The Lethal giant larvae (Lgl) tumour suppressor protein is conserved from yeast to mammals. The Lgl protein functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface [
]. The N-terminal half of Lgl members contains WD40 repeats (see ), while the C-terminal half appears specific to the protein [
].
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.
Plant specific mitochondrial import receptor subunit TOM20
Type:
Family
Description:
This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [
].
The Smr domain is an around 90-residue domain found in:The C-terminal region of the mutS2 proteins from bacteria and plants.The small mutS related (smr) proteins from bacteria and eukaryotes.These proteins could be involved in mismatch repair (MMR) or/and chromosome
crossing-over and segregation. It has been proposed that the Smr domain actsas a nicking endonuclease [
,
].
This entry represents the TIM β/α barrel found in aldolase and in related proteins. This TIM barrel usually covers the entire protein structure. Proteins containing this TIM barrel domain include class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases (FBP aldolases), and 5-aminolevulinate dehydratase (a hybrid of classes I and II aldolases) [
,
,
].
This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) splice factor proteins. This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA [
]. These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing.
In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences [
].
This entry includes flavodoxins and flavodoxin-like proteins, such as NADPH-dependent diflavin oxidoreductase NDOR1 and nitric oxide synthases. Flavodoxins act in various electron-transport systems as functional
analogues of ferredoxins []. Although flavodoxins are found only in certain bacteria and algae [] the proteins share similarity with a number of protein domains of both prokaryotic and eukaryotic origin [].
This entry represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90kDa.
This entry describes an uncharacterised domain, sometimes found in association with a PRC-barrel domain ((
, which is also found in rRNA processing protein RimM and in a photosynthetic reaction centre complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Anabaena sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known.
This entry represents Regulatory protein CII from Escherichia phage 186 (Bacteriophage 186) and similar proteins from tailed bacteriophages (Caudovirales) and prophages from Proteobacteria. CII (also known as CP76) is a transcriptional activator essential for the establishment of lysogeny [
,
,
]. The expression of this protein increases gradually with lysogenisation, which frequency increases with multiple infections [].
Members of this protein family are radical SAM proteins related to MSMEG_0568 from Mycobacterium smegmatis. Members occur within 8-gene operons in species as diverse as M. smegmatis, Rhizobium leguminosarum, Synechococcus elongatus, and Sorangium cellulosum. The function of the operon is unknown, but similarity of MSMEG_0568 to some cofactor biosynthesis radical SAM proteins suggests a similar biosynthetic function.
This winged helix-like domain is found in nuclear factor related to kappa-B-binding (NFRKB) protein. NFRKB is a component of the metazoan INO80 complex involved in chromatin remodelling, transcription regulation, DNA replication and DNA repair. This winged helix-like domain is however not involved in DNA binding but is instead thought to be involved in protein-protein interactions [
].
Members of this very narrowly defined protein are active as rhodanese (
) and are found in extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, because in many instances the genome lacks the phage shock regulon entirely.
The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species [
]. This family were previously known as 2.9 lipoprotein genes []. These surfaceexpressed genes may represent new candidate vaccinogens for Lyme disease [
]. Members of this family generally are downstream of four ORFs called A,B,C and Dthat are involved in hemolytic activity.
This protein familiy consists of glyoxalases, bleomycin/phenazine resistance proteins, and dioxygenases. It includes phenazine resistance protein EhpR. In Enterobacter agglomerans, EhpR confers resistance by binding D-alanyl-griseoluteic acid and acting as a chaperone involved in exporting the antibiotic rather than by altering it chemically. EhpR is evolutionarily related to glyoxalase I and type I extradiol dioxygenases [
,
].
This set of DNA binding proteins are found exclusively in the archaea and show homology to the origin recognition complex subunit 1/cell division control protein 6 (Orc1/Cdc6) family in eukaryotes. Several members may be found in a genome and interact with each other. The Cdc6/Orc1 protein from the archaeon Pyrococcus furiosus specifically binds to the oriC region [
].
This entry represents an extracellular domain from the envelope glycoprotein of Ebola virus sp. and Lake Victoria marburgvirus. The extracellular domain is also produced as a separate transcript that gives rise to a non-structural, secreted glycoprotein,
which is produced in large amounts and has an unknown function []. Processing of the protein may be involved in viralpathogenicity [
].
This family of sequences represents the allophycocyanin beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins [
]. Other homologous phyobiliproteins include allophycocyanin alpha chain, and the phycocyanin and phycoerythrin alpha and beta chains.
This entry represents serine/threonine-protein kinase 40 (STK40), also known as SINK-homologous inhibitory kinase (SHIK), which acts as a negative regulator of NF-kappa-B and p53-mediated gene transcription [
]. It It was identified as a protein related to SINK, a p65-interacting protein that inhibits p65 phosphorylation by the catalytic subunit of PKA, thereby inhibiting transcriptional competence of NF-kappaB.
Rhodopsin kinase (also known as G-protein-coupled Receptor Kinase 1, GRK1) is a retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade [
]. Together with recoverin (a Ca2+-binding protein), GRK1 regulates cone phototransduction during photoreceptor light adaptation [,
].This entry represents the catalytic domain of GRK1.
This family consists of several Orthopoxvirus A5L proteins. The vaccinia virus WR A5L open reading frame (corresponding to open reading frame A4L in vaccinia virus Copenhagen) encodes an immunodominant late protein found in the core of the vaccinia virion. The A5 protein appears to be required for the immature virion to form the brick-shaped intracellular mature virion [
].
This family consists of short proteins predominantly found in Firmicutes, including Uncharacterized protein YqgQ from Bacillus subtilis. YqgQ folds into a three-helical bundle, with the helix order being left-handed and with the third helix flanked by a loop. Based on sequence and structural homology, this protein is thought to be involved in single-stranded nucleic acid binding [
].
This entry represents nucleocapsid proteins from the ssRNA viruses Tenuivirus and Phlebovirus [
,
]. These are ssRNA viruses. In crystal structures, the nucleocapsid protein from the Rift Valley fever virus (RVFV) displays a ring-shaped oligomeric assembly [
]. Electron microscopy (EM) also demonstrates that, in complex with RNA, the nucleocapsid protein forms rings in solution [].
Protein import into the mitochondria involves several translocase complexes: the preprotein translocase of the outer mitochondrial membrane (TOM complex) and the two preprotein translocases of the inner mitochondrial membrane (called TIM complexes).TOM5 is a component of the TOM complex. This entry represents TOM5 from the plant complex, which consist at least of six subunits [
,
].
This entry describes a region that occurs from one to three times in proteins from Actinobacteria, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. The region is now recognized as a "choice-of-anchor"domain, since multiple members can be found anchored by sortases (e.g. LPXTG proteins) or exosortases (e.g. PEP-CTERM proteins).
The function of this structural domain is unknown. It is found to the N terminus of the biotin protein ligase catalytic domain [
]. Biotin protein ligase carries out the post-translational modification of specific proteins by the attachment of biotin. It acts on various carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and 3-methylcrotonyl CoA carboxylase.
Members of this protein family are integral proteins of the bacterial outer membrane, associated with multi-haem c-type cytochromes involved in electron transfer [
,
]. The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decahaem cytochrome MtrA and large, surface-exposed decahaem cytochrome MtrC.
This entry represents a domain that is often found as tandem repeats in proteins such as YegP from Escherichia coli. This domain covers the whole length of the protein in HVO_2922 from Haloferax volcanii ({swissprot:D4GXU1]), a small protein whose expression seem to be stress-regulated. It shows four β-strands and one α-helix []. Its specific function remains unknown.
This entry represents a family of proteins mainly found in Proteobacteria, including RsaM from Burkholderia cenocepacia (encoded by bcam1869,
) and similar proteins mainly found in Proteobacteria. RsaM is a transcriptional regulator involved in quorum sensing (QS). This protein folds into a unique domain with a five-stranded antiparallel β-sheet that wraps around two α-helices [
,
,
].
This entry represents the AAA domain found in Strawberry notch protein.Strawberry notch proteins carry DExD/H-box groups and helicase C-terminal domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes [
]. Strawberry notch was first identified in Drosophila where functions downstream of Notch and regulates gene expression during development [,
].
This domain adopts an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. It is similar in topology to many viral capsid proteins, as well as lectins and several glucanases. This domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [
].
This domain adopts an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. It is similar in topology to many viral capsid proteins, as well as lectins and several glucanases. This domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [
].
Proteins in this entry contain a UBR-type zinc finger, and include the putative E3 ubiquitin-protein ligase UBR7, which is found in mammalian spermatozoa, particularly the acrosomal cap and sperm acrosome [
]. Homologues are found in plants and fungi, including the uncharacterised protein Mlo2 from fission yeasts. Both UBR7 and Mlo2 also contain a PHD-type zinc finger.
G-protein-signaling modulator 3 (GPSM3), also known as AGS4 or G18, contains three tandem GoLoco motifs and a LSL motif that interacts with monomeric Gbeta subunits [
,
]. It interacts with Galpha and Gbeta subunits of heterotrimeric G proteins to regulate downstream intracellular signals initiated by G protein coupled receptors (GPCRs) and has been linked to immune-mediated diseases [].
This entry represents a group of plant proteins, including THH1/TOM1/TOM3 from Arabidopsis. TOM1 and TOM3 are transmembrane proteins necessary for the efficient multiplication of tobamoviruses [
]. THH1 supports tobamovirus multiplication, but to a lesser extent than TOM1 and TOM3 []. Proteins in this family belong to the GCPR superfamily and are also involved in stress tolerance [,
].
Proteins in this entry are known as bicupins as they posses two copies of the cupin domain. Two different activities have so far been identified in this group of proteins; oxalate decarboxylase activity(
) and oxalate oxidase activity (
), although the latter has more often been found in distantly related monocupin (germin) proteins [
].
Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyzes the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3. This is the carboxyl domain of Get5 (also known as Mdy2), a homodimerization domain, resulting in a heterotetrameric Get4/Get5 complex [
].
This entry describes a repeat region found mostly in cell surface proteins of various methanogens. Methanosarcina barkeri, for example, has twenty such proteins, often with either seven or fourteen repeats. These repeats resemble the beta propeller repeats of the TolB periplasmic protein of Gram-negative bacteria, part of a complex associated with various functions including biopolymer transport (see
).
This winged helix-like domain is found in nuclear factor related to kappa-B-binding (NFRKB) protein. NFRKB is a component of the metazoan INO80 complex involved in chromatin remodelling, transcription regulation, DNA replication and DNA repair. This winged helix-like domain is however not involved in DNA binding but is instead thought to be involved in protein-protein interactions [
].
This entry represents the SAM (sterile alpha motif) domain repeat 1 of SASH1, which is a predicted protein-protein interaction domain. SASH1 contains an SH3 domain and two SAM domains, and is a member of the SH3/SAM adapter molecules family. SASH1 has been identified as a tumour suppressor and critical protein in signal transduction [
,
].
SNX29 contains an N-terminal RUN domain and a C-terminal PX domain. This entry represents the PX domain. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction [
]. The RUN domain is found in GTPases in the Rap and Rab families and may play a role in Ras-like signaling pathways [].
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses have established this family to be a member of the PD-(D/E)XK superfamily [
].
In addition to the cytoplasmic proteins FtsZ and FtsA, a number of integral membrane proteins are required for cell division. Among these, FtsI, also called penicillin-binding protein 3 (PBP3), is involved in septum formation [
]. FtsI is responsible for the synthesis of septal peptidoglycan [] and is also required for FtsN localization to the septum [,
].
Ethylene-insensitive3 (EIN3) and EIN3-like (EIL) proteins are essential transcription factors in the ethylene signaling of higher plants. The EIN3/EIL proteins bind to the promoter regions of the downstream genes and regulate their expression. This superfamily represents the DNA-binding domain of EIN3 family proteins, which consist of 5 α-helices which come together to form a globular domain [
].
RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in some other genome. The longer, N-terminal domain I (this family) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (
) adds ADP to yield ADP-D-glycero-D-manno-heptose [
].
In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis. These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This entry describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of
, corresponding to phosphopantothenoylcysteine decarboxylase activity [
].
In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis. These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This entry describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of
, corresponding to phosphopantothenate--cysteine ligase activity [
].
RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in some other genome. Domain I (
) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose [
].
This entry includes glycine cleavage system T proteins (GcvT) and the bacterial tRNA-modifying protein YgfZ.YgfZ is a folate-binding protein [
] involved in regulating the level of ATP-dnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication [].
CBL proteins are calcium sensors that work with their interacting protein kinases (CIPKs) in the plant calcium signalling system [
]. In Arabidopsis there are 10 CBL Ca2+ sensors and 26 CIPK-type kinases encoded in the genome. Different combinations of CBL-CIPK proteins contribute to the complex network that connects various extracellular signals to defined cellular responses [,
].
This family of proteins includes SAV0927 from Staphylococcus aureus (
) and similar proteins predominantly found in Firmicutes. This protein forms a structure that contains five dimers. Each protomer shows an anti-parallel five-stranded β-sheet, with one strand from the other subunit in the dimer, and three α-helices at the C-terminal end. Its function is unknown [
].
This entry represents the OSK domain defined by Jeske and colleagues [
]. The domain is related to SGNH hydrolases but lacks the active site residues. The domain binds to RNA []. Proteins containing this domain include maternal effect protein oskar, which is required to keep nos RNA and staufen protein at the posterior pole in Drosophila melanogaster [].
This entry represents a non-catalytic region in eukaryotic phosphatidylinositol 4-kinase alpha (PI4K) proteins. These proteins play a role in the production of the second messenger inositol-1,4,5-trisphosphate [
,
,
]. In human PI4K alpha, this domain consists of a long sequence found in the N-terminal region of the protein. This region forms a large alpha solenoid structure [].
This entry represents Protein YfbM from Escherichia coli (strain K12) and similar proteins mainly found in bacteria. The structure of YfbM has been solved, showing alpha/beta/alpha layers with an antiparallel β-sheet. Although this protein is been suggested to be a binding site for peptide nucleic acids (PNAs, species-selective antibacterials, [
]), its function is yet to be characterised.
This family of prokaryotic GyrI-like proteins include Lin2189 protein from Listeria innocua (
), a cyclopropanoid cyclopropyl hydrolase (CCHs) that can catalyse the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065, protecting the cells. This protein shows three α-helices and six β-strands and contains a GyrI-like small molecule binding domain (
) [
].
This superfamily represents a domain with an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. It is similar in topology to many viral capsid proteins, as well as lectins and several glucanases. This domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [
].
This family consists of Phytoreovirus nonstructural proteins Pns10 and Pns11. Genome segment S11 of Rice gall dwarf virus (RGDV), a Phytoreovirus, encodes a putative protein of 40kDa that exhibits approximately 37% homology at the amino acid level to the nonstructural proteins Pns10 of rice dwarf and wound tumour viruses, which are other members of this genus [
].
This entry represents the Sed5 N-terminal and the N terminus of Syntaxin-5-like proteins. It is the region of Syntaxin that interacts with Sly1p, a positive regulator of intracellular membrane fusion, allowing SM (cytosolic Sec1/munc18-like) proteins to stay associated with the assembling fusion machinery. This allows the SM proteins to participate in late fusion steps [
].
Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein [
].
This presumed domain is found at the C terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin, C-terminal) domain is also found on its own in some proteins [
]. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.
This entry represents the N-terminal domain of a paralogous family of Plasmodium yoelii proteins that are preferentially encoded in the subtelomeric regions of the chromosomes. There are no obvious homologues to these proteins in other organisms. The C-terminal portions of the proteins are divergent and some contain other Plasmodium-specific paralogous domains such as PYST-C2 (
).
This entry represents one of several distantly related families of phage portal proteins. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90kDa [
].
Members of this protein family are PsbV2, a protein closely related cytochrome c-550 (PsbV), a protein important to the water-splitting and oxygen-evolving activity of photosystem II. Mutant studies in Thermosynechococcus elongatus showed PsbV2 can partially replace PsbV, from which it appears to have arisen first by duplication, then by intergenic recombination with a different gene [
].
This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA.
this entry represents the poxvirus Poxvirus 36kDa major membrane protein, which includes poxvirus I6. Previously uncharacterised I6 protein binds tightly and with great specificity to the hairpin form of the viral telomeric sequence. This telomere binding protein is thought to play a role in the initiation of vaccinia virus genome replication and/or genome encapsidation [
].
This is a family of bacterial putative uroporphyrinogen-III C-methyltransferase proteins. It forms one of the members of a complex of proteins involved in the biogenesis of the inner membrane in E.coli. Uroporphorphyrin-III C-methyltransferase (HemX) is a single spanning inner membrane protein that regulates the activity of NAD(P)H:glutamyl-tRNA reductase (HemA) in the tetrapyrrole biosynthesis pathway [
,
].
ABC-type thiamin-related transport system, permease component 1, predicted
Type:
Family
Description:
This group represents a predicted ABC-type thiamin-related transport system, permease component 1. It is probably part of the ABC transporter complex ykoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. It could also transport other HMP-containing products. The complex is composed of two ATP-binding proteins (ykoD), two transmembrane proteins (ykoC and ykoE) and a solute-binding protein (ykoF) [].
This entry includes proteins from bacteria, archaea and plants. Some proteins in this entry belong to peptidase family M50, hence they have been predicted to be metalloendopeptidases. This entry includes the chloroplastic protein EGY1/2/3 from Arabidopsis. EGY1 is an ATP-independent metalloprotease required for development of both thylakoid grana and a well organized lamellae system in chloroplast [
].
This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis by forming micro-pores through which endolysins and virus particles can escape from the cell. Holins accumulate in the cytoplasm and induce lysis once a critical concentration is reached [
].
The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells [
]. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.This entry represents DivIVA and related proteins, including cell cycle protein GpsB.
This domain represents the C terminus of the ARF7 effector protein (ARF7EP), also known as ARL14 effector protein. ARF7EP interacts with actin based motor protein myosin 1E (MYO1E) and may be involved in connecting MHC class II-containing cytoplasmic vesicles to the actin network in dendritic cells [
]. It contains a conserved CXCXXXXCXXCXXXCXXCXXXXCXXXCXC motif in its C-terminal half.
Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulphur clusters. The previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The new suggested name is RIC, for Repair of Iron Centres [
].
This domain is found at the N terminus of E3 ubiquitin-protein ligase Arkadia. Arkadia plays a role in embryonic development [
]. Proteins containing this domain also include protein C18orf25 from humans, the closest homologue of Arkadia. It is a novel exercise-regulated AMPK substrate that lacks the entire RING domain, suggesting that it lacks ubiquitination activity [].
RNase adapter protein RapZ is a RNA-binding protein that recruits the major endoribonuclease RNase E to sRNAs GlmZ [
]. Bacterial small RNAs (sRNAs) regulate diverse cellular processes; GlmY and GlmZ are sRNAs that act hierarchically to activate mRNA glmS, which encodes glucosamine-6-phosphate (GlcN6P) synthase. The RapZ-like family also includes many nucleotide-binding proteins, such as YvcJ [
].
Many glycoproteins of lower and higher eukaryotes are attached to the plasma membrane by means of a glycosylphosphatidylinositol (GPI) anchor, which is added onto newly synthesized proteins in the endoplasmic reticulum (ER). Precursors of GPI anchored proteins have a GPI anchoring signal at their C terminus;
GPI-anchor transamidase (MEROPS identifier C13.005) removes the C-terminal peptide and replaces it with the preformed GPI [].
This entry represents the ELL-associated factor (Eaf) family of proteins. They interact with ELL and ELL2, which are RNA polymerase II elongation factors. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation [
]. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis [].
This entry includes proteins from bacteria and plants. This domain can be found in a chloroplastic protein, LOW PSII ACCUMULATION 3 (LPA3, At1g73060), from Arabidopsis. LPA3 is involved in assisting chlorophyll a binding protein psbC assembly within photosystem II (PSII) [
]. This domain can also be found in some putative adenylate kinases, such as At5g35170 [] from Arabidopsis and Os08g0288200 from rice.
Members of this family are 19kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing [
]. The rice homologue, OsPM19L1, is induced by osmotic stress and may be associated with stress tolerance through ABA-dependent pathway [].
This entry represents lipid desaturase domains. The TMEM189 protein is a plasmanylethanolamine desaturase enzyme [
,
]. It was previously described as the B domain or probable localisation domain of the transmembrane protein TMEM189 [] which in some mammals is fused with Kua ubiquitin-conjugation E2 enzyme proteins []. The domain is also found on fatty acid saturase FAD4 in Arabidopsis [].
This entry includes folate-biopterin transporters (FBTs) from blue-green algae and plants, including Slr0642 protein from Synechocystis and its plastidial orthologue At2g32040 from Arabidopsis [
]. Both Slr0642 protein and At2g32040 mediate folate monoglutamate transport involved in tetrahydrofolate biosynthesis. However, this entry also includes 7 other
Arabidopsis FBT proteins that lack conserved critical residues and may not have folate or pterin transport activity [].
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system [
]. Several of these disulphide proteins share a common structure, consisting of a three-layer alpha/beta/alpha core.
This domain is found in FeMo cofactor biosynthesis protein NifB, PqqA peptide cyclase, Oxygen-independent coproporphyrinogen III oxidase (HemN), biotin synthase (BioB), Lipoyl synthase (LipA), Ribosomal protein S12 methylthiotransferase RimO, GTP 3',8-cyclase (MoaA) and tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (MiaB), and similar proteins found in cellular organisms. This group includes a representative in the eukaryotic elongator
subunit, Elp-3. Some members of this entry are methyltransferases [,
].
This entry represents a domain found in the human protein Hikeshi and its orthologues OPI10 from other eukaryotes. Hikeshi acts as a specific nuclear import carrier for HSP70 proteins following heat-shock stress; it acts by mediating the nucleoporin-dependent translocation of ATP-bound HSP70 proteins into the nucleus [
]. This entry covers both the dimerisation and jelly roll domains [,
].
All members of this protein are the phage shock protein PspC. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor; PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin over expression, ethanol, heat shock and protein export defects.
Adenoviruses have evolved multiple mechanisms to evade the host immune response. Several of the immunomodulatory proteins are encoded in early transcription unit 3 (E3) of human adenoviruses (Ads). These proteins appear to control viral interactions with the host [
]. This entry represents the E3_15 family, including proteins from the E3 region which may protect virus-infected cells from TNF-induced cytolysis [].
This family contains both characterised and uncharacterised bacterial and archaeal proteins; some of which are possibly transmembrane proteins involved in Na
+/H
+or K
+/H
+transport.
The characterised proteins are mnhE (Staphylococcus aureus) and PhaE (Rhizobium meliloti), which are subunits of the Na
+/H
+or K
+/H
+antiporters, that are required for sodium and potassium excretion, respectively [
,
].
Members of this protein family are putrescine-ornithine antiporters [
]. They work together with an enzyme that decarboxylates ornithine to putrescine. This two-gene system has the net effect of removing a protein from the cytosol, providing transient resistance to acid conditions []. They can function not only as a putrescine-ornithine antiporters to excrete putrescine but also as a putrescine uptake proteins [].
This family is an archaeal variant of the (normally bacterial) putative protein-sorting integral membrane protein exosortase, hence archaeosortase. The PGF-CTERM/archaeosortase A system is related to S-layer (surface layer) production [
]. Moreover, it has been shown that archaeosortase A (ArtA) is involved in carboxy-terminal post-translational processing of the S-layer glycoprotein []. Archaeosortase, similarly to sortase, mediate proteolysis-coupled, covalent cell surface attachment [].
This superfamily consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [
].
Class V myosins are well studied unconventional myosins, represented by three paralogues (Myo5a, b, c) in vertebrates. Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA [
,
,
]. They interact with several adaptor proteins, in case of Myo5b-CBD, Rab11-family interacting protein 2 [].
Serine/threonine-protein kinase MRCK (myotonic dystrophy kinase-related CDC42-binding kinase) is an serine/threonine-protein kinase which is an important downstream effector of CDC42 and plays a role in actin-myosin regulation and activities including cell adhesion, motility and invasion [
,
]. Three isoforms have been described in mammals: alpha, beta and gamma [,
]. This entry represent the N-terminal catalytic domain of Serine/threonine-protein kinase MRCK alpha.
This entry describes a type of bacterial luciferase-like monooxygenase (LLM) domain that regularly occurs within large non-ribosomal protein synthases/polyketide synthases, as well as smaller proteins. Luciferase-like monooxygenases include members that bind either FMN or F420. FMN is the more likely binding partner in the case of proteins containing this particular domain, since many are from species that lack F420 biosynthesis capability.
Human FBXL5 (F-box and leucine-rich repeat protein 5) protein plays a role in cellular iron homeostasis [
]. It is part of an E3 ubiquitin ligase complex that targets the iron regulatory protein IRP2 for proteasomal degradation []. The FBXL5's stability is regulated by iron concentration, with its iron- and oxygen-binding hemerythrin domain acting as a ligand-dependent regulatory switch [,
,
].
This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria [
].
Members of this family are flagellar hook proteins, designated FlgE, as found in the epsilon subdivision of the proteobacteria (Helicobacter, Wolinella, and Campylobacter). These proteins differ significantly in architecture from proteins designated FlgE in other lineages; the N-terminal and C-terminal domains are homologous, but members of this family only contain a large central domain that is surface-exposed and variable between strains [
].
This entry represents putative lysis proteins from Bacteriophage MS2 and Bacteriophage BZ13.The bacteriophage MS2 lysin protein
was identified as an overlapping cistron in the bacteriophage MS2 RNA [
]. This proteins induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis. Lysis may be performed via activation of host murein hydrolases [,
].
This repeat composes the C-terminal part of the Bacteriophage T4 baseplate protein Gp5. This region of the protein forms a needle like projection from the baseplate that is presumed to puncture the bacterial cell membrane. Structurally three copies of the repeated region trimerise to form a beta solenoid type structure [
]. This family also includes repeats from bacterial Vgr proteins.
This family consists of several Borna disease virus P10 (or X) proteins. Borna disease virus (BDV) is unique among the non-segmented negative-strand RNA viruses of animals and man because it transcribes and replicates its genome in the nucleus of the infected cell. It has been suggested that the p10 protein plays a role in viral RNA synthesis or ribonucleoprotein transport [
].
This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [
].
