DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].DNA topoisomerase II (
) [
,
,
] is one of the two types of enzyme that catalyze the interconversion of topological DNA isomers. Type II topoisomerases are ATP-dependent and act by passing a DNA segment through a transient double-strand break. Topoisomerase II is found in phages, archaebacteria, prokaryotes, eukaryotes, and in African Swine Fever virus (ASF). Bacteriophage T4 topoisomerase II consists of three subunits (the product of genes 39, 52 and 60). In prokaryotes and in archaebacteria the enzyme, known as DNA gyrase, consists of two subunits (genes GyrA and GyrB). In some bacteria, a second type II topoisomerase has been identified; it is known as topoisomerase IV and is required for chromosome segregation, it also consists of two subunits (genes parC and parE). In eukaryotes, type II topoisomerase is a homodimer. There are many regions of sequence homology between the different subtypes of topoisomerase II. The signature pattern used in this entry is a highly conserved pentapeptide, which is located in GyrB, in ParE, and in protein 39 of phage T4 topoisomerase.
DNA topoisomerase, type IIA-like domain superfamily
Type:
Homologous_superfamily
Description:
Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [
].Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [
]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.This superfamily represents the C-terminal of subunit B (gyrB and parE) and the N-terminal of subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent region in eukaryotic topoisomerase II composed of a single polypeptide.
SCAI is a transcriptional cofactor and tumour suppressor that suppresses MKL1-induced SRF transcriptional activity. It may function in the RHOA-DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1 [
].
This entry represents the surfeit locus protein SURF6 from mammals and its homologues from plants and fungi. In mammals, SURF6 is a component of the nucleolar matrix and has a strong binding capacity for nucleic acids [
]. SURF6 is always found in the nucleolus regardless of the phase of the cell cycle suggesting that it is a structural protein constitutively present in nucleolar substructures. A role in rRNA processing has been proposed for this protein. Saccharomyces cerevisiae member of the SURF-6 family, named Rrp14 (ribosomal RNA-processing protein 14), interacts with proteins involved in ribosomal biogenesis and cell polarity [
]. It is required for the synthesis of both 40S and 60S ribosomal subunits and may also play some direct role in correct positioning of the mitotic spindle during mitosis [,
].
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.In plants, chloride channels contribute to a number of plant-specific
functions, such as regulation of turgor, stomatal movement, nutrienttransport and metal tolerance. By contrast with Cl
-channels in animal cells, they are also responsible for the generation of action potentials.The best documented examples are the chloride channels of guard cells,
which control opening and closing of stomata. Recently, four homologousproteins that belong to the CLC family have been cloned from Arabidopsis thaliana (Mouse-ear cress) [
]. Hydropathy analysis suggests that they havea similar membrane topology to other CLC proteins, with up to 12 TM domains.
Expression in Xenopus oocytes failed to generate measurable Cl-currents,
although protein analysis suggested they had been synthesised and insertedinto cell membranes. However, similar CLC proteins have since been cloned
from other plants, and one, CIC-Nt1 (from tobacco), has been demonstrated toform funtional Cl
-channels, suggesting that at least some of these proteins
do function as Cl-channels in plants [
].
Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. This N-terminal domain is not required for transcriptional activity, and while a similar sequence has been identified in other transcription factors, and proteins that are predominantly nuclear localized [
,
], the domain is also found in proteins not directly involved in transcription. This domain is found in (amongst others):MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved [
].
Transcription factor S-II (TFIIS) induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius [
]. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [,
].TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III [
]. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding β-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre.This domain is found in the N-terminal region of transcription elongation factor S-II (TFIIS) and in several hypothetical proteins.
This entry represents the active-site-containing domain found in the trypsin family members. The catalytic activity of the serine proteases from the trypsin family is provided by a charge relay system involving an aspartic acid residue hydrogen-bonded to a histidine, which itself is hydrogen-bonded to a serine. The sequences in the vicinity of the active site serine and histidine residues are well conserved in this family of proteases [
]. A partial list of proteases known to belong to the trypsin family is shown below.Acrosin.Blood coagulation factors VII, IX, X, XI and XII, thrombin, plasminogen,
and protein C.Cathepsin G.Chymotrypsins.Complement components C1r, C1s, C2, and complement factors B, D and I.Complement-activating component of RA-reactive factor.Cytotoxic cell proteases (granzymes A to H).Duodenase I.Elastases 1, 2, 3A, 3B (protease E), leukocyte (medullasin).Enterokinase (EC 3.4.21.9) (enteropeptidase).Hepatocyte growth factor activator.Hepsin.Glandular (tissue) kallikreins (including EGF-binding protein types A, B, and C, NGF-gamma chain, gamma-renin, prostate specific antigen (PSA) and tonin).Plasma kallikrein.Mast cell proteases (MCP) 1 (chymase) to 8.Myeloblastin (proteinase 3) (Wegener's autoantigen).Plasminogen activators (urokinase-type, and tissue-type).Trypsins I, II, III, and IV.Tryptases.All the above proteins belong to family S1 in the classification of peptidases [
] and originate from eukaryotic species. It should be noted that bacterial proteases that belong to family S2A are similar enough in the regions of the active site residues that they can be picked up by the same patterns. These proteases are listed below.Achromobacter lyticus protease I.Lysobacter alpha-lytic protease.Streptogrisin A and B (Streptomyces proteases A and B).Streptomyces griseus glutamyl endopeptidase II.Streptomyces fradiae proteases 1 and 2.
Ubiquitin-conjugating enzymes (
, UBC or E2 enzymes) catalyse the covalent attachment of ubiquitin to target proteins. Ubiquitin is conjugated to the target protein through the coordinated action of three enzyme activities designated E1, E2, and E3. The E1 or ubiquitin-activating enzyme forms, in an ATP-dependent manner, a thioester linkage between its active site cysteine and the carboxy terminus of ubiquitin. The activated ubiquitin moiety is then transferred from E1 to the active site cysteine in E2 through a trans-thiol esterification reaction. The UBC enzyme later ligates ubiquitin directly to substrate proteins with or without the assistance of 'N-end' recognizing proteins (E3) [
,
,
]. In most species there are many forms of UBC (at least 9 in yeast) which are implicated in diverse cellular functions. A cysteine residue is required for ubiquitin-thiolester formation. There is a single conserved cysteine in UBC's and the region around that residue is conserved in the sequence of known UBC isozymes. The UBC core is an alpha/beta domain containing one four-stranded antiparallel β-sheet and four α-helices (
). Three of these helices flank two opposite edges of the sheet, and one helix lays diagonally across one broad face of the sheet. The other face of the sheet is exposed to solvent. One turn of a 3(10)-helix is located between the fourth strand of the sheet and the second α-helix. The active site cysteine is situated in a segment between the fourth strand of the sheet and the 3(10)-helix [
]. The signature pattern, of this entry, contains the active-site cysteine and spans the complete catalytic domain.
This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP;
), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing [
]; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.This entry also includes QDE-1 from the filamentous fungus Neurospora. QDE-1 is both an RdRP and a DNA-dependent RNA polymerase (DdRP). It is able to synthesize RNA from both ssRNA and single-stranded DNA (ssDNA) [
].
This family consists of ribonuclease III (RNase III). This ubiquitous enzyme specifically cleaves double-stranded rRNA and is found in all bacteria and eukaryotes [
]. In bacteria its main role is the processing of pre-rRNAs, where the large precursor ribosomal RNA molecules are cleaved at specific sites to produce the immediate precursors of the functional molecules. RNase III also functions in the maturation and degradation of mRNAs, and the maturation of tRNAs. In some organisms (eg. Escherichia coli) cells are viable without this enzyme, though they are impeded in growth, but in others (eg. B. subtilis and M. genitalium) this enzyme is essential.The bacterial RNase III enzymes so far characterised are homodimers with a molecular mass of ~50kDa [
,
]. The endonuclease domain is located within the N-terminal two-thirds of the protein, containing several α-helices, but no β-strands. The double-stranded RNA binding domain is found at the C-terminal third of the protein, forming the α-β(3)-α fold common to dsRNA-binding proteins. A signature box of 11 conserved amino acids found in the N-terminal region of RNase III may contain the active site, though this has not been proven.
This domain is found in eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease [
,
]. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing [,
,
].
A beta barrel of circularly permuted topology is found in the C terminus of many translation elongation and initiation factors. This domain is found in the elongation factors EF1A (or EF-Tu) of both eukaryotes and prokaryotes, which functions to recognise and transport aminoacyl-tRNA to the acceptor (A) site of the ribosome during the elongation process [
,
]. This domain is also found in the initiation factor IF2 gamma subunit of eukaryotes [], which functions to transport the initiator methionyl-tRNA to the ribosome. The C-terminal extension of mitochondrial EF1A (or EF-Tu) has structural similarities with DNA recognising zinc fingers, suggesting that the extension may be involved in recognition of RNA.
Elongation factor EF1A (also known as EF-1alpha or EF-Tu) promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. EF1A consists of three structural domains. Release factor eRF3, which governs translation termination, has a similar overall structure. RF3 has an N-terminal extension and a EF1A-like C-terminal region which comprises a GTP-binding domain (G domain) and two β-barrel domains that are similar to the three respective domains of elongation factor EF-Tu/eEF1A [
]. Archaeal EF1A is both involved in translational elongation and termination, as well as in mRNA surveillance, which explains the lack of an eRF3 orthologue in archaea [].This entry represents the C-terminal domain of both EF1A and eRF3, which adopts a β-barrel structure. In EF1A, this domain is involved in binding to both charged tRNA and to EF1B (or EF-Ts,
) [
].
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 proteins from in eukaryotic (eEF1alpha) and archaeal (aEF1alpha) organisms, these proteins being more closely related to one another than to EF1A (or EF-Tu) from bacteria (
).
Archaeal EF1-alpha is not only involved in translation elongation. It interacts with Pelota, a mRNA surveillance protein involved in no-go mRNA decay and non-stop mRNA decay; and with RF1, a tRNA-mimicking protein which recognises stop codons and catalyses polypeptide-chain release. Through these interactions archaeal EF1-alpha also has a role in translational termination and mRNA surveillance pathways [
].
This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A [
].
DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
Type:
Homologous_superfamily
Description:
The Escherichia coli DNA polymerase III gamma complex clamp loader assembles the ring-shaped beta sliding clamp onto DNA. The core polymerase is tethered to the template by beta, enabling progressive replication of the genome. The E. coli complex clamp loader contains five different subunits, clamp loading only requires 3 of these - the gamma, delta, delta' complex. Three gamma subunits, and one each of delta and delta', are arranged in a circle. Each subunit adopts the same chain topology, and folds into three domains. However, the relative orientation of these domains is different for each subunit. The carboxy-terminal domains provide the major subunit contacts of the pentamer, although other intersubunit contacts are present. The amino-terminal domains do not form a continuous circle. These domains are arranged in a highly asymmetric fashion, and appear to dangle under the carboxy-terminal pentamer 'umbrella' [
].
This entry represents the mitochondrial/chloroplastic transcription termination factors (MTERFs). In humans four MTERFs have been identified (MTERF1-4). MTERF1 was first identified as a factor responsible for terminating heavy strand transcription at a specific site at the leu-tRNA, thereby modulating the ratio of mitochondrial ribosomal RNA to mRNA [
]. Later, MTERF1 was found to stimulate transcriptional initiation [] and appeared to be in the control of mitochondrial replication pausing []. From a structural study, it binds to dsDNA containing the termination sequence and unwinds the DNA molecule, promoting base eversion, which is critical for transcription termination [].
The outer and inner segments of vertebrate rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the GTP-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A [
]. The protein is thought to participate in the regulation of visual phototransduction or in the integration of photo-receptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the functional role of the protein is the same in both retina and pineal gland [].This entry represents a domain found in members of the phosducin family. This domain has a thioredoxin-like fold [
].
This entry represents the domain that is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes which catalyse the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI and is also found in the Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN (also known as Werner syndrome helicase), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [
].Werner syndrome is a human genetic disorder causing premature ageing; the WRN protein has helicase activity in the 3'-5' direction [
,
]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein []. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.This domain is also found in some DNA polymerases from phages, including the DNA polymerase from Escherichia phage T5, exonucleolytic activity [], and the DNA polymerase DpoZ from Acinetobacter phage SH-Ab 15497, which preferentially incorporates the non-canonical base aminoadenine/dZTP instead of adenine into the synthesized DNA [].
In Saccharomyces cerevisiae, Nucleolar complex protein 2 (Noc2) forms a nucleolar complex with Mak21 that binds to 90S and 66S pre-ribosomes. It also forms a nuclear complex with Noc3 that binds to 66S pre-ribosomes [
]. Both complexes mediate intranuclear transport of ribosomal precursors []. In humans, Noc2 (also known as NIR) acts as an inhibitor of histone acetyltransferase activity; prevents acetylation of all core histones by the EP300/p300 histone acetyltransferase at p53/TP53-regulated target promoters in a histone deacetylases (HDAC)-independent manner. It also acts as a transcription corepressor of p53/TP53- and TP63-mediated transactivation of the p21/CDKN1A promoter. It is involved in the regulation of p53/TP53-dependent apoptosis [
,
,
].Nucleolar complex-associated protein 2 (Noc2) from Arabidopsis thaliana appears to be involved in pre-ribosome export from the nucleus to the cytoplasm [
]. Also from A.thaliana, Protein REBELOTE influences floral meristem (FM) determinacy in an AGAMOUS and SUPERMAN-dependent manner, thus contributing to the floral developmental homeostasis [].
The CHROMO (CHRromatin Organization MOdifier) domain [
,
,
,
] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting.
Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain
followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain [], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with
a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro [
].The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three β-strands packed against an α-helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [
].This entry represents a conserved site in the chromo domain.
The CHROMO (CHRromatin Organization MOdifier) domain [
,
,
,
] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation.These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain [
], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.This entry represents a subgroup of the Chromo domain
4-diphosphocytidyl-2C-methyl-D-erythritol kinase is a member of the family of GHMP kinases that were previously designated as conserved hypothetical protein YchB or as isopentenyl monophosphate kinase. In Solanum lycopersicum (Tomato) (Lycopersicon esculentum) and Escherichia coli the protein has been indentified as 4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an enzyme of the deoxyxylulose phosphate pathway of terpenoid biosynthesis [
]. This enzyme is involved in the non-mevalonate pathway for isoprenoid biosynthesis [] and in it is essential for for chloroplast development [].
This entry consists of a group of cysteine protease inhibitors (also known as cystatins). They can be classified as [
]:Type 1: intracellular cystatins, but may also appear in significant amounts in body fluids [
]. They are single-chain polypeptides of about 100 residues, which have neither disulphide bonds nor carbohydrate side chains. Type 1 cystatin includes cystatin-A/B. Type 2: extracellular secreted polypeptides synthesised with a 19-28 residue signal peptide. They are broadly distributed and found in most body fluids [
]. Type 2 cyctatin includes cystatin-C/D/M/F/SA/SN/G. Type 3: multidomain cystatins, including kininogens, known as kinin precursor proteins [
]. There are three different kininogens in mammals: H- (high molecular mass, ) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat.
Unclassified cystatins: cystatin-like proteins. This entry represents the type1, type2 and cystatin-like proteins.
Proteinase inhibitor I25, cystatin, conserved site
Type:
Conserved_site
Description:
Cystatins are cysteine proteinase inhibitors belonging to MEROPS inhibitor family I25, clan IH [
,
,
]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and C13 (legumain family). The cystatin family includes:The Type 1 cystatins, which are intracellular cystatins that are present in the cytosol of many cell types, but can also appear in body fluids at significant concentrations. They are single-chain polypeptides of about 100 residues, which have neither disulphide bonds nor carbohydrate side chains. The Type 2 cystatins, which are mainly extracellular secreted polypeptides synthesised with a 19-28 residue signal peptide. They are broadly distributed and found in most body fluids. The Type 3 cystatins, which are multidomain proteins. The mammalian representatives of this group are the kininogens. There are three different kininogens in mammals: H- (high molecular mass,
) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat.
Unclassified cystatins. These are cystatin-like proteins found in a range of organisms: plant phytocystatins, fetuin in mammals, insect cystatins and a puff adder venom cystatin which inhibits metalloproteases of the MEROPS peptidase family M12 (astacin/adamalysin). Also a number of the cystatins-like proteins have been shown to be devoid of inhibitory activity. All true cystatins inhibit cysteine peptidases of the papain family (MEROPS peptidase family C1), and some also inhibit legumain family enzymes (MEROPS peptidase family C13). These peptidases play key roles in physiological processes, such as intracellular protein degradation (cathepsins B, H and L), are pivotal in the remodelling of bone (cathepsin K), and may be important in the control of antigen presentation (cathepsin S, mammalian legumain). Moreover, the activities of such peptidases are increased in pathophysiological conditions, such as cancer metastasis and inflammation. Additionally, such peptidases are essential for several pathogenic parasites and bacteria. Thus in animals cystatins not only have capacity to regulate normal body processes and perhaps cause disease when down-regulated, but in other organisms may also participate in defence against biotic and abiotic stress. This entry represents a conserved region found in cystatins which includes five conserved residues proposed to be important for binding to cysteine proteases.
Cystatins are a family of cysteine protease inhibitors belonging to MEROPS inhibitor family I25, clan IH [
,
,
]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and C13 (legumain family). They occur mainly as single domain proteins. However, some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains.
Water Stress and Hypersensitive response (WHy) domain is a region of unknown function found in several plant proteins involved in either the response to water stress or the response to bacterial infection [
]. It is also found in some bacterial and archaeal proteins whose functions are not currently known. This domain is approximately 100 amino acids long and is composed of alternating hydrophobic and hydrophilic residues, with an almost invariant NPN motif at the N terminus. The predicted secondary structure is a novel fold consisting mostly of beta strands and a C-terminal alpha helix.
This entry represents the C-terminal region of plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase;
), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain [
]. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.
Squalene synthase
(farnesyl-diphosphate farnesyltransferase)(SQS) and phytoene synthase
(PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [
,
,
]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene:2 FPP ->presqualene diphosphate + NADP ->squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound.PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP)into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene.2 GGPP ->prephytoene diphosphate ->phytoene
PSY is found in all organisms that synthesize carotenoids: plants and
photosynthetic bacteria as well as some non-photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.
This family hyccin proteins (HYCC1/2) which are a component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane and it also regulates phosphatidylinositol 4-phosphate (PtdIns4P) synthesis [
]. HYCC1 plays a key role in oligodendrocytes formation [] which may explain its importance in myelination of the central and peripheral nervous system []. Defects in Hyccin are the cause of hypomyelination with congenital cataracts . This disorder is characterised by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs [,
]. These proteins may also have a role in the beta-catenin-Tcf/Lef signaling pathway.
The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 kDa alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 [
]. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes.In the crystal structure of PP2A PR65/A [
], the HEAT repeats consist of pairs of antiparallel α-helices [].
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. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters [
].
Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Atg proteins coordinate the formation of autophagosomes. The pre-autophagosomal structure contains at least five Atg proteins: Atg1p, Atg2p, Atg5p, Aut7p/Atg8p and Atg16p, found in the vacuole [
,
]. The C-terminal glycine of Atg12p is conjugated to a lysine residue of Atg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Autophagy protein 16 (Atg16) has been shown to bind to Atg5 and is required for the function of the Atg12p-Atg5p conjugate []. Autophagy protein 5 (Atg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [].This entry represents autophagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.
TAZ (Transcription Adaptor putative Zinc finger) domains are zinc-containing domains found in the homologous transcriptional co-activators CREB-binding protein (CBP) and the P300. CBP and P300 are histone acetyltransferases (
) that catalyse the reversible acetylation of all four histones in nucleosomes, acting to regulate transcription via chromatin remodelling. These large nuclear proteins interact with numerous transcription factors and viral oncoproteins, including p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1, and are involved in cell growth, differentiation and apoptosis [
]. Both CBP and P300 have two copies of the TAZ domain, one in the N-terminal region, the other in the C-terminal region. The TAZ1 domain of CBP and P300 forms a complex with CITED2 (CBP/P300-interacting transactivator with ED-rich tail), inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration []. Adaptation to hypoxia is mediated by transactivation of hypoxia-responsive genes by hypoxia-inducible factor-1 (HIF-1) in complex with the CBP and p300 transcriptional coactivators [].Proteins containing this domain also include a group of land-plant specific proteins, know as the BTB/POZ and TAZ domain-containing (BT) protein. The reports of their interaction with CUL3 are contradictory. They are multifunctional scaffold proteins essential for male and female gametophyte development [
]. The TAZ domain adopts an all-alpha fold with zinc-binding sites in the loops connecting the helices. The TAZ1 domain in P300 and the TAZ2 (CH3) domain in CBP have each been shown to have four amphipathic helices, organised by three zinc-binding clusters with HCCC-type coordination [
,
,
].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.
The BTB (for BR-C, ttk and bab) [
] or POZ (for Pox virus and Zinc finger) [,
] domain is a versatile protein-protein interaction motif involved in many cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination []. The BTB domain can occur alongside other domains: BTB-zinc finger (BTB-ZF), BTB-BACK-Kelch (BBK), voltage-gated potassium channel T1 (T1-Kv) [], MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP). Other proteins, such as Skp1 and ElonginC, consist almost exclusively of the core BTB fold. In all of these protein families, the BTB core fold is structurally conserved, consisting of a 2-layer α/β topology where a cluster of α-helices is flanked by short β-sheets []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [,
,
]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.This entry includes the BTB/POZ domain, as well as Skp1 N-terminal region which has an α/β structure similar to that of the BTB/POZ domain fold [
,
].
The BTB domain (Broad-Complex, Tramtrack and Bric a brac) is also known as the POZ domain (POxvirus and Zinc finger). It is a homodimerization domain
occurring at the N terminus of proteins containing multiple copies of eitherzinc fingers of the C2H2 type or Kelch repeats [
,
]. Many BTB proteins are transcriptional regulators that are thought to act through the control of chromatin structure.The structure of the BTB domain of the promyelocytic leukemia zinc finger
(PLZF) protein has been determined by X-ray crystallography and reveals atightly intertwined dimer with an extensive hydrophobic interface [
]. A surface-exposed groove lined with conserved amino acids is formed at the dimer interface, suggesting a peptide-binding site.
Pectate lyase
is an enzyme involved in the maceration and soft rotting of plant tissue. Pectate lyase is responsible for the eliminative cleavage of pectate, yielding oligosaccharides with 4-deoxy-alpha-D-mann-4-enuronosyl groups at their non-reducing ends. The protein is maximally expressed late in pollen development. It has been suggested that the pollen expression of pectate lyase genes might relate to a requirement for pectin degradation during pollen tube growth [
]. The structure and the folding kinetics of one member of this family, pectate lyase C (pelC)1 from Erwinia chrysanthemi has been investigated in some detail [
,
]. PelC contains a parallel β-helix folding motif. The majority of the regular secondary structure is composed of parallel β-sheets (about 30%). The individual strands of the sheets are connected by unordered loops of varying length. The backbone is then formed by a large helix composed of β-sheets. There are two disulphide bonds in pelC and 12 proline residues. One of these prolines, Pro220, is involved in a cis peptide bond. he folding mechanism of pelC involves two slow phases that have been attributed to proline isomerization. Some of the proteins in this family are allergens [
].
DNA polymerase III, subunit gamma/ tau, N-terminal
Type:
Domain
Description:
This entry represents the well-conserved first N-terminal domain of DnaX (also known as DNA polymerase III subunit gamma/tau), approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilus.This domain is also found in protein STICHEL and STICHEL-like (STI) from Arabidopsis, which share sequence similarity with DNA polymerase III gamma/tau subunits [
,
]. STI is nuclear-localized and does not participate in genome duplication; it is a key regulator of trichome branching through an endoreduplication-independent pathway [].
Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins, Sed5, present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events [
]. This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex, SFT2 protein () [
]. This is a conserved protein with four putative transmembrane helices, thought to be involved in vesicular transport in later Golgi compartments [].
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (
) (PCMT) [
] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.
Proteins containing this domain include eukaryotic phospholipase A2 enzymes (PLA2;
), small lipolytic enzymes that releases fatty acids from the second carbon group of glycerol, usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA) [
]. The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks []. These enzymes enable the of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. In eukaryotes, PLA2 plays a pivotal role in the biosynthesis of prostaglandin and other mediators of inflammation. These enzymes are either secreted or cytosolic; the latter are either Ca dependent or Ca independent. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors []. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids []. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters [,
,
]. The phospholipase domain adopts an α-helical secondary structure, consisting of five α-helices and two helical segments. PLA2 may form dimers or oligomers [
,
,
].
Quinolinate synthetase catalyses the second step of the
de novobiosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid [
]. This synthesis requires two enzymes, an FAD-containing "B protein"and an "A protein". B protein converts L-aspartate to iminoaspartate. The A protein, NadA, converts iminoaspartate to quinolate. NadA harbours a [4Fe-4S] cluster [].
This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and
the sulfur-acceptor site in SufE coincides with the location of the cysteineresidues mediating Fe-S cluster assembly in IscU. Thus, a conserved core
structure is implicated in mediating the interactions of both SufE and IscUwith the mutually homologous cysteine desulfurase enzymes present in
their respective operons [].
This group represents a high affinity nitrate transporter component from plants. It includes high-affinity nitrate transporter 3.1 (NRT3.1 or NAR2.1) from Arabidopsis, which acts as a dual component transporter with NTR2 [
,
]. The functional unit for high-affinity nitrate influx may be a tetramer consisting of two subunits each of NRT2.1 and NRT3.1 []. NRT3.1 may be involved in targeting NRT2 proteins to the plasma membrane []. Both NRT2.1 and NRT3.1 are coordinately down-regulated by high external nitrate [].
This domain represents a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. These proteins may be a family of flavocytochromes capable of moving electrons across the plasma membrane [
]. The Frp1 protein from Schizosaccharomyces pombe is a ferric reductase component and is required for cell surface ferric reductase activity. Mutants in Frp1 are deficient in ferric iron uptake [
]. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants [
]. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase []. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease [].
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. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions [
]. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in:Transcription factors P300 and CBP.Plant proteins involved in light responses, such as Hrb1.E3 ubiquitin ligases MEX and MIB2 (
).
Dystrophin and its homologues.Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel β-sheets and a short α-helix, and binds two zinc ions [
]. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues.In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain [
].ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis [
]. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination.In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain [
]. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction.
This entry represents the C-terminal domain of protein dehydration-induced19 (Di19), a protein that increases the sensitivity of plants to environmental stress, such as salinity, drought, osmotic stress and cold. the protein is also induced by an increased supply of stress-related hormones such as abscisic acid ABA and ethylene [
]. There is a zinc-finger at the N terminus, Znf-Di19.
Drought induced 19 protein type, zinc-binding domain
Type:
Domain
Description:
This zinc-binding domain is found in plant drought induced 19 (Di19) proteins, animal E3 ubiquitin-protein ligases (RNF114/KCMF1/RNF138/RNF125) and transcriptional repressors (ZEB1/ZEB2). Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [
]. KCMF1 and RNF114 are E3 ubiquitin-protein ligases [,
], while ZEB1 represses transcription by binding to the E box (5'-CANNTG-3') [].
Members of this family are glycosylphosphatidylinositol mannosyltransferase enzymes [intenz:2.4.1.-] [,
]. At least some members are localised in endoplasmic reticulum and involved in glycosyl phosphatidyl inositol (GPI) anchor biosynthesis [,
]. In Arabidopsis, mannosyltransferase APTG1 (Abnormal Pollen Tube Guidance1) is required for pollen tube micropylar guidance and embryo development []. In budding yeast, Smp3 (YOR149C) has been implemented in plasmid stability [].
This entry represents the ELMO (EnguLfment and Cell MOtility) domain, which is found in a number of eukaryotic proteins involved in the cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility, including CED-12, ELMO-1 and ELMO-2. ELMO-1 and ELMO-2 are components of signalling pathways that regulate phagocytosis and cell migration and are mammalian orthologues of the Caenorhabditis elegans gene, ced-12 that is required for the engulfment of dying cells and cell migration. ELMO-1/2 act in association with DOCK1 and CRK. ELMO-1/2 interact with the SH3-domain of DOCK1 via an SH3-binding site to enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. ELMO-1/2 could be part of a complex with DOCK1 and Rac1 that could be required to activate Rac Rho small GTPases. Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), as essential features of their actions in cells. Within the Ras superfamily, the Arf family is composed of 30 members, including 22 Arf-like (Arl) proteins. The ELMO domain has been proposed to be a GAP domain for ARL2 and other members of the Arf family [
].
Nucleoside diphosphate kinases (
) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation. In eukaryotes, there seems to be a small family of NDK isozymes each of which acts in a different subcellular compartment and/or has a distinct biological function. Eukaryotic NDK isozymes are hexamers of two highly related chains (A and B) [
]. By random association (A6, A5B...AB5, B6), these two kinds of chain form isoenzymes differing in their isoelectric point. NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP. NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [
]. The signature pattern of this entry covers the active site histidine.
Nucleoside diphosphate kinases (
) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation.
NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [
] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [].
This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene [
]. The protein is an integral member of the exon junction complex (EJC). The EJC is a multiprotein complex that is deposited on spliced mRNAs after intron removal at a conserved position upstream of the exon-exon junction, and transported to the cytoplasm where it has been shown to influence translation, surveillance, and localization of the spliced mRNA. It consists of four core proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP and is supposed to be a binding platform for more peripherally and transiently associated factors along mRNA travel. Mago and Y14 form a stable heterodimer that stabilizes the complex by inhibiting eIF4AIII's ATPase activity. Mago-Y14 heterodimer has been shown to interact with the cytoplasmic protein PYM, an EJC disassembly factor, and specifically binds to the karyopherin nuclear receptor importin 13 [
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
].The human homologue has been shown to interact with an RNA binding protein, ribonucleoprotein rbm8 (
) [
]. An RNAi knockout of the Caenorhabditis elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination [] but the protein is also found in hermaphrodites and other organisms without a sexual differentiation.
Polyadenylate-binding protein/Hyperplastic disc protein
Type:
Domain
Description:
The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (
) [
]. PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].
Polyadenylate binding protein, human types 1, 2, 3, 4
Type:
Family
Description:
These eukaryotic proteins recognise the poly-A of mRNA and consist of four tandem RNA recognition domains at the N terminus followed by a PABP-specific domain at the C terminus. The protein is involved in the transport of mRNAs from the nucleus to the cytoplasm [
]. There are four paralogs in Homo sapiens (Human) which are expressed in testis [], platelets ([
]), broadly expressed ([
]) and of unknown tissue range ().
This entry represents the filament-like plant proteins. In Arabidopsis thaliana, there are 7 filament-like plant proteins. They are coiled-coil proteins with unknown function [
].
Vid27 is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [
,
].This entry represents the C-terminal region of Vid27, which is predicted to contain a WD40 repeat domain [
].
FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons
(rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [,
,
]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently [
]. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [
] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR.To date, 3D structures of glutathione reductase [
], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. Theenzymes share similar tertiary structures based on a doubly-wound α/β fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and
NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication [].This entry describes the FAD binding domain which has a nested NADH binding domain and is found in both class I and class II oxidoreductases.
Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
Type:
Binding_site
Description:
Nitrite reductases and bacterial sulphite reductases catalyse the 6-electron reduction of nitrite (sulphite) to
ammonia (sulphide) []. On the basis of physiological function, 2 types of nitritereductase can be defined: the assimilatory type, which is involved in nitrate assimilation (denitrification);
and the dissimilatory type, which is responsible for nitrate respiration function. Assimilatory nitritereductases contain a prosthetic group termed sirohaem (an iron tetra-hydroporphyrin of the isobacteriochlorintype, with 8 carboxylic acid-containing peripheral sidechains), and an iron-sulphur cluster. Similarly, there
are 2 types of sulphite reductase: the assimilatory type, which participate in the synthesis of sulphur-containing compounds; and the dissimilatory type, which are terminal reductases in the reduction of sulphate.
Assimilatory sulphite reductases can catalyse 6-electron reduction without the formation of free intermediates,while dissimilatory reductases can produce trithionate and thiosulphate in addition to sulphide. Both types of
reductase contain sirohaem and iron-sulphur clusters. A region of sequence similarity, about 80amino acids long, is shared by assimilatory nitrite [
] and sulphite reductases [,
]. Four conserved Cys residues are suggested to be involved in binding the sirohaem group and/or theiron-sulphur centre [
].
Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure [
]. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite.SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity [
]. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain. Two copies of this domain are found in Nitrite and Sulfite reductases and form a single structural domain.
Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP) (
), and has an alpha(8)beta(4) quaternary structure [
]. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a siroheme through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite.SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity [
]. In the E. coli SiR-HP enzyme (), the iron is bound to cysteine residues at positions 433, 439, 478 and 482, the latter also forming the siroheme ligand.
Three transport protein particle (TRAPP) complexes exist in yeast (TRAPPI-TRAPPIII), which share a common core in addition to unique subunits. TRAPPI-TRAPPIII regulate endoplasmic reticulum (ER)-to-Golgi transport, intra-Golgi transport and autophagy, respectively. TRAPPC composition seems to be more complex in higher eukaryotes than in yeast, and its roles are less clear.Mammalian TRAPPC13 is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress [
]. The overall architecture of TRAPPC is not disrupted upon TRAPPC13 depletion. This is also the case for yeast TRAPP II Trs65 subunit, which was previously reported to be specific to yeast. However, Trs65 has been shown to have homology to TRAPPC13 and they are now thought to be orthologues []. This entry consists of high eukaryotes TRAPPC13 and some related yeast proteins, but it does not include S. cerevisiae Trs65 (see ).
This entry represents the predicted glutathione S-transferase omega-like protein and the glutathionyl-hydroquinone reductase YqjG. Glutathione S-transferase omega-like proteins active as '1-Cys' thiol transferase against beta-hydroxyethyl disulfide (HED), as dehydroascorbate reductase and as dimethylarsinic acid reductase, while not active against the standard GST substrate 1-chloro-2,4-dinitrobenzene (CDNB) [
]. YqjG catalyses glutathione (GSH)-dependent reduction of glutathionyl-hydroquinones (GS-HQs) to the corresponding hydroquinones [,
,
].
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 10 (
) comprises enzymes with two known activities; galactoside 3(4)-L-fucosyltransferase (
) and galactoside 3-fucosyltransferase (
).
The galactoside 3-fucosyltransferases display similarities with the alpha-2 and alpha-6-fucosyltranferases [
]. The biosynthesis of the carbohydrate antigen sialyl Lewis X (sLe(x)) is dependent on the activity of an galactoside 3-fucosyltransferase. This enzyme catalyses the transfer of fucose from GDP-beta-fucose to the 3-OH of N-acetylglucosamine present in lactosamine acceptors []. Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 3(4)-L-fucosyltransferase () belongs to the Lewis blood group system and is associated with Le(a/b) antigen.
This entry represents eukaryotic and viral proteins of approximately 140 amino acids in length. The UL139 product shares sequence homology with human CD24, a signal transducer modulating B-cell activation responses, and the sequences in the G1c variant of UL139 contained a specific attachment site of prokaryotic membrane lipoprotein lipid [
].
This domain is found in sodium, potassium, and calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channel proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices.
The following lipolytic enzymes are evolutionary related:Mammalian hormone sensitive lipase (HSL). In adipose tissue and heart, HSL
primarily hydrolyzes stored triglycerides to free fatty acids, while insteroidogenic tissues, it principally converts cholesteryl esters to free
cholesterol for steroid hormone production.Mammalian arylacetamide deacetylase (DAC).Moraxella strain TA144 lipase 2 (gene lip2), an enzyme active at a low
temperature.Acinetobacter calcoaceticus esterase which seems to be active on simple
triglycerides such as triacetin.Streptomyces hygroscopicus acetyl-hydrolase (gene bah), which removes the
N-acetyl group from the antibiotic bialaphos.Escherichia coli acetyl esterase.These enzymes contain a Ser-centred consensus sequence and a conserved His-Gly dipeptide found in most lipase N-terminal domains. These sequences are involved in the lipase active site conformation since substitution of the conserved Ser or His residues by Ala and Gln, respectively, results in the
loss of both lipase and esterase activities [].This entry represents a conserved region containing the putative His active site.
The N-terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N-terminal domain [
].
Eukaryotes have developed an evolutionarily conserved process, termed autophagy, to survive starvation conditions. The vacuole or lysosome mediates the turnover and recycling of non-essential intracellular material for re-use in critical biosynthetic reactions. ATG2 (also known as Apg2) is required for the formation and/or completion of cytosolic sequestering vesicles that are needed for vacuolar import through both the Cvt pathway and autophagy, as well as for the specific degradation of peroxisomes. ATG2 is a peripheral membrane protein that localises to the previously identified perivacuolar compartment that contains Apg9 [
].This entry represents the C-terminal domain of ATG2 and related proteins such as VPS13, which contains two to three predicted amphipathic helices (AHs) that anchors these proteins to mitochondria, late endosomes or lipid droplets [
,
,
,
]. This domain is required for membrane recruitment and localisation [].
Vacuolar protein sorting-associated protein 13-like, N-terminal domain
Type:
Domain
Description:
This is the N-terminal chorein domain of VPS13 and ATG2 proteins, which is highly conserved. ATG2 proteins are involved in autophagosome assembly, playing a key role in nonvesicular lipid transfer [
,
,
,
]. This domain has a scoop or taco shape whose concave surface is lined by hydrophobic residues which bind glycerophospholipids. This entry also includes human Bridge-like lipid transfer protein family member 3B (also known as UHRF1BP1L and SHIP164), which shares shares structural and lipid transfer properties with these proteins [,
].VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites [
,
,
]. It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on the carbon source and metabolic state. Most evidence showed that mammalian VPS13A, VPS13C and VPS13D localize at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localize to endosome-endosome contacts [,
,
]. Mutations in human VPS13 proteins (VPS13A-D) cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia, respectively which suggests they have different functions [,
]. Members of this entry belong to the repeating β-groove (RBG) superfamily. These proteins share a structure made of multiple repeating modules consisting of five β-sheets followed by a loop [].
Pexophagy is an autophagic process consisting of the rapid and selective degradation of peroxisomes. Autophagy-related protein 2 (ATG2) is required for glucose-induced micropexophagy and ethanol-induced macropexophagy in yeast [
,
]. Homologues of this protein have also been described in mammals and plants. Mammalian ATG2 proteins are thought to function both in autophagosome (a structure that enclose the cytoplasmic materials) formation and regulation of lipid droplet morphology and dispersion []. In plants they have a role in programmed cell death, senescence and disease resistance [].
Quinone oxidoreductase/zeta-crystallin, conserved site
Type:
Conserved_site
Description:
NADP-dependent quinone oxidoreductases (
) are part of the zinc-containing alcohol dehydrogenase family of enzymes.
The NADP-dependent quinone oxidoreductase (
) is found in bacteria (gene qor), in yeast and in mammals where, in some
species such as rodents, it has been recruited as an eye lens protein and isknown as zeta-crystallin [
]. The sequence of quinone oxidoreductase isdistantly related to that other zinc-containing alcohol dehydrogenases and it
lacks the zinc-ligand residues. The Torpedo fish and mammalian synaptic vesiclemembrane protein vat-1 is related to qor.
Phosphatidylinositol-specific phospholipase C, X domain
Type:
Domain
Description:
Phosphatidylinositol-specific phospholipase C, a eukaryotic intracellular enzyme, plays
an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol
and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [
,
,
]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their
tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two
regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distancebetween these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains,
and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with
significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic
counterparts.
This family includes includes Protein CHLORORESPIRATORY REDUCTION 42 (CRR42) from Arabidopsis thaliana, which is required for both formation and activity of the chloroplast NAD(P)H dehydrogenase (NDH) complex of the photosynthetic electron transport chain [
]. CRR42 functions in assembly or stabilization of the NDH complex and it is likely involved, together with CRR1 and CRR6, in the incorporation of NdhJ, NdhM, NdhK and NdhI into the NDH subcomplex A assembly intermediate (NAI500) to produce the complex NAI400 []. This family also includes uncharacterised proteins from cyanobacteria.
Acetyl-coenzyme A carboxylase (
) (ACC), a member of the
biotin-dependent enzyme family, catalyses the formation of malonyl-coenzyme A(CoA) and regulates fatty acid biosynthesis and oxidation. Biotin-dependent
carboxylase enzymes perform a two step reaction: enzyme-bound biotin is firstcarboxylated by bicarbonate and ATP and the carboxyl group temporarily bound
to biotin is subsequently transferred to an acceptor substrate such asacetyl-CoA. The carboxyltransferase domain performs the second part of the
reaction [,
].The N- and C-terminal regions of the carboxyltransferase domain share similar polypeptide backbone folds, with a central β-β-alpha superhelix [
]. The CoA molecule is mostly associated with the N subdomain.In bacterial acetyl coenzyme A carboxylase the N and C subdomains are encoded
by two different polypeptides.The acetyl-coenzyme A carboxyltransferase domain is also found in the following enzymes:Methylcrotonyl-CoA carboxylase beta chain, mitochondrial precursor.Glutaconyl-CoA decarboxylase alpha subunit.Propionyl-CoA carboxylase beta chain (PCCase).This domain is the C subdomain and recognizes also the alpha-subunit of bacterial ACC.
Acetyl-coenzyme A carboxylase (
) (ACC), a member of the biotin-dependent enzyme family, catalyses the formation of malonyl-coenzyme A (CoA) and regulates fatty acid biosynthesis and oxidation. Biotin-dependent carboxylase enzymes perform a two step reaction: enzyme-bound biotin is first carboxylated by bicarbonate and ATP and the carboxyl group temporarily bound to biotin is subsequently transferred to an acceptor substrate such as acetyl-CoA. The carboxyltransferase domain performs the second part of the reaction [
,
].The N- and C-terminal regions of the carboxyltransferase domain share similar polypeptide backbone folds, with a central β-β-alpha superhelix [
]. The CoA molecule is mostly associated with the N subdomain. In bacterial acetyl coenzyme A carboxylase the N and C subdomains are encoded by two different polypeptides.This entry represents the N-terminal subdomain and contains the bacterial ACC beta-subunit.
This entry contains ribonuclease P (Rnp) proteins from eukaryotes and archaea. Rnp is a ubiquitous ribozyme that catalyzes a Mg2 -dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA) [
,
]. Archaeal and eukaryotic RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Eukaryotic and archaeal RNase P RNAs cooperatively function with protein subunits in catalysis []. Human RNase P is composed of a singular protein Pop1 and three subcomplexes, the Rpp20-Rpp25 heterodimer, Pop5-Rpp14-(Rpp30)2-Rpp40 heteropentamer, and Rpp21-Rpp29-Rpp38 heterotrimer. Although both Pop5 and Rpp14 have similar protein structure, they share a very limited sequence similarity. Moreover, the C-terminal fragments after the conserved beta sheets in Pop5 and Rpp14 exhibit distinct structural features that mediate interactions with Pop1 and Rpp40, respectively [
].In the hyperthermophilic archaeon Pyrococcus horikoshii OT3, RNase P is composed of the RNase P RNA (pRNA) and five proteins (PhoPop5, PhoRpp38, PhoRpp21, PhoRpp29, and PhoRpp30) [
,
].Proteins in this entry include Rnp2 (also known as Pop5) from archaea and Pop5/Rpp14 from humans [
].
The domain is found in intracellular cysteine peptidase PfpI [
] and other members of the DJ-1/ThiJ/PfpI superfamily []. Some of these have been characterised:Pyrococcus horikoshii PH1704, which has both aminopeptidase and endopeptidase activity [
].Arabidopsis thaliana DJ1D, which has glyoxalase I activity [].Candida albicans glyoxalase 3 [
].It is also found in transcriptional regulators in combination with a HTH(araC) domain, such as in Pseudomonas aeruginosa cdhR [
].
Glycation is a nonenzymatic covalent reaction between proteins and endogenous reducing sugars or dicarbonyls (methylglyoxal, glyoxal) that results in protein inactivation. DJ-1 was described in vitro as a protein deglycase that repaired methylglyoxal- and glyoxal-glycated proteins [
,
]. Since then there have been reports against [], and supporting this role for DJ-1 [].Furthermore, supporting its deglycase activity, DJ-1 and its bacterial homologues have been shown to be able to repair methylglyoxal- and glyoxal-glycated nucleotides and nucleic acids [
]. This ability would make DJ-1 a target for diabetic and cancer research []. DJ-1, also known as Park7, has been associated with human parkinsonism [].Included in this family is also YajL from Escherichia coli, the bacterial homologue of DJ-1 [
,
]. This group of proteins are classified as either DJ-1 putative peptidases or non-peptidase homologues in MEROPS peptidase family C56 (clan PC(C)).
Meiosis regulator and mRNA stability factor 1 (also known as meiosis arrest female protein 1, MARF1, or Limkain-b1) was first identified as a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 [
]. Later, it was found that it is an essential regulator of oogenesis required for female meiotic progression and retrotransposon surveillance, therefore, involved in the maintenance of genomic integrity. It acts as a RNAse that efficiently cleaves ssRNAs and down-regulates RNA transcripts, either at transcriptional of post-transcriptional level [,
]. It may function both as an adaptor to recruit specific RNA targets and an effector to catalyse the specific cleavages of target RNAs. MARF1 consists of three major domains, the N-terminal NYN domain, two RNA recognition motifs (RRMs) and a C-terminal repeat of LOTUS (also known as OST-HTH) domains.
This NYN domain is found in Meiosis regulator and mRNA stability factor 1 (MARF1, also known as limkain-b1) [
,
] and in uncharacterised proteins. The NYN domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins. The NYN (for Nedd4-BP1, YacP-like Nuclease) domain shares a common protein fold with two other previously characterised groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' -->3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements it has been suggested that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' -->3' exonuclease superfamily, which binds two metal ions [
]. Based on conserved gene neighbourhoods the bacterial members are likely to be components of the processome/degradosome that process tRNAs or ribosomal RNAs.
This predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organise structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood [
,
]. The domain adopts the winged helix-turn-helix fold and binds RNA with a potential specificity for dsRNA []. In eukaryotes, this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localisation of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains, indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterised RNAse domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains [
].
This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [
,
] and is up-regulated in various cancer cells. This protein has an elongated all α-helical structure, in which the N-terminal half is similar to the HEAT repeat and the C-terminal half is similar to the ARM (Armadillo-like) repeat. This suggests that API5 is involved in protein-protein interactions and may act as a scaffold for multiprotein complexes [].
This family consists of several eukaryotic AAR2-like proteins. The Saccharomyces cerevisiae protein AAR2 is involved in splicing pre-mRNA
of the a1 cistron and other genes that are important for cell growth [].
Mitogen-activated protein (MAP) kinase, conserved site
Type:
Conserved_site
Description:
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity []:Serine/threonine-protein kinasesTyrosine-protein kinasesDual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)Protein kinase function is evolutionarily conserved from Escherichia coli to human [
]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [].Eukaryotic serine-threonine mitogen-activated protein (MAP) kinases are key regulators of cellular signal transduction systems and are conserved from Saccharomyces cerevisiae (Baker's yeast) to human beings. MAPK pathways are signalling cascades differentially regulated by growth factors, mitogens, hormones and stress which mediate cell growth, differentiation and survival. MAPK activity is regulated through a (usually) three-tiered cascade composed of a MAPK, a MAPK kinase (MAPKK, MEK) and a MAPK kinase kinase (MAPKK, MEKK). Substrates for the MAPKs include other kinases and transcription factors [
]. Mammals express at least four distinctly related groups of MAPKs, extracellularly-regulated kinases (ERKs), c-jun N-terminal kinases (JNKs), p38 proteins and ERK5. Plant MAPK pathways have attracted increasing interest, resulting in the isolation of a large number of different components of MAPK cascades. MAPKs play important roles in the signalling of most plant hormones and in developmental processes [
]. In the budding yeast S. cerevisiae, four separate but structurally related mitogen-activated protein kinase (MAPK)activation pathways are known, regulating mating, cell integrity and osmosity [].Enzymes in this family are characterised by two domains separated by a deep channel where potential substrates might bind. The N-terminal domain creates a binding pocket for the adenine ring of ATP, and the C-terminal domain contains the catalytic base, magnesium binding sites and phosphorylation lip [
]. Almost all MAPKs possess a conserved TXY motif in which both the threonine and
tyrosine residues are phosphorylated during activation of the enzyme byupstream dual-specificity MAP kinase kinases (MAPKKs).
This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.
The 33-residue LIS1 homology (LisH) motif is found in eukaryotic intracellular proteins involved in microtubule dynamics, cell migration, nucleokinesis and chromosome segregation. The LisH motif is likely to possess a conserved protein-binding function and it has been proposed that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly. The LisH motif is found associated to other domains, such as WD-40, SPRY, Kelch, AAA ATPase, RasGEF, or HEAT
[,
,
,
].The secondary structure of the LisH domain is predicted to be two α-helices [
].
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.EF-G is a large, five-domain GTPase that promotes the directional movement of mRNA and tRNAs on the ribosome in a GTP-dependent manner. Unlike other GTPases, but by analogy to the myosin motor, EF-G performs its function of powering translocation in the GDP-bound form; that is, in a kinetically stable ribosome-EF-G(GDP) complex formed by GTP hydrolysis on the ribosome. The complex undergoes an extensive structural rearrangement, in particular affecting the small ribosomal subunit, which leads to mRNA-tRNA movement. Domain 4, which extends from the 'body' of the EF-G molecule much like a lever arm, appears to be essential for the structural transition to take place. In a hypothetical model, GTP hydrolysis induces a conformational change in the G domain of EF-G, which affects the interactions with neighbouring domains within EF-G. The resulting rearrangement of the domains relative to each other generates conformational strain in the ribosome to which EF-G is fixed. Because of structural features of the tRNA-ribosome complex, this conformational strain results in directional tRNA-mRNA movement. The functional parallels between EF-G and motor proteins suggest that EF-G differs from classical G-proteins in that it functions as a force-generating mechanochemical device rather than a conformational switch [
].Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homologue to canonical (e.g. Escherichia coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis sp. (strain PCC 6803)
has a few proteins more closely related to EF-G than to any other characterised protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Elongation factor 2 (EF2 or EFG) is folded into five domains, with domains I and II forming the N-terminal block, domains IV and V forming the C-terminal block, and domain III providing the covalently-linked flexible connection between the two [
]. This entry represents the domain V of EF2 of both prokaryotes and eukaryotes (also known as eEF2). This domain is also found in elongation factor 4 and some tetracycline resistance proteins and adopts a ferredoxin-like fold [].
