Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response [
]. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis [].The MIF homologue D-dopachrome tautomerase (
) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [
,
].
Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (mouse), may act as a chromatin-associated protein [
]. The Schizosaccharomyces pombe (fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.
Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B (
) catalyses the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine.
The three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase [].Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine [
]. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a synthetase domain. The N-terminal glutaminase domain hydrolyzes glutamine to glutamic acid and ammonia [].
These sequences represent glutamine-hydrolysing asparagine synthase. The group have a poorly conserved C-terminal extension while bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis [
].
This family consists of a number of eukaryotic proteins including CXXC motif containing zinc binding protein (previously known as UPF0587 protein C1orf123). The crystal structure reveals that the protein binds a Zn2+ ion in a tetrahedral coordination with four Cys residues from two CxxC motifs. CXXC motif containing zinc binding protein was initially identified as an interaction partner for the heavy metal-associated (HMA) domain of CCS (copper chaperone for superoxide dismutase). However, it was shown that only misfolded mutant forms, lacking part of the zinc-binding sites, interact with CCS [
].
Sphingolipids are bioactive compounds found in lower and higher eukaryotes.
They are involved in the regulation of various cellular functions, such asgrowth, differentiation and apoptosis, and are believed to be essential in
a healthy diet. Sphigolipids are degraded in the lysosome, and theproducts from their hydrolysis are used in other biosynthetic and regulatory
pathways in the host.There are a number of lysosomal enzymes involved in the breakdown ofsphinogolipids, and these act in sequence to degrade the moieties [
]. These enzymes require co-proteins called sphingolipid activator proteins, (SAPs or saposins), to stabilise and activate them as necessary. SAPs are non-enzymatic and usually have a low molecular weight. They are conserved across a wide range of eukaryotes and contain specific saposin domains that aid in the activation of hydrolase enzymes. There have been four human saposins described so far, sharing significant similarity with each otherand with other eukaryotic SAP proteins.
Mutations in SAP genes have been linked to a number of conditions. A defectin the saposin B region leads to metachromatic leucodystrophy (MLD), while
a single nucleotide polymorphism in the SAP-C region may give rise toGaucher disease [
]. More recently, an opportunistic protozoan parasite protein has shown similarity both to the higher and lower eukaryotic saposins. The pore-forming protein isolated from virulent Naegleria fowleri (Brain eating amoeba) has been dubbed Naegleriapore A. It also shares structural similarity with cytolytic bacterial peptides, although this similarity does not extend to the sequence level.
Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown
of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of α-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].
The saposin B-type domain is a ~80 amino acid domain present in saposins and
related proteins that interact with lipids. The domain is named after thesmall lysosomal proteins, saposins, which serve as sphingolipid hydrolase
activator proteins in vertebrates. The mammalian saposins are synthesized as asingle precursor molecule (prosaposin) which contains two saposin A-type
domains in the extremities that are removed in the activation reaction, and four saposin B-type domains yielding the active saposins A,B, C and D after proteolytic cleavage. Saposin-like proteins (SAPLIPs) can
have different functions, such as enzymatic activities, as cofactors ofenzymes involved in lipid metabolism, as components of lung surfactant
reducing the surface tension, as part of a complex involved in stageregulation of Dictyostelium, as antimicrobial effector molecules, or as a
stimulator of dendritic outgrowth [,
,
,
].The 3D structures of different SAPLIPs have been resolved, and show that the
saposin B-type domain is formed by a four/five helical bundle. The saposin B-type domain is characterised by six conservedcysteine residues involved in three disulfide bridges: one between helices 2
and 3, one between the first and the last helix and one from the N-terminalpart of the first helix to the C terminus. In plant aspartic proteinases the
two subdomains that are connected by the disulfide bridges occur in inversedorder, these are called "swaposin"domains [
,
,
]. In these phytepsin proteinsthe two half saposin B-type domains occur in combination with the aspartyl
protease signature [,
].
This family consist of proteins found in plants and algal chloroplasts, and in cyanobacteria. It includes CGLD27 (CONSERVED IN THE GREEN LINEAGE AND DIATOMS 27), which has been described as one out of 14 Fe-responsive orthologues in Chlamydomonas and Arabidopsis, indicating that it is an important component of the iron deficiency response of the plant lineage [
].
This entry includes TMEM222 from animals and RTE1 (REVERSION-TO-ETHYLENE SENSITIVITY1) from Arabidopsis. RTE1 is positive regulator of the ETR1 ethylene receptor [
,
]. This entry also includes Arabidopsis RTE1 homologue, RTH, which acts via RTE1 in regulating ethylene responses and signaling [].
This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted [
]. The precise molecular and cellular function of members of this family is still unknown, yet they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin andhomocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (Common sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases (
), suggesting that this family may have an enzymatic function.
This entry represents a Rossmann fold-type domain found in NADH:ubiquinone oxidoreductase 20kDa subunit, [NiFe] hydrogenase small subunit and coenzyme F420 hydrogenase subunit gamma.NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 20kDa (in mammals) [], which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster.The great majority of hydrogenases (H2ases) contain iron-sulfur clusters and two metal atoms at their active centre, Ni and Fe in the case of the [NiFe]-H2ases. They catalyse the reversible oxidation of hydrogen gas and play a central role in microbial energy metabolism; in addition to their role in fermentation and H2 respiration []. The small subunit (chain A) contains the Fe4S4 clusters, whereas the large subunit (chain B) binds the binuclear NiFe active site [].
NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 20kDa (in mammals) [
], which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is mitochondrial encoded in Paramecium (gene psbG) and chloroplast encoded in various higher plants (gene ndhK or psbG).
The WH2 (WASP-Homology 2, or Wiskott-Aldrich homology 2) domain is an ~18 amino acids actin-binding motif. This domain was first recognised as an essential element for the regulation of the cytoskeleton by the mammalian Actin nucleation-promoting factor WAS (also known asWiskott-Aldrich syndrome protein, WASP). WH2 proteins occur in eukaryotes from yeast to mammals, in insect viruses, and in some bacteria. The WH2 domain is found as a modular part of larger proteins; it can be associated with the WH1 or EVH1 domain
and with the CRIB domain
, and the WH2 domain can occur as a tandem repeat. The WH2 domain binds actin monomers and can facilitate the assembly of actin monomers into newly forming actin filaments [
,
]. Some proteins known to contain a WH2 domain:Mammalian Actin nucleation-promoting factor WAS (WASP), a possible regulator of lymphocyte and platelet function. Defects in WASP are the cause of Wiskott- Aldrich syndrome (WAS), an X-linked recessive disease characterised by immune dysregulation and microthrombocytopenia. WASP proteins bind the actin nucleating protein complex Arp2/3.Mammalian N-WASP/WASL and WASF/SCAR/WAVE1-3, and yeast LAS17, which are also proteins from the WASP family that participate in the transduction of signals from the cell surface to the actin cytoskeleton.WAS protein family homologue 1 (WASH1), acts as a nucleation-promoting factor at the surface of endosomes, where it recruits and activates the Arp2/3 complex to induce actin polymerisation. Baker's yeast Verprolin, a protein involved in cytoskeletal organisation and cellular growth.Human WASP interacting protein (WASPIP/WIP), a WASP-, profilin- and actin-binding protein which induces actin polymerisation and redistribution.Nuclear polyhedrosis virus (NPV) P61/78/83 capsid protein, which may be important for the persistence and survival of the virus.Fruit fly Spir(e) protein, an actin nucleation factor involved in the development of oocytes and embryos. Spir is conserved among metazoans.Mammalian metastasis suppressor 1 or Missing in Metastasis (MIM) protein, an actin-binding protein that may be related to cancer progression or tumor metastasis.
This entry represents the Profilin family, which are small eukaryotic proteins that have different functions. In plants, they are major allergens present in pollens [
].The majority of the Profilin family members binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). They can also in certain circumstance promote actin polymerisation [
]. However, some Profilin family members, such as Profilin4 from mammals, does not binds to actin and may have functions distinct from regulating actin dynamics []. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain []. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway [,
].This entry also includes Asgard archaea profilins (Thor profilin, Loki profilin-1 and Loki profilin-2), which bind to actin and regulate the structure of the cytoskeleton. This indicates that Asgard archaea have a functional eukaryotic-like actin machinery [
].Some Profilins can also bind to polyphosphoinositides such as PIP2 [
]. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. The N-terminal region is thought to be involved in actin binding.
This entry represents the SCAR/WAVE family. Members in this family include actin-binding protein WASF1-3 (WAVE 1-3), protein SCAR 1-4, protein WAVE5 and SCAR-like proteins.SCAR/WAVE family members are downstream effector molecules receiving information from multiple signalling pathways and responding by promoting the actin nucleating activity of the ubiquitous Arp2/3 complex [
]. They are part of the WAVE complex that regulates lamellipodia formation in animals and maintains cell shape in plants [,
,
]. WAVE1 is also involved in the regulation of mitochondrial dynamics [].
The UbiA family of prenyltransferases includes bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); protohaem IX farnesyltransferase (haem O synthase) from yeast and mammals (gene COX10), and from bacteria (genes cyoE or ctaB) [
,
]; and 2-acylphloroglucinol 4-prenyltransferase and 2-acyl-4-prenylphloroglucinol 6-prenyltransferase from plant chloroplasts which catalyse prenylation steps in the beta-bitter acid pathway [,
]. These are integral membrane proteins, which probably contain seven transmembrane segments. Archaeal family members include lycopene elongase/hydratase - this type of enzyme has been shown to be involved in bacterioruberin synthesis in Halobacterium salinarum and Haloferax volcanii [].
This entry represents protein LIN-9/ALWAYS EARLY (LIN-9/ALY). LIN-9 from Caenorhabditis elegans is a homologue of the Drosophila always early (ALY) protein, which functions as a repressor of cell cycle regulated genes [
,
].LIN-9 is a component of the evolutionary conserved DREAM (MuvB/DRM) complex, which represses transcription [
]. DREAM complex undergoes a cell cycle dependent switch of subunits. DREAM core binds to the E2F4 transcription factor and to the RBL2 (p130) in quiescent cells, while associates with the transcription factor B-MYB in the S-phase []. In humans, LIN-9 acts as a tumor suppressor and plays a role in the expression of genes required for the G1/S transition [,
]. In pluripotent embryonic stem cells (ESC), LIN-9 plays an important role for proliferation and genome stability by activating genes with important functions in mitosis and cytokinesis [].In Arabidopsis thaliana, ALY is expressed ubiquitously in vegetative and reproductive tissues [
].
The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:(1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).(2) addition of a short polypeptide chain to the UDPMurNAc.(3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.Stage two involves four key Mur ligase enzymes: MurC (
) [
], MurD () [
], MurE () [
] and MurF () [
]. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid []. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that binds the incoming amino acid []. Residues found in the three domains (the Asp50, Lys130 (GKT motif), and Glu174 residues, MurC numbering) are involved in the catalytic process []. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the central domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [
].
The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:(1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).(2) addition of a short polypeptide chain to the UDPMurNAc.(3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.Stage two involves four key Mur ligase enzymes: MurC (
) [
], MurD () [
], MurE () [
] and MurF () [
]. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid []. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that binds the incoming amino acid []. Residues found in the three domains (the Asp50, Lys130 (GKT motif), and Glu174 residues, MurC numbering) are involved in the catalytic process []. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes the C-terminal domain of folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [].The C-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases, N-terminal domain (see
).
Folylpolyglutamate synthase
(FPGS) is an ATP-dependent enzyme that is responsible for the addition of a polyglutamate tail to folate and folate derivatives [
]. It plays a key role in the retention of the intracellular folate pool. In some bacteria, such as Escherichia coli, the addition of L-glutamate to dihydropteroate (dihydrofolate synthetase activity) and the subsequent additions of L-glutamate to tetrahydrofolate (FPGS activity) are catalyzed by the same enzyme, FolC [].The crystal structure of the MgATP complex of the enzyme from Lactobacillus casei reveals FPGS to be a modular protein, consisting of two domains, one with a typical mononucleotide-binding fold and the other similar to the folate-binding enzyme dihydrofolate reductase. The active site of the enzyme is located in a large interdomain cleft adjacent to an ATP-binding P-loop motif. Opposite this site, in the C domain, a cavity likely to be the folate binding site has been identified, and inspection of this cavity and the surrounding protein structure suggests that the glutamate tail of the substrate may project into the active site. A further feature of the structure is a well defined Omega loop, which contributes both to the active site and to interdomain interactions [
].
This entry represents a multi-helical domain found in the C terminus of the cryptochrome proteins and DNA photolyases. It acts as a FAD-binding domain [
].The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light photoreceptors involved in the circadian clock for plants and animals [
,
]. DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [
,
].
This entry includes fatty acid desaturase family members from bacteria, fungi, plants and animals. Proteins in this family contain the fatty acid desaturase domain (
). The eukaryotic members, including human FADS1 and FADS2, are fusion proteins containing an N-terminal cytochrome b5-like domain and a C-terminal multiple membrane-spanning desaturase portion [
].Three human fatty acid desaturase genes have been identified, fatty acid desaturase 1-3 (FADS1-3) [
]. FADS1 and FADS2 encode delta-5 desaturase (D5D) and delta-6 desaturase (D6D) respectively. They are membrane-bound enzymes that catalyse the rate-limiting formation of endogenous long-chain polyunsaturated fatty acid (PUFA). FADS3 is a ceramide desaturase that produces sphinga-4,14-dienine-containing ceramides (SPD ceramides). FADS3 also acts as a methyl-end fatty acyl coenzyme A (CoA) desaturase that introduces a cis double bond between the preexisting double bond and the terminal methyl group of the fatty acyl chain. [].
The P protein is part of the glycine decarboxylase multienzyme complex (GDC), also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T [
]. The P protein () binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. The reaction catalysed by this protein is:
Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 The subunit composition of glycine cleavage system P proteins have been classified into two types. Those from eukaryotes and some of the P proteins from prokaryotes (e.g. Escherichia coli) are in the homodimeric form. The rest of those from prokaryotes are heterotetrameric, with two different subunits which, based on sequence similarities, correspond respectively to the N and C-terminal halves of the eukaryotic subunit [
].This entry represents the P protein homodimeric subfamily, which is found in eukaryotes and some prokaryotes, such as E. coli.
Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented.This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to:Fatty acid synthase (
), a biosynthetic enzyme catalysing the formation of long-chain fatty acids
Glycine N-methyltransferase (
) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [
]
A polyketide synthase, important for the synthesis of chaetoviridin A and chaetomugilin A in the fungus Chaetomium [
].Fungal non-reducing polyketide synthases, such as ausA [
] and otaA [].Structural studies show that this domain forms the Rossman-like α-β fold typical of SAM-dependent methyltransferases [
,
,
].
This family includes tRNA N(3)-methylcytidine methyltransferases METTL2, 6 and 8, O-methyltransferase 3 and methyltransferase-like protein Metl from Drosophila. These proteins are S-adenosyl-L-methionine-dependent methyltransferases that mediate N3-methylcytidine modification of residue 32 of the tRNA anticodon loop of tRNA(Thr) and tRNA(Ser) [
,
,
,
,
,
,
].tRNA N(3)-methylcytidine methyltransferase METTL2, 6 and 8 are part of a group of proteins known as TIPs (from tension-induced/inhibited protein) required for the recruitment of histone acetyltransferase p300 to specific promoters. TIP-6 is involved in the adipogenic cascade [
]. O-methyltransferase 3 is up-regulated by phagocytic stimuli [].
Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (
), beta (
) and gamma (
) [
]. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins or by covalent modifications [].G protein alpha subunits are 350-400 amino acids in length and have
molecular weights in the range 40-45kDa. Seventeen distinct types ofalpha subunit have been identified in mammals. These fall into 4 main
groups on the basis of both sequence similarity and function: alpha-S (),
alpha-Q (), alpha-I (
)and alpha-12(
) [
].The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [
,
]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions.This family represents the plant class of G protein alpha subunits, which have been isolated from a variety of plant species. Plant G proteins are involved in signal transduction from hormone receptors, including the plant hormones gibberellin and abscisic acid that regulate gene expression, secretion and cell death in alerone []. Plant alpha subunits are highly conserved between species, but share relatively low sequence similarity with mammalian G-proteins. However, the GTP-binding and hydrolysis regions are well conserved.
This family includes preprotein translocase subunit SecG, protein transport protein Sec61 subunit beta and Sbh1.A conserved heterotrimeric integral membrane protein complex--the Sec61 complex (eukaryotes) or SecY complex (prokaryotes)--forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) [
,
]. This complex is itself a part of a larger translocase complex.The alpha subunits (
), called Sec61alpha in mammals, Sec61p in Saccharomyces cerevisiae (Baker's yeast), and SecY in prokaryotes, and the gamma subunits, called Sec61gamma in mammals, Sss1p in S. cerevisiae, and SecE in prokaryotes, show significant sequence conservation. Both subunits are required for cell viability in S. cerevisiae and Escherichia coli.
The beta subunits, called Sec61beta in mammals, Sbh in S. cerevisiae, and SecG in archaea, are not essential for cell viability. They are similar in eukaryotes and archaea, but show no obvious homology to the corresponding SecG subunits in bacteria. SecY forms the channel pore, and it is the cross-linking partner of polypeptide chains passing through the membrane [
]. SecY and SecE constitute the high-affinity SecA-binding site on the membrane []. The channel is a passive conduit for polypeptides. It must therefore associate with other components that provide a driving force. The partner proteins in bacteria and eukaryotes differ. In bacteria, the translocase complex comprises 7 proteins [
], including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF). The SecA ATPase interacts dynamically with the SecYEG integral membrane components to drive the transmembrane movement of newly synthesized preproteins []. In S. cerevisiae (and probably in all eukaryotes), the full translocase comprises another membrane protein subcomplex (the tetrameric Sec62/63p complex), and the lumenal protein BiP, a member of the Hsp70 family of ATPases. BiP promotes translocation by acting as a molecular ratchet, preventing the polypeptide chain from sliding back into the cytosol [].
Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane [
]. A cyanobacterial member of this family (proton extrusion protein PcxA) is involved in light-induced Na(+)-dependent proton extrusion and has been implicated in CO2 transport, but is probably not a CO2 transporter itself [].
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release [
]. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins [].This entry represents the C subunit that is part of the V1 complex, and is localised to the interface between the V1 and V0 complexes [
]. This subunit does not show any homology with F-ATPase subunits. The C subunit plays an essential role in controlling the assembly of V-ATPase, acting as a flexible stator that holds together the catalytic (V1) and membrane (V0) sectors of the enzyme []. The release of subunit C from the ATPase complex results in the dissociation of the V1 and V0 subcomplexes, which is an important mechanism in controlling V-ATPase activity in cells.
The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation.
The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.Members of this family represent the Med4 subunit of the Mediator (Med) complex [
,
].
PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.
The cation diffusion facilitator family (CDF) have members in both prokaryotes and eukaryotes, several of which have been shown to transport cobalt, cadmium and/or zinc. CDF transporters share a common two-modular architecture, consisting of a transmembrane domain (TMD) followed by a C-terminal domain (CTD) protruding into the cytoplasm [
].This entry represents the CDF C-terminal cytoplasmic domain. The cytoplasmic domain of Zinc transporter YiiP adopts a metallochaperone-like fold. The use of this common structural module to regulate metal coordination chemistry may enable a tunable transport activity in response to cytoplasmic metal fluctuations [
]. It is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 () exhibiting an open α-β domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed β-sheet (S1 to S3) on the other side [
].
This entry represents the C terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (
). This catalyses the hydrolysis of non-reducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides [
].
This family represents subunit 9 of the integrator complex (INTS9). The integrator complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription, and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes [
].
In eukaryotes, the Nascent polypeptide-Associated Complex (NAC) is a heterodimeric cytosolic protein complex composed of NAC alpha (NACA) and NAC beta (BTF3) [
]. NAC binds reversibly to the ribosome where it is in contact with nascent chains as they emerge from the ribosome. But the cellular function of NAC seems to be much more diverse as it is also involved in transcription regulation and mitochondrial translocation [,
]. Alpha and beta NACs share homology with each other, both contain a NAC A/B domain. In archaea no beta NAC proteins are found; the complex is an homodimer of NAC alpha [,
].The crystal structure of an archeal NAC has been solved [
]. The NAC A/B domain consists of six strands arranged in a beta barrel structure similar to the OB fold. Various OB folds interact with ribosomal RNA which could suggest a similar role for the NAC A/B domain.
In Saccharomyces cerevisiae, nascent polypeptide-associated complex subunit alpha (also known as EGD2) is a component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting [
,
,
].In human and mouse, nascent polypeptide-associated complex subunit alpha (known as NACA) prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). It binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER [
,
].
4-alpha-glucanotransferases (
) belong to the glycoside hydrolase family 77
. They transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be
glucose or (1,4)-alpha-D-glucan []. 4-alpha-glucanotransferases from prokaryotes are known as amylomaltases and those from plants, including algae, are known as disproportionating enzymes (DPE). Both belong to the disproportionating family [].
Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins (see
) from ubiquitin-conjugated proteins. All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain (see
) [
]. The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel β-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three α-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered [
]. The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition. This domain is associated with ubiquitin carboxyl-terminal hydrolase family 2 (
, MEROPS peptidase family C19). They are a family 100 to 200kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast; others include:
Mammalian ubiquitin carboxyl-terminal hydrolase 4 (USP4),Mammalian ubiquitin carboxyl-terminal hydrolase 11 (USP11), Mammalian ubiquitin carboxyl-terminal hydrolase 15 (USP15), Mammalian ubiquitin carboxyl-terminal hydrolase 20 (USP20), Mammalian ubiquitin carboxyl-terminal hydrolase 32 (USP32), Vertebrate ubiquitin carboxyl-terminal hydrolase 33 (USP33), Vertebrate ubiquitin carboxyl-terminal hydrolase 48 (USP48).
The R3H domain is a conserved sequence motif found in proteins from a diverse range of organisms including eubacteria, green plants, fungi and various groups of metazoans, but not in archaea and Escherichia coli. The domain is named R3H because it contains an invariant arginine and a highly conserved histidine, that are separated by three residues. It also displays a conserved pattern of hydrophobic residues, prolines and glycines. It can be found alone, in association with AAA domain or with various DNA/RNA binding domains like DSRM, KH, G-patch, PHD, DEAD box, or RRM. The functions of these domains indicate that the R3H domain might be involved in polynucleotide-binding, including DNA, RNA and single-stranded DNA [
].The 3D structure of the R3H domain has been solved. The fold presents a small motif, consisting of a three-stranded antiparallel β-sheet, against which two α-helices pack from one side. This fold is related to the structures of the YhhP protein and the C-terminal domain of the translational initiation factor IF3. Three conserved basic residues cluster on the same face of the R3H domain and could play a role in nucleic acid recognition. An extended hydrophobic area at a different site of the molecular surface could act as a protein-binding site [
].
The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [
].
The HIRAN domain (HIP116 Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. HIRAN is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes [
]. It has been predicted that this protein functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks [].
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1
Type:
Domain
Description:
This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [
,
]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [,
]. The precise function of this domain has not been characterised.
Based on sequence similarities a domain of homology has been identified in the following proteins [
,
]:Citron and Citron kinase. These two proteins interact with the GTP-bound forms of the small GTPases Rho and Rac but not with Cdc42.Myotonic dystrophy kinase-related Cdc42-binding kinase (MRCKalpha). This serine/threonine kinase interacts with the GTP-bound form of the small GTPase Cdc42 and to a lesser extent with that of Rac.NCK Interacting Kinase (NIK), a serine/threonine protein kinase.ROM-1 and ROM-2, from yeast. These proteins are GDP/GTP exchange proteins (GEPs) for the small GTP binding protein Rho1.This domain, called the citron homology domain (CNH), is often found after cysteine rich and pleckstrin homology (PH) domains at the C-terminal end of a group of eukaryotic proteins. It is thought to act as a regulatory domain and could be involved in macromolecular interactions [
,
,
,
]. Its structure has been solved in Rho guanyl nucleotide exchange factor (Rom2) from Neosartorya fumigata (Aspergillus fumigatus, ), where it shows a canonical β-propeller fold containing seven blades connected by small loops and arranged in a circular fashion [
].
Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2
Type:
Domain
Description:
This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [
,
]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [,
]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Fumarate reductase/succinate dehydrogenase, FAD-binding site
Type:
Binding_site
Description:
In bacteria two distinct, membrane-bound, enzyme complexes are responsible for
the interconversion of fumarate and succinate (): fumarate
reductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh)is used in aerobic growth. Both complexes consist of two main components: a
membrane-extrinsic component composed of a FAD-binding flavoprotein and aniron-sulphur protein; and an hydrophobic component composed of a membrane
anchor protein and/or a cytochrome B.In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (
)
is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphurprotein.
The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is
covalently bound to a histidine residue which is located in the N-terminalsection of the protein [
]. The sequence around that histidine is wellconserved in Frd and Sdh from various bacterial and eukaryotic species [
].
Succinate dehydrogenase and fumarate reductase are homologous enzymes reversible in principle but favoured under different circumstances. This entry represents a narrowly defined clade of the succinate dehydrogenase flavoprotein subunit as found in mitochondria, in Rickettsia, in Escherichia coli and other proteobacteria, and in a few other lineages. However, excluded are all known fumarate reductases. It also excludes putative succinate dehydrogenases that appear to diverged before the split between E. coli succinate dehydrogenase and fumarate reductase.
Succinate:quinone oxidoreductase (
) refers collectively to succinate:quinone reductase (SQR, or Complex II) and quinol:fumarate reductase (QFR) [
]. SQR is found in aerobic organisms, and catalyses the oxidation of succinate to fumarate in the citric acid cycle and donates the electrons to quinone in the membrane. QFR can be found in anaerobic cells respiring with fumarate as terminal electron acceptor. SQR and QFR are very similar in composition and structure, despite catalysing opposite reactions in vivo. They are thought to have evolved from a common ancestor, and in Escherichia coli they are capable of functionally replacing each other [].Succinate:quinone oxidoreductases consist of a peripheral domain, exposed to the cytoplasm in bacteria and to the matrix in mitochondria, and a membrane-integral anchor domain that spans the membrane (Fig. 1). The peripheral part, which contains the dicarboxylate binding site, is composed of a flavoprotein subunit, with one covalently bound FAD, and an iron-sulphur protein subunit containing three iron-sulphur clusters. The membrane-integral domain functions to anchor the peripheral domain to the membrane and is required for quinone reduction and oxidation. The anchor domain shows the largest variability in composition and primary sequence, being composed either of one large subunit, or two smaller subunits, which may, or may not, contain protoheme groups.This entry represents the flavoprotein subunit found in both the SQR and QFR enzymes. This subunit contains an N-terminal domain which binds the FAD cofactor, a central catalytic domain with an unsual fold, and a C-terminal domain whose role is unclear [
,
,
]. The dicarboxylate binding site is located between the FAD and catalytic domains.
Human YVH1, also known as dual specificity phosphatase 12 (DUSP12), is a cell survival phosphatase that prevents both thermal and oxidative stress-induced cell death. Furthermore, it associates with multiple ribonucleoprotein particles and may affect a variety of fundamental cellular processes [
]. The enzyme is known as dual specificity protein phosphatase MPK-4 in Drosophila[
]. Yeast YVH1, on the other hand, is required for a late maturation step in the 60S biogenesis pathway [].
Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity [
]. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi []. Arabidopsis thaliana has been shown to encode 2 ARV proteins (ARV1 and ARV2) both of which contain the AHD domain. This family also includes ARV2 from A. thaliana [].
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [
].Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [
]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.This entry represents subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), primarily of bacterial origin, and which functions in ATP hydrolysis and subunit interaction. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes.
This entry represents the C-terminal of the DNA gyrase B. The N terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different C terminus. The N-terminal of the DNA gyrase B protein is thought to catalyse the ATP-dependent super-coiling of DNA. The C-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This entry also contains Topoisomerase IV, which is a bacterial enzyme that is closely related to DNA gyrase [
,
].
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [
].Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [
]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.This entry represents DNA topoisomerase, type IIA.
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II [
].
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [
].Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [
]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.This entry represents the second domain found in subunit B (gyrB and parE) of bacterial gyrase and topoisomerase IV, and the equivalent N-terminal region in eukaryotic topoisomerase II composed of a single polypeptide.
Glutamate synthase (GltS)1 is a key enzyme in the early stages of the assimilation of ammonia in bacteria, yeasts, and plants. In bacteria, L-glutamate is involved in osmoregulation, is the precursor for other amino acids, and can be the precursor for haem biosynthesis. In plants, GltS is especially essential in the reassimilation of ammonia released by photorespiration. On the basis of the amino acid sequence and the nature of the electron donor, three different classes of GltS can de defined as follows: 1) ferredoxin-dependent GltS (Fd-GltS), 2) NADPH-dependent GltS (NADPH-GltS), and 3) NADH-dependent GltS (properties of the three classes have been reviewed extensively [
]). The enzyme is a complex iron-sulphur flavoprotein catalysing the reductive transfer of the amido nitrogen from L-glutamine to 2-oxoglutarate to form two molecules of L-glutamate via intramolecular channelling of ammonia from the amidotransferase domain to the FMN-binding domain.Reaction of amidotransferase domain:L-glutamine + H2O = L-glutamate + NH3Reactions of FMN-binding domain:2-oxoglutarate + NH3 = 2-iminoglutarate + H2O2e + FMNox = FMNred
2-iminoglutarate + FMNred = L-glutamate + FMNox
The central domain of glutamate synthase connects the N-terminal amidotransferase domain with the FMN-binding domain and has an alpha/beta overall topology [
].
Some membrane bound proteins possess a pair of repeats each spanning two transmembrane helices connected by a loop [
]. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes []. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought to possess a more general function; most probably this involves a glutamine residue [].
Rubrerythrin (Rr) is a fusion protein containing an N-terminal diiron-binding domain and a C-terminal domain homologous to rubredoxin [
]. This protein has been related to the response to oxidative stress [,
,
]. The 3-D structure of Desulphovibrio vulgaris rubrerythrin has been solved [
]. The structure reveals a tetramer of two-domainsubunits. In each monomer, the N-terminal 146 residues form a four-α-helix bundle containing the diiron-oxo site (centre I), and the C-terminal 45 residues form a rubredoxin-like FeS4 domain.
This entry represents the N-terminal diiron-binding domain of Rr, which has a has a ferritin-like fold [
].
Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase
Type:
Family
Description:
This family represents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions []. This enzyme is believed to utilise a binuclear iron centre and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacteria, which are differentially regulated based on the levels of copper and oxygen [,
]. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria.CRD1 (AcsF) is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (-Cu) and oxygen-deficient (-O(2)) Chlamydomonas reinhardtii cells and is localised to the thylakoid membrane. The family also contains the Rhodocyclus gelatinosus (Rhodopseudomonas gelatinosa or Rubrivivax gelatinosus) AcsF protein, which codes for a conserved, putative binuclear iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethyl ester. AcsF and homologs have a leucine zipper and two copies of the conserved glutamate and histidine residues predicted to act as ligands for iron in the Ex(29-35)DExRH motifs. Several homologs of AcsF are found in a wide range of photosynthetic organisms, including Chlamydomonas reinhardtii Crd1 and Pharbitis nil PNZIP, suggesting that this aerobic oxidative cyclization mechanism is conserved from bacteria to plants [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].The S25 ribosomal protein is a component of the 40S ribosomal subunit.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V-ATPase folding, localisation, and stability is made possible through the formation of a luminal glycan coat by the glycolipids and the glycosylated V0 subunits [
]. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [,
,
]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit E from V-ATPases and A-ATPase/synthases. Subunit E appears to form a tight interaction with subunit G, which together may act as stators to prevent certain subunits from rotating with the central rotary element, much in the same way as the F0 complex subunit B does in F-ATPases []. In addition to its key role in stator structure, subunit E appears to have a role in mediating interactions with putative regulatory subunits [].
The Nop domain is present in various pre-RNA processing ribonucleoproteins (RNP):Eukaryotic Prp31, part of a tri-snRNP complex. It is involved in pre-mRNA
splicing.Eukaryotic Nucleolar proteins 56 and 58 (Nop56 and Nop58), components of
box C/D small nucleolar ribonucleoprotein (snoRNP) particles.Archaeal Nop5, an homologue of Nop56/Nop58.The Nop domain is a RNP binding module, exhibiting RNA and protein binding surfaces. It is oval-shaped and exclusively α-helical [
,
].This entry represents the Nop domain.
This domain is found at the C terminus SPB1-like proteins. This domain interacts with the meandering tail of Erb1 and its removal is required to form the pre-mature inter-subunit surface of the Arx1/Nog2 particle [
,
].SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit [
]. In Saccharomyces cerevisiae, it specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation []. It interacts with the snoRNA-associated proteins Nop1 and Nop58 []. FTSJ3, SPB1 homologue in humans, is associated with NIP7 (involved in the biogenesis of 40S subunit) and functions in pre-rRNA processing [
].
SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit [
]. In Saccharomyces cerevisiae, it specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation []. It interacts with the snoRNA-associated proteins Nop1 and Nop58 []. FTSJ3, SPB1 homologue in humans, is associated with NIP7 (involved in the biogenesis of 40S subunit) and functions in pre-rRNA processing [
].
Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381
Type:
Domain
Description:
This uncharacterised domain is found in the central region of fungal SPB1 and mammalian homologue FTSJ3.SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit [
]. In Saccharomyces cerevisiae, it specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation []. It interacts with the snoRNA-associated proteins Nop1 and Nop58 []. FTSJ3, SPB1 homologue in humans, is associated with NIP7 (involved in the biogenesis of 40S subunit) and functions in pre-rRNA processing [
].
ADP-glucose pyrophosphorylase (glucose-1-phosphate adenylyltransferase) [
] () catalyzes a very important step in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants: synthesis of the activated glucosyl donor, ADP-glucose, from glucose-1-phosphate and ATP.
ADP-glucose pyrophosphorylase is a tetrameric allosterically regulated enzyme. It is a homotetramer in bacteria while in plant chloroplasts and amyloplasts, it is a heterotetramer of two different, yet evolutionary related, subunits.There are a number of conserved regions in the sequence of bacterial and plant ADP-glucose pyrophosphorylase subunits.
Nucleotidyl transferases transfer nucleotides from one compound to another. This domain is found in a number of enzymes that transfer nucleotides onto phosphosugars [
].
Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
Type:
Family
Description:
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Phenylalanyl-tRNA synthetase (
) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit
(pheT gene) can be designated as alpha (E. coli) or beta (see and
). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [
].This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family.
Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents a β-sandwich structural motif found in the appendage domain of the gamma subunit of coatomer complexes. This subdomain has an immunoglobulin-like β-sandwich fold containing 7 strands in 2 β-sheets in a Greek key topology [
]. The appendage domain of the gamma coatomer subunit has a similar overall fold to the appendage domain of clathrin adaptors, and can also share the same motif-based cargo recognition and accessory factor recruitment mechanisms.
Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer [
]. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This group represents the coatomer gamma subunit.
Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer [
]. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [
]. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis [].While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. The alpha and beta2 adaptor subunits can each be divided into a trunk domain and the appendage domain (or ear domain), separated by a linker region. Clathrin polymerisation is promoted by its binding to the beta2 appendage and hinge domains. The alpha appendage domain interacts with a number of accessory proteins, including eps15, epsin, amphiphysin, AP180, auxilin, numb, and Dab2, thereby regulating the translocation of these proteins to the bud site. This entry represents a subdomain of the appendage (ear) domain of alpha- and beta-adaptin from AP clathrin adaptor complexes, and the appendage domain of the gamma subunit of coatomer complexes. These domains have a three-layer arrangement, α-β-alpha, with a bifurcated antiparallel β-sheet [
,
, [
]. Although the appendage domains from AP adaptins and coatomers share a similar fold, there is little sequence identity between them. However, they also share similar motif-based cargo recognition and accessory factor recruitment mechanisms.
Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [
]. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis [].While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins [
]. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This superfamily represents a β-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, the GAE (gamma-adaptin ear) domain of GGA adaptor proteins, and the appendage domain of the gamma subunit of coatomer complexes. These domains have an immunoglobulin-like β-sandwich fold containing 7 or 8 strands in 2 β-sheets in a Greek key topology [
,
,
]. Although the appendage domains from AP / GGA adaptins and coatomers share a similar fold, there is little sequence identity between them. However, they also share similar motif-based cargo recognition and accessory factor recruitment mechanisms.
Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (), beta (
) and gamma (
) [
]. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins or by covalent modifications [].G protein alpha subunits are 350-400 amino acids in length and have
molecular weights in the range 40-45kDa. Seventeen distinct types ofalpha subunit have been identified in mammals. These fall into 4 main
groups on the basis of both sequence similarity and function: alpha-S (),
alpha-Q (), alpha-I (
)and alpha-12(
) [
].The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [
,
]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions.This entry consists of the G protein beta subunit, which assumes a barrel-shaped β-propeller structure containing WD-40 repeats preceded by an N-terminal alpha helix. The beta subunit forms a stable dimer with the gamma subunit. The alpha subunit only contacts the beta subunit in the dimer, lying on the opposite face from the gamma subunit. RGS proteins that contain GGL (G protein gamma-like) domains can interact with beta subunits to form novel dimers that prevent gamma subunit binding, and may prevent heterotrimer formation by inhibiting alpha subunit binding.
G protein is a modulator in various transmembrane signalling systems. The beta and gamma subunits are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction. This entry represents the G protein (guanine nucleotide-binding proteins) beta subunit, including Ste4 from budding yeasts [
], Git5 from fission yeasts [] and GNB1-5 from animals [].
Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [
,
,
,
]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [,
]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity.
All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase [
]. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed.This entry represents the C-terminal domain of CAP proteins, which is responsible for G-actin-binding. This domain has a superhelical structure, where the superhelix turns are made of two β-strands each [
].
Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [
,
,
,
]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [,
]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase [
]. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed.This entry represents CAP proteins from various organisms.
This entry represents the N-terminal conserved site of the CAP protein. Structurally, CAP is a protein of 474 to 551 residues, which consist of two domains separated by a proline-rich hinge. In budding and fission yeasts the CAP protein is a bifunctional protein whose N-terminal domain binds to adenylyl cyclase, thereby enabling that enzyme to be activated by upstream regulatory signals, such as Ras. The N terminus also catalyses cofilin-mediated severing of actin filaments [
]. The C-terminal domain plays a role in recycling cofilin-bound, ADP-actin monomers [].CAP is conserved in higher eukaryotic organisms. Although the role in Ras signalling does not extend beyond yeasts, the actin regulation function is conserved in all eukaryotes [
].
Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [
,
,
,
]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [,
]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed.This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [
].
Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal
Type:
Homologous_superfamily
Description:
Cyclase-associated proteins (CAPs) are highly conserved monomeric actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [
,
,
,
]. Only yeast CAPs are involved in adenylate cyclase activation. The C-terminal domain of CAP proteins is responsible for G-actin-binding that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes.In Escherichia coli, three Min proteins (MinC, MinD and MinE) negatively regulate FtsZ assembly at the cell poles in order to ensure the Z-ring only assembles at cell midpoint. MinC inhibits formation of the Z-ring by preventing FtsZ assembly. MinD binds to MinC near the cell poles, sequestering MinC away from the cell midpoint so the Z-ring can form there. MinC is an oligomer, probably a dimer, that consists of two domains: the N-terminal domain is responsible for FtsZ inhibition, while the C-terminal domain is responsible for binding to MinD and to a component of the division septum [
,
].This entry represents a structural domain found at the C-terminal of CAP proteins as well as MinC. This domain has a superhelical structure, where the superhelix turns are made of either two (CAP) or three (MinC) β-strands each.
This entry represents the CARP motif, which occurs as a tandem repeat in the C-terminal of many cyclase-associated proteins (CAPs), as well as in tubulin binding cofactor C and the X-linked retinitis pigmentosa 2 protein (RP2).
The C-CAP/cofactor C-like domain is present in several cytoskeleton-related proteins, which also contain a number of additional domains [
,
,
,
]:Eukaryotic cyclase-associated protein (CAP or SRV2), a modular actin monomer binding that directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity.Vertebrate retinitis pigmentosa 2 (XRP2). In Homo sapiens (Human), it is the protein responsible for X-linked forms of retinitis pigmentosa, a disease characterised by severe retinal degeneration.Eukaryotic tubulin-specific chaperone cofactor C (TBCC), a GTPase- activating component of the tubulin-folding supercomplex, which directs the assembly of the alpha- and beta-tubulin heterodimer.The cyclase-associated protein C-CAP/cofactor C-like domain binds G-actin and is responsible for oligomerisation of the entire CAP molecule [
], whereas the XRP2 C-CAP/cofactor C-like domain is required for binding of ADP ribosylation factor-like protein 3 (Arl3) [].The central core of the C-CAP/cofactor C-like domain is composed of six coils of right-handed parallel β-helices, termed coils 1-6, which form an elliptical barrel with a tightly packed interior. Each β-helical coil is composed of three relatively short β-strands, designated a-c, separated by sharp turns. Flanking the central β-helical core is an N-terminal β-strand, β0, that packs antiparallel to the core, and strand β7 packs antiparallel to the core near the C-terminal end of the parallel β-helix [,
].
This domain can be found in the plant NPR proteins. Arabidopsis NPR1 is a key regulator of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway [
]. Its paralogs, NPR3, and NPR4, bind SA and control the proteasome-mediated degradation of NPR1 through their interaction with NPR1 [].
This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (
) in bacteria, eukaryotes and archaea.
Lycopene cyclases generate provitamin A carotenoids which are essential building blocks for cyclic xanthophylls involved in photosynthesis and regulatory networks. The cyclization of lycopene is the final step in carotenoid biosynthesis and may proceed via one of two pathways: the formation of a beta ring by beta-cyclase, or an epsilon ring by epsilon-cyclase. Epsilon-cyclase adds only one ring, forming the monocyclic delta-carotene, whereas beta-cyclase introduces a ring at both ends of lycopene to form the bicyclic beta-carotene [
]. Lycopene cyclases are widely distributed across taxonomic groups and have structural diversity. Four partly related families of lycopene cyclases are known: CrtY, CrtL (beta-ionone end group producing), CrtL (eta-ionone end group producing) and CrtL (capsanthin/capsorubin synthase).This family includes lycopene beta- and epsilon-cyclases, which are involved in the biosynthesis of carotenoids in bacteria and plants, and the related capsanthin capsorubin synthase (Ccs) from plants, which converts antheraxanthin or violaxanthin into capsanthin or capsorubin by a mechanism similar to lycopene cyclization. This family also includes neoxanthin synthase, which is involved in the synthesis of neoxanthin, the last product of carotenoid synthesis and a precursor of abscisic acid [].
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release [
]. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins [].This entry represents the 16kDa proteolipid subunit c that is part of the V0 complex of V-ATPase in eukaryotes, and includes members from diverse groups such as fungi, plants and parasites. The three proteolipid subunits (c, c' and c'') that form part of the proton-conducting pore, each contain a buried glutamic acid residue that is essential for proton transport, and together they form a hexameric ring spanning the membrane [,
].
This entry represents the 16kDa proteolipid subunit c that is part of the V0 complex of V-ATPase in eukaryotic organelles and in certain bacteria. There are three proteolipid subunits (known as c, c' and c'' in yeast) that form part of the proton-conducting pore, each containing a buried glutamic acid residue that is essential for proton transport, and together they form a hexameric ring spanning the membrane [,
]. Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release [
]. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins [].
Ferredoxin-dependent glutamate synthase (GltS) has been implicated in a number of functions including photorespiration in Arabidopsis where it may also play a role in primary nitrogen assimilation in roots [
]. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centres, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor [,
,
].This domain is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. It contains a putative FMN binding site and Fe-S cluster [
,
].
G-box binding protein, multifunctional mosaic region
Type:
Domain
Description:
This region is often found to the N terminus of the basic-leucine zipper domain (
). It is between 150 and 200 amino acids in length. The N-terminal half of this domain is rich in proline residues and has been termed the PRD (proline rich domain) [
], whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). According to their motif composition, proteins containing this domain can be classified into three sub-families called A, B and C []. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions []. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2 []. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals [].
Creatinase or creatine amidinohydrolase (
) catalyses the conversion of creatine and water to sarcosine and urea. The enzyme works as a homodimer, and is induced by choline chloride. Each monomer of creatinase has two clearly defined domains, a small N-terminal domain, and a large C-terminal domain.
The structure of the C-terminal region represents the "pita-bread"fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (
), aminopeptidase P (
), prolidase (
), agropine synthase and creatinase (
). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [
,
,
].
Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site
Type:
Conserved_site
Description:
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role.
Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site [
]. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [].This entry represents the cataltyic core of a group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24B.A number of different enzymes from various sources have the proline dipeptidase domain. Enzymes know to have this domain include the Xaa-Pro dipeptidase (
)
(prolidase) and the Xaa-Pro aminopeptidase ().
Xaa-Pro dipeptidase (
) (prolidase) splits dipeptides with a prolyl
residue in the carboxyl terminal position. Xaa-Pro aminopeptidase () is the
enzyme responsible for the release of any N-terminal amino acid adjacent to aproline residue.
