guanosine-3',5'-cyclic-monophosphate biosynthesis
Guanosine-3',5'-cyclic-monophosphate biosynthetic process
Guanosine-3',5'-cyclic-monophosphate formation
Guanosine-3',5'-cyclic-monophosphate synthesis
Guanosine 3',5'-phosphate biosynthetic process
Protein involved in the synthesis of cGMP. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate.
Guanosine 3',5'-cyclic monophosphate-binding
Protein which binds at least one cGMP. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate.
Protein which is transiently involved in the noncovalent folding, assembly and/or disassembly of other polypeptides or RNA molecules, including any transport and oligomerisation processes they may undergo, and the refolding and reassembly of protein and RNA molecules denatured by stress. Though involved in these processes, chaperones are not an integral part of these functioning molecules. Also used for metallochaperones, which function to provide a metal directly to target proteins while protecting this metal from scavengers.
Protein which, if defective, causes Charcot-Marie-Tooth disease (CMT), a heterogeneous group of hereditary motor and sensory neuropathies (HMSN) characterized by distal muscular atrophy and weakness, hollow feet, absent or diminished deep-tendon reflexes and impaired sensation. CMT is classified into two major classes. CMT type 1 includes demyelinating neuropathies that are characterized by nerve conductance velocities (NCVs) less than 38m/s and segmental demyelination and remyelination; CMT type 2 includes axonal neuropathies that are characterized by normal or mildly reduced NCVs and chronic axonal degeneration and regeneration.
Protein involved in the movement of a cell, or organism, along a concentration gradient of a chemotactic agent, such as a protein which causes, mediates or responds to chemotaxis. Chemotactic molecules such as sugars, peptides, cell metabolites, cell-wall or membrane lipids bind to cell surface receptors and trigger activation of intracellular signaling pathways, as well as remodeling of the cytoskeleton through the activation or inhibition of various actin-binding proteins.
Protein involved in the breakdown of chitin, a linear polysaccharide consisting of (1->4)-beta-linked D-glucosamine residues, most of which are N-acetylated.
Protein which binds chitin, a linear polysaccharide consisting of (1->4)-beta-linked D-glucosamine residues, most of which are N-acetylated. The 30-43 amino acids long chitin-binding domain contains several conserved glycine and cysteines residues. The conserved cysteines form disulfide bonds. Chitin-binding domains have been found in plant, fungal and bacterial proteins.
Protein which binds at least one chloride, or protein whose function is chloride-dependent. Chloride is a negatively-charged ion, which is abbreviated Cl(-).
Protein which is part of an anion channel found in the plasma membrane and in intracellular membranes. These channels are permeable for various anions, such as iodide, bromide, but also for nitrates, phosphates and even negatively charged amino acids. They are called chloride channels, because chloride is the most abundant anion and the predominant permeating species in all organisms. They have been classified according to their gating mechanisms, which may depend on changes in the transmembrane electric field (voltage-dependent/gated chloride channels, e.g. ClC family), on a protein kinase/nucleotide mediated mechanism (CFTR), an increase in intracellular calcium (calcium activated chloride channels, e.g. CaCC), cell swelling (volume-regulated anion channels, e.g. VRAC) or binding of a ligand, e.g. glycine or - aminobutyric acid (GABA) activated channels. In contrast with cation channels, they are not involved in the initiation or spread of excitation, but in the regulation of excitability in nerve and muscle. They also participate in many housekeeping processes, such as volume regulation, pH regulation in organelles, electrogenesis and control of synaptic activity. The chloride channels are crucial for transepithelial transport and the control of water flow, and often provide unexpected permeation pathways for a large variety of anions.
Protein which interferes with the function of chloride channels which are membrane proteins forming a channel in a biological membrane selectively permeable to chloride ions. Chloride channels include voltage-gated chloride channels (ClC), ionotropic GABA receptors (ligand-gated ion channels activated by GABA) and CFTR ion channels (ABC transporter-class ion channels). Toxins that target these channels are found in venom of several species including scorpions and snakes.
Protein which interacts with chlorophyll, the major light-absorbing pigment in most oygenic green organisms. Higher plants contain chlorophyll a and chlorophyll b which are magnesium-porphyrin complexes esterified to a long hydrophobic terpenoid side chain (the alcohol phytol).
Protein involved in the synthesis of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol). Angiosperms have only a light-dependent pathway for chlorophyll biosynthesis, other oxygenic organisms seem to have both the light-dependent and the light-independent pathways. Non-oxygenic organisms, which make bacteriochlorophyll, only have a light-independent pathway.
Protein involved in the degradation of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol).
Protein encoded by or localized in the chloroplast, the most common form of plastid, found in all photosynthetic organisms except glaucophyte algae. In green (photosynthesizing) tissue they house the machinery necessary for photosynthesis and CO(2) fixation. They are surrounded by between 2 and 4 membranes and contain thylakoids in green tissue.
Photosynthetic light-harvesting complexes found in green bacteria. Chlorosomes are sac-like organelles appressed to the cytoplasmic membrane of the cell membrane.
Protein involved in the synthesis of cholesterol, the major sterol of higher animals. It is a component of cell membranes, especially of the plasma membrane.
Protein which participates in the biochemical reactions where cholesterol is involved, including transport. Cholesterol is the major sterol of higher animals and an important component of cell membranes, especially of the plasma membrane.
Protein involved in chondrogenesis, the mechanism of cartilage formation. Chondrogenesis proceeds through determination of cells and their aggregation into prechondrogenic condensations, differentiation into chondrocytes, and later maturation. The formation of the long bones requires a cartilage template.
Protein that enables bacteria and other microorganisms to withstand chromate, a salt of chromic acid (H2CrO4).
Protein controlling the opening or closing of chromatin.
Protein which interacts with one or more chromophores. A chromophore absorbs and transmits light energy. Originally it was used for visibly colored molecules, but it applies also to UV- and IR-absorbing molecules.
Protein found in or associated with a chromoplast, a plastid containing pigments other than chlorophyll. Found in flower, petals and fruit.
Protein which can be altered by a structural chromosomal rearrangement. Structural rearrangements result from chromosome breakage, followed by reconstitution in an abnormal combination. Classes of chromosomal rearrangements include: deletions, duplications, insertions, inversions, translocations and transpositions.
Protein which is associated with chromosomal DNA, including histones, protamines and high mobility group proteins.
Protein involved in chromosome partition, the process by which newly replicated plasmids and chromosomes are actively segregated prior to cell division. E.g., par and soj which contribute to efficient chromosome partitioning by serving functions analogous to centromeres (i.e. pairing or positioning of sister chromosomes).
Protein which, if defective, causes chronic granulomatous disease (CGD), a disease characterized by the failure of activated phagocytes to generate superoxide.
Protein component of the chylomicrons or involved in their catabolism. Chylomicrons are the largest lipoprotein complexes with the lowest protein-to-lipid ratio. They are present in the blood or lymph and transport exogenous (dietary) cholesterol, triacylglycerols and other lipids from the intestine to the liver or to the adipose tissue.
Protein which, if defective, causes any one of a group of diseases associated with either abnormal formation or function of cilia. Ciliopathies cover a large spectrum of often overlapping phenotypes ranging from relatively mild, tissue-restricted pathologies to severe defects in multiple organs. Although cilia play important roles in many tissues, the predominantly affected organs are kidney, eye, liver and brain. Clinical features typically include retinal degeneration, renal disease and cerebral anomalies. Additional manifestations include congenital fibrocystic diseases of the liver, diabetes, obesity and skeletal dysplasias. Ciliary dysfunction in the embryo may cause randomization of left-right body asymmetry or situs inversus, as well as severe malformations leading to embryonic lethality.
Protein found in or associated with a cilium, a cell surface projection found at the surface of a large proportion of eukaryotic cells. The two basic types of cilia, motile (alternatively named flagella) and non-motile, collectively perform a wide variety of functions broadly encompassing cell/fluid movement and sensory perception. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.
Protein which is involved in the formation, organization, maintenance and degradation of the cilium, a cell surface projection found at the surface of a large proportion of eukaryotic. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules.
Protein which allows the utilization of the 6-carbon tricarboxylic acid citrate as a sole source of carbon and energy.
2-amino-5-(carbamoylamino)pentanoic acid
Protein which is posttranslationally modified by the deimination of one or more arginine residues.
Clathrin- and caveolin-independent endocytosis of virus by host
Non-clathrin/non caveolin-mediated endocytosis by host
Viral protein involved in virus internalization into the host cell via endocytic pathways that involve neither clathrin nor caveolins. These pathways can be further defined by their dependency on various molecules such as cholesterol, DNM2/Dynamin-2, small GTPases or tyrosine kinase and possibly involve non-caveolar lipid rafts. Clathrin- and caveolin-independent pathways are used by viruses including poliovirus, human rhinovirus 14, lymphocytic choriomeningitis virus, murine norovirus-1 and SV40.
receptor-mediated endocytosis of virus by host cell
Clathrin-mediated endocytosis of virus by host
Virion endocytosis by clathrin-coated vesicle
Viral protein involved in virus internalization by the host cell via clathrin-mediated endocytosis. In response to an internalization signal, clathrin is assembled on the inside face of the cell membrane to form characteristic invaginations or clathrin coated pits that pinch off through the action of DNM1/Dynamin-1 or DNM2/Dynamin-2. The virus bound to its host cell receptor is internalized into clathrin-coated vesicles (CCV). Endocytic CCV deliver their viral content to early endosomes. The endosomal acidic pH and/or receptor binding usually induces structural modifications of the virus surface proteins that lead to penetration of the endosomal membrane via fusion or permeabilization mechanisms.
clathrin-dependent endocytosis of virus by host cell
Protein which is posttranslationally modified by the cleavage on at least one pair of basic residues, in order to release one or more mature active peptides (such as hormones).
Protein which is a component of a coated pit. Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.
Protein which contains at least one cobalamin as cofactor, e.g. methylmalonyl-CoA mutase, or which binds and/or transports cobalamin, such as intrinsic factor or transcobalamins. Cobalamin, which is synthesized by microorganisms, has equatorial sites occupied by a tetrapyrrol ring structure (corrin ring) with a cobalt(III) ion in the center, one axial site occupied by an intramolecularly-bound dimethylbenzimidazole and the other axial site occupied by a number of different ligands such as water (aquacobalamin), cyanide (cyanocobalamin=vitamin B12), glutathione (glutathionylcobalamin), 5'deoxyadenosine (adenosylcobalamin=coenzyme B12) or a methyl group (methylcobalamin). It is a prosthetic group of certain mammalian enzymes, where it is essential for the normal maturation and development of erythrocytes. A deficiency in the diet or more frequently the failure to absorb the vitamin give rise to pernicious anemia.
Protein involved in the synthesis of cobalamin. Cobalamin, which is synthesized by microorganisms, has equatorial sites occupied by a modified porphyrin ring system, with two of the four pyrrol rings fused directly (without an intervening methine bridge). The modified porphyrin system binds a cobalt(III) ion in the center, and this is called a corrin ring system. One axial site is occupied usually by an intramolecularly-bound dimethylbenzimidazole nucleotide and the other axial site is occupied by a number of different ligands such as water (aquacobalamin), cyanide (cyanocobalamine=vitamin B12), glutathione (glutathionylcobalamine), 5'deoxyadenosine (adenosylcobalamine=coenzyme B12) or a methyl group (methylcobalamin). Vitamin B12, for instance, is a prosthetic group of certain mammalian enzymes, where it is essential for the normal maturation and development of erythrocytes. A deficiency in the diet or more frequently the failure to absorb the vitamin B12 give rise to pernicious anemia.
Protein which binds at least one cobalt atom, or protein whose function is cobalt-dependent. Cobalt is a metallic element, chemical symbol Co.
Protein involved in the transport of the trace element cobalt, which is a component of vitamin B12.
Protein which, if defective, causes Cockayne's syndrome (CS), an autosomal recessive disease characterized by UV-sensitive skin (without pigmentation abnormalities), neurological dysfunction due to demyelination of neurons and calcification of basal ganglia (psychomotor retardation, deafness, optic atrophy, retinal pigmentation and hyperreflexes) and dysmorphic dwarfism (immature sexual development and microcephaly).
Keywords assigned to proteins because their sequences can differ, due to differences in the coding sequences such as polymorphisms, RNA-editing, alternative splicing.
Protein involved in the biosynthetic pathway leading from pantothenate to coenzyme A (CoA). CoA has two halves in phosphodiester linkage: a 3',5'-ADP residue, and 4-phosphopantetheine. The phosphopantetheine moiety is itself composed of three structural entities: a branched chain dihydroxy acid in amide linkage to a beta-alanyl residue, which is in turn linked to a cysteamide containing the reactive thiol. Coenzyme A functions as a carrier of acetyl and acyl groups and is essential for numerous biosynthetic, energy-yielding, and degradative metabolic pathways. Acetyl-CoA is the common cellular currency for acetyl transfers.
2-mercaptoethanesulfonic acid biosynthesis
2-mercaptoethanesulfonic acid biosynthetic process
Protein involved in the biosynthesis of coenzyme M. Coenzyme M (2-mercaptoethanesulfonic acid) is the smallest known organic cofactor. CoM serves as a methyl group carrier in key reactions within the pathway of methane formation from C1 precursors. In the alkene metabolism pathway, it is involved in aliphatic epoxyde carboxylation.
Protein which contains at least one coiled coil domain, a type of secondary structure composed of two or more alpha helices which entwine to form a cable structure. In proteins, the helical cables serve a mechanical role in forming stiff bundles of fibres.
Protein which contains one or more collagen-like domain. Collagen is a fibrous protein found in vertebrates, the major element of skin, bone, tendon, cartilage, blood vessels and teeth. It forms insoluble fibres of high tensile strength and which contains the unusual amino acids hyroxyproline and hydroxylysine. It is rich in glycine but lacks cysteine and tryptophan, and has an unusually regular amino-acid domain.
Protein involved in the degradation of collagen, a family of fibrous proteins found in skin, bones, teeth, cartilage and other tissues of vertebrates.
Protein involved in competence, the state in which a cell or organism is able to take up DNA and become genetically transformed.
establishment of competence for transformation
Protein involved in the complement activation lectin pathway which activates the proteins of the complement system. This pathway can be activated mainly by mannose-binding lectin (MBL) interacting with carbohydrate structures on microbial surfaces and by ficolins with different fine carbohydrate binding specificity.
Complement activation alternative pathway
Protein involved in the complement alternate pathway which activates the proteins of the complement system. This pathway can be activated by IgA immune complexes, but also by bacterial endotoxins, polysaccharides and cell walls, without participation of an antigen-antibody reaction.
complement activation, alternative pathway
Pathway which activates the proteins of the complement system, a group of blood proteins of the globulin class involved in the lysis of foreign cells after they have been coated with antibody, and which also promote the removal of antibody-coated foreign particles by phagocytic cells. The pathway proceeds by a cascade reaction of successive binding and proteolytic cleavage of complement components. This pathway can be activated by either IgG or IgM binding to an antigen.
complement activation, classical pathway
Toxin which interferes with the complement system. These toxins act by activating, inhibiting, or mimicking proteins of this system. They are mostly found in snake and spider venoms.
Protein which, if defective, causes cone-rod dystrophy, a disease where dystrophy of cone-rod cells is characterized by the initial degeneration of cone photoreceptor cells, thus causing early loss of visual acuity and color vision, followed by the degeneration of rod photoreceptor cells and leading to progressive night blindness and peripheral visual field loss.
Protein which, if defective, causes congenital adrenal hyperplasia, a group of inherited disorders of cortisol biosynthesis. Defective cortisol biosynthesis results in compensatory hypersecretion of corticotropin with subsequent adrenal hyperplasia and excessive androgen production. Various clinical types are recognized: "salt wasting form" is the most severe type, "simple virilizing form" with normal aldosterone biosynthesis, "non-classic form" or late onset, and "cryptic form" or asymptomatic.
Protein which, if defective, causes a congenital disorder of glycosylation. In the endoplasmic reticulum (ER) of eukaryotes, N-linked glycans are first assembled on the lipid carrier dolichyl pyrophosphate. The GlcNAc(2)Man(9)Glc(3) oligosaccharide is transferred to selected asparagine residues of nascent polypeptides. Defects along the biosynthetic pathway of N-glycans are associated with severe multisystemic syndromes called congenital disorders of glycosylation (CDG). The characteristic biochemical feature of CDG is defective glycosylation of glycoproteins due to mutations in genes required for the biosynthesis of N-linked oligosaccharides. Defects of the assembly of dolichyl-linked oligosaccharides or their transfer on to nascent glycoproteins form type I forms of CDG, whereas CDG type II comprises all defects of the trimming and elongation of N-linked oligosaccharides.
Protein which, if defective, causes congenital dyserythropoietic anemia, a heterogeneous group of disorders characterized by the occurrence of multinuclear erythroid precursors in the bone marrow, ineffective erythropoiesis, iron overload and anemia. Various forms are differentiated mainly by the morphological appearance of the erythroid precursors.
Protein which, if defective, causes congenital absolute erythrocytosis, a disorder characterized by expansion of the erythrocyte compartment in the peripheral blood. Total red cell mass is increased in the absence of a reduction of plasma volume. Erythrocytoses are usually divided into primary and secondary forms. Primary erythrocytoses are due to defects in the erythroid progenitors and are characterized by low erythropoietin levels. Secondary erythrocytoses can be due to defects in hypoxia sensing, or to conditions that cause low tissue oxygen tension with consequent increase in erythropoietin secretion.
Protein which, if defective, causes congenital generalized lipodystrophy, a disorder characterized by near complete absence of adipose tissue from birth. Affected patients manifest insulin resistance, early onset diabetes mellitus, hypertriglyceridemia, hepatic steatosis and acanthosis nigricans.
Protein which, if defective, causes congenital hypothyroidism, a condition due to thyroid hormones deficiency, presenting at birth. Congenital hypothyroidism occurs when the thyroid gland fails to develop or function properly. In most cases, the thyroid gland is absent, abnormally located, or severely reduced in size. In the remaining cases, a normal-sized or enlarged thyroid gland is present, but production of thyroid hormones is decreased or absent. If untreated, congenital hypothyroidism can lead to intellectual disability and growth failure.
The congenital muscular dystrophies (CMD) are a heterogeneous group of disorders characterized by hypotonia, muscle weakness, dystrophic changes on skeletal muscle biopsy, and joint contractures that present at birth or during the first 6 months of life. Intellectual disability with or without structural brain changes is an additional feature of several CMD syndromes.
Protein which, if defective, causes congenital myasthenic syndrome. Congenital myasthenic syndromes constitute a group of inherited diseases characterized by a congenital defect in neuromuscular transmission at the neuromuscular junction, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Congenital myasthenic syndromes are characterized by muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort.
Protein which, if defective, causes congenital stationary night blindness that is the failure or imperfection of vision at night or in dim light, with good vision only on bright days.
Protein involved in conidiation, the production of conidia which are asexual fungal spores.
Protein involved in the temporary fusion of two gametes or two cells leading to the transfer of genetic material. This process is seen in bacteria, ciliate protozoa and certain fungi.
Protein which binds at least one copper atom, or protein whose function is copper-dependent. Copper is a trace metallic element, chemical symbol Cu.
Protein involved in the transport of ions of the trace element copper.
Protein involded in the formation of the copulatory plug, a plug composed of a number of proteins which are secreted by the seminal vesicle under the influence of testosterone. Found in rodents.
Protein which, if defective, causes corneal dystrophy. The term corneal dystrophy includes a heterogeneous group of bilateral, primary alterations of the cornea that are not associated with prior inflammation or secondary to systemic disease. Most corneal dystrophies present with variable shaped corneal opacities in a clear or cloudy cornea and they affect visual acuity to different degrees. Corneal dystrophies may be present at birth but more frequently develop during adolescence and progress slowly throughout life.
Protein covalently attached to a DNA molecule. For example some viruses contains proteins that are attached to the end of a viral replicating DNA and which are necessary for DNA replication.
Protein covalently attached to a RNA molecule. For example some viruses contains proteins that are attached to the end of a viral replicating RNA and which are necessary for RNA replication.
Protein which, if defective, causes craniosynostosis, the premature closure of one or more cranial sutures which results in an abnormal head shape. Different types of craniosynostosis are known. All are characterized by skull deformities, with face and often limb involvement in the syndromic forms.
Viral protein that inhibits host defense CRISPR-cas system (Clustered Regularly Interspaced Short Palindromic Repeats). The CRISPR-cas system is composed of genomic sensors that allow prokaryotes to acquire DNA fragments from invading viruses and plasmids into the CRISPR locus. These stored fragments (called spacers) are transcribed and processed into small crRNA which are used to destroy matching DNA in future viral and plasmid invasion. Some prokaryotic viruses express specific genes that allow them to evade CRISPR-cas system.
inhibition of host CRISPR-cas system by virus
Protein involved in crown gall tumor formation, a plant tumor caused by the bacterium Agrobacterium tumefaciens.
Protein which contains at least one cysteine tryptophylquinone (CTQ) cross-link modification. CTQ is formed by oxidation of the indole ring of a tryptophan to form tryptophylquinone followed by covalent cross-linking with a cysteine residue. In the quinohemoprotein amine dehydrogenase, CTQ mediates during the catalytic cycle electron transfer from the substrate to either a copper protein, azurin, or cytochrome c-550.
Protein which, if defective, causes Cushing syndrome, a condition caused by prolonged exposure to excess levels of cortisol from endogenous or exogenous sources. Endogenous Cushing syndrome is due to excess production of cortisol by the adrenal glands. It may be caused by pituary hypersecretion of adrenocorticotropic hormone (ACTH), ectopic ACTH secretion by non-pituary tumors, or may result from cortisol hypersecretion by adrenal gland tumors (ACTH-independent Cushing syndrome). Cushing syndrome is clinically characterized by upper body obesity, osteoporosis, hypertension, diabetes mellitus, hirsutism, amenorrhea, and excess body fluid.
Protein which is a component of the cuticle, the outer protective layer produced by epidermal cells that covers the body of many invertebrates.
Protein encoded by the cyanelle genome or protein located in the cyanelle. Cyanelles are the plastids of glaucocystophyte algae. They are surrounded by a double membrane and, in between, a peptidoglycan wall. The cyanelle genome is of chloroplast size and contains genes for tRNAs, rRNAs and approx. 150 proteins, which is more than found in higher plant chloroplast genomes (this feature is also shared by other primitive plastids). Thylakoid membrane architecture is cyanobacteria-like. Historically, the term cyanelle is derived from a classification as endosymbiotic cyanobacteria, and thus is not fully correct.
Protein that belongs to the cyclin family or that contains a cyclin box-like domain. Cyclins are regulatory subunits of the cyclin-dependent protein kinases. They form kinase holoenzymes, with distinct biochemical characteristics and nonredundant biological functions, which mediate phosphorylation of cellular proteins, including key cell cycle regulatory molecules. In this way, the kinase holoenzymes promote the transit of cells through the division cycle. Cyclins accumulate during interphase of eukaryotic cell cycle and are destroyed at the end of mitosis.
Protein that confers, on an organism, the ability to withstand cycloheximide, an antibiotic produced by Streptomyces griseus, which inhibits eukaryotic elongation during protein synthesis. The resistance is often due to mutations that prevent antibiotic binding to the protein.
Protein involved in the synthesis of cysteine, the amino acid with the highly reactive sulfhydryl group (-SH). It is derived from the amino acids methionine and serine. Cysteine plays a special role in shaping some proteins by forming disulfide bonds. In enzymes the unique reactivity of this group is frequently exploited at the catalytic site.
Protein which, if defective, causes cystinuria (CSNU), an autosomal recessive condition of persistent excessive urinary excretion of cystine and three other dibasic amino acids: lysine, ornithine, and arginine. CSNU arises from impaired reabsorption of these amino acids through the epithelial cells of the renal tubule and gastrointestinal tract. It is characterized by cystine stones in the kidney, ureter and bladder. Three clinical types of cystinuria have been described: cystinuria type-I (CSNU1), type-II (CSNU2) and type-III (CSNU3).
Protein involved in cytadherence, the attachment of mycoplasma to the epithelium.
cytoadherence to microvasculature, mediated by symbiont protein
Protein involved in the biogenesis of c-type cytochromes. Cytochromes c are electron-transfer proteins having one or several heme c groups, bound to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues.
Small secreted proteins from higher eukaryotes which affect the growth, division and functions of other cells, e.g. interleukins, lymphokines, TNF and interferons. Generally, growth factors are not classified as cytokines, though TGF is an exception. Chemokines are a subset of cytokines. They differ from classical hormones in that they are produced by a number of tissues or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.
Protein involved in the synthesis of cytokinins, a class of plant hormones which promote cell division (e.g. kinetin, zeatin, benzyl adenine). They are also involved in cell growth, cell differentiation and in other physiological processes.
Protein involved in the cytokinin signaling pathway (i.e. transport or signal transduction). Cytokinins (i.e. kinetin and zeatin) are defined more by their biological activity (e.g. inducing cell division in tissue culture) rather than by structure. These phytohormones are synthesized in the root apical meristem and transported through the plant in the xylem sap. Cytokinins are involved in several physiological processes such as promoting cell division and chloroplast maturation, regulating cell growth and differentiation, and monitoring nutrient uptake and senescence. Together with auxin, they also regulate the cell cycle and tissue morphogenesis.
Protein involved in the rupture of cell membranes and loss of cytoplasm, e.g. exotoxin, cytolysin.
Protein found in the cytoplasm, the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).
Viral protein that allows the active transport of viral components along cytoskeletal filaments toward the intracellular replication sites during virus entry. Viruses such as adenoviruses, adeno-associated virus, vaccinia virus, poliovirus, canine parvovirus, African swine fever virus, rabies virus, human herpes virus 1, foamy virus are thought to use active intracellular transport of viral components.
transport of viral material towards nucleus
Protein found in or associated with cytoplasmic vesicles, which mediate vesicular transport among the organelles of secretory and endocytic systems. These transport vesicles are classified by the identity of the protein coat used in their formation and also by the cargo they contain, e.g. clathrin-, COPI-, and COPII-coated vesicles, synaptic vesicles, secretory vesicles, phagosomes, etc.
Protein involved in the biochemical reactions with the pyrimidine base cytosine.
Protein which is a component or which is associated with the cytoskeleton, a dynamic three-dimensional filamentous structure in the cytoplasm. The cytoskeleton is both a muscle and a skeleton, and its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of the organelles within the cell. This includes the major components of cytoskeleton; microfilaments (actin-like proteins), microtubules (tubulin-like proteins) and intermediate filaments (mostly in eukaryotes) and prokaryotic MinD-ParA proteins. Originally not thought to exist in prokaryotes, but now known to have the same functions as in eukyaryotes.
Protein which contains at least one D-amino acid. All of the amino acids derived from natural proteins are of the L configuration. D-amino acids are found in nature, especially as components of certain peptide antibiotics and in walls of certain microorganisms.
Protein which, if defective, causes a partial or total inability to hear. The two principal types of deafness are conductive deafness that results from changes in the middle ear, and nerve or sensorineural deafness that is caused by damages to the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information.
Enzyme that belongs to the lyase family and which catalyzes the spliting of CO(2) from the carboxylic group of amino acids, beta-keto acids and alpha-keto acids.
Viral protein involved in the degradation of host mRNAs. Viruses have evolved ways of degrading host mRNAs to inhibit cellular translation. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. Decay of host mRNAs can be achieved by endonucleotic RNA cleavage or associated with PABPC1 nuclear relocalization.
induction by virus of catabolism of host mRNA
Families of microbicidal and cytotoxic peptides. Defensins have antibacterial, antifungal and antiviral properties. Defensins kills cells by forming voltage-regulated multimeric channels in the susceptible cell's membrane.
Degradation of host capsule during virus entry
Virion protein involved in breaking down host cell capsule to reach the host cell wall, and finally the host cytoplasmic membrane. Many prokaryotic viruses carry for example glycanase, polysaccharide lyase or deacetylase activities to specifically digest host capsule.
disruption of host cell glycocalyx during viral entry
Degradation of host cell envelope components during virus entry
Virion protein involved in breaking down host cell surface components to reach the host cytoplasmic membrane. Many prokaryotic viruses for example carry enzymatic activities to degrade the host cell lipopolysaccharide layer, cell wall, or capsule.
disruption of host cell envelope during viral entry
Viral protein that rapidly degrades the host DNA at the onset of infection. The breakdown products can be reused to synthesize viral DNA or can be excreted from the host cell. Degrading host chromosome provides an advantage during the virus life cycle by reducing or eliminating competing host macromolecular synthesis. Bacteriophages such as T4 or T5 for example are known to induce degradation of the host chromosome and excretion of the host DNA degradation products.
Degradation of host lipopolysaccharides during virus entry
Virion protein involved in breaking down host cell lipopolysaccharides (LPS) to reach the cytoplasmic membrane of prokaryotes with 2 membranes. Many prokaryotic viruses carry glycanase or deacetylase activities to digest host LPS.
disruption by virus of host envelope lipopolysaccharide during virus entry
Degradation of host peptidoglycans during virus entry
Virion exolysin involved in breaking down host cell peptidoglycans (e.g. murein, pseudomurein) to reach the host cytoplasmic membrane during virus entry. Exolysins are usually part of the tail or the base plate of prokaryotic viruses. Exolysins can display various enzymatic activities such as lysozyme, transglycosylase, muramidase or even protease activity. Murein hydrolases for example are widespread in bacteriophages infecting Gram-positive or Gram-negative bacteria.
disruption by virus of host cell wall peptidoglycan during virus entry
Protein which, if defective, causes Dejerine-Sottas disease. DSS is a hereditary motor and sensory neuropathy (HMSN) of the Charcot-Marie-Tooth disease type 1 class. DSS is characterized by severe early onset, very slow nerve conduction velocities (less than 12m/sec) and raised cerebrospinal fluid protein concentrations (0.7 g/l). Clinical signs are delayed age of walking as well as areflexia.
Protein involved in dental caries or important in the prevention of dental caries. Dental caries are localized destruction of the tooth surface, initiated by decalcification of the enamel and followed by enzymatic lysis of organic structures, the result of which is cavity formation. The cavity may penetrate the enamel and dentin, and reach the pulp. The disease may be caused by acids produced by bacteria which lead to decalcification, or by microorganisms that destroy the enamel protein, or by keratolytic microorganisms producing chelates that lead to decalcification.
Deoxyribonucleotide biosynthetic process
Protein involved in the synthesis of deoxyribonucleotides, the basic repeating units in DNA. Deoxyribonucleotides consist of a purine or a pyrimidine base bonded to deoxyribose, which in turn is bound to a phosphate group. They are synthesised by reduction of ribonucleoside diphosphates.
Protein involved in the necrosis of the skin.
Protein which, if defective, causes desmin-related myopathy (DRM), a clinically and genetically heterogeneous group of muscular disorders defined morphologically by intrasarcoplasmic aggregates of desmin, usually accompanied by other protein aggregates. Both autosomal dominant and autosomal recessive inheritance have been reported. Approximately one-third of DRMs are thought to be caused by mutations in the desmin gene.
Protein involved in degrading toxic compounds. Detoxification generally takes place in the liver or kidney and inactivates toxins, either by degradation or by conjugation of residues to a hydrophilic moiety in order to promote excretion.
Protein involved in development, the process whereby a multicellular organism develops from its early immature forms, e.g., zygote, larva, embryo, into an adult.
Keywords assigned to proteins because they are expressed specifically in a given developmental stage.
Protein which, if defective, causes diabetes insipidus, a rare form of diabetes in which the kidney tubules do not reabsorb enough water resulting in excessive urine excretion (polyuria). Two types of diabetes insipidus are recognized: central or neurohypophyseal diabetes insipidus which is due to defects in the neurohypophyseal system and results in a deficient quantity of anti-diuretic hormone being produced or released; nephrogenic diabetes insipidus, a vasopressin unresponsive condition of polyuria and hyposthenuria.
Protein which, if defective, causes diabetes mellitus, a disorder of impaired carbohydrate, protein, and fat metabolism due to insufficient secretion of insulin or to target tissue insulin resistance. Diabetes mellitus can be divided into two main types, type I or insulin-dependent diabetes mellitus (IDDM), and type II, or non insulin-dependent diabetes mellitus (NIDDM). Type I diabetes mellitus normally starts in childhood or adolescence and is caused by the body's own immune system which destroys the insulin-producing beta cells in the pancreas. Classical features are polydipsia, polyphagia and polyuria, due to hyperglycemia-induced osmotic diuresis. Type II diabetes mellitus normally starts in adulthood and is caused by a lack of sensitivity to the body's own insulin. It is usually characterized by a gradual onset with minimal or no symptoms of metabolic disturbance. Both forms of diabetes mellitus lead to secondary complications (notably cardiovascular, nephropathy, retinopathy, neuropathy). Two other major subcategories of diabetes mellitus are gestational diabetes and diabetes secondary to other medical conditions. In common usage, the term diabetes, when used alone, refers to diabetes mellitus and not diabetes insipidus.
Protein involved in the synthesis of diaminopimelate, the ionic form of the amino acid diaminopimelic acid (DAP) which is found in the murein peptidoglycans of bacterial cell walls. Diaminopimelic acid is synthesised from aspartate.
Congenital hypoplastic anemia of Blackfan and Diamond
Protein which, if defective, causes Diamond-Blackfan anemia, a rare congenital non-regenerative hypoplastic anemia that usually presents early in infancy. The disease is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies.
Protein involved in differentiation, the developmental process of a multicellular organism by which cells become specialized for particular functions. Differentiation requires selective expression of the genome; the fully differentiated state may be preceded by a stage in which the cell is already programmed for differentiation but is not yet expressing the characteristic phenotype determination. Also used for fungal conidiation proteins, and for some bacteria that present specialization of function in cell types, such as Caulobacter crescentus.
Protein involved in the process whereby nutrients are rendered soluble and capable of being absorbed by the organism or cell, by action of various hydrolytic enzymes that break down proteins, carbohydrates, fats, etc.
Enzyme that reduces molecular oxygen by incorporating both atoms into its substrate(s).
Enzyme that hydrolyzes a dipeptide into its constituent amino acids.
Protein, whose amino acid sequence has been partially (more than one residue) or completely determined experimentally by Edman degradation or by mass spectrometry.
Keywords assigned to proteins because they are involved in a specific disease.
Protein for which at least one genetic variant involved in a disease is reported in the feature table of the UniProtKB/Swiss-Prot entry.
Protein which is modified by the formation of a bond between the thiol groups of two peptidyl-cysteine residues. The process of chemical oxidation that forms interchain disulfide bonds can produce stable, covalently linked protein dimers, multimers or complexes, whereas intrachain disulfide bonds can contribute to protein folding and stability. Depending on the protein environment, some disulfide bonds are more labile, forming transient redox-active disulfide bonds that are alternately reduced and oxidized in the course of an enzymatic reaction.
Protein involved in DNA condensation. In most eukaryotes, the chromosomal packing involves the wrapping of DNA around a core of histones to form nucleosomes. Adjacent nucleosomes are packaged together via Histone 1 and nucleosomes are organised into a 30 nm chromatin fibre. DNA condensation takes place as cells enter mitosis or when germ cells enter meiosis.
Protein induced by DNA damage or protein involved in the response to DNA damage. Drug- or radiation-induced injuries in DNA introduce deviations from its normal double-helical conformation. These changes include structural distortions which interfere with replication and transcription, as well as point mutations which disrupt base pairs and exert damaging effects on future generations through changes in DNA sequence. Response to DNA damage results in either repair or tolerance.
cellular response to DNA damage stimulus
Viral protein that inhibits or counteracts prokaryotic host helicase/nuclease proteins in order to escape the antiviral activity of the latter. When functioning in their exonuclease mode, helicase/nuclease proteins such as bacterial RecBCD or AddAB degrade any free DNA end as well as the linear dsDNA products resulting from restriction Type II cleavage. Any prokaryotic virus that exposes free dsDNA ends as part of its life cycle must find the means to evade destruction by these host enzymes. Prokaryotic viruses escape this host defense by expressing inhibitors or by protecting the ends of their linear genomes from digestion.
Protein involved in the repair of damages to one strand of DNA (loss of purines due to thermal fluctuations, formation of pyrimidine dimers by UV irradiation, for instance). The site of damage is recognized, excised by an endonuclease, the correct sequence is copied from the complementary strand by a polymerase and the ends of this correct sequence are joined to the rest of the strand by a ligase. In bacterial systems, the polymerase also acts as endonuclease. Excisase A and other proteins involved in recombination mediate DNA excision; a process whereby abnormal or mismatched nucleotides are enzymatically cut out of a strand of a DNA molecule.
Protein involved in DNA integration, a process that mediates the insertion of foreign genetic material, or other duplex DNA, into a chromosome, or another replicon, in order to form a covalently linked DNA continuous with the host DNA.
Specific recombinases which catalyze the inversion of a DNA segment within a nucleoprotein structure termed invertasome.
Protein involved in DNA recombination, i.e. any process in which DNA molecules are cleaved and the fragments are rejoined to give a new combination.
Protein involved in the repair of DNA, the various biochemical processes by which damaged DNA can be restored. DNA repair embraces, for instance, not only the direct reversal of some types of damage (such as the enzymatic photoreactivation of thymine dimers), but also multiple distinct mechanisms for excising damaged base; termed nucleotide excision repair (NER), base excision repair (BER) and mismatch repair (MMR); or mechanisms for repairing double-strand breaks.
Protein involved in DNA replication, i.e. the duplication of DNA by making a new copy of an existing molecule. The parental double-stranded DNA molecule is replicated semi conservatively, i.e. each copy contains one of the original strands paired with a newly synthesized strand that is complementary in terms of AT and GC base pairing.
Protein involved in the inhibition of DNA replication.
Protein involved in the synthesis of DNA from deoxyribonucleic acid monomers.
Protein which binds to DNA, typically to pack or modify the DNA, or to regulate gene expression. Among those proteins that recognize specific DNA sequences, there are a number of characteristic conserved motifs believed to be essential for specificity. Many DNA-binding domains are described in PROSITE.
Enzyme that catalyzes DNA synthesis by addition of deoxyribonucleotide units to a DNA chain using DNA as a template. They can also possess exonuclease activity and therefore function in DNA repair.
Protein of the DNA-directed RNA polymerase complexes, which catalyze RNA synthesis the by addition of ribonucleotide units to a RNA chain using DNA as a template. They can initiate a chain de novo. Prokaryotes have a single enzyme for the three RNA types that is subject to stringent regulatory mechanisms. Eukaryotes have type I that synthesizes all rRNA except the 5S component, type II that synthesizes mRNA and hnRNA and type III that synthesizes tRNA and the 5S component of rRNA.
Keywords assigned to proteins because they have at least one specimen of a specific domain.
Protein which, if defective, causes Down's syndrome, a condition due to the presence of three copies of chromosome 21 (trisomy 21), characterized by some degree of intellectual disability, short stature and poor muscle tone. Common (1 in 700 live births); incidence increases with maternal age. The cause is usually non-disjunction at meiosis but occasionally a translocation of fused chromosomes 21 and 14.
Protein which, if defective, causes dwarfism, a skeletal growth defect resulting in the condition of being undersized.
Large multimeric complex with ATPase activity, responsible for the movement of eukaryotic cilia and flagella (axonemal dynein) and for the intracellular retrograde motility of vesicles, organelles and chromosomes along microtubules (cytosolic dynein). Constitutes the side arms of the outer microtubule doublets in the ciliary axoneme and is responsible for the sliding. Also used for the dynein-associated microtubule-binding proteins (MTBs), e.g. dynactin.
Protein which, if defective, causes dyskeratosis congenita, a clinically and genetically heterogeneous disorder characterized by abnormal skin pigmentation, mucosal leukoplakia, nail dystrophy, progressive bone marrow failure, and increased predisposition to cancer.
Protein which, if defective, causes dystonia or dystonic conditions that feature persistent or recurrent episodes of dystonia as a major manifestation of disease. Dystonia is a movement disorder with a neurological basis, due to disordered tonicity of muscle. It is characterized by sustained involuntary muscle contractions that cause abnormal postures, twisting, repetitive and patterned movements. It may affect muscles throughout the body (generalized), in certain parts of the body (segmental), or may be confined to particular muscles or muscle groups (focal).
Protein which, if defective, causes any of the muscular disorders caused by aberrant glycosylation of dystroglycan. These genetically heterogeneous diseases include a range of conditions with different degrees of severity. At the most severe end of the clinical spectrum, Walker-Warburg syndrome (WWS), muscle-eye-brain disease (MEB) and Fukuyama congenital muscular dystrophy (FCMD) are characterized by congenital muscular dystrophy and severe structural brain and eye abnormalities, which in WWS result in early infantile death. At the mildest end of the clinical spectrum, affected individuals present with limb girdle muscular dystrophy (LGMD), without brain and eye involvement.
Bacteriophage or viral protein expressed in the first phase of the infectious cycle.
Protein which, if defective, causes ectodermal dysplasia, a heterogeneous group of developmental disorders affecting tissues of ectodermal origin. Ectodermal dysplasias are characterized by abnormal development of two or more ectodermal structures such as hair, teeth, nails and sweat glands, with or without any additional clinical sign. Each combination of clinical features represents a different type of ectodermal dysplasia.
Protein containing at least one EGF-like domain, a sequence of about thirty to forty amino-acid residues long found in the sequence of epidermal growth factor (EGF). It has been shown to be present, in a more or less conserved form, in a large number of proteins. The EGF-like domain contains six cysteines which form disulfide bonds within the domain (C1-C3, C2-C4, C5-C6).
Protein which, if defective, causes Ehlers-Danlos syndrome (EDS), a genetically and phenotypically heterogeneous group of connective-tissue disorders. It affects primarily the skin, ligaments, joints, and blood vessels. Typical features include skin hyperextensibility, joint hypermobility, easy bruisability, friability of tissues with bleeding and poor wound healing. Inheritance can be autosomal dominant, autosomal recessive, or X-linked recessive.
Protein involved in the transport of electrons, a process by which electrons are transported through a series of reactions from the reductant, or electron donor, to the oxidant, or electron acceptor, with concomitant energy conversion. Necessary for both photosynthesis and aerobic respiration.
Protein which, if defective, causes elliptocytosis, a disorder characterized by variable haemolytic anaemia and elliptical red blood cell shape. Caused by deficiency/dysfunction of red blood cell membrane proteins.
Protein that associates with ribosomes cyclically during the elongation phase of protein synthesis, and catalyze formation of the acyl bond between the incoming amino-acid residue and the peptide chain.
Protein which, if defective, causes Emery-Dreifuss muscular dystrophy, a heterogenous group of inherited muscular dystrophy without the involvement of nervous system. The disease is characterized by slowly progressive muscle weakness, contracture of the elbows, Achilles tendon and posterior cervical muscles, and cardiac features.
Protein located in or on an encapsulin nanocompartment, proteinaceous shells that encapsulate enzymes. The selectively permeable, self-assembling 25-42 nm shell is made of only 1 protein, unlike the larger bacterial microcompartment. The shell protein has an HK97-like fold and probably evolved from a viral protein. Artificial encapsulin nanocompartments can be expressed and filled with cargo proteins for biotechnological uses. They are found in many bacterial and a few archaeal phyla.
Protein involved in endocytosis, a process by which extracellular materials are taken up into a cell by invagination of the plasma membrane to form vesicles enclosing these materials.
Phosphodiesterase capable of cleaving at phosphodiester internal bonds within a DNA or RNA substrate.
Protein whose subcellular location is the endoplasmic reticulum, a membrane system continuous with the outer nuclear membrane. It consists of flattened, single-membrane vesicles whose inner compartments, the cisternae, interconnect to form channels throughout the cytoplasm. The rough-surface portion is studded with ribosomes.
Morphine-like peptides produced by the brain in response to neurotransmitters. They bind to neuron receptors that mediate the action of opiates and induce analgesia and sedation.
Protein found in or associated with endosomes. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.
Protein involved in the synthesis of enterobactin, a compound that transports iron from the bacterial environment into the cell cytoplasm.
Toxin which, either when ingested or when produced by enterobacteria within the intestine, acts on the intestinal mucosa and induces diarrhea by perturbing ion and water transport systems.
Protein which, if defective, causes epidermolysis bullosa, any of a group of mechano-bullous disorders characterized by blistering and/or erosion of the skin and mucous membranes which occur spontaneously or as a result of mild physical trauma. Traditionally, epidermolysis bullosa is divided into three broad categories based on the level of tissue separation: in epidermolysis bullosa simplex (EBS), tissue separation is intraepidermal and occurs within the basal keratinocytes at the bottom layer of epidermis; the junctional forms (JEB) display tissue separation within the dermo-epidermal basement membrane (basement membrane zone, BMZ), primarily within the lamina lucida; in the dystrophic forms (DEB), tissue separation occurs below the lamina densa within the upper papillary dermis. Some forms of epidermolysis bullosa display tissue separation at the basal cell/lamina lucida interface, at the level of the hemidesmosomes (hemidesmosomal variants). The hemidesmosomal variants overlap with the traditional subtypes, particularly the simplex and junctional forms. In addition to skin involvement, various extracutaneous manifestations can be associated with distinct subtypes of epidermolysis bullosa.
Protein which, if defective, causes epilepsy, any of a group of disorders characterized by paroxysmal transient disturbances of the electrical activity of the brain that may be manifested as episodic impairment or loss of consciousness, abnormal motor phenomena, psychic or sensory disturbances, or perturbation of the autonomic nervous system. Epilepsy is classified as either symptomatic or idiopathic according to whether the cause is known or unknown. Both of these types can be classified into partial and generalized epilepsy, depending on whether the seizures are due to limited or to widespread brain lesions, respectively.
Protein involved in the 'ER-to-Golgi' transport, a bidirectional membrane traffic between the endoplasmic reticulum and the Golgi apparatus which mediates the transfer of cargo molecules by means of small vesicles or tubular-saccular extensions.
Protein encoded by proviral genes of endogenous retroviruses. When a retrovirus infects a host cell, viral reverse transcriptase (RT) makes a DNA copy of the RNA viral genome. The integrated DNA form of a retrovirus is referred to as a provirus. Proviral genes are expressed by cellular mechanisms. Retroviruses that enter the germline are referred to as endogenous retroviruses (ERVs) to distinguish them from horizontally transmitted, not passed on to host progeny, "exogenous" retroviruses. Amplification of ERV copy number via retrotransposition or reinfection has given rise to numerous ERV sequences in the vertebrate genomes. As much as 8% of the human genome, and 10% of the mouse genome, consists of sequences derived from ERV insertions.
Protein involved in the maturation of erythrocytes, the predominant type of cells present in vertebrate blood and which contain the gas-transporting protein, hemoglobin.
Protein involved in the synthesis of ethylene (C2H4), an unsaturated hydrocarbon gas mainly produced in plants. It has developmental effects as a hormone, including growth inhibition, regulation of fruit development, leaf abscission and aging.
Protein involved in the ethylene signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development (e.g. seed germination, root and shoot growth, flower development, plant defense, senescence, abscission and ripening). This phytohormone can be synthesized from methionin.
Eukaryotic host gene expression shutoff by virus
Viral protein which prevents host gene expression by blocking host transcription, mRNA export or translation. This gives viral transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
Eukaryotic host transcription shutoff by virus
Viral protein involved in inhibiting host transcription to ensure the shutoff of cellular proteins expression and give virus transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Inhibition of transcription can be performed by interfering with host RNA pol-II function or interfering with general transcription factors.
suppression by virus of host transcription
Eukaryotic host translation shutoff by virus
Viral protein involved in inhibiting the host translational machinery to shutoff cellular gene expression. This gives virus transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Several virus are known to inhibit host translation mostly by inactivating translation factors.
suppression by virus of host translation
Evasion of bacteria-mediated translation shutoff by virus
Viral protein that counteracts the translation shutoff set up by the bacterial host in order to inhibit viral replication. This antiviral defense system alters a crucial cellular process thereby blocking virus multiplication and ending up with host dormancy or even cell death. For example, some E.coli strains infected by bacteriophage T4 activate an anticodon nuclease which causes depletion of tRNA(Lys) and, consequently, abolishes T4 protein synthesis and causes cell death. However, this effect is counteracted by the repair of tRNA(Lys) in consecutive reactions catalyzed by the viral enzymes polynucleotide kinase and RNA ligase. The ToxIN system functions as a toxin-antitoxin (TA) tandem which is used as a antiviral defense mechanism.
Evasion of host immunity by viral interleukin-like protein
Viral protein sharing sequence homology with host interleukins. Interleukins are produced by immune system cells such as lymphocytes, macrophages and monocytes, and modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells. Several viruses encode interleukin-like proteins playing a role in immune evasion. Additionally, viral interleukins have been shown to activate cellular signaling cascades that enhance virus replication.
mitigation of host immune response by virus
Enzyme which excises abnormal or mismatched nucleotides from a DNA strand.
Protein involved in exocytosis, a process by which a material is transported out of a cell using a vesicle that first engulfs the material and then is extruded through an opening in the cell membrane. The exocyst protein complex plays an important role in exocytosis by directing exocytic vesicles to their precise sites of fusion in the plasma membrane.
Enzyme that degrades DNA or RNA by progressively splitting off single nucleotides from one end of the chain.
Protein involved in the synthesis of exopolysaccharide (EPS), a high molecular-weight polymer composed of saccharide subunits. An example is succinoglycan (EPS I) of Rhizobium meliloti, that is important for invasion of the nodules that it elicits on its host, Medicago sativa.
Protein which is a component of the exosome, a complex of proteins that includes 3->5 exoribonucleases and that plays a major role in diverse RNA processing and degradation pathways in eukaryotes and archaea.
Protein originating from a species thought to be extinct, i.e. from a species for which no known surviving specimens are known to exist. Eg. Dodo, Mammoth or Neanderthal.
Protein found in the extracellular matrix. The extracellular matrix consists of any material produced by cells and secreted into the surrounding medium, but this term generally applies to the non-cellular components of animal tissues. The extracellular matrix forms a supportive meshwork around cells and is largely composed of collagen, laminin, fibronectin and glycosaminoglycans. It can influence the properties of the cells that it supports. In certain tissues, specific modifications to the extracellular matrix occur. For instance, the matrix of bone is mineralized to resist compression.
Protein found in the lens, a transparent body at the front of the vertebrate eye.
Protein involved in flavin adenine dinucleotide synthesis or protein which contains at least one FAD as prosthetic group, cofactor (flavoprotein) or cosubstrate such as many oxidation-reduction enzymes. FAD is an electron carrier molecule that functions as a hydrogen acceptor. The generic term "flavin" derives from the Latin word flavius ("yellow") because of the brilliant yellow color they exhibit as solids and in neutral aqueous solutions.
Familial hemophagocytic lymphohistiocytosis
Protein which, if defective, causes familial hemophagocytic lymphohistiocytosis. FHL is a genetically heterogeneous, autosomal recessive disorder characterized by immune dysregulation with hypercytokinemia and defective natural killer cell function. The clinical features of the disease include fever, hepatosplenomegaly, cytopenia, hypertriglyceridemia, hypofibrinogenemia, and neurological abnormalities ranging from irritability and hypotonia to seizures, cranial nerve deficits and ataxia. Hemophagocytosis is a prominent feature of the disease, and non-malignant infiltration of macrophages and activated T lymphocytes in lymph nodes, spleen and other organs is also found.
Protein which, if defective, causes Fanconi anemia. Fanconi anemia is a rare recessive disorder characterized by progressive pancytopenia, hypoplasia of the bone marrow and patchy brown discoloration of the skin, due to melanin deposition. It is associated with multiple congenital anomalies of the musculoskeletal and genitourinary systems.
Protein involved in the synthesis of fatty acids, long chain organic acids of the general formula CH3(CnHx)COOH. They are constituents of lipids and can be saturated or unsaturated. The esterified forms are important both as energy storage molecules and structural molecules.
Protein involved in the biochemical reactions with fatty acids. Fatty acids are long chain organic acids of the general formula CH3(CnHx)COOH. They are constituents of lipids and can be saturated or unsaturated. The esterified forms are important both as energy storage molecules and structural molecules.
Protein involved in fertilization, the union of two haploid cells, the gametes, to form a diploid cell, the zygote.
Toxin involved in fibrinogen degradation leading to a decrease of plasma fibrinogen concentration. Fibrinogenolytic toxins are mostly snake venom proteases.
Protein involved in fibrin degradation leading to the dissolving of blood clots.
Toxin involved in fibrin degradation leading to the dissolution of fibrin clots. Fibrinolytic toxins are mostly snake venom proteases.
Protein found in a fimbrium or pilus. A fimbrium or pilus is a hair-like, non-flagellar, polymeric filamentous appendage that extend from the bacterial or archaeal cell surface, such as type 1 pili, P-pili, type IV pili or curli. Pili perform a variety of functions, including surface adhesion, motility, cell-cell interactions, biofilm formation, conjugation, DNA uptake, and twitching motility.
Protein which is involved in the formation, organization or maintenance of the fimbrium, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure whose switches propels the cell through a liquid medium.
Protein involved in the movement of the flagella.
archaeal or bacterial-type flagellum-dependent cell motility
Protein present in the flagellum, a long whip-like or feathery structure which propels the cell through a liquid medium. This motile cilium is produced by unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms. The flagella commonly have a characteristic axial '9+2' microtubular array (axoneme) and bends are generated along the length of the flagellum by restricted sliding of the nine outer doublets.
Protein involved in the synthesis of flavonoids, polyphenolic compounds possessing 15 carbon atoms; two benzene rings joined by a linear three carbon chain, a C6-C3-C6 skeleton. C6 presents a benzene ring, C3 often is part of of an oxygen-containing ring. Flavonoids are coloured phenolic pigments originally considered vitamins (Vitamins P, C2) but not shown to have any nutritional role. They are responsible for the red/purple colours of many higher plants.
Enzymes which contain one or more flavin nucleotides (FAD or FMN) as redox cofactors or cosubstrates. Flavoproteins are involved, for example, in the oxidative degradation of pyruvate, fatty acids and amino acids, and in the process of electron transport.
Protein which stimulates or which is involved in flight, the act of passing through the air by the use of wings.
Protein involved in the transition from vegetative to reproductive development in plants.
Protein involved in flavin adenine mononucleotide synthesis or protein which contains at least one FMN as prosthetic group/cofactor (flavoproteins) or cosubstrate, such as many oxidation-reduction enzymes. FMN is an electron carrier molecule that functions as a hydrogen acceptor. The generic term "flavin" derives from the Latin word flavius ("yellow") because of the brilliant yellow color they exhibit as solids and in neutral aqueous solutions.
Pteroylglutamic acid biosynthetic process
Protein involved in the synthesis of folate, the ionic form of folic acid (Latin folium, 'leaf'), first found in spinach leaves. Folate is converted in a two-step reduction into its coenzyme form tetrahydrofolate, often abbreviated FH4 or THF, which acts as a carrier of one-carbon units at several oxidation levels in a variety of biosyntheses.
Protein that binds folate, the ionic form of folic acid.
A protein in which either the N-terminal N-formylmethionine has not been processed by the methionyl-tRNA formyltransferase or which is posttranslationally modified by the attachment of at least one formyl group.
Protein involved in fruit ripening. The fruit is the matured ovary of a plant, enclosing the seed(s). The plant hormone ethylene stimulates fruit ripening.
Protein involved in fruiting body formation or expressed in fruiting bodies, any specialized reproductive structure that produces spores or gametes in fungi, slime molds, algae, etc. Fruiting bodies are distinct in size, shape and coloration for each species.
Protein involved in the biochemical reactions with fucose. L-fucose (6-deoxy-L-galactose) is present in some algae and identified in the chains of glycoproteins; it is the only polysaccharides of certain bacterias.
Protein capable of killing or inhibiting growth of fungi.
Fusion of virus membrane with host cell membrane
Viral entry into host cell via plasma membrane fusion
Viral protein involved in the merging of the virus envelope with host cytoplasmic membrane during viral penetration into host cell. Virus fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. This pathway is used by viruses whose fusion protein is usually pH independent such as most paramyxoviruses, herpesviruses and retroviruses. MHV-JHM coronavirus has been shown to fuse directly with the host cytoplasmic membrane. Prokaryotic viruses such as Tectiviridae fuse their inner membrane with the host cytoplasmic membrane whereas Cystoviridae fuse their outer membrane with the host cytoplasmic membrane.
fusion of virus membrane with host plasma membrane
Fusion of virus membrane with host endosomal membrane
Viral protein involved in the merging of the virus envelope with host endosomal membrane during viral penetration into host cell. Viral fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. The specific trigger is mainly endosome acidification which induce activation of the fusion protein by conformational change. This pathway is used by enveloped viruses which are endocytosed and whose fusion protein is usually pH-dependent like influenza A virus, rhabdoviruses, bornaviruses, filoviruses, asfarviridae, flaviviridae, alphaviruses, HIV-1, avian leukosis virus, SARS, 229E, and MHV-2 coronaviruses.
fusion of virus membrane with host endosome membrane
Fusion of virus membrane with host membrane
Viral entry into host cell via membrane fusion
Viral protein involved in the merging of the virion membrane with a host membrane during viral penetration into host cell. Viral fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. The specific trigger depends on the virus and can be exposure to low pH in the endocytic pathway or interaction of the virion with the host receptor(s). In prokaryotic viruses, host-virus membrane fusion can occur either at the host outer membrane or plasma membrane. Bacteriophages such as cystoviridae fuse their external envelope with the host outer membrane, whereas others like tectiviridae fuse their inner envelope with the host plasma membrane.
membrane fusion involved in viral entry into host cell
Fusion of virus membrane with host outer membrane
Viral entry into host cell via outer membrane fusion
Viral protein involved in the merging of the virion external lipidic membrane (envelope) with the prokaryotic host outer membrane during viral penetration into host cell. Bacteriophages such as Cystoviridae for example fuse their membrane with the host outer membrane.
G-protein coupled acetylcholine receptor impairing toxin
Muscarinic acetylcholine receptor regulator
Toxin which interferes with the function of the muscarinic acetylcholine receptor (mAChR). The mAChR is a specific class of G-protein coupled receptor (GPCR) that binds acetylcholine. These toxins are mostly found in snake venoms.
Receptors which transduce extracellular signals across the cell membrane. At the external side they receive a ligand (a photon in case of opsins), and at the cytosolic side they activate a guanine nucleotide-binding (G) protein. These receptors are hydrophobic proteins that cross the membrane seven times.
G protein-coupled receptor signaling pathway
G-protein coupled receptor impairing toxin
Toxin which interferes with the function of G-protein coupled receptors (GPCRs). These toxins are mostly found in snake and scorpion venoms.
G0/G1 host cell cycle checkpoint dysregulation by virus
Viral protein involved in the modulation of host cell cycle progression by dysregulating the G0/G1 transition. Some viruses benefit from keeping cells in resting state (G0), while others favor entry through G1 and subsequent cell division to replicate more efficiently.
modulation by virus of host G0/G1 transition checkpoint
G1/S host cell cycle checkpoint dysregulation by virus
Viral protein involved in the modulation of host cell cycle progression by dysregulating the G1/S transition. Some viruses benefit from an arrest in G1 to S phase transition, while others force through S phase to favor their own replication.
modulation by virus of host G1/S transition checkpoint
Protein involved in the biochemical reactions with galactitol. This sugar alcohol is derived from galactose. It can be found in certain bacteria, yeasts, fungi and plants. In humans, the congenital galactosemic cataracts are due to an accumulation of galactitol within the lens.
Protein involved in the biochemical reactions with the monosaccharide galactose. This optical isomer (epimer) of glucose is a constituent of various oligosaccharides (e.g. lactose, raffinose), polysaccharides (e.g. galactans, agar, gum arabic) and also of sphingolipids (galactocerebrosides).
Protein which possesses at least one gamma-carboxyglutamic acid, a vitamin K dependent post-translational modification of a glutamate residue found in blood coagulation proteins and in the proteins of calcified tissues. Gamma-carboxyglutamyl residues are good chelators of calcium ions. There are two natural forms of vitamin K, which are phylloquinone (vitamin K1 or phytylmenaquinone) in green vegetables and menaquinone (vitamin K2 or menaquinone-n, depending of the number of isoprene units of the side-chain or MK-n) in intestinal bacteria, as well as one synthetic provitamin form, menadione (vitamin K3). In infants, the primary symptom of a deficiency of this fat-soluble vitamin is a hemorrhagic syndrome.
Protein which, if defective, causes gangliosidosis. Gangliosidosis defines any of a group of autosomal recessive lysosomal storage diseases characterized by the accumulation of gangliosides GM1 or GM2 and related glycoconiugates, and by progressive psychomotor deterioration. Subtypes include GM1-gangliosidoses and GM2-gangliosidoses.
Protein component of gap junctions which are specialized regions of the plasma membrane formed by a cluster of channels allowing small molecules to diffuse from the cytosol of one cell to that of an adjacent cell. A current model of the gap junction consists of a cluster of gap-junction channels. Both membranes contain connexon hemichannels, composed of a hexamer of an integral membrane protein which is often referred to as connexin. The junction of two adjacent connexons forms a gap-junction channel.
A group of insect proteins which are crucial for the development of proper embryonic segmentation. These are the first proteins that define the coarsest subdivisions. Generally, gap gene mutations are lethal and eliminate a large block of contiguous segments from the embryo.
Protein component of, or involved in the formation of, gas vesicles, which are a rigid, hollow structure found in five phyla of the Bacteria and two groups of the Archaea, but mostly restricted to planktonic microorganisms, in which they provide buoyancy. By regulating their relative gas vesicle content, aquatic microbes are able to perform vertical migrations. The gas vesicle is impermeable to liquid water, but is highly permeable to gases and is normally filled with air. Two proteins have been shown to be present in the gas vesicle: GVPa, which makes the ribs that form the structure, and GVPc, which binds to the outside of the ribs and stiffens the structure against collapse.
Protein involved in the exchange of gases.
respiratory gaseous exchange by respiratory system
Protein involved in gastrulation, a stage in early embryogenesis in which cell movements result in a massive reorganization of the embryo from an initially unstructured group of cells, the blastula, into a multi-layered organism. During gastrulation, the primary germ layers (endoderm, mesoderm, and ectoderm) are formed and organized in their proper locations for further development.
Protein which, if defective, causes Gaucher disease, the most prevalent sphingolipid storage disorder caused by a recessively inherited deficiency of the enzyme glucocerebrosidase. Most common in Ashkenazi Jews, it is associated with hepatosplenomegaly (enlargement of liver and spleen) and, in severe early onset forms of the disease, with neurological dysfunction.
Any protein used in a biotechnological process that results in the modification of a naturally occurring food (crop or livestock). Examples include proteins introduced to enable herbicide or insect resistance or proteins that act in fruit ripening.
Protein involved in germination, the physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Protein involved in the gibberellin (GA) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth including seed germination, hypocotyl elongation, stem elongation, leaf expansion, trichome development, pollen maturation and flower and fruit development. GAs are tetracyclic diterpenoid phytohormones found in plants, fungi and bacteria. They are named GA1....GAn in order of discovery. The term "gibberellin" was first given to a substance, produced by the fungus Gibberella fujikuroi, which caused overgrowth symptoms in rice. This substance was later proven to be a mixture of GAs, with GA1 and GA3 being the active factors.
gibberellic acid mediated signaling pathway
Protein which, if defective, causes glaucoma, a group of eye diseases characterized by pathological changes in the optic disk, progressive loss of optic nerve axons and visual field defects. Most of the patients with glaucoma have an increased intraocular pressure. The disease is painless and often diagnosed at a late stage, when visual field defects are severe. Glaucoma is one of the leading causes of blindness worldwide.
Protein involved in the biochemical pathway(s) in which gluconate is the carbon source.
Protein involved in the biosynthesis of "new" glucose from such noncarbohydrate precursors as pyruvate, lactate, certain amino acids and intermediates of the tricarboxylic acid cycle.
Protein involved in the biochemical reactions with the 6-carbon aldose sugar glucose.
Protein involved in the synthesis of the acidic amino acid glutamate. Glutamate is a component of proteins and can also act as a neurotransmitter in the central nervous system.
Enzyme that catalyzes the removal of the ammonia group from glutamine and transfers it to a substrate to form a new carbon-nitrogen group. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides or as domains in larger multifunctional proteins. There exist two classes of glutamine amidotransferases domains: I and II.
Protein which, if defective, causes glutaricaciduria (GA), a metabolic disorder characterized by the excretion of glutaric acid in the urine. Type I GA is caused by the deficiency of glutaryl-CoA dehydrogenase, a mitochondrial enzyme involved in the metabolism of lysine, hydroxylysine and tryptophan. Type II GA differs from type I in that multiple acyl-CoA dehydrogenase deficiencies result in a large excretion not only of glutaric acid but also of lactic, ethylmalonic, butyric, isobutyric, 2-methyl-butyric, and isovaleric acids. GA II can result from a deficiency of any one of 3 mitochondrial molecules: the alpha and beta subunits of electron transfer flavoprotein and electron transfer flavoprotein-ubiquinone oxidoreductase.
Protein involved in the synthesis of the tripeptide glutathione (Gamma-Glu-Cys-Gly). Glutathione sulphydryl group is kept largely in the reduced state; this allows it to act as a sulphydryl buffer, reducing any disulphide bonds formed within cytoplasmic proteins to cysteines. Glutathione is also important as a cofactor for the enzyme glutathione peroxidase, in the uptake of amino acids and participates in leucotriene synthesis. Glutathione contains an unusual peptide linkage between the carboxyl group of the glutamate side chain and the amine group of cysteine.
Protein which is posttranslationally modified by the attachment of a glutathione molecule by a disulfide bond.
Protein containing one or more covalently linked glucose residues, resulting from a non-enzymatic spontaneous reaction. The carbohydrate is attached to an amino-acid nitrogen atom (e.g. from a lysine side chain, or the amino-terminal group). This modification is a side effect of diabetes and aging. Glycation is the first step toward the formation of advanced glycation endproducts (AGEs). Some AGEs are benign, but others are implicated in age-related chronic diseases such as: type II diabetes mellitus, cardiovascular diseases, Alzheimer's disease, etc.
Protein involved in the biochemical reactions with the 3-carbon sugar alcohol glycerol. Glycerol is primarily of interest as the central structural component of the major classes of biological lipids, triglycerides and phosphatidyl phospholipids. It is also an important intermediate in carbohydrate and lipid metabolism.
Protein involved in the synthesis of glycogen, a branched polymer of D-glucose (mostly -(1-4) linked, but with some -(1-6) linked residues at branch points). Glycogen is the major short term storage polymer of animal cells and is particularly abundant in liver and to a lesser extent in muscles.
Protein involved in the biochemical reactions with glycogen, a branched polymer of D-glucose (mostly -(1-4) linked, but with some - (1-6) linked residues at branch points). Glycogen is the major short term storage polymer of animal cells and is particularly abundant in liver and to a lesser extent in muscles.
Protein which, if defective, causes glycogen storage disease, a group of inherited metabolic disorders involving the enzymes responsible for the synthesis and degradation of glycogen. At least thirteen types of this disease have been described.
Protein involved in the glycolate pathway, synthesis of the amino acids serine and glycine from glycolate via a glyoxylate intermediate.
Protein involved in the anaerobic enzymatic conversion of glucose to lactate or pyruvate, resulting in energy stored in the form of adenosine triphosphate (ATP), as occurs in skeletal muscle and in embryonic tissue.
Protein containing one or more covalently linked carbohydrates of various types, i.e. from monosaccharides to branched polysaccharides, including glycosylphosphatidylinositol (GPI), glycosaminoglycans (GAG).
Hydrolases which attack glycosidic bonds in carbohydrates, glycoproteins and glycolipids. The glycosidases are not highly specific. Usually they distinguish only the type of bond, e.g. O- or N-glycosidic, and its configuration (alpha or beta).
hydrolase activity, acting on glycosyl bonds
Protein present in the glycosome, a microbody-like organelle found in all members of the protist order Kinetoplastida examined. Nine enzymes involved in glucose and glycerol metabolism are associated with these organelles. These enzymes are involved in pathways which, in other organisms, are usually located in the cytosol.
Enzymes that catalyze the transfer of glycosyl (sugar) residues to an acceptor, both during degradation (cosubstrates= water or inorganic phosphate) and during biosynthesis of polysaccharides, glycoproteins and glycolipids. In biosynthetic glycosyl transfers, the common activated monomeric sugar intermediate is a nucleoside diphosphate sugar.
Protein involved in the glyoxylate bypass, an alternate route in bacteria, plants, and fungi which bypasses the CO2-evolving steps of the tricarboxylic acid cycle, thus permiting the utilization of fatty acids or acetate, in the form of acetyl-CoA, as sole carbon source, particularly for the net biosynthesis of carbohydrate from fatty acids. The glyoxylate bypass is especially prominent in plant seeds.
Protein present in the glyoxysome, a membrane-surrounded plant cell organelle, especially found in germinating seeds, and involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass. Since it is also rich in catalase, the glyoxysome may be related to the microbodies or peroxisomes or derived from them.
Guanosine 5'-monophosphate biosynthetic process
Protein involved in the synthesis of GMP. GMP is the abbreviation for the nucleotide guanosine 5'-monophosphate.
Protein found in the Golgi apparatus, an organelle present in eukaryotic cells that appears as a stack of 6-8 plate-like membranous compartments and associated vesicles and vacuoles, often located near the centrosome. It has four functionally distinct compartments: cis, medial and trans Golgi stacks, and the trans Golgi network (TGN). The first three are involved in posttranslational modifications of proteins (e.g., N- or O-glycosylation, sulfation, processing of acid hydrolases), while the TGN is involved in sorting the proteins to their final destination (e.g., to lysosomes, to secretory vesicles, or to plasma membrane).
Protein involved in gonadal differentiation, the progressive restriction of the developmental potential and increasing specialization of function which takes place during the embryonic development and leads to the formation of gamete-producing glands, such as ovary or testis.
Protein which, if defective, causes gout, a recurrent acute arthritis of peripheral joints caused by the precipitation of monosodium urate crystals in articular cartilage. Gout is usually due to overproduction of uric acid secondary to an inherited abnormality of purine metabolism, but may be a result of urate under-excretion.
Protein bound to the lipid bilayer of a membrane through either a GPI-anchor (glycosylphosphatidylinositol anchor), a complex oligoglycan linked to a phosphatidylinositol group, or a GPI-like-anchor, a similar complex oligoglycan linked to a sphingolipidinositol group, resulting in the attachment of the C-terminus of the protein to the membrane.
Glycosylphosphatidylinositol anchor anabolism
Glycosylphosphatidylinositol anchor biosynthesis
Glycosylphosphatidylinositol anchor biosynthetic process
Glycosylphosphatidylinositol anchor formation
Glycosylphosphatidylinositol anchor synthesis
Protein involved in the synthesis or the attachment to a protein of a GPI-anchor (glycosylphosphatidylinositol anchor) or a GPI-like-anchor (glycosylsphingolipidinositol anchor), both of which have complex oligoglycan linked to a phospholipidinositol molecule that serves to attach the C-terminus of some extracellular membrane proteins to the lipid bilayer of a membrane. The core glycolipid is composed of a tetraglycan: three mannose units and one glucosamine linked to a phospholipidinositol. The terminal mannose is linked to the protein via an ethanolamine attached to the C-terminal of the mature protein. The core structure is conserved from protozoa to humans. There are, however, marked differences in the glycosyl side chains attached to the core glycolipid. The phospholipid component may be either a phosphatide (two long chain fatty acids attached by ester linkage to glycerol phosphate) or a sphingolipid (a long chain fatty acid attached by amide linkage to a ceramide phosphate). Some yeast and Dictyosteliida synthesize the GPI-like anchor de novo, whereas other organisms may interconvert the lipid components by a "resculpting" process after the anchor is attached to the protein.
Protein involved in growth arrest, a phenomenon occurring when a cell does not proceed through the cell cycle.
Protein which, by binding to a cell-surface receptor, triggers an intracellular signal-transduction pathway leading to differentiation, proliferation, or other cellular response.
Protein other than a receptor that binds to a cell's growth factor.
Protein involved in growth regulation, which usually implies the control of the rate of division rather than that of the size of an individual cell.
Protein which binds guanosine 5'-triphosphate (GTP), a ribonucleotide guanosine (a purine base guanine linked to the sugar D-ribofuranose) that carries three phosphate groups esterified to the sugar moiety.
GTPase-activating protein (GAP) by itself does not hydrolyze GTP but, by binding to a GTPase, accelerates its intrinsic GTPase activity.
Protein which catalyzes the release of GDP (guanosine 5'-diphosphate).
guanyl-nucleotide exchange factor activity
Protein or apolipoprotein associated with High-Density Lipoproteins (HDL), a class of proteins involved in lipid (cholesterol, phospholipids and triacylglycerol) metabolism in the body fluids. HDL are formed in the liver and are involved in reverse cholesterol transport, the transport of cholesterol from peripherical tissues to the liver. Apolipoproteins are proteins which are specifically associated with lipoproteins, which is not the case for all the proteins associated with HDL or with the other lipoprotein classes.
Protein involved in hearing, the special sense by which an organism is able to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
Viral protein that forms a helical capsid to protect the viral genome. Viral helical capsids are about 7-30 nm in diameter and 200-2000 nm long.
Protein with an helicase activity. Helicases are ATPases that catalyze the unwinding of double-stranded nucleic acids. They are tightly integrated (or coupled) components of various macromolecular complexes which are involved in processes such as DNA replication, recombination, and nucleotide excision repair, as well as RNA transcription and splicing.
Protein which causes agglutination of erythrocytes or other cell types: In viruses, a protein which is responsible for attaching the virus to cell receptors and for initiating infection.
Protein containing at least one heme, an iron atom coordinated to a protoporphyrin IX. In myoglobin and hemoglobin, one of the coordination positions of iron is occupied by oxygen or other ligands, such as carbon monoxide. Hemes are also found in cytochromes of the electron-transport chain where they bind electrons, in reducing peroxides (catalases and peroxidases), and act as terminal components in multienzyme systems involved in hydroxylation. Cytochrome c is the only common heme protein in which the heme is covalently bound.
Protein involved in the synthesis of heme, an iron atom coordinated to a protoporphyrin IX.
Protein which binds hemoglobin, a gas-carrying protein found in red blood cells.
Protein involved in the coagulation of hemolymph, the circulatory fluid of invertebrate animals which is functionally comparable to the blood and lymph of vertebrates.
Protein involved in hemolysis, the disruption of the integrity of the red cell membrane, thus causing the release of hemoglobin.
Protein which, if defective, causes hemolytic uremic syndrome, a disorder characterized by non-immune hemolytic anemia, thrombocytopenia and renal failure. The vast majority of cases are sporadic, occur in young children and are associated with epidemics of diarrhea due to bacterial infections. This typical form of the disease has a good prognosis and death rate is very low. In contrast to typical hemolytic uremic syndrome, atypical forms present without a prodrome of enterocolitis and diarrhea and have a poor prognosis, with frequent development of end-stage renal disease or death.
Protein which, if defective, causes hemophilia, a genetic disease characterized by uncontrollable bleeding due to a sex-linked recessive deficiency of blood-clotting factor (usually of Factor VIII).
Toxin which induces the leakage of blood components into tissues by damaging endothelial cells or disturbing endothelial cell interactions with the basement membrane. Hemorrhagic toxins are mostly found in snake venoms.
Protein involved in the arrest of bleeding through blood clotting and contraction of blood vessels.
Toxin which interferes with hemostasis regrouping all mechanisms implicated in the cessation of blood loss through damaged vessels. Hence, hemostasis impairing toxins not only interfere with platelet aggregation, the coagulation cascade, fibrinogen depletion, and fibrin clot degradation (fibrinolysis), but also provoke hemorrhage by damaging endothelial cells or disturbing their interaction with the basement membrane. Numerous snake venom families have the capacity to interfere with hemostasis.
Protein containing at least one heparan sulfate, a highly sulfated glycosaminoglycan, closely related to heparin, which consists of repeating units of disaccharides composed of iduronic acid, glucosamine and N-acetylglucosamine.
Protein which binds heparin, a highly sulfated glycosaminoglycan which consists of repeating units of disaccharides composed of D-glucosamine, D-glucuronic acid or L-iduronic acid. This anticoagulant is found in the granules of mast cells.
Protein that confers, on plants, bacteria or other microorganisms, the ability to withstand herbicide action. Herbicides are chemicals that selectively kill plants. Herbicide resistance occurs usually as a result of mutation or amplification of a gene, e.g. 3-phosphoshikimate 1-carboxyvinyltransferase.
Protein which, if defective, causes hereditary hemolytic anemia, a hereditary disease characterized by the premature destruction of red blood cells.
Protein which, if defective, causes hereditary multiple exostoses (EXT). It is an autosomal dominant disease characterized by the formation of cartilage-capped benign tumors (exostoses), developing from the juxtaepiphyseal regions of the long bones and often accompanied by skeletal deformities and short stature.
Hereditary nonpolyposis colorectal cancer
Protein which, if defective, causes hereditary non-polyposis colorectal cancer (HNPCC), also known as Lynch's syndrome. It is an autosomal dominant syndrome which confers an increased risk for colorectal and endometrial cancers as well as others tumors. Clinically, HNPCC is often divided into two subgroups: type I, characterized by a hereditary predisposition to colorectal cancer, a young age of onset, and carcinoma observed in the proximal colon; type II, characterized by an increased risk for cancers in certain tissues such as the uterus, ovary, breast, stomach, small intestine, skin, and larynx in addition to the colon.
Protein which, if defective, causes hereditary spastic paraplegias (HSPs). HSPs are a diverse class of hereditary degenerative spinal cord disorders characterized by a slow, gradual, progressive weakness and spasticity (stiffness) of the legs. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. Rate of progression and the severity of symptoms are quite variable.
Protein which, if defective, causes Hermansky-Pudlak syndrome, a rare autosomal recessive disorder characterized by oculocutaneous albinism and storage pool deficiency due to an absence of platelet dense bodies. Lysosomal ceroid lipofuscinosis, pulmonary fibrosis and granulomatous colitis are occasional manifestations of the disease.
Protein which is implicated in heterocyst formation. A heterocyst is a differentiated cyanobacterial cell that carries out nitrogen fixation. The heterocysts function as the sites for nitrogen fixation under aerobic conditions. They are formed in response to a lack of fixed nitrogen (NH4 or NO3). The morphological differentiation is accompanied by biochemical alterations. The mature heterocysts contain no functional photosystem II and cannot produce oxygen. Instead, they contain only photosystem I, which enables them to carry out cyclic photophosphorylation and ATP regeneration. These changes provide the appropriate conditions for the functioning of the oxygen-sensitive nitrogenase.
Protein which, if defective, causes heterotaxy, a broad group of disorders caused by failure to correctly establish left-right patterning during embryogenesis with consequent abnormal segmental arrangements of cardiac chambers, vessels, lungs, and/or abdominal organs. Heterotaxy include complex cardiac malformations, situs inversus, situs ambiguus, isomerism. Situs inversus indicates complete left-right reversal of organ position and is not usually associated with structural anomalies. Situs ambiguus is an abnormal arrangement of viscera almost invariably associated with complex cardiovascular malformations as well as anomalies of the spleen and the gastrointestinal system. Isomerism is a defect in asymmetry of paired organs that usually have distinct right and left forms, but in this condition, are mirror images.
Protein involved in the process of hibernation. Hibernation is a state of inactivity in an animal brought about by short day lengths, cold temperatures and limitations of food.
Hirschsprung's disease (HSCR); a genetic disorder of neural crest development characterized by the absence of intramural ganglion cells in the hindgut; often resulting in intestinal obstruction.
Protein involved in the synthesis of the weakly basic amino acid histidine.
Protein involved in the biochemical reactions with the weakly basic amino acid histidine.
A clinically variable and genetically heterogeneous malformation in which the developing forebrain fails to correctly separate into right and left hemispheres. In its most severe form (alobar holoprosencephaly), the forebrain consists of a single ventricle, and midbrain structures may be malformed as well. In the most extreme cases, anophthalmia or cyclopia is evident along with a congenital absence of the mature nose. In milder forms (semilobar or lobar holoprosencephaly), rudimentary midline structures are present. The less severe form features facial dysmorphia characterized by ocular hypertelorism, defects of the upper lip and/or nose, and absence of the olfactory nerves or corpus callosum. The majority of cases are sporadic, although families with both autosomal dominant and autosomal recessive holoprosencephaly have been described.
Protein which contains at least one homeobox, a conserved sequence originally detected, on the nucleotide level, in many of the genes which give rise to homeotic and segmentation mutants in Drosophila. The homeobox, also termed homeodomain, consists of about 60 amino acids and is involved in DNA-binding.
Protein which functions as a hormone, a biochemical substance secreted by specialized cells that affects the metabolism or behavior of other cells which possess functional receptors for the hormone. Hormones may be hydrophilic, like insulin, in which case the receptors are on the cell surface, or lipophilic, like the steroids, where the receptor can be intracellular.
Protein found in or associated with the prokaryotic host cell inner membrane, a selectively permeable membrane which separates the host cytoplasm from the host periplasm in prokaryotes with 2 membranes.
Protein found in or associated with a host cell junction, a host cell-host cell or host cell-host extracellular matrix contact within a tissue of a host multicellular organism, especially abundant in host epithelia. In vertebrates, there are three major types of cell junctions: anchoring junctions (e.g. adherens junctions), communicating junctions (e.g. gap junctions) and occluding junctions (e.g. tight junctions).
Viral protein involved in the lysis of the host cell allowing the release of mature, newly formed virions. Viruses use different way to lyse their host cell. They can express viroporins as Adenoviridae or Picornaviridae do in the late phase of infection. Phycodnaviridae for their part seem to express lytic phospholipids. In dsDNA prokaryotic viruses, lysis-specific proteins are expressed: a holin, which permeabilizes the inner membrane and an endolysin which then gains access to and degrades the host peptidoglycans. Some bacterioviruses express a signal-containing endolysin and thus do not need the holin function.
viral release from host cell by cytolysis
Protein found in or associated with the host cytoplasmic membrane, a selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the host cell inner membrane in prokaryotes with 2 membranes.
Protein found in or associated with the prokaryotic cell outer membrane, a selectively permeable membrane which separates the prokaryotic periplasm from its surroundings in prokaryotes with 2 membranes. Traditionally only Gram-negative bacteria were thought of as having an outer membrane, but recent work has shown some Actinobacteria, including Mycobacterium tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.
Protein found in or associated with a host cell projection, a host cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, pili or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as host cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.
Cell surface protein used by a virus as an attachment and entry receptor. In some cases, binding to a cellular receptor is not sufficient for infection: an additional cell surface molecule, or coreceptor, is required for entry. Some viruses are able to use different receptors depending on the target cell type. In prokaryotic viruses, cell receptor for virus entry can also be localized on host outer membrane, pilus or flagellum.
Protein found in the host cytoplasm, the content of a host cell within the plasma membrane and, in eukaryotics cells, surrounds the host nucleus.
Protein found in or associated with host cytoplasmic vesicles, which mediate vesicular transport among the organelles of host secretory and endocytic systems.
Protein which is a component or which is associated with the host cytoskeleton, a dynamic three-dimensional structure that fills the host cytoplasm of eukaryotic cells. It is responsible for cell movement, cytokinesis, and the organization of the organelles or organelle-like structures within the host cell.
Protein whose subcellular location is the host endoplasmic reticulum (ER), which is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic host cell, especially those responsible for the production of hormones and other secretory products.
Protein found in or associated with host endosomes, which are highly dynamic membrane systems involved in transport within the host cell, they receive endocytosed host cell membrane molecules and sort them for either degradation or recycling back to the host cell surface. They also receive newly synthesised proteins destined for host vacuolar/lysosomal compartments.
Viral protein involved in the modulation of host cell cycle by inhibiting the G2/M transition. A variety of viruses have been associated with G2/M arrest, including some DNA viruses, some RNA viruses and retroviruses but the mechanisms by which arrest is achieved greatly differs between those viruses.
suppression by virus of G2/M transition of host mitotic cell cycle
Viral protein which prevents host gene expression by blocking for example host transcription, mRNA export or translation. This gives virus transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
suppression by virus of host gene expression
Protein found in the host Golgi apparatus, a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the host Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the host Golgi exists as many copies of discrete stacks dispersed throughout the host cytoplasm. It is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the host plasma membrane and compartments of the host endocytic pathway.
Host monolayer-surrounded lipid storage body
Protein characteristic of host lipid droplet, a dynamic cytoplasmic host organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. They may play a role in host lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.
Protein found in the host lysosome, a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the host lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.
Protein which is membrane-bound or membrane-associated with the host membrane, a lipid bilayer which surrounds host enclosed spaces and compartments. This selectively permeable structure is essential for effective separation of a host cell or organelle from its surroundings.
Protein found in host microsomes, which are a heterogenous set of vesicles 20-200 nm in diameter and formed from the host endoplasmic reticulum when host cells are disrupted.
host intracellular membrane-bounded organelle
Protein encoded by or localized in the host mitochondrion, a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, host eukaryotes. Each host mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. They are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP.
Protein found in or associated with the host mitochondrion inner membrane, the membrane which separates the host mitochondrial matrix from the host mitochondrial intermembrane space.
Protein found in or associated with the host mitochondrion outer membrane, the host mitochondrial membrane facing the host cytoplasm.
Viral protein involved in suppressing host mRNAs expression to maximize expression of viral mRNAs. Decimating cellular mRNAs eventually leads to shutoff of host proteins expression and gives virus transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Suppression of host mRNA can be performed by interfering with host pre-mRNA processing function (splicing or polyadenylation), by degrading mRNAs or blocking their export from the nucleus to the cytoplasm.
Protein located in the host nucleus, which is the most obvious organelle in any host eukaryotic cell. It is a membrane-bound organelle and is surrounded by double membranes. It communicates with the surrounding cytosol via numerous nuclear pores.
Protein located in the host periplasm, the space between the inner and outer membrane in host Gram-negative bacteria. In Gram-positive bacteria a smaller periplasmic space is found between the inner membrane and the peptidoglycan layer. Also used for the host intermembrane spaces of host fungi and host organelles.
Protein located in the host synapse, the communicating cell-cell junctions that allow signals to pass from a host nerve cell to a host target cell. In a chemical synapse, the signal is carried by a neurotransmitter which diffuses across a narrow synaptic cleft and activates a receptor on the postsynaptic membrane of the target cell.
Protein located in or on the host thylakoid, a membranous cellular structure containing the photosynthetic pigments, reaction centers and electron-transport chain. In host chloroplast, thylakoids stack up to form the grana or stay as single cisternae and interconnect the grana. Thylakoid, where photosynthesis occurs, are found in chloroplasts, cyanelles and in photosynthetic bacteria where they are the extensive invaginations of the plasma membrane.
Viral or cellular protein involved in a host-virus interaction. Viruses interact with many cellular pathways to achieve their replication cycle. Entry into the host cell, transport to the viral replication sites or viral exit from the host cell are all steps that require specific interactions between the virus and its host. Additionally, the evasion from the host immune response requires a lot of viral proteins to associate with and inhibit cellular proteins with antiviral functions.
Protein which binds hyaluronic acic, an acidic glycosaminoglycan which consists of repeating units of the disaccharide composed of D-glucuronic acid and N-acetyl-D-glucosamine. This linear polymer is present in cell coats and in the extracellular ground substance of the connective tissues of vertebrates; it also occurs in the synovial fluid in joints and in the vitreous humor of the eye.
Protein sequenced from a hybridoma, an artificially produced hybrid cell line created by fusion of a lymphocyte and a myeloma cell. These cells can multiply indefinitely in culture and produce monoclonal antibodies.
Protein involved in the transport of hydrogen ions across a membrane. Used to power processes such as ATP synthesis and bacterial flagellar rotation.
Protein involved in hydrogen peroxide (H(2)O(2)) decomposition, e.g., catalase. H(2)O(2) is generated by the body as a byproduct of aerobic cellular respiration.
Protein characteristic of the hydrogenosome, a redox organelle of anaerobic unicellular eukaryotes which contains hydrogenase and produces hydrogen and ATP by glycolysis. They are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Most hydrogenosomes lack a genome, but some like that of the anaerobic ciliate Nyctotherus ovalis, have retained a rudimentary genome.
Enzyme which catalyzes hydrolysis reaction, i.e. the addition of the hydrogen and hydroxyl ions of water to a molecule with its consequent splitting into two or more simpler molecules.
Protein which is posttranslationally modified by the attachment of at least one hydroxyl (-OH) group.
Protein which, if defective, causes hyperlipidemia, a condition characterized by the elevation of lipids in the bloodstream. There are different types of hyperlipidemias: type I (lipoprotein lipase deficiency), IIa (hypercholesterolemia; LDL receptor deficiency), IIb (combined hyperlipidemia), III (dysbetalipoproteinemia), IV (hypertriglyceridemia) and V (mixed hyperlipidemia).
Protein involved in hypersensitive response, a complex and early defense response that causes necrosis and cell death to restrict the growth of a pathogen. Local and systemic biochemical changes include generation of active oxygen species (oxidative burst), cell death, overproduction of lignin-related materials, and the induction of certain proteins such as pathogen related (PR) proteins.
Proteins involved in hypersensitive response (HR) elicitation. HR is a rapid defense-associated programmed cell death of plant cells at the site of invasion.
modulation by symbiont of host defense-related programmed cell death
Idiopathic hypogonadotropic hypogonadism
Protein which, if defective, causes hypogonadotropic hypogonadism, a disorder characterized by a deficiency of the pituitary secretion of follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Affected individuals present with absent or impaired sexual development due to sex-steroid-hormone deficiency, low serum levels of the pituitary gonadotropins FSH and LH, and infertility.
Protein which can cause hypotension, i.e. low blood pressure or a sudden drop in blood pressure.
Protein which, if defective, causes hypotrichosis, a condition characterized by reduced pilosity over the body and scalp (with sparse, thin, and short hair).
Protein which is posttranslationally modified on at least one lysine residue to form hypusine (N-epsilon-(4-aminobutyl)lysine). This spermidine-dependent reaction is catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase. eIF-5A is the only protein in eukaryotes and archaebacteria known to contain hypusine.
Protein involved in the synthesis of hypusine, an amino acid formed by the two posttranslational steps in the modification of a lysine: (i) deoxyhypusine synthase catalyzes the transfer of a 4-aminobutyl moiety from spermidine to a specific lysine residue to form a deoxyhypusine residue, N-epsilon-(4-aminobutyl)lysine, and (ii) deoxyhypusine hydroxylase catalyzes the hydroxylation of the deoxyhypusine residue to form hypusine (N-epsilon-(4-amino-2-hydroxybutyl)lysine).
peptidyl-lysine modification to peptidyl-hypusine
Protein which promotes the nucleation of ice. The proteins catalyzes the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation.
Protein which, if defective, causes ichthyosis, any of a group of cutaneous disorders characterized by increased or aberrant keratinization and resulting in non-inflammatory scaling of the skin. Most ichthyoses are genetically determined, while some may be acquired and develop in association with various systemic diseases or be a prominent feature in certain genetic syndromes.
Viral protein allowing host innate defense evasion by methylating the first and second ribonucleotide of viral mRNAs (cap1 and cap2). These methylations allow viral RNA to escape cellular antiviral process mediated by host IFIT proteins which degrade non cap1-methylated mRNAs. Also prevents IFIH1/MDA5 sensor activation by cap0 mRNAs, which would trigger interferon beta synthesis.
Protein binding to immunoglobulin A, the major class of antibodies found in external secretions such as saliva, tears, gastric fluid, milk and mucosal secretions.
Protein binding to immunoglobulin E, the antibody class involved in local inflammatory reactions, reactions to parasites, and also in allergic responses.
Protein binding to immunoglobulin G, the main type of immunoglobulin produced towards the end of a primary immune response and in a secondary response.
Protein involved in immunity, any immune system process that functions in the response of an organism to a potential internal or invasive threat. The vertebrate immune system is formed by the innate immune system (composed of phagocytes, complement, antimicrobial peptides, etc) and by the adaptive immune system which consists of T- and B-lymphocytes.
A glycoprotein produced in membrane-bound or secreted form by B lymphocytes. The basic structural unit of an immunoglobulin (Ig) is composed of two identical covalently linked heavy chains and two identical light chains. Both the heavy chains and light chains contain a series of repeating homologous structural units called Ig domains. The N-terminal variable regions of the heavy and light chains form the antigen binding sites, whereas the C-terminal constant regions of the heavy chains interact with other molecules in the immune system. The membrane-bound antibodies serve as receptors that mediate the antigen-triggered activation of B cells. Secreted antibodies function as mediators of specific humoral immunity by engaging various effector mechanisms that serve to eliminate the bound antigen.
A globular structural motif found in many proteins of the immune system, including immunoglobulins (Igs), T cell receptors (TCRs) and major histocompatibility complex (MHC) molecules. Ig domains are approximately 110 amino acid residues in length, include an internal disulfide bond, and contain two layers of beta-pleated sheets, each layer composed of three to five strands of antiparallel polypeptide chains. Ig domains are classified as V-like or C-like on the basis of closest homology to either Ig V or C domains.
Component of the inflammasome complex involved in innate immunity and inflammation. Inflammasomes are supramolecular micron-sized complexes that assemble in the cytosol adjacent to the nucleus in response to pathogens and other damage-associated signals. The core of inflammasomes consists of at least 2 components: a signal sensor and an effector inflammatory caspase (mostly CASP1). However, most inflammasomes contain a third element, an adaptor (often ASC/PYCARD). In response to a danger signal, the sensor homooligomerizes and interacts with the adaptor that polymerizes and forms a platform to recruit caspase precursors. This results in increased local concentration of the enzyme, leading to trans-autocleavage and activation. Active caspases process proinflammatory IL1B and IL18 cytokine precursors, which are then secreted in the extracellular milieu and induce inflammatory responses. In adaptor-independent inflammasomes, the sensor directly recruits the caspase. Additional proteins may interaction with the core complex. Inflammasomes also induce pyroptosis, an inflammatory form of programmed cell death.
Protein involved in the localized protective response to tissue damage, microbial infection, or the presence of foreign matter. It is characterized by swelling, redness, heat and pain and involves a complex series of events including vascular changes and accumulation of blood cells, such as neutrophil leucocytes and mononuclear phagocytes, at the site of injury.
Inhibition of eukaryotic host transcription initiation by virus
Viral protein involved in the disruption of the host transcriptional machinery. Viruses have evolved ways of interacting with the cellular preinitiation complex (PIC) to shutoff host transcription initiation. For example, the TATA binding protein and TFIIH are targeted by some viral proteins and thus cannot assemble properly to form a functional PIC.
suppression by virus of host transcription initiation from RNA polymerase II promoter
Inhibition of eukaryotic host translation factors by virus
Viral protein that inhibits or degrades host translation initiation factor(s). Viruses have evolved ways of interacting with the cellular translational machinery to shutoff host gene expression. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. Some viruses are known to cleave host translation initiation factors like EIF3 or EIF4G, while others achieve translation inhibition by promoting dephosphorylation of some host translation initiation factors or their binding partners.
suppression by virus of host translation initiation factor activity
Inhibition of host adaptive immune response by virus
Viral protein involved in the evasion of host adaptive immune response. Upon infection, the innate immune system provides mechanisms for the rapid sensing and elimination of viruses. Adaptive immunity has evolved to provide a broader and more finely tuned repertoire of recognition for both self- and nonself-antigens. A lot of viruses escape the adaptive immune response by different mechanisms including interference with the presentation of antigenic peptides at the surface of infected cells.
suppression by virus of host adaptive immune response
Inhibition of host apoptosis by viral BCL2-like protein
Viral protein sharing sequence similarity with host BCL2 protein. Cellular BCL2 family members are divided in two groups, some having anti-apoptotic activity (such as BCL2 itself) while others have pro-apoptotic function (such as BAX). If the level of proapoptotic members are higher than inhibitors, then the cell undergoes apoptosis. So far, all viral homologues display anti-apoptotic activity.
suppression by virus of host apoptotic process
Inhibition of host apoptosis by viral FLIP-like protein
Viral protein sharing sequence similarity with host FLIPs (FLICE-inhibitory proteins). Cellular FLIPs play an essential role in apoptosis functioning as a link between cell survival and cell death pathways . Viral FLIPs inhibit apoptosis by interfering with death receptor signaling.
Viral protein involved in the inhibition of host autophagy. Autophagy is a major intracellular pathway in the delivery of cytoplasmic material to lysosomes for degradation. It is also essential for the removal of pathogenic protein aggregates from the cell during infection. Several viruses including influenza and HIV-1 block autophagosome maturation by interacting with and inhibiting host Beclin-1, an essential protein playing a central role in autophagy.
Viral protein involved in the evasion of host cell apoptosis by inhibiting host caspases. Many viruses from diverse families have evolved mechanisms to evade or delay cell death by suppressing the activity of cytoplasmic proteases termed caspases which have a central role in apoptosis induction.
suppression by virus of host cysteine-type endopeptidase activity involved in apoptotic process
Viral protein involved in the evasion of host immune response by inhibiting chemokines. Chemokines have several roles including Th1/Th2 differentiation, T_cell costimulation, or promotion of leukocyte migration. Due to the importance of chemokines in immunity, viruses have evolved mechanisms to counter the chemokine network. They encode chemokine-like proteins, chemokine receptors, or chemokine-binding proteins to inhibit cellular chemokines.
suppression by virus of host chemokine activity
Inhibition of host complement factors by virus
Viral protein involved in the evasion of host humoral response by inhibiting the complement factors. The activation of complement involves the sequential proteolyis of proteins to generate enzymes with catalytic activities. The biological functions of the complement include opsonization, inflammation, lysis of immune complexes, or enhancement of the humoral immune response. Some herpesviruses, poxviruses and retroviruses mimic or interact with complement regulatory proteins to block complement activation and neutralization of virus particles.
suppression by virus of host complement activation
Inhibition of host DNA replication by virus
Viral protein that blocks host DNA replication without inhibiting host transcription or translation. Inhibiting host replication provides an advantage during the virus life cycle by reducing or eliminating competing host macromolecular synthesis. Bacteriophage N4 for example is known to shut off the host DNA replication while the host genome remains structurally intact. Bacteriophage lambda prevents host DNA replication initiation and Staphylococcus bacteriophages target the replicative DNA polymerase processivity clamp and the helicase.
Viral protein involved in the evasion of host innate defenses by inhibiting the IKBKE/IKK-epsilon kinase. Upon viral infection, the DDX58/RIG-I or IFIH1/MDA5 receptors recognize foreign material and transmit the signal to downstream components MAVS and IKBKE. In turn, the IKBKE kinase phosphorylates and activates IRF3 and/or IRF7. Once phosphorylated, IRF3 and IRF7 translocate into the nucleus to drive transcription of interferons. Several viruses including arenaviruses or ebola virus interact directly with and inhibit IKBKE/IKK-epsilon to prevent IRFs activation.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity
Inhibition of host innate immune response by virus
Viral protein involved in the evasion of host innate immune response. Upon viral infection, the innate immune system initially defends the host in a non-specific manner. Many viral proteins interact with and inhibit components the host innate system to replicate more efficiently.
suppression by virus of host innate immune response
Inhibition of host interferon receptors by virus
Viral protein involved in the evasion of the interferon pathway by inhibiting interferon receptors. Interferon signaling exerts antiviral effects through cell surface receptors termed interferon receptors. In response to binding of extracellular interferons, they activate the JAK/STAT pathway causing transcriptional activation of IFN-regulated genes. To avoid this antiviral response, several viruses target the interferon receptors and send them to degradation via the proteasome.
suppression by virus of host interferon receptor activity
Inhibition of host interferon signaling pathway by virus
Viral protein involved in the evasion of host innate defense by inhibiting the interferon signaling pathway leading to the production of interferon-induced genes. Interferons bind to the IFN receptors (IFNAR) on the cell surface and activate Jak/Tyk kinases. These kinases phosphorylate STAT1 and STAT2 that translocate to the nucleus and induce the expression of interferon stimulated genes (ISGs). Many viruses interact with components of this pathway to prevent expression of ISGs and inhibit the host immune response.
suppression by virus of host type I interferon-mediated signaling pathway
Viral protein involved in the evasion of host innate defense by inhibiting the interferon regulatory factor-3 (IRF3) protein. Viral infection triggers the phosphorylation and activation of IRF3. The activated IRF3 migrates to the nucleus, where it complexes with the transcription coactivator CREBBP/EP300, leading to the transcriptional activation of the IFN-alpha and IFN-beta genes. Several viral proteins directly bind to IRF3 and inhibit its transcriptional activity while others target it to the proteasome for degradation.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity
Viral protein involved in the evasion of host innate defense by inhibiting the interferon regulatory factor-7 (IRF7) protein. Viral infection triggers the phosphorylation and activation of IRF7. The activated IRF7 migrates to the nucleus leading to the transcriptional activation of the IFN-alpha and IFN-beta genes. Some viral proteins prevent IRF7 phosphorylation and nuclear activation. Ebola virus VP35 interacts with IRF7 and hijacks the cellular SUMOylation machinery for its advantage to increase IRF7 SUMOylation thereby disabling its activity.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity
Viral protein involved in the evasion of the type I and III interferon pathway by inhibiting the interferon regulatory factor-9 (IRF9) protein. Viral infection triggers the phosphorylation and activation of IRF9. The activated IRF9 migrates to the nucleus leading to the transcriptional activation of several hundred IFN-responsive genes. Some viral proteins inhibit IRF9 activation by preventing its nuclear localization upon infection or by sending it to the nucleus in an inactive state.
suppression by virus of host JAK-STAT cascade via inhibition of host IRF9 activity
Viral protein involved in the evasion of host immune defense by inhibiting the ISG15 protein, an ubiquitin-like modifier playing important roles in the innate immune response. Like ubiquitin, ISG15 is conjugated to lysines on numerous target proteins through its conserved C-terminal region. Viruses escape from the antiviral activity of ISG15 by direct interaction or by cleavage of ISG15 derivatives.
suppression by virus of host ISG15-protein conjugation
Viral protein involved in the evasion of the type I, II and III interferon pathways by inhibiting the JAK1 protein. Upon viral infection, JAK1 is activated by the interferon-alpha/beta, -gamma, and -lambda signal transduction pathways. Several viral proteins can directly interact with JAK1 to prevent its ability to phosphorylate the downstream partners STAT1 or STAT2.
suppression by virus of host JAK-STAT cascade via inhibition of JAK1 activity
Viral protein involved in the evasion of host innate defense by inhibiting the MAVS protein. During viral replication, dsRNA is produced and detected by DDX58/RIG-I or IFIH1/MDA5 that will activate MAVS to coordinate pathways leading to induction of antiviral cytokines. Several viral proteins including NS3/4A from Hepatitis C, or protease 3C from hepatitis A virus, cleave MAVS to abrogate its activity.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity
Viral protein involved in the evasion of host innate defense by inhibiting the IFIH1/MDA5 protein. Upon recognition of long viral dsRNAs, IFIH1/MDA5 initiates an antiviral signaling cascade by interacting with downstream partners. Some viral proteins including paramyxovirus V proteins interact with IFIH1/MDA5 and blocks its binding with its downstream partner MAVS.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host MDA-5 activity
Inhibition of host MHC class I molecule presentation by virus
Viral protein involved in the evasion of host adaptive immune response by inhibiting the presentation of loaded MHC class I molecules at the cell surface. Many viruses 'intercept' the loaded MHC class I molecules and retain them in the endoplasmic reticulum or target them to degradation in order to prevent presentation of the peptides at the cell surface.
suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I
Inhibition of host MHC class II molecule presentation by virus
Viral protein involved in the evasion of host adaptive immune response by inhibiting the presentation of loaded MHC class II molecules at the cell surface. MHC class II molecules are found only on a few specialized cells termed professional antigen-presenting cells (APCs). This group includes macrophages, dendritic cells and B-cells. Many viruses 'intercept' the loaded MHC class II molecules and retain them in the endoplasmic reticulum or target them to degradation in order to prevent presentation of the peptides at the cell surface.
suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II
Inhibition of host mitotic exit by virus
Viral protein involved in the inhibition of host cell cycle progression by preventing cells to exit mitosis.
suppression by virus of host exit from mitosis
Inhibition of host mRNA nuclear export by virus
Viral protein involved in the disruption of the mRNA nuclear export machinery. Viruses have evolved ways of interacting with the nuclear export machinery to inhibit cellular translation and maximize the expression of their own mRNAs. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response.
suppression by virus of host mRNA export from nucleus
Viral protein involved in the inhibition of host NF-kappa-B. This protein is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. Many viruses have developed strategies to inhibit the NF-kappa-B pathway in order to evade host immunity and inhibit production of proinflammatory cytokines.
suppression by virus of host NF-kappaB cascade
Viral protein involved in the evasion of the interferon pathway by inhibiting the interferon induced PKR/EIF2AK2 protein. During viral replication of RNA viruses, dsRNA is produced leading to the activation of the PKR/EIF2AK2 kinase. Once activated, PKR/EIF2AK2 autophosphorylates and catalyzes the phosphorylation of many substrates including the translation initiation factor EIF2S1, leading to the inhibition of the initiation of protein synthesis. Several viral proteins prevent PKR/EIF2AK2 activation by direct interaction while others target PKR/EIF2AK2 to degradation.
protein serine/threonine kinase inhibitor activity
suppression by virus of host PKR signaling
Inhibition of host poly(A)-binding protein by virus
Viral protein involved in the inhibition of host translation by inhibiting the poly(A)-binding protein PABPC1. Viruses have evolved ways of interacting with the host translational machinery to shutoff host gene expression. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. One common target is the translation initiation factor PABPC1. Some viruses proteolytically cleave PABPC1, while others displace PABPC1 from EIF4G1.
Inhibition of host pre-mRNA processing by virus
Viral protein involved in the disruption of host pre-mRNA processing. Viruses have evolved ways of interacting with the cellular RNA splicing machinery and regulate splicing of cellular pre-mRNAs as a part of the mechanism for shutting down the synthesis of host proteins. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response.
suppression by virus of host mRNA processing
Inhibition of host proteasome antigen processing by virus
Viral protein involved in the evasion of host adaptive immune response by inhibiting MHC class I peptide antigen generation by the proteasome. The processing of foreign proteins leads to the presentation of viral peptides by MHC class I molecules to cytotoxic T lymphocytes and triggers immune response. Several viral proteins have evolved mechanisms to avoid synthesis of antigenic peptide by the proteasome. Epstein-Barr virus EBNA-1 for example contains an internal repeat exclusively composed of glycines and alanines that inhibits its proteasomal degradation.
suppression by virus of host antigen processing and presentation
Viral protein involved in the evasion of host innate defense by inhibiting the DDX58/RIG-I protein. Upon recognition of viral RNA, the cytosolic receptor DDX58/RIG-I initiates an antiviral signaling cascade by interacting with downstream partners. Several viral proteins inhibit DDX58/RIG-I via direct interaction while others via proteolytic cleavage.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host RIG-I activity
Viral protein involved in the evasion of host innate defense by inhibiting the DDX58/RIG-I-like receptor (RLR) pathway leading to the triggering of interferon-mediated response. This pathway starts with the recognition of viral RNA by host proteins including DDX58/RIG-I or IFIH1. Then, the signal is transmitted through MAVS and TRAFs leading to the activation and nuclear localization of transcription factors IRF3 and IRF7 to induce IFNalpha/beta transcription and protein production. Many viruses interact with components of this pathway to inhibit production of interferons and establishment of the antiviral state.
negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
Inhibition of host RNA polymerase II by virus
Viral protein involved in the disruption of the host RNA polymerase II. Many viruses induce alterations in the cellular gene expression. Among these, shutoff of host transcription by targeting RNA polymerase II is commonly used. Indeed, many viruses are able to modify RNAP II CTD including Herpes virus, HIV, Epstein-Barr virus or Bunyamwera virus.
suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity
Viral protein involved in the evasion of the type I, II and III interferon pathways by inhibiting the STAT1 protein. Upon viral infection, STAT1 is activated by IFN-gamma, IFN-alpha/beta, or IFN-lambda that bind to specific cell surface receptors. While IFN-gamma induces STAT1 homodimerization, IFN-alpha/beta and IFN-lambda stimulate heterodimerization of STAT1 and STAT2, both leading to STAT1 nuclear localization and subsequent induction of IFN-stimulated genes. Many viruses interfere with STAT1 activation, often by preventing STAT1 phosphorylation and nuclear localization.
suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity
Viral protein involved in the evasion of type I and III interferon pathways by inhibiting STAT2 protein. Upon viral infection, STAT2 is activated by IFN-alpha/beta or IFN-lambda that bind to specific cell surface receptors. In turn, IFN-alpha/beta (or IFN-lambda) induces heterodimerization of STAT1 and STAT2 by phosphorylation, leading to STAT2 nuclear localization and subsequent induction of IFN-stimulated genes. Many viruses interfere with STAT2 activation, often by preventing STAT2 phosphorylation and nuclear localization.
suppression by virus of host JAK-STAT cascade via inhibition of STAT2 activity
Viral protein involved in the evasion of host adaptive immune response by inhibiting the TAP complex. Transporter associated with antigen (TAP), composed of two subunits TAP1 and TAP2, is required for the translocation of peptides into the ER, where they are loaded onto MHC class I. Thereafter, the viral peptides are presented to cytotoxic T lymphocytes at the cell surface and trigger immune response. The loading of peptide on MHC by TAP is targeted by several viruses including herpesviruses and retroviruses.
Viral protein involved in the evasion of host adaptive immune response by inhibiting the tapasin/TAPBP protein. tapasin/TAPBP is a type I transmembrane protein essential for the optimal expression of stable MHC class I molecules on host cell surface. Its helps the MHC class I molecules to remain in a peptide receptive state, avoiding irreversible denaturation. Several retroviruses and DNA viruses encode proteins interacting with tapasin/TAPBP and inhibiting its activity.
Viral protein involved in the evasion of host innate defenses by inhibiting the TBK1 kinase. Upon viral infection, Toll-like receptors (TLRs) or DNA recognition receptors recognize foreign material and transmit the signal to TBK1 that in turn phosphorylates and activates IRF3 and IRF7. Once phosphorylated, IRF3 and/or IRF7 translocate into the nucleus to drive transcription of interferons. Several viruses including herpes simplex virus 1 or vaccinia virus interact directly with and inhibit TBK1 to prevent IRFs activation.
suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity
Viral protein involved in the evasion of host immune defense by inhibiting the BST2/tetherin protein. BST2/tetherin is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses, including human immunodeficiency virus type 1 (HIV-1), HIV-2, as well as other retroviruses. Several viruses manage to circumvent the antiviral activity of BST2/tetherin either by sending BST2/tetherin to degradation (HIV-1) or by lowering the presence of BST2 on cell surfaces (HIV-2).
suppression by virus of host tetherin activity
Viral protein involved in the evasion of host innate defenses by inhibiting the Toll-like recognition receptor (TLR) pathway. This pathway usually starts with the recognition of viruses by host TLRs including TLR3 or TLR4. Then, the signal is transmitted through MYD88 (or TRIF) and then to TBK1 leading to the activation and nuclear localization of transcription factors IRF3 and/or IRF7 to induce IFNalpha/beta transcription and production of proinflammatory cytokines through activation of the NF-kappaB signaling pathway. Many viruses interact with components of this pathway to inhibit production of interferons and establishment of the antiviral state.
suppression by virus of host toll-like receptor signaling pathway
Viral protein involved in the evasion of host innate defense by inhibiting TRAF proteins. After viral infection, the cellular signaling pathway leading to production of interferons is activated and several TRAF family members including TRAF2, TRAF3, and TRAF5 participate in this cascade. Many viruses encode protein able to interact with TRAF members to inhibit their antiviral activity.
suppression by virus of host TRAF activity
Viral protein involved in the evasion of the type I and III interferon pathways by inhibiting the host TYK2 protein. Upon viral infection, the TYK2 protein is activated by IFNalpha/beta or IFN-lambda stimulation leading to a series of phosphorylation events that induce transcription of several hundred IFN-responsive genes. Several viruses have evolved mechanisms to inhibit TYK2 activity thereby preventing the subsequent activation of downstream partners STAT1 and STAT2.
suppression by virus of host JAK-STAT cascade via inhibition of host TYK2 activity
Protein which plays an important role in initiating the translation of a mRNA molecule into a polypeptide. Initiation factors help to form the complex between the mRNA and a ribosome.
Protein involved in innate immunity, an inborn defense mechanism used by organisms to defend themselves against invasion by pathogens (bacteria, fungi, viruses, etc.). Initially discovered in insects which are devoid of an adaptive immune system and rely only on innate immune reactions for their defense, this immediate response accomplishes many activities including recognition and effector functions. Recognition is mediated by broad specificity, pattern recognition, receptors which recognize many related molecular structures (e.g. polysaccharides, polynucleotides) present in microorganisms but not found in the host. The innate responses include the release of antimicrobial peptides, production of cytokines, acute-phase proteins, complement. Although many different innate immune mechanisms are deployed for host defence, a unifying theme of innate immunity is the use of germline-encoded pattern recognition receptors for pathogens or damaged self components, such as the Toll-like receptors, nucleotide-binding domain leucine-rich repeat (LRR)-containing receptors, retinoic acid-inducible gene I-like RNA helicases and C-type lectin receptors.
Viral protein that is a component of the inner layer of a double or triple concentric icosahedral capsid. Inner capsids are part of reoviridae and cystoviridae virions.
Protein involved in the synthesis of inositol, a cyclic hexahydric alcohol. It occurs in various forms, of which myo-inositol, a constituent of phospholipids, is the most important.
Protein that confers, on insect vectors and pests, the ability to withstand insecticide action. Insecticides are chemicals that selectively kill insects. Insecticide resistance usually occurs by two broad mechanisms. The first is where the insect may produce large amounts of enzymes, such as esterases which either break down the insecticide molecule or bind to it so tightly that it cannot function (a process known as sequestration). The second mechanism involves mutation of the insecticide target site, such as the acetylcholinesterase enzyme in the nervous system. This effectively blocks the action of the insecticide.
Protein of the integrin family of cell surface heterodimeric receptors that mediates dynamic cell-to-cell as well as cell-to-matrix adhesion. Integrins function as mechanochemical sensors and transducers able to change rapidly and reversibly their adhesive functions by modulating their ligand-binding affinity. Each subunit has a large N-terminal extracellular domain followed by a transmembrane domain and a short C-terminal cytoplasmic region. Some subclasses of integrins share a common beta chain while having different alpha chains.
Protein which, if defective, is involved in intellectual disability, a disorder appearing during development and characterized by subnormal intellectual functioning and impaired adaptive behavior.
Viral protein which prevents the activation of the antiviral state induced by interferon (IFN) in the host cell, thereby allowing the virus to replicate optimally. The antiviral state is the result of a signaling pathway induced by IFN-alpha or IFN-beta following viral infection. It leads to the transcription of various cellular antiviral genes coding for host defense proteins.
Viral protein that is a component of the intermediate layer of a triple concentric icosahedral capsid. Intermediate capsids are part of reoviridae virions.
Intermediate filaments (IF) are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide and intermediate in size between microtubules and microfilaments. This family of protein includes cytokeratins, vimentin, desmin, glial fibrillary acidic protein, neurofilament proteins and nestin. All IF proteins are structurally similar in that they consist of: a central rod domain which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; an N-terminal non-helical domain (head) of variable length; and an C-terminal domain (tail) which is also non-helical and shows extreme length variation between different IF proteins.
Protein which, if defective, causes intrahepatic cholestasis, a condition characterized by stoppage or suppression of the bile flow from the liver to the duodenum without extrahepatic bile duct obstruction.
Endonucleases involved in intron homing, a genetic event leading to the transfer of an intron DNA sequence. This type of intron mobility depends on site-specific restriction endonucleases encoded by the mobile introns.
Protein which is posttranslationally modified by the replacement of at least one hydrogen by iodine.
Protein which is part of a transmembrane protein complex that forms a hydrophilic channel across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients. The channels are usually gated and only open in response to a specific stimulus, such as a change in membrane potential (voltage-gated) or the binding of a ligand (ligand-gated channel).
Protein which interferes with the function of ion channels, which are hydrophilic channels across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients.
Protein involved in the transport of ions. Such proteins are usually transmembrane and mediate a movement of ions across cell membranes. Transport may be passive (facilitated diffusion; down the electrochemical gradient), or active (against the electrochemical gradient). Active transport requires energy which may come from light, oxidation reactions, ATP hydrolysis, or cotransport of other ions or molecules.
Protein that inhibits ionotropic glutamate receptor (iGluR). iGluRs are glutamate-gated ion channels that mediate excitatory neurotransmission in the central nervous system. Based on both molecular and pharmacological criteria, iGluRs have been divided into two major classes, the non-NMDA class, which includes both AMPA and kainate subtypes of receptors, and the NMDA class.
Protein which binds at least one iron atom, or protein whose function is iron-dependent. Iron is a metal, chemical symbol Fe.
Protein involved in the storage of iron.
Protein involved in the transport of iron.
Protein which binds at least one iron-sulfur cluster, e.g. 2Fe-2S, 3Fe-4S, 4Fe-4S.
Protein involved in the synthesis of the hydrophobic amino acid isoleucine.
Enzyme that catalyzes the 1,1-, 1,2- or 1,3-hydrogen shift. The 1,1-hydrogen shift is an inversion at an asymmetric carbon center (racemases, epimerases). The 1,2-hydrogen shift involved a hydrogen transfer between two adjacent carbon atoms, one undergoing oxidation, the other reduction (aldose-ketose isomerases). The 1,3-hydrogen shifts are allylic or azaallylic (when nitrogen is one of the three atoms) isomerizations.
Protein which is posttranslationally modified by the formation of an amide bond between an amino-group and a carboxyl-group at least one of which is not an alpha group. An isopeptide bond involves the side chain of one or two amino acid residues. Because there are few enzymes that hydrolyze isopeptide bonds, the formation of interchain isopeptide bonds can produce stably linked protein dimers, multimers or complexes, such as blood clots.
Protein involved in the synthesis of isoprene, an important organic unit of 5 carbons in plants. It is used to build up isoprenoids, including carotenoids, terpenes and natural rubber.
Protein involved in the jasmonic acid (jasmonate, JA) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth, development and cellular signaling (e.g. growth inhibition, senescence, tuber formation, response to wounding, plant defense, and leaf abscission). This phytohormone and its derivatives such as methyl jasmonate (MeJA) can be synthesized from the fatty acid linolenic acid in the oxylipin octadecanoid pathway.
Protein which, if defective, causes Joubert syndrome, an autosomal recessive multisystem disorder characterized by cerebellar ataxia, developmental delay, hypotonia, neonatal breathing abnormalities and oculomotor apraxia. Neuroradiologically, it is characterized by cerebellar vermis hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of the 'molar tooth sign' on transaxial slices. A wide clinical variability with a marked variation in severity and inconsistent presence of the following features is observed: episodic apnea-hyperpnea, abnormal eye movements, occipital meningoencephalocele, polydactyly, nephronophthisis or cystic dysplasia of the kidney, chorioretinal coloboma and retinal dysplasia. The variable association of ocular and renal abnormalities with cerebellar features typical of Joubert syndrome defines the cerebello-oculo-renal syndromes (CORSs).
Dysplasia olfactogenitalis of De Morsier
Hypogonadotropic hypogonadism and anosmia
Protein which, if defective, causes Kallmann syndrome, a disorder characterized by the association of hypogonadotropic hypogonadism with anosmia or hyposmia. Kallmann syndrome is caused by impaired embryonic development of the olfactory system and the GnRH-synthesizing neurons. The main clinical features consist of the association of micropenis and cryptorchidism in young boys, the absence of spontaneous puberty, and a partial or total loss of the sense of smell (anosmia). In some patients other developmental anomalies can be present such as renal agenesis, cleft lip/palate, selective tooth agenesis and bimanual synkinesis.
Dextrocardia-bronchiectasis-sinusitis syndrome
Protein which, if defective, causes Kartagener syndrome, a rare and genetically heterogeneous disorder characterized by the combination of primary ciliary dyskinesia and situs inversus viscerum.
Protein involved in the fusion of the nuclei of two gametes after cytoplasmic fusion.
Protein containing at least one Kelch repeat.
Fibrous proteins rich in cysteine and the chief constituent of horn, nails, hair, epidermis and feathers. Two major conformational groups have been characterized, alpha-keratin, whose peptide backbone forms an alpha-helix, and beta-keratin, whose backbone forms a zigzag or pleated sheet structure.
Protein involved in keratinization, the process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns.
Enzyme that catalyzes the transfer of phosphate (phosphoryl or pyrophosphoryl transfer) usually from ATP to a second substrate.
The kinetochore is a complex assembled at centromeric region of DNA, which provides the major attachment point for the spindle microtubules. In monocentric chromosomes, the kinetochores of point centromeres bind a single microtubule and the larger kinetochores of regional centromeres interact with a number of microtubules. In holocentric chromosomes, the kinetochores bind the diffuse centromere along the length of the chromosomes.
Protein associated with the kinetoplast DNA (kDNA), the mitochondrial DNA of trypanosomatid protozoa. kDNA is a massive network, composed of thousands of topologically interlocked DNA circles. Each cell contains one network condensed into a disk-shaped structure within the matrix of its single mitochondrion. The kDNA circles are of two types, maxicircles present in a few dozen copies and minicircles present in several thousand copies.
Small disulfide-rich protein characterized by a special 'disulfide through disulfide knot'. This knot is obtained when one disulfide bridge crosses the macrocycle formed by two other disulfides and the interconnecting backbone (disulfide III-VI goes through disulfides I-IV and II-V). The knottin structure is found in some plant protease inhibitors, cyclotides, toxins from cone snails, spiders, insects, horseshoe crabs and scorpions, gurmarin-like peptides, agouti-related proteins, and some antimicrobial peptides.
Protein containing at least one kringle domain, a triple-looped, disulfide cross-linked domain of approximately 80 amino acids in length and involved in protein-protein interactions.
Protein which, if defective, causes lacrimo-auriculo-dento-digital syndrome. Lacrimo-auriculo-dento-digital syndrome, a form of ectodermal dysplasia, is an autosomal dominant multiple congenital anomaly. It is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed.
Protein involved in lactation, the secretion of milk by mammary glands.
Protein involved in the synthesis of lactose, a disaccharide of glucose and galactose present in milk.
Protein involved in the biochemical reactions with lactose, a disaccharide of glucose and galactose, found in milk.
Protein containing at least one laminin EGF-like domain. Laminins are the major noncollagenous components of basement membranes. Their subunits contain consecutive repeats of about 60 amino acids, which include 8 conserved cysteines that form disulfide bonds (C1-C3, C2-C4, C5-C6, C7-C8). The tertiary structure of this domain is remotely similar, in its N-terminal, to that of the EGF-like module.
Lanthionine-containing peptide antibiotics are peptides produced by Gram-positive bacteria which cause cell death of other Gram-positive bacteria.
Bacteriophage or viral protein expressed in a later phase of the infectious cycle.
Viral protein part of a genetic system that takes part in the decision of the outcome of the infection: latency or replication. Expression of genetic switch proteins control the expression of viral genes that act as effectors in either the establishment of latency (lysogeny) or in promoting productive replication (lytic cycle). Interactions between proteins involved in switch regulatory processes and host proteins often influence the decision.
Protein constituent of the low-density lipoproteins or protein which binds LDLs. LDLs are plasma lipoproteins rich in cholesterol esters, synthesized from the very low-density lipoprotein (VLDL), and which transport cholesterol to peripheral tissue and regulate de novo cholesterol synthesis.
Protein which binds at least one lead atom, or protein whose function is lead-dependent. Lead is a metal, chemical symbol Pb.
Short peptide sequences translated from bacterial leader RNA sequences which are involved in transcriptional or translation attenuation, mechanisms that modulate mRNA transcription or translation.
Protein which, if defective, causes Leber congenital amaurosis, a clinically and genetically heterogeneous type of blindness transmitted as an autosomal recessive trait and occurring at or shortly after birth. It is associated with an atypical form of diffuse pigmentation and commonly with optic atrophy and attenuation of the retinal vessels.
Protein which, if defective, causes Leber hereditary optic neuropathy, a mitochondrial disease leading to bilateral, painless loss of central vision due to selective degeneration of the retinal ganglion cells and their axons. The disease arises during young adult life and displays sex-dependent incomplete penetrance and male predominance.
Protein which specifically binds carbohydrates. Lectins are obtained particularly from seeds of leguminous plants but also from other plant and animal sources. They contain binding sites for specific mono-and oligosaccharides. They agglutinate cells by binding to specific sugar residues in membrane glycoproteins.
Protein which, if defective, causes Leigh syndrome, a neurodegenerative disorder characterized by the subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, dysphagia, and lactic acidosis. Pathological features include spongy degeneration of the neuropile of the basal ganglia, thalamus, brain stem, and spinal cord. The syndrome is caused by a variety of defects of enzymes involved in energy metabolism, including cytochrome c oxidase (COX), the mitochondrial encoded ATP6 subunit of ATP synthase, and the X-linked E1-alpha subunit of pyruvate dehydrogenase.
Protein involved in the synthesis of the hydrophobic amino acid leucine.
Protein containing at least one leucine-rich repeat (LRR).
Protein which, if defective, causes leukodystrophy, any of a group of diseases that affect the formation or maintenance of myelin in the central nervous system.
Protein involved in the synthesis of leukotrienes, eicosanoid hormones first isolated from leukocytes. They are thought to mediate the allergic response that causes lung constriction and muscle contraction in asthma.
Sarcoma family syndrome of Li and Fraumeni
Protein which, if defective, causes Li-Fraumeni syndrome (LFS), an autosomal dominant familial cancer predisposition syndrome associated with soft-tissue sarcoma, breast cancer, leukemia, osteosarcoma, melanoma, and cancer of the colon, pancreas, adrenal cortex and brain. Individuals with LFS are at increased risk for developing multiple primary cancers.
Keywords assigned to proteins because they bind, are associated with, or whose activity is dependent of some molecule.
Protein which forms or is a component of a ligand-gated channel. Ligand-gated channels are transmembrane ion channels whose permeability is increased by the binding of a specific ligand, such as neurotransmitters, ionositol triphosphates, and cyclic nucleotides.
Enzyme that catalyzes the joining of two molecules coupled with the breakdown of a pyrophosphate bond in ATP or a similar triphosphate. Sometimes the terms "synthase", "synthetase" or "carboxylase" are also used for this class of enzymes.
Proteins which form part of the antenna complex, a light-harvesting system found in photosynthetic bacteria which absorb light radiation and transfer the excitation energy to the reaction centres.
Protein involved in the synthesis of lignin, a polymer of phenylpropanoid subunits found in the walls of plant cells such as xylem and sclerenchyma fibres. Lignin imparts strength to the wall and protects against degradation by microorganisms.
Protein involved in the breakdown of lignin, a polymer of phenylpropanoid subunits found in the walls of plant cells such as xylem and sclerenchyma fibres. It imparts strength to the wall and protects against degradation by microorganisms.
Protein which contains at least one LIM domain, a conserved cysteine-rich domain of approximately 60 amino acids with seven conserved cysteines and a histidine. The LIM domain binds two zinc ions and seems to be involved in protein-protein interactions.
Protein which, if defective, causes limb-girdle muscular dystrophy, a degenerative myopathy without nervous system involvement. The disease is characterized by slowly progressive wasting and weakness of the proximal muscles of arms and legs around the pelvic or shoulder girdles, elevated creatine kinase levels and dystrophic features on muscle biopsy. Onset of symptoms is in late childhood, adolescence or even adult life. Limb-girdle muscular dystrophy is a genetically heterogeneous disorder. Inheritance can be autosomal dominant or autosomal recessive.
Protein involved in the synthesis of lipid A (endotoxin), the hydrophobic anchor of lipopolysaccharide (LPS). Lipid A is a glucosamine-based phospholipid that makes up the outer monolayer of the outer membranes of most Gram-negative bacteria.
Protein involved in the synthesis of lipids, a diverse class of compounds which are insoluble in water but soluble in organic solvents. They include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
Protein involved in the breakdown of lipids, a diverse class of compounds, insoluble in water but soluble in organic solvents, and which include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
Protein characteristic of a lipid droplet, a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.
Protein involved in the biochemical reactions of lipids. Lipids are a diverse class of compounds which are insoluble in water but soluble in organic solvents. They include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
Protein involved in the transport of lipids, a diverse class of compounds which are insoluble in water but soluble in organic solvents. They include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
Protein involved in the synthesis of lipopolysaccharides (LPS), the main constituents of the outer cell wall of Gram-negative bacteria. LPS are composed of lipid molecules joined to polysaccharides and are highly immunogenic.
Protein which is posttranslationally modified by the attachment of at least one lipid or fatty acid, e.g. farnesyl, palmitate and myristate.
Protein which contains at least one lipoyl-binding domain. Lipoic acid is an essential cofactor for E2 acyltransferases and some other proteins.
Protein which, if defective, causes lissencephaly, a brain malformation characterized by the absence (agyria) or reduction (pachygyria) of brain surface convolutions (gyri), in association with abnormal organisation of the cortical layers. It results from neuronal migration defects during embryogenesis. Two large groups can be distinguished: classical lissencephaly (and its variants) and cobblestone lissencephaly. Lissencephaly means "smooth brain".
Protein whose function is lithium-dependent. Lithium is an alkali metal, chemical symbol Li.
Protein which, if defective, causes the long QT syndrome, a heart disease which manifests itself by a prolonged QT interval on the ECG and, clinically, by a propensity for tachyarrhythmias, causing syncopes and sudden cardiac death. LQTS may be drug-induced, but mutations in genes coding for cardiac ion-channels are the cause of the hereditary forms: Romano-Ward syndrome (RWS), and Jervell and Lange-Nielsen Syndrome (JLNS).
Protein which contains at least one lysine tyrosylquinone (LTQ) cross-link modification. LTQ is formed by oxidation of the phenol ring of a tyrosine to form tyrosylquinone (topaquinone) followed by covalent cross-linking with a lysine residue.
Protein involved in luminescence, the property of giving off light without emitting a corresponding degree of heat.
Enzyme that catalyzes the cleavage of C-C, C-O, C-S, C-N or other bonds by other means than by hydrolysis or oxidation, with two substrates in one reaction direction, and one in the other. In the latter direction, a molecule (of carbon dioxide, water, etc) is eliminated, thus creating a new double bond or a new ring.
Protein involved in the synthesis of the essential basic amino acid lysine.
Protein found in the lysosome, a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for the intracellular degradation of macromolecules.
Protein which binds at least one magnesium atom, or protein whose function is magnesium-dependent. Magnesium is a metallic element, chemical symbol Mg.
Protein located in or on the magnetosome, a membrane-bound bacterial organelle that envelops crystals of magnetic iron minerals in magnetotactic bacteria. Magnetosomes form linear chains that align along the cellular motility axis at midcell and function in bacterial navigation along the Earth's magnetic field. They are formed by invagination of the cell inner membrane; in some species they remain connected to the inner membrane, in others they pinch off to form independent intracellular vesicles.
Protein involved in malaria, a human disease caused by Plasmodium, a parasitic protozoan that grows by sexual reproduction in the Anopheles mosquito.
Protein involved in the biochemical reactions with maltose, a disaccharide of glucose. Maltose is produced by the hydrolysis of starch.
Enzyme involved in the mandelate pathway. These enzymes enable various microorganisms to grow using D(-)-, L(+)- or DL-mandelate (2-hydroxy-2-phenylacetate) as the sole source of carbon and energy.
Protein which binds at least one manganese atom, or protein whose function is manganese-dependent. Manganese is a metallic element, chemical symbol Mn.
Protein which binds mannose, a 6-carbon aldose sugar, that is found in many glycoproteins and polysaccharides.
Protein which, if defective, causes maple syrup urine disease, an autosomal recessive disorder characterized by mental and physical retardation, feeding problems and a maple syrup odour to the urine.
Protein involved in mast cell degranulation. Mast cell is a large, ovoid cell of hematopoietic lineage, with a centrally located nucleus and numerous large, intensely basophilic granules. The binding of an antigen to its specific immunoglobulin-E antibody on the mast cell surface triggers the release of the MC granules. Mast cells are involved in hypersensitivity reactions.
Protein which, if defective, causes Meckel syndrome, an autosomal recessive disorder characterized by a combination of renal cysts and variably associated features, including developmental anomalies of the central nervous system (usually occipital encephalocele), hepatic ductal dysplasia and cysts, and polydactyly.
Protein involved in meiotic processes or in regulation of meiosis. Meiosis is the nuclear division which results in the daughter nuclei each containing half the number of chromosomes of the parent. It comprises two distinct nuclear divisions, the first and second meiotic divisions (which may be separated by cell division), the actual reduction in chromosome number takes place during the first division.
Protein involved in the synthesis of melanin. Melanins are brown or black pigments found in skin, hair, feathers, etc. They are irregular polymeric structures produced from tyrosine. Melanins can be divided into 3 groups: allomelanins in the plant kingdom, and eumelanins and phaeomelanins in the animal kingdom.
Protein which, if defective, causes mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome, a genetically heterogeneous disorder, characterized by episodic vomiting, seizures, and recurrent cerebral insults resembling strokes and causing hemiparesis, hemianopsia, or cortical blindness.
Protein involved in the synthesis of melatonin (N-acetyl 5-methoxytryptamine), a neurohormone synthesized by lower plants and in the pineal gland in animals. In humans, it is involved in the regulation of sleep, mood, puberty, ovarian cycles and in the establishment of circadian rhythms. In lower vertebrates, it causes aggregation of pigment in melanophores, and thus lightens skin.
Protein which is membrane-bound or membrane-associated. A membrane is the layer which forms the boundary of cells and intracellular organelles. It is composed of two oriented lipid layers in which proteins are embedded and acts as a selective permeability barrier.
Component of the membrane attack complex which groups the complement plasma glycoproteins C5b, C6, C7, C8 and polymeric C9 on biological membranes. The complex forms transmembrane channels which displace lipid molecules and other constituents, thus disrupting the phospholipid bilayer of target cells leading to cell lysis by osmotic leakage. The formation of the membrane attack complex is the terminal step in the complement cascade.
Protein involved in the synthesis of menaquinone, a derivative of 2-methyl-1,4-naphthoquinone in which the 3-position is substituted with a variable-length polyisoprene chain. In mammals, menaquinone is an important component of the blood coagulation system. Mammals need to obtain this vitamin by their diet or from the bacterial flora of the gut.
Protein that confers bacteria or other microorganisms the ability to withstand mercury salts.
Protein which binds mercury and/or is involved in the cleavage of carbon-mercury bonds. Mercury is the only liquid metallic element, chemical symbol is Hg.
Protein expressed in the merozoite stage of sporozoite parasites, an invasive stage in the life cycle produced by schizogony or asexual reproduction in which the nucleus of a cell undergoes division several times. This results in a multinucleate schizont which subsequently gives rise to a number of uninucleate cells called merozoites.
Protein which, if defective, causes metachromatic leukodystrophy, a disease characterized by intralysosomal or myelin membrane storage of cerebroside-3-sulfate. Whereas storage occurs in many cells, the disease almost exclusively affects oligodendrocytes. Patients suffer from a progressive demyelination, which causes a variety of neurological symptoms, including gait disturbances, ataxias, optical atrophy, dementia, seizures and spastic tetraparesis.
Protein which binds at least a cluster composed of metal coordinated via cysteinyl thiolate bridges to cysteine ligands.
Protein that inhibits metalloenzymes, enzymes which contains metal ions.
Proteolytic enzyme which use a metal for its catalytic mechanism. Most metalloproteases are zinc-dependent, some use cobalt.
Protein that inhibits metalloproteases, which are peptide hydrolases that use a metal in the catalytic mechanism.
Protein involved in methanogenesis, the energy yielding formation of methane by methanogenic bacteria.
Protein involved in the utilization of methanol.
Protein involved in the synthesis of the hydrophobic amino acid methionine, an essential amino acid in human diets which contains a thioether linkage.
Protein that confers the ability to withstand methotrexate, an inhibitor of dehydrofolate reductase (DHFR). Methotrexate resistance occurs usually as a result of mutation or amplification of the DHFR gene.
Protein which is posttranslationally modified by the attachment of at least one methyl group.
Enzyme that transfers methyl groups from one compound to another.
A heterodimeric membrane protein composed of two non-covalently linked polypeptide chains, a major histocompatibility complex (MHC)-encoded alpha chain and a non-MHC-encoded subunit B2M/beta2-microglobulin. Each MHC molecule consists of an extracellular peptide-binding cleft, followed by an immunoglobulin (Ig)-like domain and transmembrane and cytoplasmic domains. The amino-terminal alpha-1 and alpha-2 segments of the alpha chain form the peptide-binding cleft. Expressed on all nucleated cells, displays peptides derived from cytosolic proteins for recognition by CD8-positive T cells. By scanning MHC I molecules, CD8-positive T cells can detect infected or tumor cells and eliminate them.
antigen processing and presentation of peptide antigen via MHC class I
A heterodimeric membrane protein composed of two non-covalently linked alpha and beta polypeptide chains, both major histocompatibility complex (MHC)-encoded. Each MHC molecule consists of an extracellular peptide-binding cleft followed by an immunoglobulin (Ig)-like domain and transmembrane and cytoplasmic domains. The amino-terminal alpha-1 and beta-1 segments interact to form the peptide-binding cleft. Expressed on professional antigen presenting cells, displays peptides derived from endocytosed proteins for recognition by CD4-positive helper T cells. By scanning MHC II molecules, CD4-positive T cells activate effector mechanisms that eliminate extracellular microbes.
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
Protein which, if defective, causes microphthalmia, a developmental anomaly in which the eyeballs are abnormally small. Disease severity ranges from moderate reduction of the size of a single eye to complete bilateral absence of ocular tissues. Microphthalmia can occur in isolation or as part of a syndrome.
Protein found in microsomes, a heterogenous set of vesicles 20-200 nm in diameter and formed from the endoplasmic reticulum when cells are disrupted. The vesicles are isolated by differential centrifugation and are composed of three structural features: rough vesicles, smooth vesicles and ribosomes. Numerous enzyme activities are associated with the microsomal fraction.
intracellular membrane-bounded organelle
Viral protein that allows the active transport of complete particles and viral components along microtubules toward the intracellular replication sites during virus entry. This transport, which usually involves motor proteins like dynein or polymerization/depolymerization reactions as a driving force, is mostly used by viruses that replicate their genome near or in the nucleus. Neurotropic viruses for example, often enter neurons at the terminal axon and their viral genome must be moved retrogradely to cell bodies. Viruses such as adenovirus, Adeno-associated virus, rabies virus, canine parvovirus, vaccinia, foamy virus, human papillomavirus 16 and herpes virus utilize this type of intracellular transport.
microtubule-dependent intracellular transport of viral material towards nucleus
Viral protein that allows the active transport of viral components and assembled, complete particles along microtubules toward the cell periphery during virus egress. This transport, which usually involves interaction with motor proteins like kinesin or polymerization/depolymerization reactions as a driving force, is mostly used by viruses that replicate their genome near or in the nucleus and allows newly assembled viral progeny to reach the plasma membrane. Herpes simplex virus for example is transported anterogradely along the axon.
microtubule-dependent intracellular transport of viral material towards cell periphery
Protein associated with or component of the microtubule. The microtubule is formed by the arrangement of 13 parallel protofilaments arising from end-to-end aggregation of the tubulin alpha/beta-dimers. Microtubules are associated with various other proteins (MAPs, dynein, kinesin) and are involved in structures responsible for cellular movement such as flagella or cilia. Microtubules of the ciliary axoneme are more permanent than cytoplasmic and spindle microtubules. Microtubule formation is inhibited by agents such as colchicine, vinblastine or vincristine.
Protein found in milk, a fluid secreted by female mammals to provide food for their offspring. It consists of water, proteins, soluble carbohydrates, electrolytes, lipids and vitamins.
Protein that influences the equilibrium of minerals present in bone, e.g., fetuin.
Protein encoded by or localized in the mitochondrion, a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.
Protein found in or associated with the inner membrane of a mitochondrion, the membrane which separates the mitochondrial matrix from the intermembrane space.
Protein found associated with the mitochondrial nucleoid, the mitochondrial pseudocompartment formed by the chromatin-dense area. This region, which is functionally equivalent to the eukaryotic nucleus, is not surrounded by a membrane.
Protein found in or associated with the outer membrane of a mitochondrion, the mitochondrial membrane facing the cytoplasm.
Protein which can induce mitosis of certain eukaryotic cells, i.e. it stimulates cellular proliferation.
Protein involved in mitosis, the nuclear division in eukaryotic cells involving the exact duplication and separation of the chromosome threads so that each daughter nucleus carries a chromosome complement identical to that of the parent nucleus. Mitosis is divided into four substages: prophase, metaphase, anaphase and telophase.
Protein localized in the mitosome, an organelle found in "amitochondrial" unicellular organisms which do not have the capability of gaining energy from oxidative phosphorylation. Mitosomes are almost certainly derived from mitochondria, they have a double membrane and most proteins are delivered to them by a targeting sequence. Unlike mitochondria, mitosomes do not contain any DNA. The mitosome functions in iron-sulphur cluster assembly.
Protein involved in the conjugative transfer of plasmid DNA. These proteins provide the function of nicking the DNA at a certain point, guiding the 5' end of the nicked strand into the recipient cell, recircularization, and perhaps the priming of complementary strand synthesis in the recipient.
Modulation of host cell apoptosis by virus
Viral protein involved in the modulation of host cell apoptosis by acting different steps of the process. Several viruses encode proteins that inhibit apoptosis while other viruses use apoptosis to their advantage to suppress immune response or to disseminate.
modulation by virus of host apoptotic process
Modulation of host cell cycle by viral cyclin-like protein
Viral protein sharing sequence homology with cellular cyclins. Most viral cyclin homologues are closely related in sequence to the cellular D-type cyclins, which are implicated in regulating the transit of cells from G1 into S and are thought to operate via the inactivation of the retinoblastoma tumour suppressor protein.
Viral protein involved in the modulation of host cell cycle. The cell cycle can be divided into four stages: G1, S, G2 and mitosis, while cells resting are termed quiescent cells (G0). Viruses have evolved strategies to modulate cell cycle progression including stimulation of S phase entry from G1 or G0 or cell cycle arrest at G2/M for example. This regulation allows viruses to maximize their own replication.
Viral protein involved in the regulation of host chromatin structure. Chromatin has a major role in life cycle of many viruses, and a lot of them have evolved mechanisms to modulate chromatin-related processes. For example, histone acetyltransferases, histone deacetylases or histones are common targets of viruses.
modulation by virus of host chromatin organization
Modulation of host dendritic cell activity by virus
Viral protein involved in the modulation of host dendritic cell activity. Dendritic cells operate at the interface between the innate and adaptive immune response by their ability to sample their environment for pathogenic products, to process them, and to present viral antigens to T-cells. This results in T cell proliferation and the induction of virus-specific adaptive immune responses. Therefore impairing dendritic cell function by viruses is an effective strategy to disrupt the host immune response.
evasion by virus of host dendritic cell activity
Modulation of host E3 ubiquitin ligases by virus
Viral protein involved in the modulation of cellular E3 ubiquitin ligases. In general, viral proteins redirect cellular E3 ubiquitin ligases to select specific host proteins for proteasomal degradation. The aim of this subversion is the creation of a favorable environment for virus replication and dissemination.
modulation by virus of host ubiquitin-protein ligase activity
Modulation of host immunity by viral IgG Fc receptor-like protein
Viral protein acting as an IgG Fc receptors, able to bind IgG and inhibit host Fc-dependent immune activation. Fc receptors are proteins found at the surface of certain cells of the immune system including macrophages, monocytes, natural killer cells or B-cells. They allow these cells to bind to antibodies that are attached to the surface of infected cells or pathogens, helping these cells to identify and eliminate pathogens.
modulation by virus of host immune response
Modulation of host NK-cell activity by virus
Viral protein involved in the modulation of host NK-cell activity. Natural killer (NK) cells are critical in defense against viral infections, since they provide host protection by releasing cytokines such as IFN-gamma or by direct lysis of infected targets. Therefore, during viral infections, viruses and NK cells are in a constant battle and many viruses have developed a variety of strategies to modulate NK cell activity.
evasion by virus of host natural killer cell activity
Modulation of host PP1 activity by virus
Protein phosphatase-1 (PP1) is a member of the Serine/Threonine phosphatases. The enzyme regulates many important physiological processes, including gene transcription, translation, metabolism, cell growth and division. Different viruses including asfivirus, herpes simplex virus or papillomavirus interact with and modulate PPP1 phosphatase activity to dephosphorylate specific cellular substrates including EIF2S1. Upon viral infection, the host PKR/EIF2AK2 triggers the phosphorylation of EIF2S1 leading to a complete translational shut-off. By dephosphroylating EIF2S1 with PPP1CA, viruses manage to circumvent this antiviral response and prevent translational shut-off.
modulation by virus of host PP1 activity
Modulation of host ubiquitin pathway by viral deubiquitinase
Viral protein possessing deubiquitinating activity. Hijacking the ubiquitin system plays an essential role during viral replication. Therefore, several viruses including EBV or HCMV encode for proteins able to remove ubiquitin or ubiquitin-like proteins from their substrate.
modulation by virus of host protein ubiquitination
Modulation of host ubiquitin pathway by viral E3 ligase
Viral protein functioning as a cellular E3 ubiquitin ligase. These viral proteins usually target several host proteins for proteasomal degradation.
Modulation of host ubiquitin pathway by viral ubl
Viral protein sharing sequence similarity with host ubiquitin. Several of these homologues are present in large DNA viruses such as entomopoxvirus or canarypoxvirus and are thought to modulate host ubiquitin pathway.
Modulation of host ubiquitin pathway by virus
Viral protein involved in the modulation of the host ubiquitin pathway. The ubiquitination pathway comprises E1, E2, and E3 ligases that conjugate ubiquitin to protein substrate. Usually, the host E3 ligase determines the substrate specificity. Some viruses encode E3 ligases that modulate the substrate specificity of host E3 ligases. Alternatively, some viruses encode deubiquitinases able to remove ubiquitin or ubiquitin-like proteins from their substrate.
Viral factor that modulates its bacterial host's virulence against a third organism. These virulence factors are mostly expressed from integrated viral genomes and have diverse functions. Bacterial host, and populations, and the encoding (pro)virus probably benefit from the expression of such factors. For example, Bor and Lom outer membrane proteins encoded by bacteriophage lambda modify the virulence of the host bacteria against a eukaryotic target. Some enteric bacterioviruses direct alterations in lipopolysaccharide biosynthesis, resulting in bacterial immune evasion of its eukaryotic target. Other prokaryotic viruses encode exotoxins changing their host bacteria into serious pathogens. A well-known bacterial exotoxin encoded by a provirus is the diphtheria toxin.
Keywords assigned to proteins due to their particular molecular function.
Protein which binds molybdenum (or molybdopterin) or protein involved in the transport of molybdenum, a metallic element, chemical symbol Mo. It plays an essential role in the active site of all eukaryotic Mo-containing enzymes. In plants, Mo enzymes are important for nitrate assimilation, phytohormone synthesis, and purine catabolism. Mo is often coordinated to the sulfur atoms of a pterin derivative (molybdopterin [MPT]), thereby forming the active Molybdenum cofactor (Moco), which is highly conserved in eukaryotes, eubacteria, and archaebacteria.
Molybdenum cofactor biosynthetic process
Protein involved in the synthesis of the molybdenum cofactor (Moco), a molybdenum atom coordinated to the sulfur atoms of a pterin derivative (molybdopterin [MPT]). It is highly conserved in eukaryotes, eubacteria, and archaebacteria. In prokaryotes, two operons are directly associated with biosynthesis of the pterin moiety and its side chain while additional loci play a role in the acquisition of molybdenum and/or activation of the cofactor.
Mo-molybdopterin cofactor biosynthetic process
Antibody produced by a single clone of B cells and thus consisting of a population of identical antibody molecules all specicfic for a single antigenic determinant. They are produced from cultured hybridoma cell lines for research and commercial purposes.
Enzymes that reduce molecular oxygen by incorporating one oxygen atom into its substrate and the other one in water.
Diffusible protein that influence morphogenesis or embryonic development. These proteins carry information relating, for example, to a position in the embryo, and thus, determine the differentiation that cells perceiving this information will undergo. They are thought to act as a function of a threshold of their concentration.
Protein that walks or slides along microtubules or microfilaments using the energy provided by ATP or GTP hydrolysis, e.g. dyneins, myosins and kinesins. Or protein which mediates motility by other non enzymatic processes, e.g. prestin, a bidirectional voltage-to-force converter.
Protein involved in the modification (capping) of the 5' end of eukaryotic mRNAs. This modification occurs after the beginning of transcription in the nucleus, and consists of adding a guanosine nucleotide to the 5'-end of mRNAs and then, methylating the guanosine. Capping protects mRNAs at their termini against attack by phosphatases and other nucleases and promotes mRNA function at the level of initiation of translation.
Protein involved in the processing of the primary mRNA transcript to yield a functional mRNA. This includes 5' capping, 3' cleavage and polyadenylation, as well as mRNA splicing and RNA editing.
Protein involved in the process by which nonsense sequences or intervening sequences (introns) are removed from pre-mRNA to generate a functional mRNA (messenger RNA) that contains only exons.
Protein which is involved in the mechanism of export of mRNAs from the nucleus to the cytoplasm.
Protein which, if defective, causes mucolipidosis, a group of inherited metabolic diseases characterised by the accumulation of excessive amounts of acid mucopolysaccharides, sphingolipids, and/or glycolipids in visceral and mesenchymal cells. Abnormal amounts of sphingolipids or glycolipids are present in neural tissue. Mental retardation and skeletal changes are common. All mucolipidosis are lysosomal disorders and are inherited in an autosomal recessive manner.
Protein which, if defective, causes mucopolysaccharidosis. These inherited diseases are characterized by excessive accumulation and secretion of oligomucopoloysaccharide due to the deficiency of enzymes involved in the degradation of glycosaminoglycans (mucopolysaccharides). They are progressive and often display a wide spectrum of clinical severity within one enzyme deficiency.
Protein that contains at least two distinct enzymatic activities and two distinct active sites.
Characteristic protein of a muscle cell. The major ones are myosin and actin, which are responsible for the contraction and relaxation of muscles.
Protein which is encoded by a mutator gene (mutator). Generally, these are genes within which certain mutations cause an increase in frequency of spontaneous mutations in other genes. Mutator proteins are therefore thought to be responsible for inaccurate DNA replication.
Protein which, if defective, causes myofibrillar myopathy, a group of morphologically homogeneous, but genetically heterogeneous neuromuscular disorders. The morphologic changes in skeletal muscle result from disintegration of the sarcomeric Z disc and the myofibrils, followed by abnormal ectopic accumulation of multiple proteins involved in the structure of the Z disc. Clinical manifestations are variable and can involve the skeletal, cardiac and smooth muscle.
Protein involved in the differentiation and development of the muscle. Myogenesis is controlled by myogenic factors, a family of muscle-specific transcription factors that contain a conserved helix-loop-helix domain which is homologous to the myc family of proteins.
A motor protein which uses the energy provided by the hydrolysis of ATP to drive movements along actin filaments. Different types of myosin are found in eukaryotic cells.
Protein which causes muscle necrosis. Myotoxins are principally found in snake venoms. The myotoxic activity can be monitored by morphological analysis and by the increase of plasma creatine kinase (CK) activity. The increase in plasma CK levels results from sarcolemmal damage due to myotoxic components of the venom.
Protein which is posttranslationally modified by the attachment of at least one myristate group. The myristate (14-carbon saturated fatty acid) group is attached through an amide bond to the N-terminal glycine residue of the mature form of a protein or to an internal lysine residue. Myristoylproteins may be cytoplasmic or membrane-associated.
Enzymes which use NAD(H) as an electron acceptor or as a cofactor. Nicotinamide adenine dinucleotide, an important redox coenzyme that participates in a variety of enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). NAD also functions as an ADP-ribose donor in ADP-ribosylation reactions.
Nicotinamide adenine dinucleotide phosphate
Nicotinic adenine dinucleotide phosphate
Enzymes which use NADP(H) as an electron acceptor or as a cofactor. Nicotinamide adenine dinucleotide phosphate, a redox coenzyme that participates in a variety of enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NADP+) and reduced (NADPH). Analogue of NAD, but NADPH is used extensively in biosynthetic, rather than catabolic pathways as well as in photosynthesis.
Protein involved in necrotic programmed cell death. Necrosis is a form of traumatic cell death that results from acute cellular injury due infection, toxins, trauma, etc. Necrosis is characterized by blebbing, mitochondrial fission, loss of cell membrane integrity and an uncontrolled release of products of cell death into the intracellular space. This initiates an inflammatory response in the surrounding tissue often resulting is a build-up of dead tissue and cell debris at, or near, the site of the cell death.
Protein which, if defective, causes nemaline myopathy, a hereditary neuromuscular disorder characterized by generally non-progressive muscle weakness of varying severity, and abnormal thread- or rod-like structures in muscle fibers on histologic examination. The age of onset varies from birth to adulthood. The main clinical manifestations include weakness (usually most severe in the face, the neck flexors, and the proximal limb muscles), hypotonia, and depressed or absent deep tendon reflexes. Nemaline myopathy is divided into several broad groups classified by onset and severity of motor and respiratory involvement.
Protein localized in the nematocyst, an organelle found in nematoblast (cnidoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the nematocyst) is stimulated by a prey or another stimulus. These proteins are principally found in anemones and jellyfishes.
Protein which, if defective, causes nephronophthisis, a chronic tubulo-interstitial nephritis that progresses to end-stage renal failure. Clinical features include anemia, polyuria, polydipsia, isosthenuria, and death in uremia. Some children present with extrarenal symptoms such as tapeto-retinal degeneration, mental retardation, cerebellar ataxia, bone anomalies or liver involvement.
Protein which, if defective, causes neurodegeneration.
Protein involved in neurogenesis, which involves the differentiation and development of the nervous system.
Protein which, if defective, causes neuronal ceroid lipofuscinosis, a group of neurodegenerative, lysosome storage disorders characterized by intracellular accumulation of autofluorescent wax-like lipid materials in brain and other tissues. Neuronal ceroid lipofuscinoses are associated with variable yet progressive symptoms including seizures, dementia, visual loss, and/or cerebral atrophy.
Protein which, if defective, causes neuropathy, a functional disturbance or pathological change in the peripheral nervous system, sometimes limited to non-inflammatory lesions as opposed to those of neuritis. Neuropathies affecting a specific nerve may be named for the nerve. The terms mononeuropathy and polyneuropathy may be used to denote whether one or several nerves are involved.
Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells. They have direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators).
Proteins, often exquisitely toxic, that inhibit neuronal function. Neurotoxins act typically against sodium channels or block or enhance synaptic transmission. Most venoms contain neurotoxic substances.
Protein, released by the axon terminal in response to an electrical impulse, which travels across the synapse to either excite or inhibit the target cell.
Protein involved in the synthesis of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
Protein involved in the breakdown of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
Protein involved in the transport of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
Protein which binds at least one nickel atom, or protein whose function is nickel-dependent. Nickel is a metal, chemical symbol Ni.
Protein which is involved in the creation and/or insertion of a nickel metallocenter into another protein, without necessarily binding the metal itself.
Protein involved in the transport of nickel.
Protein which, if defective, causes Niemann-Pick disease. Niemann-Pick disease comprises an inherited group of congenital lipidoses in which sphingolipids accumulate in cells, especially in the reticuloendothelial system, due to defective lysosomal storage. The disease is clinically characterized by progressive degeneration of the central nervous system with visceral accumulation of cholesterol and sphingomyelin. The clinical phenotype is highly variable and different types are distinguished by age of onset, degree of central nervous system involvement and by the amount of sphingomyelin phosphodiesterase activity.
Protein involved in the uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid. This includes the uptake and transport into cells by nitrate transporters, with the sequential reduction to nitrite and ammonium, catalyzed by the enzymes nitrate reductase and nitrite reductase, respectively.
Protein which is posttranslationally modified by replacement of a hydrogen on an aromatic ring of one or more tyrosine or tryptophan residues by a nitro (NO2) group.
Protein involved in nitrogen fixation, the reduction of gaseous nitrogen to ammonia. This process is carried out only by prokaryotes who are either free-living or form symbiotic associations with plants or other organisms (e.g. termites, protozoa).
Protein involved in nodulation, the formation of nitrogen-fixing nodules on roots of both leguminous plants and the Parasponia genus.
Protein which, if defective, causes inability to hear in the absence of other clinical signs and symptoms. Most forms of non-syndromic deafness are associated with permanent hearing loss caused by damage to structures in the inner ear.
Protein involved in nonsense-mediated messenger RNA (mRNA) decay, a critical process of selective degradation of mRNAs that contain premature stop codons.
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Protein involved in the Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Notch proteins are transmembrane receptors, which are cleaved by the gamma-secretase complex upon activation and released from the cell membrane and turn into transcriptional activators after their association with SU(H) proteins.
Protein associated predominantly with the nuclear pore complex (NPC). NPCs constitute the exclusive means of nucleocytoplasmic transport in eukaryotes during interphase. NPCs allow the passive diffusion of ions and small molecules (up to about 20 kDa or 5 nm) and the active, nuclear transport receptor (karyopherin: importin and exportin)-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoprotein (RNPs), and ribosomal subunits (up to about 10 MDa) across the double-membrane nuclear envelope. NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. The NPC is composed of at least 30 distinct subunits, shows 8-fold rotational symmetry with specialized structures on the cyto- and nucleoplasmic side and in the nuclear envelope embedded core. The MW varies from about 44-60 MDa in S. cerevisiae to 60-120 MDa in vertebrates, yet the overall architecture is conserved.
Enzyme that degrades nucleic acids into shorter oligonucleotides or single nucleotide subunits by hydrolyzing sugar-phosphate bonds in the nucleic acid backbone.
Protein associated with the nucleomorph. A nucleomorph is a remnant nucleus found between the outer two and inner two membranes of the plastid in cryptomonads and chlorarachniophyte algae.
Protein characteristic of the nucleosome, a repeating structural unit in chromatin that packages DNA to give the chromatin a 'beads-on-a-string' appearance. Each repeat consists of approximately 146 base pairs of DNA wound around a disk-shaped protein core which is composed of two of each of the nucleosomal histones H2A, H2B, H3 and H4.
Protein involved in the synthesis of a nucleotide, a phosphate ester of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
Protein involved in the biochemical reactions of nucleotides. Nucleotides are phosphate esters of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
Protein which binds a nucleotide, a phosphate ester of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
Enzyme which transfers a nucleotide from one compound to another.
Protein located in the nucleus of a cell.
Protein involved in the degradation of nylon, a polymer whose main chain comprises recurrent amide groups. These compounds are generally formed from combinations of diamines, diacids and amino acids.
Protein which, if defective, causes obesity, a disorder characterized by excessive deposition of fat.
Protein involved in olfaction, the process of smelling.
Protein encoded by an oncogene, which promotes cell transformation. Examples include viral homologs of cellular proto-oncogenes such as the transcription factors v-myc and v-jun, the growth factor v-fgr, the regulatory GTPase v-ras, and papillomavirus protein E6.
Protein involved in the biochemical reactions with one-carbon groups, e.g., methyl and formyl groups.
Protein involved in egg development and maturation. A process whereby primordial germ cells form mature ova.
Endogenous peptides with opiate-like activity.
Protein encoded by the organellar chromatophore genome or a protein targeted to the organellar chromatophore. The organellar chromatophore is the photosynthetic inclusion found in Paulinella species, which are photosynthetic thecate amoeba. It probably derives from a different endosymbiotic event than that which led to all other plastids. Houses the machinery necessary for photosynthesis and CO(2) fixation; it also has the genetic capacity to synthesize some amino acids, some fatty acids and a few cofactors. It contains thylakoid membranes, and a residual peptidoglycan wall between the 2 envelope membranes. There are 1 or 2 chromatophores per cell.
Protein which is posttranslationally modified by the formation of a stable radical. E.g., P09373 is posttranslationally interconverted, under anaerobic conditions, from an inactive to an active form that carries a stable radical localized to a specific glycine at the C-terminal region of the polypeptidic chain.
Protein involved in osteogenesis, the mechanism of bone formation wether intramembranous or endochondral. In intramembranous ossification, bone is formed by differentiation of mesenchymal cells into osteoblasts with absence of a cartilaginous model. The flat bones of the skull, the sternum, and the scapula are examples of bones that develop by intramembranous ossification. The term endochondral refers to the close association of the developing bone with the pre-existing hyaline cartilage model of that bone. The long bones of the limbs (including the phalanges) and the ribs develop by endochondral ossification.
Protein which, if defective, causes osteogenesis imperfecta, a bone disorder characterized by low bone mass, and brittle, osteoporotic and easily fractured bones. It may also present with blue sclerae, loose joints, and imperfect dentin formation.
Protein which, if defective, causes osteopetrosis, an hereditary disorder characterized by abnormally dense bone due to reduced bone resorption, and by the common occurrence of fractures of affected bones.
Viral protein that is a component of the outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
Protein which is posttranslationally modified by oxidation of a residue.
Enzyme that catalyzes the oxidation of one compound with the reduction of another.
Protein involved in the transport of oxygen (e.g. hemoglobin and myoglobin).
Protein involved in the synthesis of oxygenated fatty acids (oxylipins), including jasmonic acid (jasmonate) (JA) and its derivatives. Oxylipins regulate many defense and developmental pathways in plants. JA is involved in wound-mediated signaling pathways, plant defense, and reproductive development. It acts as a growth inhibitor and promotes senescence.
A protein encoded by a pair-rule gene. These are developmental genes in Drosophila involved in delimiting segments in the early embryos. Mutations in pair rule genes affect every alternate segment.
Protein which contains a paired box domain, a conserved domain of about 120 amino acids, which is generally located in the N-terminal section of various proteins.
Protein which is posttranslationally modified by the attachment of at least one palmitate group. The palmitate (16-carbon saturated fatty acid) group is usually attached to cysteine via a thioester bond. Lysine, serine and threonine may also serve as palmitate acceptors. Many palmitoylproteins are membrane associated either directly through the palmitate moiety or as transmembrane proteins anchored by the fatty acid. However, a few are actually secreted from cells.
Protein which, if defective, causes hereditary palmoplantar keratoderma (PPK), a genetically and clinically diverse group of cutaneous disorders characterized by abnormal thickening of the skin on the palms and soles. It results from excessive keratin formation leading to hypertrophy of the stratum corneum (hyperkeratosis). PPKs are distinguished from each other on the basis of mode of inheritance, presence of transgrediens (defined as contiguous extension of hyperkeratosis beyond the palmar and/or plantar skin), association with other skin findings and/or abnormalities of other organs, and extent of epidermal involvement (diffuse, focal, punctate). Diffuse PPK is characterized by uniform involvement of the palmoplantar surface; focal PPK consists of localized areas of hyperkeratosis located mainly on pressure points and sites of recurrent friction; punctate PPK shows multiple small, hyperkeratotic papules or nodules on the palms and soles.
Protein involved in the synthesis of pantothenate.
Protein which, if defective, causes classic Parkinson disease. Parkinson disease is a complex multifactorial neurodegenerative disorder, usually occurring in late life, although an early onset and a juvenile form are known. Typical features are masklike facies, tremor of resting muscles, a slowing of voluntary movements (bradykinesia), festinating gait and postural instability. The signs and symptoms of the disease are the consequence of a striatal deficiency of dopamine, resulting from neuronal death in the substantia nigra. Parkinson disease is characterized by the presence of Lewy bodies, intraneuronal inclusions found in many brain regions which are not entirely specific to, but are a highly sensitive marker for, Parkinson disease.
Protein which, if defective, causes parkinsonism. Parkinsonism refers to disorders, both genetic and non-genetic, characterized by four primary parkinsonian symptoms: tremor, rigidity, postural instability and bradykinesia, resulting from the loss or dysfunction of dopamine-producing neurons in the substantia nigra. Lewy bodies, intraneuronal accumulations of aggregated proteins, may or may not be present in the brain of the patients.
Protein induced in several plant species when they are infected by viruses, viroids, fungi or bacteria. The occurrence of these proteins is not pathogen-specific, but determined by the type of reaction of the host plant. They form a protective barrier against pathogens by collecting at infection sites and act to decrease susceptibility of plants. They may have anti-fungal or anti-bacterial activity.
Protein involved in the pentose shunt, the biochemical pathway in which glucose-6-phosphate is oxidized to 6-phosphogluconate with the production of NADPH. Then 6-phosphogluconate is converted to ribulose-5-phosphate and CO2 and a second molecule of NADH. This pathway is an important source of NADPH and ribose-5-phosphate.
Protein involved in the transport of peptides.
Protein involved in the synthesis of peptidoglycan which consists of a glycosaminoglycan formed by alternating residues of D-glucosamine and either muramic acid {2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose} or L-talosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), which are usually N-acetylated or N-glycoloylated. The carboxyl group of the muramic acid is commonly substituted by a peptide containing residues of both L- and D-amino acids, whereas that of L-talosaminuronic acid is substituted by a peptide consisting of L-amino acids only. These peptide units may be cross-linked by a peptide bond, thereby giving rise to a giant macromolecule that forms the rigid cell wall (sacculus or murein sacculus). This macromolecule is known to occur as a monomolecular layer between the inner and outer membrane in Gram-negative bacteria and as a multimolecular layer, often associated covalently or non-covalently with various additional compounds (teichoic acids, neutral polysaccharides. etc.) in Gram-positive bacteria. In the archaebacteria, several organisms contain a peptidoglycan, also called pseudomurein, which differs in certain respects from those of the eubacteria.
Protein that is covalently anchored to the peptidoglycan of a cell wall envelope. In Gram-positive bacteria, binding proceeds through a transpeptidation mechanism which requires a C-terminal sorting signal with a conserved LPXTG or LPXAG motif; an amide bond is created between the alpha-carboxyl group of the conserved threonine, alternatively alanine, and the amino group of peptidoglycan cross-bridges. In Gram-negative bacteria, binding proceeds through the formation of an isopeptide bond between the epsilon-amino group of a lysine and the alpha-carboxyl group of a peptidoglycan diaminopimelic acid.
Protein located in the space between the inner membrane and the outer membrane (cell wall) of Gram negative bacteria and some eukaryotic algae. Also used for proteins located in the region between the plasma membrane and the cell wall in fungi.
Enzyme that catalyzes the oxidation of a substrate by reducing peroxide to water. These enzymes are often located in peroxisomes.
Protein found in or associated with the peroxisome, a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.
Protein which is involved in the formation, organization and maintenance of the peroxisome. The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions.
Protein which, if defective, causes peroxisome biogenesis disorder, a group of peroxisomal disorders arising from a failure of protein import into the peroxisomal membrane or matrix. The PBD group is comprised of four disorders: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata type 1 (RCDP1). ZWS, NALD and IRD are distinct from RCDP1 and constitute a clinical continuum of overlapping phenotypes known as Zellweger spectrum. The PBD group is genetically heterogeneous with at least 12 distinct genetic groups as concluded from complementation studies.
Protein which, if defective, causes Peters anomaly, an ocular disorder characterized by congenital central corneal leukoma, absence of the posterior corneal stroma and Descemet membrane, and a variable degree of iris and lenticular attachments to the central aspect of the posterior cornea.
Poly(3-hydroxyalkanoate) biosynthetic process
Protein involved in the synthesis of poly(3-hydroxyalkanoates) (PHA). In Pseudomonas oleovorans large amounts of this polyester are synthesized when cells are grown under nitrogen-limiting conditions. When nitrogen is further supplied in the medium, the accumulated PHA is degraded.
Protein that is involved in phagocytosis or that renders the organism resistant to phagocytosis, the process by which a cell is engulfed and broken down by another for purposes of defense or sustenance.
Protein which is used or may be used as a pharmaceutical drug, e.g. to treat specific diseases.
Poly-(3-hydroxybutyrate) biosynthetic process
Poly-beta-hydroxybutyrate biosynthetic process
Poly-hydroxybutyrate biosynthetic process
Protein involved in the synthesis of poly-hydroxybutyrate (PHB). It accumulates in a variety of bacteria as an energy source. This polyester is thermoplastic with biodegradable properties.
Protein involved in the biosynthesis of the aromatic amino acid phenylalanine.
Protein involved in the degradation of the aromatic amino acid phenylalanine.
Protein which, if defective, causes phenylketonuria, an autosomal recessive disorder in which the body is unable to break down the amino acid phenylalanine. The resulting buildup of phenylalanine in the body causes intellectual disability, mental disturbances, eczema and skin pigmentation.
Protein involved in the biochemical reactions with phenylpropanoids.
Proteins which acts as a pheromone. Pheromones are odours of conspecifics which elicit an adaptive behavioral response, e.g. insect sex pheromones. Generally, they are comprised of mixtures of compounds and behavioral responsiveness to them is largely instinctual, sexually-dimorphic, and attributable to a specialized component(s) of the olfactory system.
Protein involved in the pheromone response.
Protein which binds pheromones, the odours of conspecifics which elicit an adaptive behavioral response, e.g. insect sex pheromones.
Protein involved in the transport of phosphate.
Protein which inhibits phospholipase A2 (EC 3.1.1.4) (PA2), an enzyme which releases fatty acids from the second carbon group of glycerol. Phospholipase A2 inhibitors are widely distributed in venoms and digestive secretions.
Protein involved in the synthesis of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
Protein involved in the breakdown of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
Protein involved in the metabolism of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
Protein involved in the transport of phosphonates. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as Escherichia coli can use alkylphosphonates as a phosphorus source.
Protein which contains at least one phosphopantetheine as the prosthetic group. In acyl carrier proteins (ACP) for example, it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups.
Protein which is posttranslationally modified by the attachment of either a single phosphate group, or of a complex molecule, such as 5'-phospho-DNA, through a phosphate group. Target amino acid is usually serine, threonine or tyrosine residues (mostly in eukaryotes), aspartic acid or histidine residues (mostly in prokaryotes).
Phosphoenolpyruvate-dependent sugar phosphotransferase system
Protein involved in the phosphotransferase system, the major carbohydrate transport system in bacteria. This phosphotransferase system catalyzes the transfer of the phosphoryl group from phosphoenolpyruvate to incoming sugar substrates concomitant with their translocation across the cell membrane.
Luminescent proteins, which are involved in the phenomenon of light emission in certain living organisms. E.g., green fluorescent protein which is unique among fluorescent proteins in that its chromophore is not a separately synthesized prostethic group but is composed of modified amino acid residues within its polypeptide chain.
Protein involved in the convertion of light directly into a signal. These proteins are classified in a limited number of families based on the chemical structure of the light-absorbing chromophores involved, and also on protein sequence similarities to discriminate the many photoreceptor proteins that bind a flavin derivative. Accordingly, the most important families are the rhodopsins, the phytochromes, the xanthopsins, the cryptochromes, the phototropins and the BLUF proteins.
Protein involved in a light-dependent process to convert 2-phospho-glycolate (2-PG) into 3-phospho-D-glycerate (3-PG), where oxygen is consumed and carbon dioxide released. It takes place in plants and cyanobacteria during the light period, since in the presence of O(2) their type of Rubisco can catalyze the oxidative fragmentation of ribulose 1,5-biphosphate to 3-PG and 2-PG. 2-PG inhibits the Calvin cycle enzyme triose-phosphate isomerase, and so must be eliminated quickly. In plants 2-PG is recycled to 3-PG via reactions in peroxisomes, mitochondria as well as chloroplasts. For every 2 molecules of 2-PG, one molecule of 3-PG is formed and one molecule of CO(2) is lost. In cyanobacteria it seems there are two mechanisms to deal with 2-PG; a path similar to that described for plants and the bacterial-like glycerate pathway.
Protein involved in photosynthesis, the process in which light energy is absorbed by photosynthetic pigments (e.g. chlorophyll) and converted to chemical energy (usually ATP and NADPH, =light reaction). This energy is subsequently used as an energy source for the reduction of carbon dioxide to carbohydrate (=Calvin cycle). The general reaction is: CO(2) + 2H(2)A = (CH(2)O) + 2A + H(2)O, where 2H(2)A is any reduced compound that can serve as an electron donor. In plants, algae and cyanobacteria H(2)O serves as a reductant, generating O(2). Non-oxygenic organisms use other electron donors, for example H(2)S in purple sulfur bacteria, generating sulfur.
Protein involved in photosystem I (PSI), a complex that uses light energy to mediate electron flow in the chloroplast thylakoid membrane of plants and in cyanobacteria. In linear electron flow, PSII is coupled to PSI and produces a pH gradient, ATP and NADPH. In cyclic electron flow, PSI generates a pH gradient and ATP. PSI is excited best by light at about 700 nm, and is thus sometimes called P700. PSI is an iron-sulfur type reaction center (RC), sharing a common ancestor with the RCs of Heliobacteriaceae, green sulfur and green non-sulfur bacteria.
Protein involved in photosystem II (PSII), a complex that uses light energy to mediate electron flow in the chloroplast thylakoid membrane of plants and in cyanobacteria. PSII splits water, releasing hydrogen ions and molecular oxygen. PSII cannot use photons of a wavelength greater than 680 nm, and is thus sometimes called P680. PSII is a quinone type rection center (RC), sharing a common ancestor with the RCs of purple bacteria.
Protein found in phycobilisome, an accessory light energy harvesting structure on the outer face of the thylakoid membranes in cyanobacteria and red algae. Phycobilisomes are mainly composed of phycobiliproteins (such as allophycocyanin, phycocyanin and phycoerythrin) together with linker polypeptides.
Protein involved in the relay of information from the activated phytochrome molecule to target genes. Different phytochromes use both separate and common early signaling pathways. These pathways converge downstream in a process of signal integration that regulates photomorphogenesis and the circadian clock. This provides the means by which information from specific wavelengths of light may be amplified and coordinated.
Protein which binds or transport pigments, any coloring matter in animals, plants or microorganisms.
Protein involved in plant defense, either as part of preexisting, developmentally regulated defense barriers (such as thionins, defensins or hydroxyproline-rich glycoproteins fortifying the cell wall) or as components of the defense responses induced upon pathogen infection during hypersensitive cell death (HR), local acquired resistance (LAR) or systemic acquired resistance (SAR). This includes proteins involved in various pathways, such as the gene-for-gene resistance, the salicylic acid (SA)-dependant resistance, the jasmonate (JA) and/or ethylene (ET)-dependant resistance and the induced systemic resistance (ISR), as well as the final products of those pathways such as the pathogenesis-related proteins.
Protein encoded on a plasmid, a self-replicating circular DNA that is found in a variety of bacterial, archaeal, fungal, algal and plant species, and can be transferred from one organism to another. Plasmids often carry antibiotic-resistant genes and are widely used in molecular biology as vectors of genes and in cloning.
Protein involved in the plasmid copy control, the ability of a plasmid to control its own copy number in a cell. Copy number is a function of the rate at which DNA synthesis is initiated.
Protein involved in plasmid partition, the process whereby newly replicated plasmids are distributed properly to daughter cells during cell division.
Protein involved in the plasminogen activation which occurs when an heterogeneous group of proteolytic enzymes convert plasminogen to plasmin.
Protein encoded by or localized in a plastid, a semi-autonomous, self-reproducing organelle. Plastids are remnants of a photosynthetic organism that was engulfed by the host, although not all are now photosynthetic. Plastid genomes encode genes for rRNAs, tRNAs and between about 28 and 150 proteins. Plastids can be categorized in 4 main groups: chloroplasts, cyanelles, apicoplasts and non-photosynthetic. The latter are found is some land plants (Epifagus virginiana), chlorophyte algae (Prototheca wickerhamii) and euglenoids (Astasis longa), which do not encode the genes necessary for photosynthesis and so are not photosynthetic but still contain a plastid. Non-photosynthetic plastids probably do not contain thylakoids.
Protein found in or associated with the inner membrane of a plastid, which separates the plastid stroma from the intermembrane space.
Protein found in or associated with the outer membrane of a plastid, which is the membrane facing the cytoplasm.
Protein which interacts with plastoquinone, a substituted quinone called plastoquinone because it appeared concentrated in the chloroplasts of higher plants. Plastoquinone transfers electrons from the photosystem II reaction center to the cytochrome bf complex and carries protons across the photosynthetic membrane.
Toxin which induces agonist-induced platelet aggregation, the self-adhesion of platelets via adhesion molecules. Numerous snake venom families have the capacity to induce platelet aggregation.
Toxin which inhibits agonist-induced platelet aggregation, the self-adhesion of platelets via adhesion molecules. Numerous snake venom families have the capacity to inhibit platelet aggregation.
Protein involved in polyamine biosynthesis. The polyamines, e.g. putrescine, cadaverine, agmatine, spermidine and spermine, are wide-spread in all organisms, and have been shown to play a role in the regulation of growth and differentiation of virtually all types of cells.
Protein involved in polysaccharide degradation, the breakdown of polysaccharides.
Protein involved in the transport of polysaccharides.
Protein which, if defective, causes pontocerebellar hypoplasia, a heterogeneous group of congenital disorders characterized by hypoplasia and atrophy of the cerebellar cortex, dentate nuclei, pontine nuclei and inferior olives. Additional defects of other brain and spinal cord structures can be present, resulting in clinical manifestations that vary among cases.
Pore-mediated penetration of viral genome into host cell
Membrane puncture-mediated penetration of viral genome into host cell
Virion-associated pore-forming protein that induces the formation of a transmembrane pore or channel in the host membrane(s) to allow the viral genome to enter the host cytoplasm. This mechanism is used by non-enveloped viruses such as human rhinovirus 2 or poliovirus. Many tailed bacteriophages carry specialized proteins which open a pore or a channel in the host membrane(s) to allow penetration of the virion tail into host envelope and genome delivery into host cytoplasm.
pore-mediated entry of viral genome into host cell
Membrane protein which in a multimeric form constitutes a water-filled transmembrane channel (a pore). This pore allows the passage of ions and numerous other, non-specific molecules through the membrane. Found in the mitochondrial and plastid outer membrane of eukaryotes, in many Gram-negative bacteria, at least some Corynebacterineae, archaea and in sea anemones.
Protein involved in the synthesis of porphyrins which are compounds that contain the porphin structure, e.g. four pyrrole rings connected by methine bridges in a cyclic configuration to which a variety of side chains are attached. Porphyrins often chelate metal ions (Fe, Mg, Co, Zn, Cu, Ni). Examples are, heme proteins (which contain iron porphyrins) like myoglobin, hemoglobin, cytochromes, or related macrocycles including chlorophylls (which have a central magnesium ion) and pheophytins (which are metal free) and vitamin B-12 (which has cobalt).
porphyrin-containing compound biosynthetic process
Protein characteristic of the postsynaptic membrane. In a chemical synapse, the postsynaptic membrane is the membrane that receives a signal (binds neurotransmitter) from the presynaptic cell and responds via depolarisation or hyperpolarisation. The postsynaptic membrane is separated from the presynaptic membrane by the synaptic cleft.
Protein which acts as a neurotoxin at the postsynaptic membrane. They bind to acetylcholine receptors and so inhibit their activity.
Protein which binds at least one potassium, or protein whose function is potassium-dependent. Potassium is an alkali metal, chemical symbol K.
Protein which is part of a transmembrane protein complex that forms a hydrophilic channel across the lipid bilayer through which potassium ions can diffuse down their electrochemical gradient. The channels are gated and only open in response to a specific stimulus, such as a change in membrane potential (voltage-gated). They are important for the regulation of the resting membrane potential and for the control of the shape and frequency of action potentials.
Protein which interferes with the function of potassium channels which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions. They are found in various venoms from snakes, scorpions and spiders.
Protein involved in the transport of potassium ions.
Protein which non-covalently binds at least one pyrroloquinoline quinone (PQQ) cofactor.
Protein involved in the biosynthesis of the cofactor pyrroloquinoline quinone (PQQ).
pyrroloquinoline quinone biosynthetic process
Protein which plays a role in pregnancy, the condition of having a developing embryo or fetus in the body, after union of an ovum and spermatozoon.
Protein which, if defective, causes premature ovarian failure, a condition characterized by the arrest of normal ovarian function before the age of 40 years, due to a primary ovarian defect. It is characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles (secondary amenorrhea).
Protein which is posttranslationally modified by the attachment of at least one prenyl group (e.g. farnesyl, geranylgeranyl) usually on cysteine residues which are at or near the C-terminal extremity.
Enzyme that catalyzes the transfer of an isoprenoid (farnesyl or geranylgeranyl) usually on cysteine residues, which are three residues away from the C-terminal extremity.
Protein which acts as a neurotoxin at the presynaptic membrane and usually blocks neuromuscular transmission.
Protein which, if defective, causes primary ciliary dyskinesia, a rare and genetically heterogeneous disorder characterized by sino-pulmonary disease, laterality defects and male infertility. Primary ciliary dyskinesia is due to dysfunction of motile cilia and flagella in various organ systems.
Protein which, if defective, causes primary hypomagnesemia. Primary hypomagnesemia defines a heterogeneous group of disorders characterized by low magnesium serum content due to primary renal or intestinal magnesium wasting. Primary hypomagnesemia disorders generally share symptoms of magnesium depletion, such as tetany and generalized convulsions. They often include associated disturbances in calcium excretion.
Protein which, if defective, causes primary microcephaly. This is a neurodevelopmental condition characterized by a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean, and absence of other syndromic features or significant neurological deficits. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Primary microcephaly is also known as true microcephaly or microcephaly vera.
Protein which, if defective, causes any one of a clinically heterogeneous group of disorders arising from dysfunction of the mitochondrial respiratory chain. The phenotypic spectrum ranges from isolated diseases affecting single organs to severe multisystem disorders. Common clinical features include ptosis, external ophthalmoplegia, proximal myopathy and exercise intolerance, cardiomyopathy, sensorineural deafness, optic atrophy, pigmentary retinopathy, encephalopathy, seizures, stroke-like episodes, ataxia, and spasticity. Mitochondrial disorders can be caused by mutations of mitochondrial DNA or nuclear DNA that either affect oxidative phosphorylation proteins directly, or affect respiratory chain function by impacting the production of the complex machinery needed to run this process.
Component of the complex involved in the synthesis of RNA primer sequences used in DNA replication. Main components are primases and replicative DNA helicases that move as a unit along the replication fork.
DNA replication, synthesis of RNA primer
Protein which is able to form a prion, a self-propagating protein conformation (infectious protein). Formation of prions involves conversion of the native proteins into an infectious, amyloid form. This class of proteins includes the members of the prion family which can form proteinaceous infectious particles responsible for transmissible spongiform encephalopathies (TSE) in many animals, such as Kuru and Creutzfeldt-Jakob syndrome in humans, scrapies in sheep and BSE in cattle. These prion diseases represent special cases of neurodegenerative amyloidoses, because they result from the transmissibility and infectivity of the amyloid.
Protein which, if defective, causes progressive external ophthalmoplegia with mitochondrial DNA deletions. Progressive external ophthalmoplegia (PEO) is characterized by ptosis and weakness of the extraocular muscles. Typical symptoms are ophthalmoparesis and exercise intolerance. Some people also may develop cardiomyopathy, cataracts, ataxia, peripheral neuropathy, hypogonadism or major depression. The diagnosis depends on the demonstration, by Southern blotting, of multiple deletions of mtDNA in muscle biopsy specimens. Both autosomal dominant and autosomal recessive inheritance can occur. The autosomal recessive form, which is often associated with multisystemic disorders, is clinically more heterogenous than the autosomal dominant form and can be more severe.
Protein involved in the biosynthesis of the cyclic amino acid proline. The structure of proline differs from the structure of other amino acids in that its side chain is bonded to the nitrogen of the amino group as well as to the carbon atom. This makes the amino group a secondary amine, and because of this, proline is also described as an imino acid. The presence of proline residues strongly influences the secondary structure of proteins.
Protein involved in a biochemical reaction with the cyclic amino acid proline. The structure of proline differs from the structure of other amino acids in that its side chain is bonded to the nitrogen of the amino group as well as to the carbon atom. This makes the amino group a secondary amine, and because of this, proline is also described as an imino acid. The presence of proline residues strongly influences the secondary structure of proteins.
Protein involved in the biosynthesis of prostaglandins. Prostaglandins are fatty acids composed of 20 carbons with a substituted cyclopentane ring. There are four major classes of prostaglandin, which differ in the position of the double bonds and/or the oxygen substituents on the ring: PGA, PGB, PGE, and PGF. They are found in many mammalian tissues.
Protein involved in a biochemical reaction with prostaglandins. Prostaglandins are fatty acids composed of 20 carbons with a substituted cyclopentane ring. There are four major classes of prostaglandin, which differ in the position of the double bonds and/or the oxygen substituents on the ring: PGA, PGB, PGE, and PGF. They are found in many mammalian tissues.
Protein which inhibits or antagonizes the biosynthesis of proteases or their activity.
Protein which is part of the proteasome, a large protein complex in the cytosol that is responsible for degrading proteins which have been marked for destruction by ubiquitination or by some other means.
Protein involved in the biosynthesis of proteins from mRNA molecules. This process, called translation, is carried out by ribosomes, where activated amino acids are added to the nascent polypeptide chain.
Protein which inhibits the activity of a protein kinase.
Enzyme that catalyzes the hydrolysis of phosphate monoesters bonds of phosphoserines, phosphothreonines, phosphotyrosines or phosphoaspartic acids. While many protein phosphatases inhibit the activities of phosphorylation cascades, some activate them.
Protein which inhibits the activity of a protein phosphatase.
Protein which undergoes protein self-splicing, a posttranslational modification involving the excision of an intervening protein sequence (intein) from a protein precursor and the concomitant ligation of the flanking protein fragments (exteins) to form a mature extein protein and the free intein.
Protein which blocks the synthesis of proteins (translation) through various mechanisms, including hydrolysis of cellular tRNA, and inactivation of the 60S subunits of eukaryotic ribosome.
Protein involved in the intracellular transport of proteins from one location to another. All proteins (except the ones synthesized in mitochondria and plastids) are synthesized on ribosomes in the cytosol. Most proteins remain in the cytosol. Proteins with a signal sequence either become plasma membrane components or are exported from the cell of origin.
Protein containing one or more covalently linked and usually sulfated glycosaminoglycans, (e.g., chondroitin sulfate, dermatan sulfate, heparan sulfate, heparin, keratan sulfate). Glycosaminoglycans are polysaccharides made of repeating disaccharides (usually 40-100 times), which consist of uronic acid (or galactose) and hexosamines. Aggrecan, for example, is the major component in articular cartilage.
Protein whose amino acid sequence has been partially or completely confirmed using publicly available mass spectrometry based data. The mapping from the mass spectrometry data to UniProtKB sequences may be subject to quality metrics from both UniProt and the data providers.
Protein which activates prothrombin, the inactive precursor of thrombin. For example, staphylocoagulase, an extracellular protein produced by Staphylococcus aureus, forms a complex with prothrombin which can clot fibrinogen without any proteolytic cleavage of prothrombin.
positive regulation of peptidase activity
Protein whose normal cellular gene can be converted into a cancer-promoting oncogene by activating mutations, chromosomal translocation or DNA amplification. Once activated a proto-oncogene can promote cell transformation in culture or tumorigenesis in animals. Examples include the regulatory GTPase HRAS, which is commonly activated by dominant gain of function point mutations, and the transcription factor MYC, which can be activated by both chromosomal amplification and chromosomal translocation.
Proton-gated sodium channel impairing toxin
Protein which interferes with the function of proton-gated sodium channels (ASICs) which are membrane proteins forming a channel in a biological membrane selectively permeable to sodium ions, and open in response to an increase of extracellular protons. These toxins are found in various venoms from snakes, spiders, sea anemones, and cone snails.
Protein which, if defective, causes pseudohermaphroditism, a condition in humans in which the individual has gonads of one sex but shows ambiguous morphologic criteria of sex.
Keywords assigned to proteins because their sequences can differ from the mere translation of their corresponding genes, due to some post-translational modification.
Protein involved in the biosynthesis of purine, a nitrogenous heterocyclic base, e.g. adenine, guanine, hypoxanthine and xanthine. De novo synthesis involves a complex, energy-expensive pathway that yields inosine 5'-monophosphate (IMP), a purine ribonucleotide. AMP and GMP are then formed from IMP in separate pathways. Adenine and guanine are found in both DNA and RNA. Hypoxanthine and xanthine are important intermediates in the synthesis and degradation of the purine nucleotides.
Protein involved in a biochemical reaction with purines. Purines are nitrogenous heterocyclic bases, e.g. adenine, guanine, hypoxanthine and xanthine. The degradation of purines leads to uric acid, which is excreted in primates, birds and some other animals. In many other vertebrates uric acid is degraded further to the excretory product allantoin.
Protein involved in the biosynthesis of purine nucleotides from free purines salvaged from their catabolism. This process is less expensive energetically and exerts feedback control on the de novo synthesis.
Protein involved in the biosynthesis of putrescine, a foul-smelling polyamine. This metabolic precursor of the polyamines spermine and spermidine is often produced during breakdown of some of the amino acids by bacteria.
Protein involved in the biosynthesis of the pyridine nucleotides NAD and NADP. NAD may be synthesized de novo from aspartate and dihydroxyacetone phosphate or from tryptophan. NAD may also be synthesized from nicotinamide or nicotinic acid. NADP is formed via the phosphorylation of NAD by NAD+ kinase.
pyridine nucleotide biosynthetic process
Protein which uses at least one pyridoxal phosphate as cofactor or protein required for its synthesis. This coenzyme, derived from vitamin B6, is important in amino acid metabolism, e.g., in reactions involving transamination, decarboxylation, racemization, elimination or replacement.
Protein involved in the biosynthesis of pyridoxine, a precursor to the coenzyme pyridoxal phosphate.
Protein involved in the biosynthesis of pyrimidine, a nitrogenous heterocyclic base, e.g. uracil, thymine, cytosine and orotic acid. Pyrimidines are synthesized from carbamoyl phosphate and aspartate. Ribose-5-phosphate is then attached to yield pyrimidine ribonucleotides. Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine is normally found in DNA. Sometimes tRNA contains some thymine as well as uracil.
pyrimidine nucleotide biosynthetic process
Protein producing fever. The major endogenous pyrogen in mammals is probably interleukin-1, which is produced by activated macrophages and acts on the hypothalamic thermoregulatory centre.
Protein which, if defective, causes hereditary pyropoikilocytosis (HPP), a recessively inherited hemolytic anemia characterized by microspherocytosis, poikilocytosis (deformation of the erythrocytes), and an unusual thermal sensitivity of red cells. Frequently associated with abnormalities in alpha-spectrin, one of the principal structural proteins of the erythrocyte membrane skeleton.
Protein which is posttranslationally modified by the cyclization of a N-terminal glutamine.
Protein which contains a pyrrolysine, a naturally occurring amino acid so far only found in some archaeal proteins. Pyrrolysine is a lysine in an amide linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate.
Protein which uses at least one pyruvate as cofactor (pyruvoyl) or substrate, or protein required for pyruvate synthesis or degradation. Pyruvate is an intermediate compound in the metabolism of carbohydrates, proteins and fats.
Protein involved in the synthesis of queuosine (nucleoside Q), a modified guanosine derivative found only in tRNAs for aspartic acid, asparagine, histidine and tyrosine. It can pair with either C or U.
Protein involved in the biochemical reactions of quinate. Quinate is the ionized form of quinic acid which is found in plants, e.g. in cinchona bark.
Protein which interacts with quinones. Quinones are aromatic dicarbonyl compounds, where the two carbonyl groups are usually in the para position. Most naturally occuring quinones contain a long isoprenoid side chain, and are divided in two major structural groups, the naphtoquinones and benzoquinones; the number of isoprene units depends on the organism. These highly hydrophobic molecules are mainly involved in electron transport, as electron carriers in redox reactions. For example, ubiquinone (coenzyme Q) and menaquinone (vitamin K2) are essential components of the respiratory electron transport chain. Plastoquinone, found in chloroplasts and in cyanobacteria, functions as one of the carrier molecules of the electron transport chain in photosynthesis. Phylloquinone (vitamin K1) is the major form of vitamin K found in plants. Chlorobiumquinone, demethylmenaquinone, alpha-tocopherolquinone, rhodoquinone, epoxyubiquinone and caldariellaquinone are other quinones found in several species.
Protein involved in quorum sensing (QS). QS is a phenomenon whereby the accumulation of signaling molecules enables a single cell to sense the number of bacteria (cell density). The bacterial reponse to QS includes adaptation to availability of nutrients, defence against other microorganisms which may compete for the same nutrients and the avoidance of toxic compounds potentially dangerous for the bacteria.
Protein which is a component of the reaction center, a system consisting of proteins and cofactors which facilitate light energy and electron transfer in plants. The system also acts as a light-driven electron pump across the photosynthetic membrane of photosynthetic bacteria.
Protein which binds to, or responds to, a ligand with high specificity.
Protein which possesses at least one active center which mediates its participation in redox reactions, usually via reversible oxidation of a cysteine residue leading to a cysteine-sulfenic acid that can either be stabilized, or react with an unmodified cysteine residue and form a stable but reversible disulfide bond.
Protein which is part of a reference proteome. Reference proteomes are a subset of proteomes that have been selected either manually or algorithmically according to a number of criteria to provide a broad coverage of the tree of life and a representative cross-section of the taxonomic diversity found within UniProtKB, as well as the proteomes of well-studied model organisms and other species of interest for biomedical research.
Protein which contains a stretch of amino acids present in multiple copies.
Protein which interferes with transcription, usually by binding to specific sites on DNA. Also used for proteins which repress translation.
Protein involved in respiratory chain. In aerobic respiration electrons are transferred from metabolites to molecular oxygen through a series of redox reactions mediated by an electron transport chain. The resulting free energy is used for the formation of ATP and NAD. In anaerobic respiration analogous reactions take place with an inorganic compound other than oxygen as ultimate electron acceptor.
Protein involved in the restriction system present in many bacteria and archaea. This defense mechanism is composed principally of a restriction endonuclease and a methylase. The restriction endonuclease cuts the invading DNA of viruses (or phages) at a specific recognition site. The bacterial DNA is protected by the methylase which adds a methyl group to a specific nucleotide, immediately following replication, in the same target site as the restriction enzyme.
Restriction-modification system evasion by virus
Viral anti-restriction protein that counteracts the host restriction-modification (R-M) system. R-M system is a prokaryotic host defense system that recognizes incoming unmodified viral DNA and rapidly degrades it. Methylation and phosphorothioation (S-modification) are two known modifications used by the host to to label its genomic DNA as 'self'. Many prokaryotic viruses have evolved antirestriction strategies such as expressing their own methylase, stimulating the host methylase so that it confers protection to the virus genome or shutting down host restriction endonuclease.
Protein found in the retina or, in the case of bacteriorhodopsin, in the purple membrane of halobacteria, and which acts as a photoreceptor and which binds a retinal chromophore.
Protein which, if defective, causes retinitis pigmentosa, a hereditary progressive degeneration of the neuroepithelium of the retina,.
Protein which binds retinol, one of the active form of Vitamin A, a fat-soluble vitamin derived from carotenes. It is a precursor of retinal, the light-absorbing group of visual pigments. Vitamin A is also required for growth.
Protein involved in the biochemical reactions of rhamnose. Rhamnose is a methylpentose sugar structurally derived from mannose. The L-isomer occurs naturally as a component of many plant glycosides and in lipopolysaccharides of some bacteria with 2 membranes (Gram-negative bacteria).
Protein which, if defective, causes rhizomelic chondrodysplasia punctata (RCDP). This lethal autosomal recessive disease is characterized by proximal limb shortening, severely disturbed endochondrial bone formation, and intellectual disability. RCDP type 1 (RCDP1) is the classical and most common form. It is a peroxisome biogenesis disorder caused by mutations in the PEX7 gene, which encodes the PTS2-receptor peroxin-7. RCDP type 2 (RCDP2) and RCDP type 3 (RCDP3) result from single peroxisomal enzyme deficiencies: dihydroxyacetone phosphate synthase is deficient in RCDP2 and dihydroxyacetone phosphate acyltransferase in RCDP3. Both enzymes are involved in the biosynthesis of plasmalogens.
Protein involved in the synthesis of riboflavin (Vitamin B2), which consists of ribose attached to a flavin moiety. It is synthesized by all green plants and most microorganisms and occurs free in milk, the retina, whey and urine. It is found in most cells as a component of the coenzymes flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN).
Proteins conjugated with ribonucleic acid (RNA). Ribonucleoprotein are involved in a wide range of cellular processes. Besides ribosomes, in eukaryotic cells both initial RNA transcripts in the nucleus (hnRNA) and cytoplasmic mRNAs exist as complexes with specific sets of proteins. Processing (splicing) of the former is carried out by small nuclear RNPs (snRNPs). Other examples are the signal recognition particle responsible for targetting proteins to endoplasmic reticulum and a complex involved in termination of transcription.
Protein produced by programmed ribosomal frameshifting, a translational recoding mechanism which causes the ribosome to alter its reading of the genetic code to produce either an alternative product not directly encoded by the mRNA or two or more different isoforms.
Protein of the ribosome, large ribonucleoprotein particles where the translation of messenger RNA (mRNA) into protein occurs. They are both free in the cytoplasm and attached to membranes of eukaryotic and prokaryotic cells. Ribosomes are also present in all plastids and mitochondria, where they translate organelle-encoded mRNA.
Protein produced by ribosomal 'skipping', in which a specific sequence in the nascent peptide chain prevents the ribosome from creating the peptide bond with the next proline. Nevertheless, translation continues and gives rise to a second chain. This mechanism results in apparent co-translational cleavage of the polyprotein. This process is induced by a '2A-like', or CHYSEL (cis-acting hydrolase element) sequence.
Protein involved in the synthesis of ribosomes.
Protein which is derived from an RNA which has been modified by RNA editing, a process that changes the nucleotide sequence of an RNA from that of the DNA template encoding it. RNA editing can be due to nucleotide conversion, insertion and/or deletion.
Protein involved in the repair of RNA, the various biochemical processes by which damaged RNA can be restored.
Protein which is derived from an mRNA by suppression of termination, a process in which a tRNA misreads a termination codon thereby producing a longer protein. RNA secondary structure after the stop codon plays a role in this process. The efficiency of suppression of termination is about 10% for most viruses. Termination suppression is involved in polyprotein synthesis of gamma and epsilon retroviruses, as well as all togaviridae.
Protein which is derived from an mRNA by termination-reinitiation, a process in which ribosomes translate the upstream ORF but following termination, a proportion of 40S subunits remain tethered to the mRNA and reinitiates at the start codon of the downstream ORF to another open reading frame. Termination-reinitiation operates in animals and yeast translational systems.
Protein which is derived from an mRNA by translational shunting, a process in which ribosomes are loaded onto mRNA at the 5'-cap structure, start scanning for a short distance before bypassing the large internal leader region and initiating at a downstream start site. Shunting operates in plants, animals, and yeast translational systems, both in vivo and in vitro.
Enzyme (EC 2.7.7.49) which synthesizes (-)DNA on a (+)RNA template. They are encoded by the pol gene of retroviruses and by certain retrovirus-like elements.
Enzyme (EC 2.7.7.48) which synthesizes (+)RNA on a (-)RNA template. They are encoded by many viruses.
RNA-directed 5'-3' RNA polymerase activity
Protein involved in RNA-mediated gene silencing. This term describes a number of related processes which use 21- to 25-nucleotide RNAs to repress the expression of specific target genes. These processes include the post-transcriptional regulation of mRNA by either RNA interference (RNAi) or endogenously encoded microRNAs (miRNAs) and the transcriptional regulation of mRNA by RNAi-mediated chromatin silencing. RNAi is generally triggered by the presence of dsRNA produced by bidirectional transcription or by the transcription of an inverted repeat or hairpin sequence. dsRNA is processed into small interfering RNAs (siRNAs) of around 21 nucleotide which are then incorporated into the RNA-induced silencing complex (RISC), which cleaves mRNAs with sequences fully complementary to the siRNA. miRNAs differ from siRNAs principally in their biogenesis. miRNA genes encode precursors with complex hairpin structures which are processed by endonucleolytic cleavage to form mature miRNAs. Like siRNAs, miRNAs function in RISC-like complexes. Animal miRNAs generally inhibit translation of target mRNAs following imperfect base pairing to the 3'-untranslated region (3'-UTR), while most plant miRNAs show nearly precise complementarity to coding regions of target mRNAs and trigger mRNA degradation similar to siRNAs. Finally, in RNAi-mediated chromatin silencing, siRNAs derived from repeat element transcripts are incorporated into the nuclear RNAi-induced initiator of transcriptional silencing complex (RITS), where they guide chromatin modifications such as histone methylation which lead to transcriptional silencing.
Enzyme (EC 5.2.1.8) which accelerates the folding of proteins by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
peptidyl-prolyl cis-trans isomerase activity
Protein involved in the processing of the primary rRNA transcript to yield a functional rRNA. This includes the cleavage and other modifications.
Ryanodine-sensitive calcium-release channel impairing toxin
Protein which interferes with the function of ryanodine receptors (Ryr) which are a class of intracellular calcium channels in various forms of excitable animal tissue like muscles and neurons. These toxins are mostly found in scorpion and snake venom.
Protein which binds at least one S-adenosyl-L-methionine (SAM), or protein whose function is SAM-dependent. S-adenosyl-L-methionine, a conjugate of the nucleotide adenosine and the amino acid methionine, is a substrate/cofactor in numerous enzyme-catalyzed reactions. Enzymatic reactions that involve interactions of proteins with S-adenosyl-L-methionine include transfer of methyl, thiomethyl, aminoalkyl and adenosyl groups. It not only provides methyl groups to be transferred in numerous biological reactions, but also acts as a precursor in the biosynthesis of polyamines and metal ion chelating compounds. It is also a source of catalytic 5'-deoxyadenosyl radicals produced as reaction intermediates by a superfamily of radical enzymes. It is also involved in decarboxylation reactions.
Protein of the paracrystalline mono-layered assembly which coats the surface of bacteria and archaea.
Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues.
Protein found in a special form of agranular reticulum located in the sarcoplasm of striated muscle. The agranular reticulum comprises and comprising a system of smooth-surfaced tubules which form a plexus around each myofibril.
Enzyme which forms a covalent enzyme-substrate complex, a Schiff's base or ketimine between the amino group of a lysine residue of the enzyme and the carbonyl group of the substrate.
Protein which, if defective, is associated with schizophrenia, a multifactorial psychotic disorder characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior).
Severe combined immunodeficiency disease
Severe congenital immunodeficiency disease
Protein which, if defective, causes severe combined (or congenital) immunodeficiency disease. An heterogeneous group of inherited disorders characterized by gross functional impairment of the immune system.
Protein secreted into the cell surroundings.
Protein required for the development or growth of seeds.
Protein involved in the division of the embryo into segments and which is responsible for determining the internal polarity of the segments. Segment polarity gene mutations are lethal and change the pattern and, often the polarity, of every segment.
Protein which binds at least one selenium, or protein whose function is selenium-dependent. Selenium is a nonmetallic trace element, chemical symbol Se.
Protein which contains a selenocysteine, a naturally occurring amino acid in both eukaryotic and prokaryotic organisms.
Protein involved in the self-incompatibility system, which is to say the inability of pollen grains to fertilize flowers of the same plant or a close relative. This mechanism ensures out-breeding in certain plant species.
Juvenile nephronophthisis with Leber amaurosis
Protein which, if defective, causes Senior-Loken syndrome, a genetically and clinically heterogeneous disease characterized by nephronophthisis and retinal abnormalities manifesting as congenital retinal blindness or retinitis pigmentosa. Senior-Loken syndrome can be associated with manifestations such as cerebellar ataxia and skeletal abnormalities including cone epiphyses.
Protein involved in sensory transduction, the process by which a cell converts an extracellular signal, such as light, taste, sound, touch or smell, into electric signals.
Protein involved in septation, the formation of a separating wall (septum) between daughter cells during cell division.
Protein involved in the synthesis of the amino acid serine, a constituent of proteins and precursor of several metabolites, including cysteine, glycine and choline. Serine is mostly formed from 3-phosphoglycerate in a 3-step reaction pathway.
Enzyme which catalyzes the hydrolysis of esters and is characterized by a catalytically active serine residue in its active site.
Proteolytic enzyme with a serine residue (Ser) in its active site. The reactivity of the serine residue is ensured by the vicinity of a histidine and an aspartate residue (catalytic triad), all three residues are required for the charge relay system to take place.
Protein which is related to serine proteases but seems to have no proteolytic activity.
Protein which inhibits serine proteases, a group of proteolytic enzymes which are characterized by a catalytically active serine residue in their active site.
serine-type endopeptidase inhibitor activity
Protein which catalyzes the phosphorylation of serine or threonine residues on target proteins by using ATP as phosphate donor. Such phosphorylation may cause changes in the function of the target protein. Protein kinases share a conserved catalytic core common to both serine/ threonine and tyrosine protein kinases.
protein serine/threonine kinase activity
Protein involved in the synthesis of the biochemical messenger and regulator serotonin which is formed by the hydroxylation and subsequent decarboxylation of L-tryptophan. In humans, serotonin mediates several important physiological functions, including neurotransmission, gastrointestinal motility, hemostasis and cardiovascular integrity.
Protein involved in both the determination of cells to become sexual tissue in embryonic development and in the process by which male and female tissue becomes structurally and functionally specialized during embryonic development.
Protein with at least one Src homology 2 (SH2) domain. The SH2 domain, which was first identified in the oncoproteins Src and Fps, is about 100 amino-acid residues long. It functions as a regulatory module of intracellular signaling cascades by interacting with high affinity to phosphotyrosine-containing target peptides in a sequence-specific and strictly phosphorylation-dependent manner.
Protein with at least one Src homology 3 (SH3) domain It is a small protein domain of about 50 amino-acid residues first identified as a conserved sequence in the non-catalytic part of several cytoplasmic protein tyrosine kinases (e.g. Src). Since then, it has been found in a great variety of other intracellular or membrane-associated proteins. The SH3 module might mediate the assembly of specific protein complexes by binding to proline-rich peptides.
Protein with at least one SH3-binding site and which mediates the binding to the Src homology 3 (SH3) region, a module present in a large group of proteins, including cytoskeletal elements and signaling proteins.
Protein which, if defective, causes short QT syndrome, a heart disorder characterized by the presence of a short QT interval on ECG, associated with syncope, palpitations, cardiac arrest and sudden death.
Protein with at least one sialic acid. The term "sialic acid" refers to the group of sugars including neuraminic acid and its derivatives, not to a specific sugar. They are widely distributed in bacteria and animal tissue as components of polysaccharides, glycoproteins and glycolipids. They are typically the terminal residues on cell surface oligosaccharides.
Initiation factors that bind to bacterial DNA-dependent RNA polymerases and promote attachment to specific initiation sites on DNA. Following attachment, the sigma factor is released.
regulation of transcription, DNA-templated
Protein which has a signal sequence, a peptide usually present at the N-terminus of proteins and which is destined to be either secreted or part of membrane components. The signal sequence (usually 20-30 amino acids long) interacts with the signal recognition particle and directs the ribosome to the endoplasmic reticulum where co-translational insertion takes place. Signal peptides are highly hydrophobic but have some positively charged amino acids. Normally, the signal sequence is removed from the growing peptide chain by specific peptidases (signal peptidases) located on the cisternal face of the endoplasmic reticulum.
Protein of the signal recognition particle (SRP) which is a cytosolic ribonucleoprotein complex that induces elongation arrest of nascent presecretory and membrane proteins until the ribosome becomes associated with the rough endoplasmic reticulum or the prokaryotic cytoplasmic membrane.
signal recognition particle, endoplasmic reticulum targeting
Protein which inhibits signal transduction, the process by which extracellular signals induce intracellular responses. Usually a hormone or neurotransmitter binds to a cell surface receptor which is coupled to a second messenger system, such as that involving cAMP, or to an ion channel. The final downstream consequence of signal transduction is a change in the cell's function, such as a modification in glucose uptake or in cell division. Such a change may be the result of an activation or an inhibition event.
negative regulation of signal transduction
Single-pass transmembrane protein (type II, III, and IV) possessing a membrane-spanning domain which targets the protein to the ER membrane. Typical features of signal-anchors are the presence of positively charged residues on the amino terminal side followed by an apolar segment of approx. 20 residues. The amino-acid composition is not very different from typical signal sequences.
Protein of the signalosome complex, a multifunctional protein complex essential for development and possibly involved in the regulation of protein degradation.
Protein found in silk, a strong, soft, lustrous fiber made of fibroin, a structural protein consisting almost entirely of stacked antiparallel beta pleated sheets. It is produced by certain spiders and by the larvae of certain bombycine moths.
Protein which binds at least one sodium, or protein whose function is sodium-dependent. Sodium is an alkali metal, chemical symbol Na.
Protein which is part of a cation channel permeable for sodium found in the plasma membrane and in intracellular membranes. Sodium channels have been classified according to their gating mechanisms, which may depend on changes in the transmembrane electric field (voltage-gated sodium channels) or not (non-voltage-gated sodium channels, e.g. degenerins which are permeable also to lithium and potassium). Voltage-gated sodium channels, by opening in response to membrane depolarization, allow sodium entry and thus the propagation of depolarization along the plasma membrane of nerve, muscle and other electrically excitable cells. They play a role in different processes such as sensation, emotions, thought and movement. Another class of sodium channel is the degenerin/epithelial sodium channel (ENaC) superfamily, which is a group of proteins involved in diverse biological processes, including sodium homeostasis, salt taste, nociception, pain transduction, touch sensation and mechanotransduction.
Protein involved in the movement of sodium ions across energy-transducing cell membranes. Primary active sodium transport is coupled to an energy-yielding chemical reaction such as ATP hydrolysis. Secondary active transport utilizes the voltage and ion gradients produced by the primary transport to drive the cotransport of other ions or molecules. These may be transported in the same (symport) or opposite (antiport) direction.
Protein involved in the active transport system which simultaneously moves two potassium ions into the cell and three sodium ions out of the cell.
Protein involved in the DNA repair system also known as error-prone repair in which apurinic DNA molecules are repaired by the incorporation of a base that may be the wrong base but that permits replication.
Protein involved in an SOS response, which implies the coordinated activation of diverse unlinked genes (ca. 20 in E.coli) involved in DNA repair, error-prone DNA replication, etc., in response to severe DNA damage. The SOS system is tightly regulated and its expression only occurs when absolutely required.
Protein involved in sperm cell development. A process whereby primordial germ cells form mature spermatozoa, which includes spermatocytogenesis (successive mitotic and meiotic divisions) and spermiogenesis (a metamorphic change).
Protein involved in the synthesis of spermidine, a widely distributed polyamine which acts as a growth factor for some microorganisms and stabilizes the membrane structure of bacteria, as well as the structure of ribosomes, some viruses and the DNA of many organisms.
Protein involved in the biochemical reactions of sphingolipids. These are structurally complex saponifiable lipids which contain a fatty acid covalently linked to the amino alcohol sphingosine (or a related base), as backbone structure, to which is attached a polar head group. They are synthesized in the Golgi complex and are important membrane components in both plant and animal cells. They are present in especially large amounts in brain and nerve tissue.
Autosomal dominant spinocerebellar ataxia
Protein which, if defective, causes autosomal dominant spinocerebellar ataxia, a clinically and genetically heterogeneous group of autosomal dominant cerebellar ataxias (ADCA). Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements. Spinocerebellar ataxia is caused by degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. Three clinical types are distinguished, according to the extent of extra-cerebellar signs: cerebellar ataxia with additional features like optic atrophy, ophthalmoplegia, bulbar and extrapyramidal signs, peripheral neuropathy and dementia, is known as ADCA type I; cerebellar ataxia with retinal degeneration and pigmentary macular dystrophy is defined as ADCA type II; pure cerebellar ataxia without additional signs is classified as ADCA type III.
Protein of the spliceosome, a very large complex of small nuclear RNA/protein particles (snRNPs) which assemble with pre-mRNA to achieve RNA splicing.
Protein expressed in the sporozoite stage which is the infectious stage of the malaria parasite. Malaria is transmitted by mosquitos to the vertebrate host. This term also refers to the motile infectious stage of other sporozoans (parasitic protozoans).
Protein involved in the production of spores, i.e. sporulation.
sporulation resulting in formation of a cellular spore
Protein involved in the synthesis of starch, the carbohydrate storage of plants. Starch consists of amylose (a linear alpha(1-4)-glucan) and amylopectin (an alpha(1-4)-glucan with alpha(1-6)-branch points). Starch (glucans and amylopectins) is synthesised via the ADP-glucose pathway by three key enzymes: ADP-glucose pyrophosphorylase, starch synthases and starch branching enzymes. The randomly branched glucan molecules are then specifically debranched via a debranching enzyme in order to produce amylopectins. Amylopectins are branched in highly ordered clusters and are crystalline in nature, but also contain covalently bound phosphate.
Protein which, if defective, causes Stargardt disease (SD). SD is a hereditary degeneration of the macula lutea occurring between the ages of six and twenty, marked by rapid loss of visual accuity and by abnormal appearance and pigmentation of the macular aerea.
In vivo synthesis of steroids (steroidogenesis), a large group of complex polycyclic lipids that consist of a 17-carbon ring system. Examples are bile acids, sterols, various hormones and saponins.
Protein involved in the biochemical reactions of steroids. Steroids are a large group of complex tetracyclic lipids that consist of a 17-carbon-ring system. Examples are bile acids, sterols, various hormones and saponins.
Biosynthesis of steroid hormones which takes place in the mitochondria of the adrenal cortex. Oxidation of two adjacent carbon atoms in the side chain of cholesterol, followed by the cleavage between them, produces pregnenolone, a precursor of all other steroid hormones. The hydroxylation and oxygenation reactions are catalyzed by cytochrome P450 and mixed-functions oxidases that use NADPH and O2.
Protein involved in the synthesis of sterols, any steroid alcohol which are components of cell membranes in plants, animals and fungi.
Protein involved in the metabolism of sterols, any steroid alcohol. Sterols are components of cell membranes in plants, animals and fungi.
Protein which, if defective, causes Stickler syndrome (STL), also known as hereditary progressive arthro-ophthalmopathy. It is a genetically and phenotypically heterogeneous disorder with ocular, oro-facial, auditory and skeletal manifestations. Clinical features include high myopia, vitreo-retinal degeneration, retinal detachment, cleft palate, midfacial hypoplasia, osteoarthritis, and sensorineural hearing loss. Inheritance is autosomal dominant.
Protein which is a source of nutrients for the development or growth of an organism.
Protein involved in the synthesis of streptomycin, an antibiotic substance produced by the soil actinomycete Streptomyces griseus. The three parts of the molecule (streptidine-6-P, dTDP-dihydrostreptose and N-methyl-glucosamine) are synthesized by separate biochemical pathways and the subunits brought together at the end. The final intermediate in the pathway, streptomycin P, becomes biologically active upon removal of the phosphate. The synthesis of the key streptomycin biosynthesis enzymes is mainly regulated by differing levels of factor A. Streptomycin binds to the small subunit of ribosomes of prokaryotic cells and causes inhibition and misreading.
Protein involved in the response to stress, a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of some stressful conditions. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation, hypertonicity, amino acid deprivation).
Protein involved in the transfer of sugars across a biological membrane by a carrier protein.
Protein involved in sulfate respiration, which is the use of sulfate (or other oxidized compounds of sulfur) as the terminal electron acceptor in the anaerobic respiratory metabolism of sulfate- or sulfur-reducing bacteria.
Protein involved in the translocation of sulfate, or sulfate-containing compounds, such as thiosulfate, across a biological membrane.
Protein which is posttranslationally modified by the attachment of at least one sulfate group to a tyrosine residue. Serine and threonine may also serve as sulfate group acceptors.
Bacterial or virus secreted protein that induces a strong T-lymphocyte activity. When a normal antigen stimulates 0,001% of the body's T-cells, superantigens can stimulate up to 20% of body's T-cells. They simultaneously interact with the Vb domain of the T-cell receptor (TCR) and with the class II major histocompatibility complex (MHC) molecules on the surface of an antigen-presenting cell. This compels the MHC to interact with the TCR, thereby inducing T-cells activation. Most superantigens are bacterial toxins, but some are produced by viruses. Staphylococcal enterotoxins are the best known superantigens.
Viral protein that is expressed by a prokaryotic virus, integrated or not, to help protect the host cell from superinfection, a process by which a cell that has previously been infected by one virus subsequently gets coinfected with a different strain of the virus, or another virus. Superinfection exclusion can be achieved for example by expressing viral enzymes that alter a portion of a surface receptor thereby blocking entry of incoming viruses with this receptor specificity. Exclusion protein can also target and block the ejection and/or DNA delivery by new incoming phages.
Protein which suppresses host RNA-mediated gene silencing. The most common form of RNA-mediated gene silencing is RNA interference (RNAi), a sequence-specific RNA-degradation mechanism that operates as a natural antiviral system in plants and invertebrates cells. RNAi is mediated by small interfering RNAs (siRNA) of about 21- to 25-nt that target homologous RNAs for destruction. RNA silencing by endogenous micro-RNAs (miRNAs) may also play a role in the antiviral defences of mammals. miRNAs differ from siRNAs in that they generally base pair imperfectly with target RNAs and inhibit their translation by an unknown mechanism.
Protein found in the film of pulmonary surfactants which cover the alveolar surface of the mammalian lung. These surfactants are composed of 90% phospholipids and 10% proteins.
Protein which contains at least one sushi domain, a motif of approximately 60 amino acids characterized by a framework of four conserved half-cystine residues (1-3 and 2-4 disulfide-bonded) and several other highly conserved residues including proline, tryptophan, tyrosine/phenylalanine and cysteine. This type of structure, also designated SCR (Short Consensus Repeat), is predominantly present in proteins associated with the complement system.
Protein involved in the transport of solutes across a biological membrane in one direction, which depends on the transport of another solute in the same direction. One molecule can move up an electrochemical gradient because the movement of the other molecule is more favorable. Example: the sodium/glucose co-transport.
Protein found in the synapses. Synapses are the communicating cell-cell junctions that allow signals to pass from a nerve cell to a target cell. In a chemical synapse, the signal is carried by a neurotransmitter which diffuses across a narrow synaptic cleft and activates a receptor on the postsynaptic membrane of the target cell. The target may be a dendrite, cell body, neuronal axon, a specialized region of a muscle or a secretory cell. In an electrical synapse, a direct connection is made between the cytoplasms of two cells via gap junctions.
Protein found in synaptosomes, the pinched-off nerve endings and their contents of vesicles and cytoplasm together with the attached subsynaptic area of the membrane of the postsynaptic cell. They are largely artificial structures produced by fractionation after selective centrifugation of nervous tissue homogenates.
Syncytium formation induced by viral infection
Induction by virus of host cell-cell fusion
Polykaryons formation in virally infected cells
Viral protein that mediates fusion of an infected cell with neighboring cells leading to the formation of multi-nucleate enlarged cells called syncytia. Usually these syncytia are the result of expression of a viral fusion protein at the host cell membrane during viral replication. Viruses such as herpesviruses are known to induce the formation of syncytia.
positive regulation of syncytium formation by virus
Protein involved in the systemic lupus erythematosus (SLE), a chronic autoimmune disease where the immune system is over-active and produces too many abnormal antibodies that react with the patient's own tissues. The exact cause of lupus is not known, but heredity, environment and hormonal changes may be involved. The immune complex deposition in many tissues leads to the manifestations of the disease. Immune complexes can be deposited in glomeruli, skin, lungs, synovium, mesothelium, and other places. Many SLE patients develop renal complications.
The T cell receptor (TCR) is the antigen receptor expressed on CD4-positive and CD8-positive T lymphocytes that recognizes complexes of peptides bound to self-MHC molecules on the surface of antigen presenting cells. Structurally, TCR is composed of a heterodimer of two disulfide-linked transmembrane polypeptide chains designated alpha and beta, each containing one terminal immunoglobulin (Ig)-like variable domain, one Ig-like constant domain, a hydrophobic transmembrane region and a short cytoplasmic region. A less common type of TCR, composed of gamma and delta chains, is found on a small subset of T cells and recognizes different forms of antigens. Each T cell expresses a unique TCR that is generated by randomly assorting genes. This ensures that T cells can respond (at the population level) to almost any infection.
Viral protein that forms an icosahedral capsid with a T=1 symmetry to protect the viral genome. The T=1 capsid is composed of 60 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 18 to 35 nm.
Viral protein that forms an icosahedral capsid with a T=13 symmetry to protect the viral genome. The T=13 capsid is composed of 780 subunits, each subunit occupying a quasi-equivalent position. Its diameter ranges from 70 to 80 nm.
Viral protein that forms an icosahedral capsid with a T=147 symmetry to protect the viral genome. The T=147 capsid is composed of 8820 subunits. Its diameter is about 185 nm.
Viral protein that forms an icosahedral capsid with a T=16 symmetry to protect the viral genome. The T=16 capsid is composed of 960 subunits, each subunit occupying a quasi-equivalent position. Its diameter is about 100 nm.
Viral protein that forms an icosahedral capsid with a T=169 symmetry to protect the viral genome. The T=169 capsid is composed of 10140 subunits. Its diameter is about 165-190 nm.
Viral protein that forms an icosahedral capsid with a T=2* symmetry to protect the viral genome. The T=2* capsid is composed of 120 subunits. The T=2* symmetry does not exist under the rules described by Caspar and Klug, strictly speaking the capsid has a T=1 symmetry composed of 60 dimeric subunits. The capsid diameter is about 40 nm.
Viral protein that forms an icosahedral capsid with a T=219 symmetry to protect the viral genome. The T=219 capsid is composed of 13140 subunits. Its diameter is about 130-160 nm.
Viral protein that forms an icosahedral capsid with a T=25 symmetry to protect the viral genome. The T=25 capsid is composed of 1500 subunits, each subunit occupying a quasi-equivalent position. Its diameter is about 90 nm.
Viral protein that forms an icosahedral capsid with a T=3 symmetry to protect the viral genome. The T=3 capsid is composed of 180 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 26 to 40 nm.
Viral protein that forms an icosahedral capsid with a T=4 symmetry to protect the viral genome. The T=4 capsid is composed of 240 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 30 to 40 nm.
Viral protein that forms an icosahedral capsid with a T=7 symmetry to protect the viral genome. The T=7 capsid is composed of 420 subunits, each subunit occupying a quasi-equivalent position. Papillomavirus and Polyomavirus T=7 capsids are composed of pentameric capsomeres for a total of 360 capsid proteins. Its diameter ranges from 45 to 60 nm.
Viral protein that forms an icosahedral capsid with a pseudo T=3 symmetry to protect the viral genome. The pseudo T=pseudo3 capsid is composed of 180 subunits. Each subunit does not occupy a quasi-equivalent position, therefore the structure is called pseudo. The capsid diameter ranges from 26 to 40 nm.
Protein expressed in the infectious tachyzoite stage, a rapidly growing, lytic and disease-causing stage in the life stage of coccidians (e.g. Toxoplasmy). Tachyzoites, which can infect most nucleated cells, replicate inside a parasitophorous vacuole, egress, and then infect neighboring cells. Aggregates of numerous tachyzoites are called clones, terminal colonies, or groups.
Protein found in a target cell cytoplasm, the contents of a target cell within the plasma membrane and which, in eukaryotic cells, surrounds the host nucleus. This term is used to describe a toxin located in the cytoplasm of a target cell.
Protein found in or associated with a target cell membrane, the selectively permeable membrane which separates the target cell cytoplasm from its surroundings. This term is used to describe a toxin located to the cell membrane of a target cell.
Protein which is membrane-bound or membrane-associated with the target membrane, a lipid bilayer which surrounds target cell enclosed spaces and compartments. This selectively permeable structure is essential for effective separation of a target cell or targeet cell organelle from its surroundings. This term is used to describe a toxin located to a membrane of a target cell.
Protein involved in taste signal transduction. Human perceives five basic taste qualities: bitter, salty, sour, sweet, and umami, the taste of glutamate. Taste perception begins when a taste-eliciting molecule, or tastant, interacts with specialized receptors in the membrane of taste receptor cells. Taste responses to bitter, sweet, and umami compounds are initiated by G-protein-coupled receptors and transduced via G-protein signaling cascades. Salty and sour tastes are transduced by ion channels.
Protein that function as a natural sweetener or flavor enhancer. TMPs are found in the fruit or seed of several plants and show no primary sequence similarity. TMPs interact with taste receptors in a potent and specific manner. TMPs are natural and have been used by some cultures for centuries. West Africans have long used TMPs to improve flavor and suppress bitterness of food and drink.
Protein involved in the synthesis of taxol, a complex diterpenoid isolated from the bark of yew (Taxus) species. Taxol is a potent antimitotic agent with activity against a number of leukamias and solid tumors. It has become a chemotherapeutic drug under the generic name of paclitaxel.
Keywords assigned to proteins according to 'technical' reasons.
Protein involved in the synthesis of teichoic acid, a polymer of mainly glycerol phosphate or ribitol phosphate substituted extensively with amino acids and/or sugars. Teichoic acid occurs in the cell wall of Gram-positive bacteria.
Protein that confers resistance to tellurium.
Protein involved in telomere replication, length regulation, structure, etc. The telomere is a nucleoprotein structure comprising the terminal section of a eukaryotic chromosome. It has a specialized structure which is replicated by a special process, thereby counteracting the tendency of a chromosome to be shortened during each round of replication.
Protein involved in the random addition of deoxynucleoside 5'-triphosphate to the 3'end of a DNA initiator.
Protein involved in the synthesis of tetrahydrobiopterin, the reduced form of dihydrobiopterin, a reduced pteridine derivative related to folic acid. It is a coenzyme for the enzyme phenylalanine-4-hydroxylase which is involved in phenylalanine degradation.
tetrahydrobiopterin biosynthetic process
Protein involved in the synthesis of thiamine, a water-soluble vitamin member of the vitamin B complex. It occurs in cells largely as its active coenzyme form thiamine pyrophosphate, formerly called cocarboxylase. Thiamine is necessary in the diet of most vertebrates and some microorganisms. Its deficiency causes beriberi in man and polyneuritis in birds. Thiamine pyrophosphate serves as coenzyme in aldehyde-group transfers.
Protein involved in the degradation of thiamine, a water-soluble vitamin which is a member of the vitamin B complex. It occurs in cells largely as its active coenzyme form thiamine pyrophosphate, formerly called cocarboxylase. Thiamine is necessary in the diet of most vertebrates and some microorganisms. Its deficiency causes beriberi in man and polyneuritis in birds. Thiamine pyrophosphate serves as a coenzyme in aldehyde-group transfers.
Protein which contains at least one thiamine pyrophosphate, the active form of vitamin B1 (thiamine). It is a required coenzyme for the pyruvate decarboxylase, pyruvate dehydrogenase and ketoglutarate dehydrogenase reactions.
Protein found in, or associated with, the thick filaments which are formed by bipolar myosin-II filaments (12-14 nm in diameter, 1.6 mm long) found striated muscle. Myosin filaments elsewhere are often referred to as 'thick filaments', although their length may be considerably less. The myosin heads project from the thick filament in a regular fashion.
Protein which is posttranslationally modified by the formation of a thioester crosslink between two amino acids in the polypeptidic chain(s), usually formed between a cysteine side chain and the carboxamide group of an asparagine or glutamine side chain.
Protein which is posttranslationally modified by the formation of a thioether crosslink between two amino acids in the polypeptidic chain(s), usually formed between a cysteine side chain and the side chain of a serine or a threonine.
Proteolytic enzyme with a cysteine residue (Cys) in its active site. There are many families of thiol proteases. The most well known one is the papain family (C1 in MEROPS classification) which is known to exist in most eukaryotes.
Protein which inhibits the activity of a thiol protease, a class of proteases that contains an active site cysteine residue (Cys), e.g. papain, cathepsins, etc.
cysteine-type endopeptidase inhibitor activity
Protein involved in the synthesis of the essential amino acid threonine.
Proteolytic enzyme with a threonine residue (Thr) in its active site. The prototype members of this class of enzymes are the proteasome catalytic subunits.
Protein which, if defective, causes thrombophilia, a disorder of hemostasis in which the individuals are prone to serious spontaneous thrombosis.
Protein located in or on the thylakoid, a membranous cisterna of the chloroplast. Thylakoids stack up to form the grana or stay as single cisternae and interconnect the grana. The thylakoid contains the photosynthetic pigments, reaction centers and electron-transport chain. Thylakoid, where photosynthesis occurs, are also found in cyanelles and in photosynthetic bacteria where they are the extensive invaginations of the plasma membrane.
Protein precursor of thyroid hormones which are secreted by the thymus gland and participate in the development of the lymphoid system as well as the maturation of the cellular immune response. Also used for proteins which bind thyroid hormones or thyroid hormone receptor antagonists.
Protein involved in the synthesis of thyroid hormones.
Protein which is a component of the tight junction or are associated with it. These specialized regions of the plasma membrane prevent the diffusion of dissolved molecules between adjacent epithelial cells, seal off body cavities such as intestine or stomach lumen and prevent the diffusion of membrane proteins and glycolipids between the apical and basolateral regions of the plasma membrane.
Protein involved in tissue remodeling. As an example the matrix-degrading plasminogen activators (PAs) and matrix metalloproteinases (MMPs) are general proteolytic enzyme systems which mediate tissue remodeling and tissue destruction in a variety of physiological and pathological conditions, including ovulation, angiogenesis, implantation, tumor invasion and inflammatory diseases such as rheumatoid arthritis (RA).
Protein with a TonB box. In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB these receptors bind their substrates but do not carry out active transport. TonB also interacts with some colicins and is involved in the energy dependent, irreversible steps of bacteriophages phi-80 and T1 infection.
Enzymes capable of altering the degree of supercoiling of double-stranded DNA molecules. Various topoisomerases can increase or relax supercoiling, convert single-stranded rings to intertwined double-stranded rings, tie and untie knots in single stranded and duplex rings or catenate and decatenate duplex rings. Any enzyme that cleaves only one strand of a DNA duplex and then reseals it is classified as a type I topoisomerase (Topo I). Type II topoisomerases (Topo II) change DNA topology by breaking and rejoining double-stranded DNA.
Naturally-produced poisonous protein that damages or kills other cells, or the producing cells themselves in some cases in bacteria. Toxins are produced by venomous and poisonous animals, some plants, some fungi and some pathogenic bacteria. Animal toxins (mostly from snakes, scorpions, spiders, sea anemones and cone snails) are generally secreted in the venom of the animal.
Bacterial, archaeal or viral protein belonging to a toxin-antitoxin (TA) system. Toxin protein expression is poisonous to the cell and is counteracted by its co-expressed, short-lived "antidote" antitoxin. Antitoxins can be protein (type II, IV, V, VI) or RNA (type I, III) and act directly or indirectly on the toxin protein or transcript. Genes for the 2 components are closely linked; in many type II TA systems the toxin-antitoxin complex regulates transcription of its operon. Toxins belong to recognizable protein families, antitoxins usually do not. Orphan toxin genes are occasionally found in complete genomes.
Protein which is posttranslationally modified on a tyrosine residue to form TPQ. This modification of a strictly conserved active-site tyrosine residue proceeds via the hydroxylation of tyrosine to Topa (Trihydroxyphenylalanine) and then to TPQ (Topaquinone). It is a self-processing pathway requiring only the protein, copper and molecular oxygen. TPQ is the redox cofactor of most copper-containing amine oxidases.
Protein with at least one TPR repeat. The TPR repeat of typically 34 amino acids was first described in the yeast cell division control protein 23 (CDC23) and later found to occur in a large number of proteins. A function for this repeat seems to be protein-protein interaction.
Protein involved in the transfer of genetic information from DNA to messenger RNA (mRNA) by DNA-directed RNA polymerase. In the case of some RNA viruses, protein involved in the transfer of genetic information from RNA to messenger RNA (mRNA) by RNA-directed RNA polymerase.
Protein involved in transcription antitermination, the process whereby RNA polymerase is allowed to read through specific RNA secondary structures that normally terminate transcription.
Protein involved in the regulation of the transcription process.
Protein involved in transcription termination.
DNA-templated transcription, termination
Protein which converts an input signal into an output signal of a different form.
Enzyme that transfers a chemical group, e.g. a methyl group or a glycosyl group from one compound (donor) to another compound (acceptor).
Proteins which have an N-terminal presequence which directs them to an organelle (chloroplast, mitochondria, microbody, cyanelle). The transit peptide is required for their transport across the relevant membranes from their site of synthesis in the cytoplasm.
Protein involved in the regulation of peptide formation on ribosomes, directed by messenger RNA (mRNA).
Protein which is involved in the translational shunt, an unusual translation process in which ribosomes are loaded onto mRNA at the 5'-cap structure, start scanning for a short distance before bypassing the large internal leader region and initiating at a downstream start site. Shunting operates in plants, animals, and yeast translational systems, both in vivo and in vitro.
Protein that uses enzyme activity to effect transmembrane transport, as exemplified by transmembrane transport coupled to ATP hydrolysis and oxidoreductases involved in transmembrane proton or electron transport. Not to be confused with ligand-gated ion channels or other transmembrane transporters without enzyme activity.
Protein involved in the transport of proteins across a membrane. As an example translocation into the nucleus occurs via nuclear pores which allow rapid diffusion of small molecules. Larger molecules (maximum 9 nm) take longer. Translocation into the mitochondria or chloroplast occurs at sites of adhesion between the outer and inner membranes and is driven by ATP hydrolysis as well as the electrochemical gradient of the inner membrane.
Protein with at least one transmembrane domain, a membrane-spanning helical or beta-stranded domain embedded in a membrane.
Protein with at least one transmembrane beta stranded domain, a membrane-spanning stretch, typically 5-10 amino acids long, whose peptide backbones are almost fully extended with the sidechains of two neighboring residues projected in the opposite direction from the backbone. Two or more hydrogen bonded (parallel or anti-parallel) beta strands form a beta sheet. A beta barrel is formed by a closed beta sheet around a central pore. Beta barrels consist usually of an even number of beta strands (between 8 and 24), they are found only in bacterial outer membranes, mitochondria and plastids.
Protein with at least one transmembrane helical domain, a membrane-spanning domain with an hydrogen-bonded helical configuration, including alpha-, 3-10-, and pi-helices. The transmembrane alpha-helix is very common, while the 3-10-helix is found at the ends of alpha-helices and the pi-helix, is more rare.
Protein involved in the transport of a molecule (metabolite, protein, etc), a ion or an electron across cell membranes, inside the cell or in a tissue fluid.
Protein encoded by a transposable element, or transposon, a mobile DNA segment that can replicate and insert a copy at another site within the genome. Simple transposons only contains genes needed for insertion. More complex types also carry genes with functions unrelated to insertion, e.g. genes for resistance to antibiotics or heavy metals.
Protein involved in the movement of a specific DNA sequence - generally known as a transposable element or transposon - to another location within the genome by replication of the sequence and insertion of the copy at its target site, at random or at some specific site. Proteins necessary for the transposition, such as the enzyme transposase, are usually encoded by the transposable element itself.
Protein involved in the tricarboxylic acid cycle, a series of metabolic reactions in aerobic cellular respiration, which occurs in the mitochondria of animals and plants and in which acetyl-CoA, formed from pyruvate produced during glycolysis, is completely oxidized to CO2 via the interconversion of various carboxylic acids. It results in the reduction of NAD and FAD to NADH and FADH2, whose reducing power is then used indirectly in the synthesis of ATP by oxidative phosphorylation. The TCA cycle also provides intermediates for many other biosynthetic processes.
Protein that confers, on bacteria or other microorganisms, the ability to withstand the antibacterial agent trimethroprim that inhibits dihydrofolate reductase (DHFR), an enzyme required for de novo glycine and purine synthesis.
Protein encoded by a gene which has a triplet repeat expansion, i.e. the increase of triplet (trinucleotide) repeats within the gene sequence. The length of such repeats is frequently polymorphic, and there is often a correlation between repeat length and disease severity.
Protein involved in the processing of the primary tRNA transcript to yield a functional tRNA. Transcription of tRNA genes results in a large precursor molecule which may even contain sequences for several tRNA molecules. This primary transcript is subsequently processed by cleavage and by modification of the appropriate bases.
Protein which binds transfer RNA, for example some ribosomal proteins or some aminoacyl-tRNA synthetases.
Protein expressed in the trophozoite stage, a motile replicating and disease-causing stage of in the life cycle of some sporozoan parasites.
Protein involved in trypanosomiasis, a human or animal disease caused by Trypanosoma, a genus of parasitic flagellate protozoa. Such diseases include African sleeping sickness, Nagana and American Chagas' disease.
Protein involved in the synthesis of the aromatic amino acid tryptophan (Trp) in bacteria, fungi and plants from chorismate. Trp is needed to synthesize proteins and as a precursor to niacin, serotonin and melatonin.
Protein involved in the degradation of the aromatic amino acid tryptophan (Trp).
Protein which contains at least one tryptophan tryptophylquinone (TTQ) cross-link modification. TTQ, the cofactor of methylamine dehydrogenase (MADH), is formed by oxidation of the indole ring of a tryptophan to form tryptophylquinone followed by covalent cross-linking with another tryptophan residue. MADH converts primary amines to their corresponding aldehydes plus ammonia. During the catalytic cycle, TTQ mediates electron transfer from the substrate to a copper protein, amicyanin. These electrons are transferred to the respiratory chain via a C-type cytochrome.
Protein on the surfaces of tumor cells detected by cell-mediated immunity. Different categories of tumor antigens which induce cytotoxic T lymphocyte (CTL) responses in vitro and in vivo, have been identified. These are, namely, "cancer testis" (CT) antigens expressed in different tumours and normal testis, melanocyte differentiation antigens, point mutations of normal genes, self antigens that are overexpressed in malignant tissues and viral antigens.
Protein that suppresses tumorigenesis. Tumor suppressors generally function as negative regulators of cell cycle progression or cell proliferation. They may act to enforce cell cycle arrest in response to specific signals, such as DNA damage, thereby allowing DNA repair to occur prior to DNA replication. Tumor suppressors that act in this way include TP53 and its downstream effector CDKN1A/p21. They may also act to induce programmed cell death (apoptosis) in response to specific developmental signals or under circumstances where DNA repair cannot be completed. Tumor suppressors that act in this way include PTEN and BAX.
Protein which binds at least one tungsten atom, or protein whose function is tungsten-dependent. Tungsten is a metallic element, chemical symbol W.
Two-component sensory transduction system
Two-component signal transduction system
Protein involved in a system responding to environmental changes characterized usually by a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and a response regulator to which the phosphoryl group is transferred. The responder is typically a DNA-binding protein that regulates transcription. Several of these systems are quite complex, involving many proteins in a signaling cascade or contributing to several responses simultaneously. They are involved in a variety processes such as chemotaxis, osmoregulation, magnesium transport, pH tolerance, sporulation, or response of virulent species to host cell's environments.
Protein involved in the synthesis of the aromatic amino acid tyrosine. In microorganisms and plants, tyrosine is synthesized from chorismate via a simple pathway using prephenate as an intermediate. In rat, this nonessential amino acid is produced by hydroxylating the essential amino acid phenylalanine.
Protein involved in the degradation of the aromatic amino acid tyrosine. In mammals, tyrosine degradation is catalyzed by a series of 5 enzymatic reactions which yield acetoacetate (ketogenic) and the Krebs cycle intermediate fumarate (glucogenic).
Enzyme which catalyzes the transfer of the terminal phosphate of ATP to a specific tyrosine residue on its target protein. Many of these kinases play significant roles in development and cell division. Tyrosine-protein kinases can be divided into two subfamilies: receptor tyrosine kinases, which have an intracellular tyrosine kinase domain, a transmembrane domain and an extracellular ligand-binding domain; and non-receptor (cytoplasmic) tyrosine kinases, which are soluble, cytoplasmic kinases.
Protein which interacts with ubiquinone. This fat soluble benzoquinone has a long isoprenoid side chain, which varies in length depending on the species. For example, S.cerevisiae has CoQ-6, E.coli has CoQ-8, rat and R.capsulatus have CoQ-9 and S.pombe, G.suboxydans and humans have CoQ-10. Ubiquinone is a carrier of hydrogen atoms (protons plus electrons) and functions as an ubiquitous coenzyme in redox reactions, where it is first reduced to the enzyme-bound intermediate radical semiquinone and in a second reduction to ubiquinol (Dihydroquinone; CoQH2). Ubiquinone is not tightly bound or covalently linked to a protein complex but is very mobile.
Protein involved in the synthesis of ubiquinone which involves the conversion of chorismate into 4-hydroxy-benzoate, to which is added six to ten isoprene units to form polyprenyl phenol. The addition of a further oxygen atom at C3, followed by the transfer of three methyl groups from S-adenosine methionine gives rise to ubiquinol, which is further reduced to ubiquinone (6-polyprenyl-2,3-dimethoxy-5-methyl-1,4-benzoquinone).
Protein which is posttranslationally modified by the attachment of at least one ubiquitin-like modifier protein, such as ubiquitin, SUMO, APG12, URM1 or RUB1. Ubiquitin, for example, is linked through a isopeptide bond between its C-terminus and the epsilon group of a lysine residue present on either another ubiquitin-like modifier protein or a target protein.
Ubiquitin-like modifier conjugation pathway
Protein involved in ubiquitin-like modifier processing, activation, conjugation or deconjugation such as Ubl-activating enzymes (E1s), Ubl-conjugating enzymes (E2s), Ubl-protein ligases (E3s), some thiol proteases (Ubiquitin carboxyl-terminal hydrolases (UCH), Ubiquitin-specific processing proteases (UBP) and ubiquitin-like proteases) and the ubiquitin-like modifier proteins. Besides signaling proteolysis, ubiquitination for example can be a signal for trafficking, kinase activation and other nonproteolytic fates.
Protein involved in the unfolded protein response. An accumulation of unfolded proteins in the ER lumen triggers a stress response, resulting in the transcriptional induction in the nucleus of a set of genes, whose products are involved in protein folding, assembly and modification as well as in phospholipid biosynthesis. The unfolded protein response (UPR) is the intracellular pathway that mediates signaling from the endoplasmic reticulum (ER) to the nucleus. UPR is also tightly linked to ER-associated protein degradation (ERAD). UPR is a ubiquitous mechanism observed in all eukaryotes from humans to yeast.
Protein involved in the urea cycle. This is a metabolic pathway in which ammonia, produced during amino acid degradation, is converted to urea in the liver, through a series of reactions that are distributed between the mitochondrial matrix and the cytosol.
Sensorineural deafness with retinitis pigmentosa
Protein which, if defective, causes Usher syndrome, an autosomal recessive disorder characterized by sensorineural hearing loss and retinitis pigmentosa leading to visual impairment. There are three clinical subtypes: Usher syndrome type 1 (USH1), characterized by congenital profound deafness, constant vestibular dysfunction, and prepubertal onset of retinitis pigmentosa; Usher syndrome type 2 (USH2), associated with moderate to severe hearing loss, normal vestibular function, and onset of retinitis pigmentosa during the second decade of life; and Usher syndrome type 3 (USH3), characterized by progressive hearing loss, variable vestibular function, and adult onset retinitis pigmentosa.
Protein related to the vacuole of a cell. The precise form and function of vacuoles may vary between phyla. Plant vacuoles are among the best characterized. They are generally large fluid-filled compartments in the cytoplasm, bounded by a membrane called the tonoplast; individual vacuoles can fuse to form larger species. Examples include the lytic vacuole, the storage vacuole and the lutoid. One important function of plant vacuoles is the maintenance of hydrostatic pressure. Other eukaryotes employ vacuoles for a variety of purposes, including storage (as in the yeast lysosome/vacuole), secretion and phagocytosis. In Protozoa, contractile vacuoles can be used to discharge water from the cytoplasm to the external environment. Aquatic microorganisms may employ gas vacuoles (composed of clusters of inert gas vesicles) to provide buoyancy.
Protein whose function is vanadium-dependent. Vanadium is a transition metal, chemical symbol V.
Protein which is vasoactive, i.e. has a constricting or dilating effect on the caliber of blood vessels.
Protein which constricts the caliber of blood vessels.
Protein which dilates the caliber of blood vessels.
Viral attachment to host adhesion receptor
Virion surface protein implicated in the initial binding to a specific host adhesion molecule. Adhesion receptors can be for example proteoglycans, sialic acids or a protein receptor. This initial attachment is not sufficient for triggering virus entry into host cell. In prokaryotic viruses, the primary attachment is called reversible adsorption.
adhesion receptor-mediated virion attachment to host cell
Viral surface protein implicated in the binding to specific host surface molecule(s). This binding can lead to virion entry into the host cell, it can trigger signaling pathways, or it can allow the virion to be carried by the host cell to a specific organ.
Virion protein involved in the primary attachment to host flagellar receptor. This attachment allows the prokaryotic virus to move along the host flagellum to find its entry receptor for viral genome penetration. Some prokaryotic viruses such as bacteriophages Chi or PV22 specifically interact with their host's flagellum, move toward the base of the flagellum to come in contact with the host cytoplasmic membrane and deliver the viral genome into the host cytoplasm.
virion attachment to host cell flagellum
Virion protein involved in the interaction with bacterial pili, which are retractile filaments that protrude from bacteria with 2 membranes (Gram-negative bacteria). Binding to the pilus is followed by retraction of the pilus, which translocates the bound virion to the bacterial surface and allows subsequent viral genome penetration into host cytoplasm. Bacteriophages M13, f1, fd, R17, Qbeta, Pf1, Pf3, phiKMV or phi6 for example utilize the host cell pilus as an attachment structure.
Virion surface protein implicated in the binding to a secondary specific host surface molecule(s), which triggers the internalization of viral genome and possibly other viral components into the host cell. In prokaryotic viruses, the attachment to a host entry receptor is called irreversible adsorption.
entry receptor-mediated virion attachment to host cell
Viral protein part of the virion base plate of tailed prokaryotic viruses such as Caudovirales. The baseplate is a multiprotein component at the end of the tail and to which fibers of tailed phages may be attached. Sometimes referred to as the tail tip or tip structure in Siphoviridae.
Viral protein involved in the budding of a viral particle through a cellular membrane into the extracellular space or into a cellular compartment.
Viral budding via the host ESCRT complexes
Viral protein which recruits the cellular ESCRT (Endosomal Sorting Complex Required for Transport) to mediate host-assisted viral budding. Specific motifs in enveloped viruses' proteins called late assembly domains (L-domains) are responsible for recruiting the ESCRT machinery directly or via ESCRT-associated proteins like PDCD6IP.
Viral protein involved in the assembly of the capsid. In most cases virion assembly is spontaneous, but viruses like adenoviruses, herpesviruses, microviruses and tailed bacteriophages need the help of scaffolding proteins to assemble their capsid. Maturation steps that remove the scaffolding proteins and induce structural changes in the assembled capsid are also often part of the assembly process.
Viral protein involved in the refolding and structural rearrangements of the procapsid shell that give rise to the more stable mature capsid structure. These maturation events occur during the intracellular capsid assembly process. In many cases, procapsid maturation is initiated by the activation of a viral protease. Most bacterial viruses as well as Herpesviruses assemble as a procapsid that mature through a massive conformational change of the surface shell.
Viral genome injection via long contractile tail
Viral protein that constitutes the contractile ejection system carried by some tailed prokaryotic viruses such as the Myoviridae. This structure is able to penetrate the host cell envelope, to deliver the viral genome, and possibly some specific proteins, into the cell cytoplasm. A contractile ejection system is composed at least of the contractile sheath, the internal noncontractile tube, the baseplate and the terminator complex. Sheath contraction drives the rigid internal tube through the host cell envelope. Proteins of the ejection apparatus can play an active or a structural role in ejection.
viral genome ejection through host cell envelope, contractile tail mechanism
Viral protein involved in the synthesis of multiple copies of the viral DNA genome. The replicated genomes provide support for further viral transcription or are assembled into progeny virions.
Protein of the viral envelope, a lipoprotein membrane which forms the outermost layer of the virion in certain viruses.
Virally encoded toxin that acts as a host virulence factor against another organism. Viral exotoxins are mostly expressed from integrated viral genomes. Bacterium host, bacterial populations, and the encoding virus/provirus probably benefit from the expression of such exotoxins. Although prokaryotic viruses can kill their host if they switch to the lytic cycle, provirus encoding exotoxins (e.g. shiga toxin, diphtheria toxin) are often retained for the sake of bacterial utility.
Viral protein involved in the extrusion of viral particles from the host prokaryotic cell. Extrusion is a concerted mechanism of assembly and secretion used by filamentous phages to release mature viral particles without inducing host cell lysis.
Viral protein that is involved in or facilitates the conversion of a linear double stranded DNA viral genome into a circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). Circular genomes can support rolling circle replication and, for many viruses, genome circularization is also necessary for latency.
Viral genome ejection through host cell envelope
Viral genome ejection through host membranes
Viral protein that constitutes the ejection system carried by some prokaryotic viruses. These structures are able to penetrate the host cell envelope in order to deliver the viral genome, and possibly also some specific proteins, into the cell cytoplasm.
Viral protein involved in latent provirus DNA excision from the host genome following induction. Bacteriophage lambda for example expresses an excisionase that manages excision of the viral genome from the host genome.
Viral protein involved in the integration of a virus genome into the host DNA. Integrated viral DNA is referred to as a provirus in the case of retroviruses or prophage in the case of prokaryotic viruses. The integrated viral genome does not necessarily make new DNA copies of itself while integrated into a host genome. Instead, it can remain latent and be passively replicated along with the host genome and passed on to the original cell's offspring; all descendants of the infected cell will also bear it in their genomes. The host's environmental conditions changes can however reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection). Integration is a crucial step in replication of retroviruses, as well as some phages. Integration is not part of the viral replication cycle of phycodnaviruses, adeno-associated virus type 2, and human herpesvirus 6A genome, but can occasionally occur.
establishment of integrated proviral latency
Protein involved in actively packaging the replicated viral genome into a protective shell or envelope. Such packaging proteins are present for example in adenoviruses, herpesviruses and tailed bacteriophages. In bacteriophages, the packaging proteins complex is involved in recognizing and selecting a neo-synthesized viral genome in order to translocate it into a pre-assembled empty procapsid. DNA cleavage is sometimes coupled to genome packaging as well as maturation steps that induce structural changes in the assembled capsid.
Viral protein involved in host immune evasion thereby optimizing viral growth and dissemination. Viral immune evasion strategies are typical of viruses which persist in their host throughout life. For example: Herpesviridae, Adenoviridae, Poxviridae and Retroviridae have developed subversions of the MHC class I antigen-presentation pathway. In order to reduce the effectiveness of cytotoxic T-lymphocytes immunity, they express proteins that either down-modulate MHC class I expression (degradation or mislocalization) or interfere with the antigen binding/presentation process (down-regulation of the expression of the transporter associated with antigen processing TAP). Some proteins of these virus families also down-regulate other molecules involved in immune recognition.
Small transmembrane protein that homo-oligomerizes to form a viral ion channel usually expressed in the viral envelope and host cell membranes. These channels affect membrane permeability to ions and play an important role in facilitating virus entry, assembly and release, as well as modulating the ion homeostasis of host cells. Viral ion channels are not necessarily required for the production of infectious virions, although their expression usually significantly increases growth. During influenza A virus entry for example, the M2 proton channel allows protons from the acidic endosome to enter the enveloped virion, initiating pH-dependent uncoating of the genome. In certain influenza A subtypes, M2 also equilibrates the intraluminal pH of the trans-Golgi network with the cytoplasm, preventing premature conformational changes in the viral fusion protein during budding.
pore formation by virus in membrane of host cell
Viral protein expressed primarily to establish, maintain or terminate latency, the part of the viral life cycle during which a virus lies dormant (latent) within a cell. This part of the virus life cycle is called the lysogenic part in prokaryotic viruses. During latency, the viral genome can either exist as a provirus integrated in the host genome (proviral latency) or as a linear or circular plasmid in the host cell (episomal latency). The virus does not replicate, but is passively duplicated when the host divides. In eukaryotes for example, HHV-1 and HHV-3 establish episomal latency in neurons. HIV is integrated as a provirus in the genome of resting CD4-positive T cells, allowing the virus to persist for years. Following changes in the environmental conditions of the host, reactivation of the virus can occur leading to viral transcription and production of new infectious viruses.
Viral latency initiation and maintenance
Viral protein expressed primarily to establish and maintain latency, the part of the viral life cycle during which a virus lies dormant (latent) within a cell. This part of the virus life cycle is called the lysogenic part in prokaryotic viruses. During latency, the viral genome can either exist as a provirus integrated in the host genome (proviral latency) or as a linear or circular plasmid in the host cell (episomal latency). The virus does not replicate, but is passively duplicated when the host divides.
Viral long flexible tail ejection system
Viral genome injection via long noncontractile tail
Viral protein that constitutes the noncontractile ejection system carried by some long-tailed prokaryotic viruses such as the Siphoviridae. This ejection system is composed at least of a noncontractile tube and a tail tip which is able to penetrate the host cell envelope to deliver the viral genome, and possibly some specific proteins, into the cell cytoplasm. Proteins of the ejection apparatus can play an active or a structural role in ejection.
viral genome ejection through host cell envelope, long flexible tail mechanism
Protein that organises and maintains virion structure. It usually interacts directly with cellular membranes and is involved in the budding process. In some enveloped RNA viruses, it acts as a bridge between virion membrane and nucleocapsid.
Plant viral protein that enables the viral nucleic acid to move between adjacent plant cells via the plasmodesmata.
transport of virus in host, cell to cell
Viral protein conjugated with nucleic acid (DNA or RNA).
Protein component of the viral occlusion body, a crystalline protein matrix which surrounds the nucleocapsids of some insect viruses (baculoviridae, entomopoxvirinae, cypovirus). Viral occlusion bodies are produced either in the nucleus (baculoviridae) or in the cytoplasm (poxvirinae and cypovirus) of the infected cells and confer resistance to adverse environmental conditions on viruses. They are made from polyhedrin (nucleopolyhedrovirus, cypovirus), granulin (granulovirus), spheroidin and spherulin (entomopox-virinae) and are dissolved by the alkaline pH of the insect gut, thus resulting in the release of infectious virus particles.
Viral protein involved in the entry of the entire virion, some of its contents or at least its genetic material into the host cell cytoplasm. Entry is achieved through pore formation, membrane fusion, pilus retraction, ejection, permeabilization and/or endocytosis mechanisms. Penetration reactions occur mainly in five locations: the cell membrane, early and late endosomes, caveosomes, and the ER. In prokaryotes, membrane fusion, pore formation through a puncturing device, ejection, pilus retraction or permeabilization occur at the plasma membrane, as well as at the outer membrane in prokaryotes with 2 membranes.
Viral penetration into host cytoplasm via pilus retraction
Viral protein involved in the entry of the virion into the host cytoplasm via the host pili, which are retractile filaments that protrude from bacteria with 2 membranes (Gram-negative bacteria). Entry of bound prokaryotic viruses such as filamentous viruses is achieved through the retraction of host pilus and translocation of the virion through the basis of the pilus to reach the host cytoplasm. Examples of bacteriophages which utilize the host cell pilus to penetrate into host cytoplasm are bacteriophages M13, f1, fd, R17.
viral entry into host cell via pilus retraction
Viral protein necessary for the penetration of the viral genome into the host cell nucleus either via active nuclear transport through nuclear pore complexes (NPCs) or DNA injection through the nuclear membrane. Nuclear membrane permeabilization might also be possible. Viruses can also enter the nucleus during mitosis when the nuclear membrane temporarily disintegrates (e.g. most retroviruses). All these strategies to cross the nuclear envelope barrier are associated with various levels of capsid disassembly, since virus can pass intact (e.g. papovaviruses) or, in the case of injection, only the viral genome enters the nucleus (e.g. herpesviruses).
Viral penetration via lysis of host organellar membrane
Viral membrane-lytic protein, usually associated with the viral capsid or released through partial programmed disassembly of the capsid, that induces major rupture of the bilayer integrity of host endosomal, lysosomal, or caveosomal membrane to allow viral escape and penetration into the cytoplasm. These viral lytic proteins may need to be activated, mostly through endosomal acidic pH or receptor binding to display membrane lytic activity. Viruses such as human adenoviruses group C and D lyse the host endosomal membrane to penetrate into the host cytoplasm.
lysis of host organelle involved in viral entry into host cell
Viral penetration via permeabilization of host membrane
Viral penetration via host membrane disruption by virus
Viral penetration via perforation of host membrane by virus
Viral membrane-penetration protein, usually associated with the viral capsid or released through partial programmed disassembly of the capsid, that locally permeabilizes the bilayer of a host membrane to allow virion penetration into the cytoplasm. Viral membrane-penetration proteins often need to be activated, mostly through endosomal acidic pH or receptor binding to display their membrane penetrating activity. Non-enveloped viruses such as parvovirus, human reovirus, BDV, BTV, rotavirus, papillomavirus, Flock house virus permeabilize the host endosomal membrane to penetrate the host cytoplasm.
permeabilization of host organelle membrane involved in viral entry into host cell
viral entry via permeabilization of inner membrane
Viral primary envelope fusion with host outer nuclear membrane
Viral protein implicated in fusion of the herpesviruses' primary envelope with the host outer nuclear membrane during egress. During egress, herpesviruses acquire a transitory, primary envelope as they bud at the inner nuclear membrane and gain access to the perinuclear space. This membrane is lost by fusing with the outer nuclear membrane during nuclear exit.
fusion of viral membrane with host outer nuclear membrane
Viral protein involved in virus reactivation from latency to replication, thereby putting an end to the latency phase in the viral life cycle. Changes in the environmental conditions of the host often reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection).
A switch in the host range specificity occurs in some bacterial viruses through massive sequence variation of their host-binding receptor. Sequence variation can be induced by site-specific inversion of a DNA segment in their genome or by a diversity-generating retroelement. Inversion is catalyzed by a specific recombinase called invertase and consists of a reciprocal recombination event within two inverted repeats present in the viral genome that leads to the alternate expression of two different sets of genes involved in tail fiber biosynthesis. Mu-like viruses and P1-like viruses, for example, encode a recombinase responsible for the switch in the targeted host. Diversity-generating retroelements (DGR) like in BPP-1 virus also allow tropism switching by creating a mutant copy of an invariant DNA template repeat by transcription and reverse transcription and introducing this mutated sequence in the receptor-binding protein sequence.
Viral protein involved in the release of virions from an infected cell to allow cell-to-cell spread of virus. Once assembled at the replication site, viral particles can be released by budding, exocytosis, extrusion or host cell lysis. Some viruses also mediate direct transport of their viral genome to adjacent cells thanks to movement proteins.
Viral protein involved in the SYnthesis of multiple copies of the viral RNA genome. The replicated genomes provide support for further viral transcription or are assembled into progeny virions.
Viral genome injection via short noncontractile tail
Virion protein that constitutes the noncontractile ejection system carried by some short-tailed prokaryotic viruses such as some Podoviridae. This ejection system is composed at least of the tail tube and ejection proteins. Upon receptor binding, proteins located inside the capsid (head) rearrange to extend the tail tube, creating a channel spanning the periplasmic space. This hydrophilic channel directs the viral genome, and possibly some specific proteins, into the cytoplasm and protects it from periplasmic nucleases. Once the viral genome is in the host cytoplasm, the channel collapses and seals. Bacteriophage T7 for example expresses ejection proteins that partition into the host outer and cytoplasmic membranes and allow transport of viral DNA across the host envelope. Proteins of the ejection apparatus can play an active or a structural role in ejection.
viral genome ejection through host cell envelope, short tail mechanism
Viral protein involved in tail assembly. Some tailed bacteriophages need chaperones that help with the assembly of their tail.
Viral protein involved in tail fibers or spike assembly. Some tailed bacteriophages need chaperones that help with the assembly of their fibers or spikes. T4 for example encodes a general tail fiber chaperone that is needed for the correct assembly of the short and long tail fiber proteins.
Viral fibrous protein part of the virion fiber, which is a thin long rod like structure, unique or multiple, appended to the tail of prokaryotic viruses and used for attachment to the host cell. Shorter appendages are called tail spikes (e.g. Podoviridae) or whiskers.
Viral protein part of the virion tail of prokaryotic viruses such as Caudovirales. The tail is usually composed of a tube, a tail sheath when contractile, a base plate or tip and tail long or short fibers.
Viral protein part of the virion tail sheath of prokaryotic viruses. The tail sheath is an external contractile envelope wrapping the tail tube in some viruses (e.g. Myoviridae).
Viral protein part of the virion tail tube of prokaryotic viruses such as Caudovirales. The tail tube is the channel for DNA ejection into the host cytoplasm and can be wrapped in an external contractile envelope in some viruses (e.g. Myoviridae). Also called tail shaft in some Siphoviridae.
Viral Protein involved in the synthesis of messenger RNAs. The process can occur in the host cell nucleus or cytoplasm, and the genomic template can be viral DNA or RNA, single- or double-stranded.
Viral protein involved in the maturation of the immature virion into the mature virion, once the virion has been released from the host cell. Maturation usually involves proteolysis events and changes in the folding of the virion proteins.
Viral structural protein of the tegument, a protein structure that resides between the capsid and envelope of herpesviruses and which appears amorphous in electron micrographs.
Protein involved in virulence, the degree of pathogenicity within a group or species of microorganisms or viruses, as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. In some cases, the virulence factor can be borne by another organism in symbiosis with the one whose virulence is increased. Some prokaryotic viruses/proviruses for example bear exotoxins that increase the virulence of their host. A well-known bacterial exotoxin encoded by a provirus is the diphtheria toxin.
Viral protein involved in virus internalization by the host cell via endocytosis. Endocytosis can occur via: clathrin-mediated endocytosis, caveolin-mediated endocytosis or clathrin- and caveolae-independent endocytosis.
endocytosis involved in viral entry into host cell
Viral protein involved in the virion entry into a host cell. Entry is a multistep process that mostly requires binding to the target cell, penetration into the host cell cytoplasm, intracellular transport of viral components and genome release to the replication site of the virus.
Protein involved in vision, the special sense by which objects in the external environment are perceived by the light they give off or reflect, which stimulates the photoreceptors in the retina.
Protein which interacts with any form of the fat-soluble vitamin A. There are three active forms of vitamin A: retinol, retinal (retinaldehyde) and retinoic acid, which are all derived from the plant beta-carotene (provitamin A). Vitamin A is essential to night vision and is also required for epithelium differentiation, bone development, reproduction and the immune response. Symptoms associated with a deficiency of vitamin A are night blindness, changes in the eyes, poor bone development, weak tooth enamel and dry skin.
Protein which contains at least one vitamin C as cofactor. This water-soluble vitamin is a reducing agent in a number of reactions. As cofactor, it is required for the hydroxylation of proline residues in collagen, and in many other metabolic reactions such as in the catabolism of tyrosine and the synthesis of bile acids. Deficiency in vitamin C leads to the disease scurvy.
Protein which interacts with any form of the fat-soluble vitamin D or protein whose transcription is regulated by the biologically active form of vitamin D, i.e. 1,25-dihydroxy vitamin D3 (1,25 dihydroxycholecalciferol) also termed calcitriol. Active calcitriol is derived from ergosterol (produced in plants) and 7-dehydrocholesterol (produced in the skin). Ergocalciferol (vitamin D2) and cholecalciferol (vitamin D3) are formed by UV irradiation of ergosterol and 7-dehydrocholesterol, respectively, and processed by the same enzymatic pathway in the body to D2-calcitriol and D3-calcitriol. Deficiency in vitamin D leads to the disease rickets, in children, and osteomalacia, in adults.
Protein present in particles of Very Low-Density Lipoproteins or protein which interacts with them. VLDL are composed of 50% triacylglycerols, 12% cholesteryl esters, 7% free cholesterol, 18% phospholipids, and 10% proteins including apoB-100, apoC-I, apoC-II, apoC-III and apoE. Excess fatty acids or carbohydrate in the diet can be converted into triacylglycerols in the liver and packaged into VLDL. These lipoproteins are transported by the blood to muscle and adipose tissue, where activation of lipoprotein lipase by apoC-II causes the release of free fatty acids from the triacylglycerols of the VLDL.
Voltage-gated calcium channel impairing toxin
Protein which interferes with the function of voltage-gated calcium channels (Cav) which are membrane proteins forming a channel in a biological membrane selectively permeable to calcium ions and open in response to a change in membrane potential. They are mostly found spider and cone snail venoms.
Protein which is a component of a voltage-gated channel. Voltage-gated ion channels are responsible for the electrical activity in a variety of cell types. They probably exist in all life forms.
regulation of ion transmembrane transport
Voltage-gated chloride channel impairing toxin
Protein which interferes with the function of voltage-gated chloride channels (ClC) which are membrane proteins forming a channel in a biological membrane selectively permeable to chloride ions, and open in response to a change in membrane potential. They are found in venoms from scorpions.
Voltage-gated potassium channel impairing toxin
Protein which interferes with the function of voltage-gated potassium channels (Kv) which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions and open in response to a change in membrane potential. They are mostly found in scorpion and spider venoms.
Voltage-gated sodium channel impairing toxin
Protein which interferes with the function of voltage-gated sodium channels (Nav) which are membrane proteins forming a channel in a biological membrane selectively permeable to sodium ions, and open in response to a change in membrane potential. They are found in various venoms from snakes, scorpions and spiders.
Protein which, if defective, causes von Willebrand disease, a hemorrhagic disorder in which the von Willebrand factor is either quantitatively or qualitatively abnormal. Usually inherited as an autosomal dominant trait though rare kindreds are autosomal recessive. Symptoms vary depending on severity and disease type but may include prolonged bleeding time, deficiency of factor VIII and impaired platelet adhesion.
Protein which, if defective, causes Waardenburg syndrome, an autosomal dominant disorder, characterized by sensorineural deafness associated with pigmentary changes of the irides, hair and skin; each of these features may be uni- or bilateral. On the basis of the presence or absence of dystopia canthorum (lateral displacement of the inner corner of the eye), Waardenburg syndrome type 1 (WS1) and type 2 (WS2) are distinguished. Additionally, the association of WS1 with limb anomalies defines Waardenburg syndrome type 3 (WS3), while the association of Waardenburg features with Hirschsprung disease defines Waardenburg syndrome type 4 (WS4).
Protein which contains at least one WD repeat, a conserved domain of about 40 amino acids in length. Most copies contain a central conserved Trp-Asp motif.
Protein involved in the induction of whooping cough, a respiratory infection caused by the very small Gram-negative aerobic coccobacillus Bordetella pertussis. It is characterized by paroxysmal coughing often ending in a characteristic inspiratory gasp (whoop). The bacterium is a pathogen for humans and possibly for higher primates.
Protein which, if defective, causes Williams-Beuren syndrome (WBS), a contiguous gene deletion syndrome involving genes from chromosome band 7q11.23. It is a rare developmental autosomal dominant disorder characterized by cardiovascular abnormalities, elfin face, mental and statural deficiency, characteristic dental malformation, and infantile hypercalcemia.
Protein involved in the Wnt signaling pathway. Wnts are a large family of cysteine-rich secreted glycoproteins that control development in organisms ranging from nematodes to mammals. Wnt genes are defined by sequence homology to the original members of the family, Wnt1 in the mouse and wingless (wg) in Drosophila. Wnt signaling is a very complex pathway which includes numerous ligands, receptors and transcriptional effectors. There is a well-characterized canonical pathway as well as diverse, less-characterized noncanonical pathways. Several components of Wnt signaling are implicated in the genesis of human cancer.
Protein which, if defective, causes xeroderma pigmentosum, an autosomal recessive disease characterized by extreme photosensitivity to ultraviolet light and the development of multiple skin cancers.
Protein involved in the hydrolysis of xylan to xylose and other sugars. Xylan is a major component of hemicellulose, which is the second most common plant material in nature. The structures of xylans are complex, and several enzymes are involved in their breakdown. Xylan degrading enzymes are produced by a variety of microorganisms.
Protein involved in the biochemical reactions with the 5-carbon sugars xylose or xylulose. Xylose is the second most abundant sugar found in hardwood and agricultural residues.
Protein which, if defective, causes Zellweger syndrome, a fatal peroxisome biogenesis disorder associated with severe abnormalities in the brain, liver and kidney and death soon after birth. This disease is characterized by the presence of empty peroxisomes in the cells due to impaired transport of peroxisomal proteins into the peroxisomes.
Protein which binds at least one zinc atom, or protein whose function is zinc-dependent. Zinc is a metallic trace element, chemical symbol Zn.
Protein involved in the transport of zinc.
Protein which contains at least one zinc finger. A small, functional, independently folded domain that requires coordination of one or more zinc ions to stabilize its structure. Zinc fingers vary widely in structure, as well as in function, which ranges from DNA or RNA binding to protein-protein interactions and membrane association.
The enzymatically inactive precursor of mostly proteolytic enzymes.