Glycerol-3-phosphate (1)-acyltransferase(G3PAT) catalyzes the incorporation of an acyl group from either acyl-acyl carrier proteins (acylACPs) or acyl-CoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol-3-phosphate [
]. Glycerol-3-phosphate (G3P) plays an important role in carbohydrate and lipid metabolic processes [].
The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG). 8-OxoG can mispair with 2'-deoxycytidine 5'-triphosphate or with 2'-deoxyadenosine triphosphate during DNA replication, forming C*8-oxoG and A*8-oxoG mispairs. If unrepaired, the A=8-oxoG mispairs can result in deleterious C:G to A:T transversions. MutY, with its DNA glycosylase activity, excises adenine paired with guanine or 8-oxoG [
].Multiple forms of the mammalian homologue of MutY are formed by alternative splicing and locate to the nucleus or mitochondrion, where they have been shown to interact with several other proteins involved in the repair of DNA damage [
,
]. The HhH-GPD domain within the protein binds the phosphate backbone of the substrate.
Translation initiation factor 1A (eIF-1A), conserved site
Type:
Conserved_site
Description:
Eukaryotic translation initiation factor A (eIF-1A) (formerly known as eiF-4C) is a protein that seems to be required for maximal rate of protein biosynthesis. It enhances ribosome dissociation into subunits and stabilises the binding of the initiator Met-tRNA to 40S ribosomal subunits [
]. The archaea possess an eIF-1A homologue.
This domain is found associated with BTB/POZ domain (
) and Kelch repeats (
). BTB (broad-complex, tramtrack and bric a brac) is a Kelch related domain, also known as the POZ domain [
]. BTB proteins are divided into subgroups depending on what domain lies at the C terminus. Despite the divergence in sequences, the BTB fold is highly conserved.BTB-Kelch proteins have Kelch repeats that form a β-propeller that can interact with actin filaments [
]. BTB and C-terminal Kelch (BACK) together constitute a novel conserved domain, which is thought to have a possible role in substrate orientation in Cullin3-based E3 ligase complexes.Four domains, namely the BTB domain, a kelch domain, a BACK domain, and an intervening region (IVR) make up the aryl hydrocarbon receptor (AHR); a ligand-activated transcription factor [
]. This entry represents the domain associated with BTB and Kelch.
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [
,
]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta).This entry represents EF1A (or EF-Tu) proteins found primarily in bacteria, mitochondria and chloroplasts. Eukaryotic and archaeal EF1A (
) are excluded from this entry. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors [
].
Proteins of this family are predominantly nucleolar. Myb-binding protein 1A (MYBBP1A) is a transcription regulator that may play an important role in the cellular stress response [
,
,
,
]. This family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units [
]. This protein was originally thought to be a DNA polymerase, however, later reseach indicated its involvement in ribosome assembly [,
].
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 [
,
].A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The small ribosomal subunit protein S12 contains 130-150 amino acid residues, and is thought to be involved in the translation initiation step. This family consists of eukaryotic S12 ribosomal proteins, including those from vertebrates [
], Trypanosoma brucei [], Caenorhabditis elegans, Drosophila and Saccharomyces cerevisiae (Baker's yeast).
This entry represents the EKC/KEOPS complex subunit Cgi121 from fungi and its homologue, TPRKB from mammals. This entry also includes archaeal homologues [
]. CGI121 is part of the KEOPS complex, which is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine [
]. The KEOPS complex also plays an important part in telomere uncapping and telomere elongation and is required for efficient recruitment of transcriptional coactivators []. TPRKB has been shown to bind to the p53-related protein kinase (PRPK) [
]. PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53.
This entry includes animal NOSIP (nitric oxide synthase-interacting protein) and plant CSU1. They are ubiquitin E3 ligases [
,
]. Human NOSIP negatively regulates nitric oxide production by inducing NOS1 and NOS3 translocation to actin cytoskeleton and inhibiting their enzymatic activity [,
,
].Arabidopsis CSU1 plays a important role in maintaining COP1 homeostasis by targeting COP1 for ubiquitination and degradation in dark-grown seedlings [
].
This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins [
]. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif [].
Otubain family members include OTUB1, OTUB2 from mammals and otubain-like proteins from insects, worms and plants. They are a group of deubiquitylating enzymes that can remove conjugated ubiquitin from proteins and plays an important regulatory role at the level of protein turnover by preventing degradation [
]. A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. Four clans of cysteine peptidases share structural similarities with serine and threonine peptidases and asparagine lyases. From sequence similarities, cysteine peptidases can be clustered into over 80 different families [
]. Clans CF, CM, CN, CO, CP and PD contain only one family.Cysteine peptidases are often active at acidic pH and are therefore confined to acidic environments, such as the animal lysosome or plant vacuole. Cysteine peptidases can be endopeptidases, aminopeptidases, carboxypeptidases, dipeptidyl-peptidases or omega-peptidases. They are inhibited by thiol chelators such as iodoacetate, iodoacetic acid,
N-ethylmaleimide or
p-chloromercuribenzoate.
Clan CA includes proteins with a papain-like fold. There is a catalytic triad which occurs in the order: Cys/His/Asn (or Asp). A fourth residue, usually Gln, is important for stabilising the acyl intermediate that forms during catalysis, and this precedes the active site Cys. The fold consists of two subdomains with the active site between them. One subdomain consists of a bundle of helices, with the catalytic Cys at the end of one of them, and the other subdomain is a β-barrel with the active site His and Asn (or Asp). There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. Peptidases in clan CA are usually sensitive to the small molecule inhibitor E64, which is ineffective against peptidases from other clans of cysteine peptidases [
].Clan CD includes proteins with a caspase-like fold. Proteins in the clan have an α/β/α sandwich structure. There is a catalytic dyad which occurs in the order His/Cys. The active site His occurs in a His-Gly motif and the active site Cys occurs in an Ala-Cys motif; both motifs are preceded by a block of hydrophobic residues [
]. Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds.Clan CE includes proteins with an adenain-like fold. The fold consists of two subdomains with the active site between them. One domain is a bundle of helices, and the other a β-barrel. The subdomains are in the opposite order to those found in peptidases from clan CA, and this is reflected in the order of active site residues: His/Asn/Gln/Cys. This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other.Clan CL includes proteins with a sortase B-like fold. Peptidases in the clan hydrolyse and transfer bacterial cell wall peptides. The fold shows a closed β-barrel decorated with helices with the active site at one end of the barrel [
]. The active site consists of a His/Cys catalytic dyad.Cysteine peptidases with a chymotrypsin-like fold are included in clan PA, which also includes serine peptidases. Cysteine peptidases that are N-terminal nucleophile hydrolases are included in clan PB. Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. Cysteine peptidases with an intein-like fold are included in clan PD, which also includes asparagine lyases.
This is the C-terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [
,
].
This entry represents replication factor C subunit 1 (RFC1), which is the large subunit of replication factor C (RF-C), a five subunit DNA polymerase accessory protein. RF-C is a DNA binding protein complex and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon [
]. It also may have a role in telomere stability [].
This entry represents the N-terminal domain of the DNA polymerase III, delta subunit (
), which is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [
]. The delta subunit is also known as HolA.
Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase;
) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [,
]. The PTP superfamily can be divided into four subfamilies []:(1) pTyr-specific phosphatases(2) dual specificity phosphatases (dTyr and dSer/dThr)(3) Cdc25 phosphatases (dTyr and/or dThr)(4) LMW (low molecular weight) phosphatasesBased on their cellular localisation, PTPases are also classified as:Receptor-like, which are transmembrane receptors that contain PTPase domains [
]
Non-receptor (intracellular) PTPases [
]
All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel β-sheet with flanking α-helices containing a β-loop-α-loop that encompasses the PTP signature motif [
]. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [
,
]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 α-helices and 4 β-strands forming a 3-layer α-β-alpha sandwich architecture.
Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase;
) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [
,
]. The PTP superfamily can be divided into four subfamilies []:(1) pTyr-specific phosphatases(2) dual specificity phosphatases (dTyr and dSer/dThr)(3) Cdc25 phosphatases (dTyr and/or dThr)(4) LMW (low molecular weight) phosphatasesBased on their cellular localisation, PTPases are also classified as:Receptor-like, which are transmembrane receptors that contain PTPase domains [
]
Non-receptor (intracellular) PTPases [
]
All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel β-sheet with flanking α-helices containing a β-loop-α-loop that encompasses the PTP signature motif [
]. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase), which act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates [
,
]. The structure of a LMW PTPase has been solved by X-ray crystallography [] and is found to form a single structural domain. It belongs to the alpha/beta class, with 6 α-helices and 4 β-strands forming a 3-layer α-β-alpha sandwich architecture.
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 subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow [
]. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal α-helical domain with a similar superhelical topology to an armadillo repeat [].
The sialyltransferase family represents a group of enzymes that transfers sialic acid from its common nucleotide sugar donor, CMP-beta-N-acetylneuraminate, to the terminal carbohydrates group of various glycoproteins and glycolipids. Animal sialyltransferases have type II transmembrane topology, and are thought to localise to the Golgi body. Gene homologues of animal sialyltransferases have been detected in plants [
,
].This entry includes a subset of sialyltransferases that belong to the glycosyltransferase family 29 [
]. Beta-galactoside alpha-2,6-sialyltransferase 2 is not included in this entry.
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described [
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.Glycosyltransferase family 29 (
) comprises enzymes with a number of known activities; sialyltransferase (
), beta-galactosamide alpha-2,6-sialyltransferase (
), alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (
), beta-galactoside alpha-2,3-sialyltransferase (
), N-acetyllactosaminide alpha-2,3-sialyltransferase (
), alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase (
); lactosylceramide alpha-2,3-sialyltransferase (
). These enzymes use a nucleotide monophosphosugar as the donor (CMP-NeuA) instead of a nucleotide diphosphosugar.
Sialyltransferase may be responsible for the synthesis of the sequence NEUAC-Alpha-2,3-GAL-Beta-1,3-GALNAC-, found on sugar chains O-linked to thr or ser and also as a terminal sequenec on certain gagnliosides. These enzymes catalyse sialyltransfer reactions during glycosylation, and are type II membrane proteins.
This entry describes a family of proline iminopeptidases (
), which are Mn2+-requiring enzymes present in the cytosol of mammalian and microbial cells. They release an N-terminal residue from a peptide, preferably (but not exclusively) a proline.
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [
]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [].Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [
]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [,
].This entry represents a group of serine peptidase belonging to peptidase family S33 (clan SC). They include prolinases (Pro-Xaa dipeptidase,
), prolyl aminopeptidases (
), and L-amino acid amidases.
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups [
]. The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [,
,
,
,
]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].GPCR family 3 receptors (also known as family C) are structurally similar to other GPCRs, but do not show any significant sequence similarity and thus represent a distinct group. Structurally they are composed of four elements; an N-terminal signal sequence; a large hydrophilic extracellular agonist-binding region containing several conserved cysteine residues which could be involved in disulphide bonds; a shorter region containing seven transmembrane domains; and a C-terminal cytoplasmic domain of variable length [
]. Family 3 members include the metabotropic glutamate receptors, the extracellular calcium-sensing receptors, the gamma-amino-butyric acid (GABA) type B receptors, and the vomeronasal type-2 receptors [,
,
,
]. As these receptors regulate many important physiological processes they are potentially promising targets for drug development.
Inorganic pyrophosphatase (
) (PPase) [
,
] is the enzyme responsible for the hydrolysis of pyrophosphate (PPi) which is formed principally as the product of the many biosynthetic reactions that utilise ATP. All known PPases require the presence of divalent metal cations, with magnesium conferring the highest activity. Among other residues, a lysine has been postulated to be part of or close to the active site. PPases have been sequenced from bacteria such as Escherichia coli (homohexamer), Bacillus PS3 (Thermophilic bacterium PS-3) and Thermus thermophilus, from the archaebacteria Thermoplasma acidophilum, from fungi (homodimer), from a plant, and from bovine retina. In yeast, a mitochondrial isoform of PPase has been characterised which seems to be involved in energy production and whose activity is stimulated by uncouplers of ATP synthesis.The sequences of PPases share some regions of similarities, among which is a region that contains three conserved aspartates that are involved in the binding of cations.
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 family contains putative zinc metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). The N-terminal region of contains a perfectly conserved motif HEXGH, where the Glu is the active site and the His residues coordinate the metal cation.
The family of bacterial and plant proteins also includes a region that hits the PDZ domain (), found in a number of proteins targeted to the membrane by binding to a peptide ligand []. The family includes EcfE, which is a homologue of human site-2 protease (S2P), a membrane-bound zinc metalloprotease involved in regulated intramembrane proteolysis. In Escherichia coli EcfE activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA.
Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome (APC) [
]. The APC subunits are cullin family proteins with ubiquitin ligase activity []. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. Apc11 contains a canonical RING-H2-finger domain, which includes one histidine and seven cysteine residues that coordinate two Zn2+ ions. In addition, it contains a third Zn2+-binding site and the third Zn2+ ion is not essential for its ligase activity []. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability [].This entry represents the RING-H2 finger found in Apc11.
This entry represents the C-terminal β-sandwich domain of the splicing factor cactin [
], which is necessary for the association of cactin with the IkappaB protein cactus, as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival []. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development and in the establishment of dorsal-ventral polarity in the early embryo []. Members of this entry play a role in pre-mRNA splicing by facilitating excision of a subset of introns [].Most members of the family also have the conserved mid region of cactin (
) further upstream.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β hairpin and an α helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 [
]. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets [].A specific C2H2 Zn-finger is conserved in matrin and several RNA-binding proteins. The Zn-finger follows the general pattern C-x2-C-x(12,16)-H-x5-H, and is different from the 'classical' DNA-binding C2H2 Zn-finger.
Respiratory-chain NADH dehydrogenase (
) [
] (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 24 Kd (in mammals), which is a component of the iron-sulfur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulfur cluster. The 24 Kd subunit is nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa.The 24 Kd subunit is highly similar to [
,
]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) and Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase.
This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway [
]. These enzymes are primarily from bacteria, and have both DNA glycosylase activity () and AP lyase activity (
). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei).
Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity;
) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;
). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge [
]. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [,
].Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (
,
), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [
].These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger [
]. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a β-hairpin loop formed by the zinc finger [].
This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway [
]. These enzymes are primarily from bacteria, and have both DNA glycosylase activity () and AP lyase activity (
). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei).
Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity;
) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;
). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge [
]. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [
,
].Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (
,
), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [
].These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger [
]. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a β-hairpin loop formed by the zinc finger [].This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [
].
Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologues. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115.3-isopropylmalate dehydrogenase (IPMDH or LeuB) is the third enzyme in leucine biosynthesis. It catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate [
]. In the yeast Glarea lozoyensis, 3-isopropylmalate dehydrogenase gloI (EC 1.1.1.85) is required for the biosynthesis of the mycotoxin pneumocandin, a lipohexapeptide of the echinocandin family [
].
Signal recognition particle, SRP54 subunit, eukaryotic
Type:
Family
Description:
The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [
,
]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor []. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [].This entry represents the 54kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.
Signal recognition particle, SRP54 subunit, M-domain
Type:
Domain
Description:
The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [
,
]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor []. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [].This entry represents the M domain of the 54kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.
This entry represents the SRP54 subunit of the signal recognition particle protein translocation system.The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [
,
]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor []. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [].The bacterial homologues of the SRP54 protein and SRP RNA are Ffh and 4.5S RNA. They comprise a minimal bacterial SRP that can target ribosome-nascent chain complexes to the plasma membrane via interaction with FtsY, the bacterial
homologue of the SRP receptor [,
].
The PRO8NT domain is found at the N terminus of pre-mRNA splicing factors of PRO8 family [
]. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region [].
The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis [
]. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [].
This entry represents the interacting site for U6-snRNA, which is part of U4/U6.U5 tri-snRNPs complex of the spliceosome is a prime candidate for the role of cofactor in the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [
].
This entry represents Prp8 domain IV, which adopts a RNase H like fold within its core structure but with little sequence similarity. Pre-mRNA-splicing factor 8 (Prp8), a spliceosome protein, interacts directly with the splice sites and branch regions of precursor-mRNAs and spliceosomal RNAs associated with catalysis of the two steps of splicing. Catalysis of RNA cleavage by RNase H-like proteins involves a two-metal mechanism in which adjacently-bound divalent magnesium ions promote hydrolysis by activation of a water nucleophile and stabilization of the transition-state. However, the Prp8 domain IV contains only one of the canonical metal-binding sites and the coordinating side chains are spatially conserved with respect to Mg2+-coordinating residues within the RNase H fold [].
The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is the pre-mRNA-processing-splicing factor 8 (PrP8) which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa [
]. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RNA- recognition-motif (RRM) are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain [
].
Pre-mRNA-processing-splicing factor 8 (Prp8) is a central component of the spliceosome, which may play a role in aligning the pre-mRNA 5'- and 3'-exons for ligation. It interacts with U5 snRNA, and with pre-mRNA 5'-splice sites in B spliceosomes and 3'-splice sites in C spliceosomes. It is part of the U5 snRNP complex, and of U5.4/6 and U5.U4atac/U6atac snRNP complexes in U2- and U12-dependent spliceosomes, respectively. It is also found in a mRNA splicing-dependent exon junction complex (EJC) with SRRM1 where it interacts with U5 snRNP proteins SNRP116 and WDR57/SPF38 [
,
].Mutations of human Prp8 cause retinitis pigmentosa 13, a retinal dystrophy belonging to the group of pigmentary retinopathies [
].
Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria:
[
]. The enzyme acts as a monomer and binds a single metal ion, catalysing the reaction:N-formyl-L-methionine + H2O = formate + methionyl peptide
Catalytic efficiency strongly depends on the identity of the bound metal []. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents [
,
,
,
].The structure of these enzymes is known [
,
]. PDF, a zinc metalloenzyme from the mitochondrion, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel β-strands that surround two perpendicular α-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of metalloproteases such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloenzymes [
].
Members of this family have two highly conserved cysteine residues within the DxxCxxC motif at the N-terminal. This motif is conserved in the thiol-disulfide oxidoreductase family [
]. This family includes At5g50100 (also known as DCC1) from Arabidopsis thaliana, a thioredoxin that modulates ROS homeostasis resulting in de novo shoot initiation and may be involved in the improvement of the capacity of plant regeneration []. Uncharacterised proteins from bacteria are also included in this family.
Nup93/Nic96 is a component of the nuclear pore complex. It is required for the correct assembly of the nuclear pore complex [
]. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].
These proteins are members of the ATP:ADP Antiporter (AAA) family, which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers.This family contains bacterial proteins as well as chloroplastic proteins found in plants.
Cytochrome c oxidase (
) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen [
]. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [
,
]. Two of these cysteines are clustered in the C-terminal section of the subunit.
This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein, also known as MLN51) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide [
,
].
This entry represents mammalian centromere protein C (CENP-C), budding yeast Mif2 and fission yeast centromere protein 3 (cnp3) [
]. They play an important role in assembly of the kinectochore, which is the microtubule-attachment sites that allow chromosome segregation on the mitotic spindle. It binds to the centromere and interacts with histones [,
]. In budding yeast, it is phosphorylated by Aurora kinase Ipl1 []. In humans, CENP-C is a component of the CENPA-NAC complex, which is at least composed of CENPA, CENPC, CENPH, CENPM, CENPN, CENPT and MLF1IP/CENPU [,
].
This entry represents a domain found in Nup2, 50 and 61, which are components of the nuclear pore complex. Nucleoporin 50kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha [
]. NUP2 encodes a non-essential nuclear pore protein that has a central domain similar to those of Nsp1 and Nup1[
,
]. Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope [,
,
]. The structure of the vertebrate NPC has been studied extensively; recent reviews include [,
,
,
]. The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate [,
]. Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches [,
,
,
]. nup2 mutants show genetic interactions with nsp1 and nup1 conditional alleles [,
]. Nup1 interacts with the nuclear import factor Srp1 [] and with the small GTPase Ran (encoded by GSP1) [].
This domain of unknown function is found in the Xeroderma pigmentosum group D (XPD) proteins which belong to a family of ATP-dependent helicases characterised by a 'D-E-A-H' motif. This resembles the
'D-E-A-D-box' of other known helicases, which represents a special version of the B motif of ATP-binding proteins. In XPD,His replaces the second Asp. The DEAD box helicases are involved in
various aspects of RNA metabolism, including nuclear transcription, pre-mRNA splicing, ribosome biogenesis,nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [
].
This domain of unknown function is found at the C terminus of some
ATP-dependent helicases characterised by a 'D-E-A-H' motif. This resembles the 'D-E-A-D-box' of other known helicases,
a special version of the B motif of ATP-binding proteins however His replaces the second Asp. The DEADbox helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre-mRNA splicing,
ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP and, consequently, all of them carry the classical Walker A
(phosphate-binding loop or P-loop) and Walker B(Mg2+-binding aspartic acid) motifs. For the two largest groups, commonly
referred to as SF1 and SF2, a total of seven characteristic motifs has beenidentified [
]. These two superfamilies encompass a large number of DNA andRNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be
active as monomers or dimers. RNA and DNA helicases are considered to beenzymes that catalyze the separation of double-stranded nucleic acids in an
energy-dependent manner [].The various structures of SF1 and SF2 helicases present a common core with two
α-β RecA-like domains [,
]. Thestructural homology with the RecA recombination protein covers the five
contiguous parallel beta strands and the tandem alpha helices. ATP binds tothe amino proximal α-β domain, where the Walker A (motif I) and Walker
B (motif II) are found. The N-terminal domain also contains motif III (S-A-T)which was proposed to participate in linking ATPase and helicase activities.
The carboxy-terminal α-β domain is structurally very similar to theproximal one even though it is bereft of an ATP-binding site, suggesting that
it may have originally arisen through gene duplication of the first one.Some members of helicase superfamilies 1 and 2 are listed below:
DEAD-box RNA helicases. The prototype of DEAD-box
proteins is the translation initiation factor eIF4A. The eIF4A protein isan RNA-dependent ATPase which functions together with eIF4B as an RNA
helicase [].DEAH-box RNA helicases. Mainly pre-mRNA-splicing factor
ATP-dependent RNA helicases [].Eukaryotic DNA repair helicase RAD3/ERCC-2, an ATP-dependent 5'-3' DNA
helicase involved in nucleotide excision repair of UV-damaged DNA.Eukaryotic TFIIH basal transcription factor complex helicase XPB subunit.
An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIHbasal transcription factor, involved in nucleotide excision repair (NER) of
DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.It acts by opening DNA either around the RNA transcription start site or
the DNA.Eukaryotic ATP-dependent DNA helicase Q. A DNA helicase that may play a
role in the repair of DNA that is damaged by ultraviolet light or othermutagens.Bacterial and eukaryotic antiviral SKI2-like helicase. SKI2 has a role in
the 3'-mRNA degradation pathway, repressing dsRNA virus propagation byspecifically blocking translation of viral mRNAs, perhaps recognizing the
absence of CAP or poly(A).Bacterial DNA-damage-inducible protein G (DinG). A probable helicase
involved in DNA repair and perhaps also replication [].Bacterial primosomal protein N' (PriA). PriA protein is one of seven
proteins that make up the restart primosome, an apparatus that promotesassembly of replisomes at recombination intermediates and stalled
replication forks.Bacterial ATP-dependent DNA helicase recG. It has a critical role in
recombination and DNA repair, helping process Holliday junctionintermediates to mature products by catalyzing branch migration. It has a
DNA unwinding activity characteristic of helicases with a 3' to 5'polarity.A variety of DNA and RNA virus helicases and transcription factorsThis entry represents the ATP-binding domain found within bacterial DinG and eukaryotic Rad3 proteins, differing from other SF1 and SF2 helicases by the presence of a large insert after the Walker A motif [
].
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 beta' subunit.
Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex,
, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum.
Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain
Type:
Domain
Description:
Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport in eukaryotic cells, playing essential roles in cellular homeostasis. The NPC is a modular structure composed of multiple copies of ~30 proteins (nucleoporins, Nups) arranged into distinct subcomplexes [
,
]. A number of these peptides are synthesised as precursors and undergo self-catalyzed cleavage. The largest NPC sub-complex is the heptameric Y-shaped mammalian Nup107-Nup160 complex (called Nup84 complex in budding yeast), an essential scaffolding component of the NPC [
,
,
]. Nup98 and Nup96 are encoded by the same gene that produces a 190 kDa polyprotein with autoproteolytic activity which generates the N-terminal NUP98 and C-terminal NUP96 proteins, part of the Nup107-Nup160 subcomplex [
,
]. The yeast homologue Nup145 undergoes the similar proteolytic event to produce Nup145N and Nup145C, which are part of the Nup84 complex. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96, which is predicted to be an alpha helical solenoid, complexes with Sec13 in the middle of the heptamer. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex [,
].The proteolytic cleavage site of yeast Nup145p has been mapped upstream of an evolutionary conserved serine residue. Then, Nup145C form the heptameric Y-complex together with six other proteins while Nup145N shuttle between the NPC and the nuclear interior. [
,
].Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs, is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-terminal domain reveals a novel protein fold, and thus a new class of autocatalytic proteases. The structure further reveals that the suggested nucleoporin RNA binding motif is unlikely to bind to RNA [
].The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [
,
]:Vertebrate Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs.
Yeast Nup100, plays an important role in several nuclear export and import pathways including poly(A)+ RNA and protein transport.
Yeast Nup116, involved in mRNA export and protein transport.
Yeast Nup145, involved in nuclear poly(A)+ RNA and tRNA export.The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59
autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145each occur immediately C-terminal to the NUP C-terminal domain. Thus, although
this domain occurs in the middle of each precursor polypeptide, it winds up atthe C-terminal end of the N-terminal cleavage product. Cleavage of the peptide
chains are necessary for the proper targeting to the nuclear pore [,
].The NUP C-terminal domain adopts a predominantly β-strand structure. The molecule consists of a six-stranded β-sheet sandwiched against a two-stranded β-sheet and flanked by α-helical regions. The N-terminal helical region consists of two short helices, whereas the stretch on the opposite side of molecule consists of a single, longer helix [
,
].
Aspartate racemase (
) and glutamate racemase (
) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity [
]. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S.In addition to characterised aspartate and glutamate racemases, this family also includes a hypothetical protein from Erwinia carotovora and one from Escherichia coli (ygeA).
Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate. This entry represents a conserved region containing the first cysteine.
This entry represents a domain found in some members of the S26A family of serine endopeptidases. Peptidases S26A (signal peptidase I) removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism [
]. Peptidases S26B includes eukaryotic microsomal signal peptidases involved in the removal of signal peptides from secretory proteins as they pass into the endoplasmic reticulum lumen []. Peptidases 26C (TraF signal peptidase) are found in operons that encode elements of conjugative transfer systems.
This entry consists of the E3 SUMO-protein ligase Nse2 (also known as Mms21). Nse2 is an E3 SUMO-protein ligase component of the SMC5-SMC6 complex [
,
]. Nse2 acts as an E3 ligase targeting several proteins for sumoylation and is required for efficient DNA repair and maintenance of genome stability [,
,
,
]. Nse2 and SMC5 may also be required for sister chromatid cohesion during prometaphase and mitotic progression; this role is apparently independent of SMC6 []. Nse2 is necessary for normal cell cycle progression in Arabidopsis, where Nse2 mutation results in abnormal root development [].
This entry represents a conserved region of 80 residues which defines a family of coiled-coil proteins known as Biogenesis of lysosome-related organelles complex 1 subunit KXD1 in yeast and KXDL1 in animals [
,
,
]. This domain contains the characteristic KxDL motif towards the C terminus. Members of this entry are components of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) involved in endosomal cargo sorting. They may play a role in lysosomes movement and localization at the cell periphery [,
,
].
Thymidylate kinase (
; dTMP kinase) catalyses the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:
ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate
Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages [
].
Thymidylate kinase (
; dTMP kinase) catalyses the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:
ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate
Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages [
].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [
,
,
]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class E cytochrome P450 proteins that fall into sequence cluster group II. Group II enzymes are distributed widely in life, i.e., in bacteria (family CYP102), cyanobacteria (CYP110), fungi (CYP52, CYP53 and CYP56), insects (CYP4 and CYP6) and mammals (CYP3, CYP4 and CYP5). Many group II enzymes catalyse hydroxylation of linear chains, such as alkanes (CYP52), alcohols and fatty acids (CYP4, CYP5, CYP102); Aspergillus niger CYP53 carries out para-hydroxylation of benzoate; yeast CYP56 is possibly involved in oxidation of tyrosine residues; insect CYP6 metabolises a wide range of toxic compounds; and members of the CYP3 family are omnivorous.
This entry represents a group of DNA binding proteins, known as SBP (SQUAMOSA-pROMOTER BINDING PROTEIN) family. They are putative transcription factors characterised by a highly conserved SBP-box of 76 amino acids involved in DNA binding and nuclear localisation [
]. They are involved in the control of early flower development []. This entry includes Arabidopsis SPL3 and SPL4 []. SPL3/SPL4 promote vegetative phase change and flowering, and are strongly repressed by miR156 [].
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 [
,
].Ribosomal protein L3 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui
HmaL3 (HL1), and yeast mitochondrial YmL9 [,
,
].This entry represents bacterial, mitochondrial and chloroplast L3 proteins. The organellar proteins typically contain a transit peptide sequence located N-terminal to the region covered by this entry.
This enzyme is the enolase-phosphatase of methionine salvage, a pathway that regenerates methionine from methylthioadenosine (MTA). Adenosylmethionine (AdoMet) is a donor of different moieties for various processes, including methylation reactions. Use of AdoMet for spermidine biosynthesis, which leads to polyamine biosynthesis, leaves MTA as a by-product that must be cleared. In Bacillus subtilis and related species, this single protein is replaced by separate enzymes with enolase and phosphatase activities. This entry also matches a number of probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 enzymes.
Methylthioribulose-1-phosphate dehydratase catalyses the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). It functions in the methionine salvage pathway. This entry also includes probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 from plants.
Proteins in this family are probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 from plants. They share protein sequence similarity to both
and
.
Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine.Proteins in this entry also include the bifunctional enzyme MtnB/MtnX from bacteria and the probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 from plants.
This entry represents the alpha/beta/alpha domain found in class II aldolases and in adducin (usually at the N terminus of adducin). Proteins containing this domain include: rhamnulose-1-phosphate aldolase (
), L-fuculose phosphate aldolase (
) [
,
] that is involved in the third step in fucose metabolism, L-ribulose- 5-phosphate 4-epimerase () involved in the third step of L-arabinose catabolism, a probable sugar isomerase SgbE and the metazoan adducins, which have not been ascribed any enzymatic function but which play a role in cell membrane cytoskeleton organisation [
].
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 [
,
].A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.
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 [
,
].A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.
D-alanine--D-alanine ligase (
) is a bacterial enzyme involved in cell-wall biosynthesis. It participates in forming UDP-N-acetylmuramoyl pentapeptide, the peptidoglycan precursor. These enzymes are proteins of 300 to 360 amino acids containing many conserved regions. The N-terminal Gly-rich region could be involved in ATP-binding.
This family of enzymes represent chromosomal versions of species not specifically resistant to glycopeptide antibiotics such as vancomycin. The mechanism of glycopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). This model attempts to exclude the VanA/VanB and VanC subfamilies while capturing most other D-Ala-D-Ala ligases above the trusted cut-off. However, changes in small numbers of amino acids, as demonstrated crystallographically, can alter specificity. In chlamydial species, this enzyme is found as a fusion protein with UDP-N-acetylmuramate--alanine ligase.
This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (
) which is thought to be involved in substrate binding [
,
]. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].
This domain is found in the RNase Z enzymes, which are closely related structurally to the Lactamase B family members. tRNase Z (ribonuclease Z) is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Trz1, is targeted to the nucleus and has an SV40 nuclear localisation signal at its N terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Trz2, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues [].
Photosystem I, a membrane complex found in the chloroplasts of plants and cyanobacteria
uses light energy to transfer electrons from plastocyanin to ferredoxin. The electron transfer components of the photosystem include the primary electron donor
chlorophyll P-700 and 5 electron acceptors: chlorophyll (A0), phylloquinone (A1) and three 4Fe-4S iron-sulphur centres, designated Fx, Fa and Fb. The role of this protein, subunit VI or PsaH, may be in docking of the light harvesting
complex I antenna to the core complex.
This entry describes an N-terminal domain found regularly in proteins encoded near a variant form of signal peptidase I such as the SipW protein of Bacillus subtilis. Many though not all members are homologues of camelysin (a casein-cleaving metalloprotease) and TasA (CotN), a metalloprotease that is secreted, along with extracellular polysaccharide (EPS), to be the major protein constituent of the Bacillus subtilis biofilm matrix. Sequencing from several known TasA/CotN proteins shows the cleavage location to be near the centre of the alignment and typical of type I signal peptidases, with small residues at -3 and -1.
The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [
]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specificaffinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.
The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.This ribosomal protein family includes 30S ribosomal protein S17 and 40S ribosomal protein S11.
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 ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [
]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [
] has revealed that S17 has virtually no groups exposed on the ribosomal surface.This entry represents a short conserved sequence region located towards the C terminus of S17.
This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes [
]. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
This is the middle region of a family of TATA element modulatory factor 1 (TMF1) proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [
] and plant [] cells.
Protein kinase A anchor protein, nuclear localisation signal domain
Type:
Domain
Description:
This entry represents the nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes [
]. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. The domain is also found in a number of other proteins, such as activating signal cointegrator 1 complex subunit 1 and leukocyte receptor cluster member 9.
The nuclear pore complex (NPC) mediates the transport of macromolecules across
the nuclear envelope (NE). The NPC is composed of a relatively small number ofproteins (~30), termed nucleoporins or Nups. The vertebrate nuclear pore
protein Nup35, the ortholog of Saccharomyces cerevisiae Nup53p, is suggestedto interact with the NE membrane and to be required for nuclear morphology.
The highly conserved region between vertebrate Nup35 and yeast Nup53p ispredicted to contain an RNA-recognition motif (RRM) domain.
The sequences of the RRM Nup-35-type domain are highly conserved in alleucaryotes. The RRM Nup35-type domain adopts the characteristic BetaAlphaBeta
BetaAlphaBeta topology of the secondary structure elements, with a four-stranded antiparallel β-sheet packed against two alpha helices. The RRM
Nup35-type domain forms a homodimer and contains atypicalrinonucleoprotein (RNP) motifs, which lack the conserved residues that
typically bind RNA in canonical RRM domains. The dimer interface involves theβ-sheet surface, with its atypical RNP motifs, which is generally used to
bind RNA in typical RRM domains [].This entry represents the RRM Nup35-type domain.
This entry represents the C-terminal domain of MMS19. This domain shares homology with some HEAT repeat sequences. MMS19 is a key component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into apoproteins specifically involved in DNA metabolism and genomic integrity [
,
,
]. In humans, MMS19 acts as an adapter between early-acting CIA components and a subset of cellular target iron-sulfur proteins such as ERCC2/XPD, FANCJ and RTEL1, thereby playing a key role in nucleotide excision repair (NER) and RNA polymerase II (POL II) transcription [
,
]. It is also part of the MMXD (MMS19-MIP18-XPD) complex, which plays a role in chromosome segregation, probably by facilitating iron-sulfur cluster assembly into ERCC2/XPD [
].In budding yeasts, the mms19 mutants were originally isolated in a screening for mutants hypersensitive to the alkylating agent methyl methanesulfonate (MMS) [
]. Different from human MMS19, Mms19 in budding yeasts (also known as Met18) does not participate directly in NER []. In fission yeast, Mms19 is part of a silencing complex named Rik1-Dos2 complex, which contains Dos2, Rik1, Mms19 and Cdc20. This complex regulates RNA Pol II activity in heterochromatin, and is required for DNA replication and heterochromatin assembly [
].
Profilin [
,
] is a small eukaryotic protein that binds to monomeric actin(G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into
filaments (F-actin). It can also, in certain circumstance promotes actinpolymerisation. Profilin also binds 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-terminalregion is relatively well conserved. That region is thought to be involved in
the binding to actin. This entry represents a conserved site at the N-terminal extremity of profilin. A protein structurally similar to profilin is present in the genome of variola and vaccinia viruses (gene A42R).
This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides [
].
Acetolactate synthases are a group of biosynthetic enzymes apparently found in plants, fungi and bacteria that are capable of
de novosynthesis of the branched-chain amino acids [
]. They can all synthesize acetolactate from pyruvate in the biosynthesis of valine, while some are also capable of synthesizing acetohydroxybutyrate from pyruvate and ketobutyrate during the biosynthesis of isoleucine. These enzymes generally require thiamin diphosphate, FAD and a divalent metal ion for catalysis, though some enzymes specific for acetolactate synthesis do not require FAD. They are composed of two subunits, a large catalytic subunit, and a smaller regulatory subunit which binds the natural modulators (valine, and in some cases leucine or isoleucine).These enzymes are the target for currently-used herbicides such as sulphonylureas and imidazolinones. Their restricted distribution also makes them potential targets for the development of novel antibacterial and antifungal compounds.This entry represents the small regulatory subunit of acetolactate synthase. It contains an ACT domain, which is a predicted regulatory ligand-binding fold often found in proteins regulated by small-molecule effectors [
].
RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in MEROPS peptidase family S16 (lon protease family, clan SJ).RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks [
,
].
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups [
]. The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [,
,
,
,
]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].GPCR Fungal pheromone mating factor receptors form a distinct family of G-protein-coupled receptors, and are also known as Class D GPCRs.The Fungal pheromone mating factor receptors STE2 and STE3 are integral membrane proteins that may be involved in the response to mating factors on the cell membrane [
,
,
]. The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains,in a manner reminiscent of the rhodopsins and other receptors believed tointeract with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence similarity either between STE2 and STE3, or between these and the rhodopsin-type family: the receptors thereofore bear their own unique '7TM' signatures which is why they have been given their own GPCR group: Class D Fungal mating pheromone receptors.
This entry represents the STE3-type family of fungal pheromone mating factor receptors. The STE3 gene of Saccharomyces cerevisiae (Baker's yeast) is the cell-surface receptor that binds the 13-residue lipopeptide a-factor. Several related fungal pheromone receptor sequences are known: these include pheromone B alpha 1 and B alpha 3, and pheromone B beta 1 receptors from Schizophyllum commune; pheromone receptor 1 from Ustilago hordei; and pheromone receptors 1 and 2 from Ustilago maydis. Members of the family share about 20% sequence identity.
