This entry consists of movement proteins of the genus of negative-strand RNA viruses Emaravirus (related to the family Bunyaviridae), which infect plants. This entry includes P4 protein, which is a movement protein of the 30K superfamily [
].
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA [
]. However, more recent work has cast doubt on the importance of SspB in wild-type cells []. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [].
TrfB (also known as KORA) is a Gram-negative bacterial protein that acts as global repressors of genes involved in plasmid replication, conjugative transfer and stable inheritance in the IncP group of plasmids. KORA operates as a symmetric dimer, and contacts the DNA via the helix-turn-helix region at the N terminus [
].
The portal protein of P22 and similar Podoviridae tail phages is a dodecameric structure consisting of a hip (2), a leg(1) and a barrel(3). DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Domains 1 and 3 are mostly helical and form the majority of the DNA-translocating channel. Domain 2 adopts an α-β-fold characterised by two sheets of eight β-strands, which cross each other to form a β-barrel-like structure [
].
Members of this protein family include TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process [
]. Other members are DsrC [], a functionally similar protein in species where the sulphur relay system exists primarily for sulphur metabolism [], rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulphite reductases.
This is a small family of proteins from Saccharomyces and related species. The function is not known but member proteins are highly induced in zinc-depleted conditions [
,
] and have increased expression in NAP1-deletion mutants []. The S. cerevisiae genes are named Vel1 by association with Velum formation in the wine making process.
This domain (Mid) is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded β-sheet core surrounded by four α-helices and two additional short α-helices. It most closely resembles the amino terminal tryptic core of the E.coli lactose repressor. There is an extensive interface between the Mid and the Piwi domains. The conserved C-terminal half or the Mid has extensive interactions with Piwi, with a deep basic pocket on the surface of the `Mid adjacent to the interface with Piwi. The Mid carries a binding pocket for the 5' phosphate overhang of the guide strand of DNA [
]. The N, Mid, and Piwi domains form a base upon which the PAZ domain sits, resembling a duck. The 5' phosphate and the U1 base are held in place by a conserved network of interactions from protein residues of the Mid and Piwi domains in order to place the guide uniquely in the proper position observed in all Argonaute-RNA complexes [].
Saccharomyces cerevisiae respond and cope to starvation by ceasing growth and entering a non-proliferating state referred to as stationary phase [
]. Expression of SPG4 has been shown to be higher in stressed cells, and stationary phase cells compared to active cells. It is not required for growth on non-fermentable carbon sources [].
The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF [
].
SP24, or structural protein of 24kD, is a family of putative virion membrane proteins of plant and insect viruses. These viruses are ssRNA positive-strand viruses, with no DNA stage. The family corresponds to the central region of the ORF3 of insect chroparaviruses and negeviruses and plant cileviruses, higreviruses and blunerviruses. It contains four transmembrane regions. Chronic bee paralysis virus (CBPV) is one of the more common member virions. SP24 is probably one of the major structural components of the virions [
].
This is the C-terminal domain of a bacterial lipoate protein ligase [
]. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with , further upstream. This C-terminal domain is more stable than
and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Peroxisomes are single membrane bound organelles, present in practically all eukaryotic cells, and involved in a variety of metabolic pathways; the deduced protein is extremely basic, a characteristic of many other peroxisomal intrinsic membrane proteins. They carry two short stretches of hydrophobic residues shown to be necessary for the correct targeting of these proteins. This entry represent Pmp4.
Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated [
]. This protein is known as Huntington-interacting protein-1 in humans.
This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation [
]. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology.
This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with
, further towards the N terminus.
Trappin-2,a protease inhibitor, has a unique N-terminal domain that enables it to become cross-linked to extracellular matrix proteins by transglutaminase [
]. This domain contains several repeated motifs (rpresented by this entry) with the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing and transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond []. Cementoin is associated with the WAP family, , at the C terminus.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding
site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of anancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites [
].The spinach plastid 50S subunit comprises 33 proteins, of which 31 are orthologues of Escherichia coli ribosomal proteins and two are plastid-specific ribosomal proteins (PSRP-5 and PSRP-6) having no homologues in other types of ribosomes [
].
This family consists of UL17 proteins from Cytomegalovirus, mainly from Human cytomegalovirus (HCMV), also known as Human herpesvirus 5 (HHV-5). Its function is not known [
].
Poly-beta-1,6-N-acetyl-D-glucosamine synthesis protein IcaD
Type:
Family
Description:
IcaD is essential for the synthesis of poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also known as PIA), a biofilm adhesin polysaccharide. IcaD is required for full IcaA N-acetylglucosaminyltransferase activity [
].
The MRP (mitochondrial ribosomal protein); MRP-S23, is one of the proteins that makes up the 55S ribosome in eukaryotes. It does not appear to carry any common motifs; either RNA binding or ribosomal [
]. All of the mammalian MRPs are encoded in nuclear genes that are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble in co-ordination with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system []. MRP-S23 is significantly up-regulated in uterine cancer cells [].
Small proline-rich (SPRR) proteins are structural components of the cornified cell envelope of stratified squamous epithelia. They are subdivided into three families: SPRR1, SPRR2, and SPRR3 [
].This entry represents SPRR2, a family of small proteins rich in proline, cysteine and glutamate. They contain a tandemly repeated nonamer, PKCPEPCPP [
]. They are components of the cornified envelope of keratinocytes [].
The translational GTPase BipA (also known as TypA or YihK) regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. BipA is composed of five domains. Domain I consists of a central six-stranded β-sheet surrounded by five α-helices, which is characteristic for the G domain found in translational GTPases. Domain II has the distinctive OB-fold of oligonucleotide/oligosaccharide binding domains. Domains III and V both have the same double-split beta-α-β fold. The C-terminal domain of BipA spatially occupies a position between domains III and V and consists of a unique mixed alpha + beta fold composed of eight β-sheets and two α-helices [
].This superfamily represents the C-terminal domain found in GTP-binding protein TypA/BipA.
This entry represents CcmM, which functions as a scaffold protein for the assembly of β-carboxysomes, initiates carboxysome assembly via its N-terminal domain binding to CcaA, CcmK and CcmL. Binds HCO3-, suggesting it may play a role in the activity or regulation of bicarbonate dehydration [
].Aquatic photosynthetic organisms, like cyanobacteria, respond to low-CO(2) conditions by inducing a CO(2) concentrating mechanism (CCM) in the carboxysome. The CCM allows photosynthesis to proceed in CO2-limited aquatic environments [
]. Carbonic anhydrases (CAs) and zinc metalloenzymes are important parts of the CCM. They catalyse the interconversion of CO(2) and HCO(3)(-) [
]. The CCM components include at least four modes of active inorganic carbon uptake, including two bicarbonate transporters and two CO(2) uptake systems associated with the operation of specialised NDH-1 complexes. This results in the accumulation of HCO(3)(-) in the cytosol of the cell, which is subsequently used by the ribulose 1.5-bisphosphate carboxylase/oxygenase (RubisCO)-containing carboxysome protein micro-compartment within the cell to elevate CO(2) around RubisCO [
]. Carboxysomal carbonic anhydrase is thought to dehydrate abundant cytosolic bicarbonate and provide RubisCO, sequestered within the carboxysome, with sufficiently high concentrations of CO(2) to permit its efficient fixation onto ribulose 1,5-bisphosphate [].
This entry includes the RNA-binding protein KhpB, also known as RNA-binding protein Jag/EloR, a RNA chaperone that forms a complex with KhpA and binds to cellular RNA, controlling its expression. It plays a role in peptidoglycan (PG) homeostasis and cell length regulation, cell division and maintenance of cell shape [
,
,
]. Bacillus subtilis KhpB/Jag is associated with SpoIIIJ, a gene necessary for the third stage of sporulation []. This domain is found at the N terminus of the KhpB/Jag proteins, whose function is unknown.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].This superfamily represents the ribosomal protein L31, a protein of the large ribosomal subunit.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Members in this family are found in various hypothetical prokaryotic proteins. Their function is not clear. They contain a probable winged helix DNA-binding domain.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
This entry contains proteins that are related to glutamate carboxypeptidase and classed as non-peptidase homologues belonging to MEROPS peptidase family M20 (glutamate carboxypeptidase, clan MH) [
].The bacterial amidohydrolase abgB catalyses the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate is a natural end product of folate catabolism, and its utilization is initiated by the abg region gene product, AbgT, by enabling uptake of its into the cell in a concentration-dependent, saturable manner. It is subsequently cleaved by AbgA and AbgB (sometimes referred to as AbgAB) [
,
].
This entry represents the C-terminal domain of the Nck-associated protein 5 (NCKAP5), also known as the Peripheral clock protein. NCKAP5 interacts with the SH3-containing region of the adaptor protein Nck. Nck is a protein that interacts with receptor tyrosine kinases and guanine nucleotide exchange factor Sos. The role of Nck can be thought of as similar to Grb2. The role of NCKAP5 is to assist Nck with its adaptor protein role [
].
This group includes two members of the TGF-beta superfamily: bone morphogenetic protein 3 (BMP3) and bone morphogenetic protein 3B (BMP3B), also known as growth differentiation factor 10 (GDF10). Together they represent a subgroup of the BMP family. They are involved in development and organogenesis. In developing embryos, they have different dorsalising activities [
]. BMP3 is a negative regulator of bone density []. BMP3B plays an inhibitory role in the process of osteoblast differentiation [].
TEX12 is a meiosis-specific protein [
]. TEX12 contributes to the formation of the central element of the synaptonemal complex (SC) in mouse meiocytes [,
].
Prion protein (PrP) is intimately linked with transmissible spongiform encephalopathies (TSEs). The human PrP gene (PRNP) locus contains three genes: PRNP, DOPPEL and PRND. A novel gene, designated PRNT, has been identified 3kb 3' to PRND and is transcribed to generate at least three alternatively spliced mRNAs. PRNT constitutes a family of putative prion-related proteins expressed in the testis [
,
]. This group of eukaryotic proteins are typically between 52 and 94 amino acids in length.
This entry represents a group of eukaryotic proteins, TMEM71 (also known as parturition-related protein 2). They are typically between 242 and 326 amino acids in length.
Myc target protein 1 (MYCT1) is regulated by the c-Myc oncoprotein; its promoter is a direct c-Myc target. Furthermore, MYCT1 regulates the expression of several other c-Myc target genes [
].
REC114-like is necessary for meiotic DNA double-strand break formation. It works in conjunction with Mei4 [
]. This family of proteins is found in eukaryotes.
This entry represents a group of plant NAC domain-containing proteins, including SOG1 (At1g25580) and NAC10/73/75 from Arabidopsis. They are a group of transcription activators that function in genomic stress response and plant development. SOG1 regulates the transcriptional activation response to gamma irradiation [
]. NAC10 and NAC73 plays a regulatory role in the development of secondary cell wall fibres [,
], while NAC75 is involved in xylem formation [,
].
This family includes the chromatin modification-related protein EAF1A/B from Arabidopsis. They are components of the NuA4 histone acetyltransferase complex involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A [
].
Pentatricopeptide repeat-containing protein THA8L-like
Type:
Family
Description:
This entry represents a group of plant pentatricopeptide repeat-containing proteins, including Protein THYLAKOID ASSEMBLY 8-like (THA8L) and the uncharacterised Arabidopsis protein At1g62350. THA8L resembles THA8 and binds weakly to specific single strand RNA [
].
The exon-junction complex (EJC) is involved in post-transcriptional regulation of mRNA. The core of EJC consists of Y14, Magoh, MLN51 and eIF4AIII, a DEAD-box RNA helicase. EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery, and its core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism. Human MLN51 has been shown to stimulate the ATPase activity of eIF4AIII [
]. This entry represents the plant MLN51 homologues. Similar to animal MLN51, Arabidopsis MLN51 is also a core component of the plant EJC [].
This entry represents a group of plant Rho GTPase-activating proteins, including RopGAP1-5 from Arabidopsis. RopGAP4 is a Rop deactivator, elevates ADH expression in response to oxygen deprivation but decreases tolerance to stress [
]. RopGAP3 and RopGAP4 mediate local activation of ARAC10/ROP11 to initiate the distinct pattern of secondary cell walls in xylem cells [].
Pentatricopeptide repeat-containing protein At5g10690-like
Type:
Family
Description:
This is a family of plant pentatricopeptide repeat-containing proteins, including At5g10690 from Arabidopsis thaliana. Its exact function is not clear.
This entry represents the C terminus of CKAP2 (cytoskeleton-associated protein 2) and CKAP2L (cytoskeleton-associated protein 2-like). Mouse CKAP2 has been shown to possess microtubule stabilising properties [
] and is involved in regulating aneuploidy, cell cycle, and cell death in a p53-dependent manner []. In human, CKAMP2 is up-regulated in primary gastric cancers []. It has been shown that human CKAP2 is degraded by APC/C-Cdh1 during mitotic exit and that a tight regulation of CKAP2 protein level is important for mitotic progression [].
Pcp2, also known as Purkinje cell-specific protein L7, is a member of the GoLoco protein family with highly cell-specific expression, being restricted to cerebellar Purkinje cells and retinal bipolar neurons in various species. It may function as guanine nucleotide dissociation inhibitor, or a guanine nucleotide exchange factor [
].
Vesicle-associated membrane protein 5 (Vamp5) is part of the Vamp family of SNAREs (soluble NSF attachment protein receptor), whose members are proteins responsible for the last stage of docking and subsequent fusion in diverse intracellular membrane transport events [
].
Homeobox-leucine zipper protein GLABRA2/ANL2/PDF2/ATML1-like
Type:
Family
Description:
This entry represents a group of plant proteins that belong to transcription factors of the class IV homeodomain-leucine zipper (HD-Zip IV) protein family. This entry includes GLABRA2, ANTHOCYANINLESS2 (ANL2), ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), and PROTODERMAL FACTOR2 (PDF2) from Arabidopsis. GLABRA2 regulates the frequency of trichome initiation and is involved in determining trichome spacing [
]. ANL2 is involved in anthocyanin distribution and root development []. PDF2 and ATML1 are involved in shoot epidermal cell differentiation. ATML1 and PDF2 function redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development [,
].
PHF12, also known as Pf1, is a PHD zinc finger protein that binds TLE (transducin-like enhancer) in an mSin3A-independent manner and recruits functional TLE complexes to repress transcription [
].
This entry represents a group of J-domain proteins from plants, including AtJ13 (also known as OWL1, At2g35720) from Arabidopsis. It is involved in perception of very low light fluences [
].
Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins in this family are involved in the formation of gas vesicles [
].
Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are
permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
This entry represents the DinB family, and includes DinB from Bacillus subtilis. DNA damage-inducible genes (dinA, dinB, and dinC) in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon [
].
Serine/threonine-protein kinase-like protein CCR3/CCR4
Type:
Family
Description:
This family includes plant serine/threonine receptor-like kinases related to CRINKLY4 (CR4), a protein involved in developmental processes in plant and endosperm that was first isolated in maize [
,
]. Mutations in this protein affects the cell wall thickness and structure, cuticle formation, and vesicle trafficking, and tumor like outgrowths, with similar effects seen in rice [,
,
]. Arabidopsis thaliana contains an orthologue of CR4, ACR4, and four CRINKLY4-related proteins (CRR or CCR) AtCRR1, AtCRR2, AtCRR3 and AtCRR4 (also known as CRINKLY 4-related kinase 1, AtCRK1) []. Phylogenetic analysis showed that the CR4 family of receptor kinases can be divided in three clades, one including CR4, CCR1 and CCR2, a second including CCR3 and CCR4 family members, and a third and more distant clade including members from algae and Selaginella moellendorffii sequences with transmembrane and/or kinase domains []. Kinase assays showed that ACR4 is an active serine/threonine kinase, while CCR1 and CCR2 are nearly inactive in autophosphorylation assays []. CR4 family are characterised by the presence of seven 'crinkly' repeats in the extracellular part which is required both for signalling and normal protein internalisation, including a conserved C(X~10)CWG sequence motif. The Cys residues in the extracellular 'crinkly' repeat domain are likely to form stabilizing disulfide bridges [
]. Another feature of the CR4 family is that the extracellular domain shows homology to the three Cys-rich repeats of the TUMOR NECROSIS FACTOR RECEPTOR (TNFR) extracellular domain [].This family represents the CRINKLE4-related proteins CCR3 and CCR4.
This protein family, GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [
]. However, members of this protein family are found also in several members of the Bacteriodetes that appear not to be motile. The best conserved region, toward the N terminus, is centred on a highly hydrobobic probable transmembrane helix. Two paralogs are found in Cytophaga hutchinsonii.
This family contains sugar fermentation stimulation protein SfsA, which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA [
]. The structure of SfsA has been solved (,
)
Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in C. johnsonae. Over expression of GldE partially suppresses the effects of a GldB point mutant suggesting that GldB and GldE interact []. Gliding motility appears closely linked to chitin utilization in the model species C. johnsonae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to have the gliding phenotype.
Members of this family all have a C-terminal SPASM domain (
), a region usually found as a C-terminal second 4Fe-4S domain of radical SAM domain proteins. A majority of rSAM/SPASM proteins modify ribosomally produced peptides. In a few members of this family, the key Cys residues of the radical SAM domain have been lost, making this a pseudo-rSAM family. Members of this family are restricted so far to Haloarchaea, always occur next a member of family
, and are often accompanied by another rSAM/SPASM domain protein. The function of this two or three gene cassette is unknown.
This family is related to the ABC-2 membrane transporter family [
]. Proteins in this entry include NatB from Bacillus subtilis. NatB is part of an ABC transporter that catalyses ATP-dependent electrogenic sodium extrusion [].
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
This family consists of paralogous proteins in the Verrucomicrobium spinosum and Chthoniobacter flavus. All members contain the prepilin-type N-terminal cleavage/methylation domain (
) at the N terminus. These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain.
This family consists of paralogous proteins in the Verrucomicrobium spinosum and Chthoniobacter flavus. All members contain the prepilin-type N-terminal cleavage/methylation domain (
) at the N terminus. These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain.
This is a family of SNARE associated Golgi proteins. The yeast member of this family,Tvp38, localises with the t-SNARE Tlg2 [
] and is involved in vesicular trafficking and spindle migration [].
This model describes a nearly twenty member protein family in Verrucomicrobium spinosum and a somewhat smaller paralogous family in Chthoniobacter flavus. All members share a type IV pilin-like N-terminal leader sequence (
). These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain.
In Verrucomicrobium spinosum and Chthoniobacter flavus, a four-gene operon that includes proteins with an N-terminal signal sequence for cleavage and methylation recurs many times. Each operon is likely to encode a membrane complex, the function of which is unknown. This entry represents a long protein from this putative membrame complex, with members averaging about 1300 amino acids. The N-terminal region includes an apparent signal sequence. The function is unknown. Most cassettes are adjacent to an unusually large protein with both an outer membrane autotransporter region and PEP-CTERM putative protein-sorting motif.
FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction
of FtsA-FtsZ has arisen through coevolution in different bacterial strains [].
This is a family of uncharacterised tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis.
This superfamily consists of several plant specific allene oxide cyclase proteins (
). The allene oxide cyclase (AOC)-catalysed step in jasmonate (JA) biosynthesis is important in the wound response of tomato [
].The superfamily also contains Dirigent proteins. Dirigent proteins impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of coniferyl alcohol in the biosynthesis of lignans, flavonolignans, and alkaloids and thus plays a central role in plant secondary metabolism [,
].Dirigent proteins and allene oxide cyclases exert stereochemical control on a cyclization reaction. Both share common structural features [
].
PmrA/PmrB and PhoP/PhoQ are a pair of two-component systems (TCSs) that allow the Gram-negative bacteria to survive the cationic antimicrobial peptide polymyxin B. The two TCSs are linked by the polymyxin resistance protein, PmrD [
]. This entry represents a domain found in PmrD. This domain can also be found in anti-adapter protein IraM, a protein which inhibits rpoS proteolysis by regulating rssB activity, thereby increasing the stability of the sigma stress factor rpoS during magnesium starvation []. The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope [
].The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop [,
].
This entry represents WBP2 and related proteins from animals, fungi and plants.
WBP2 encodes the WW domain-binding protein 2 that acts as a transcriptional coactivator for the estrogen and progesterone receptors [
,
]. WBP2 binds to the target gene promoter and is required for the binding of the phosphorylated form of RNA polymerase II to the same promoter. Furthermore, it is also essential for histone acetylation at the same target region [].WWP2 N-terminal-like (WBP2NL), also known as post-acrosomal sheath WW domain-binding protein (PAWP), is a testis-specific protein localized in the post-acrosomal sheath of spermatozoa [
]. The WBP2NL protein enters the oocyte during fertilization, and induces meiotic resumption and oocyte activation events [,
]. It may be associated with cellular proliferation and tumourigenic processes [,
].
WD repeat protein 35 (WDR35) is a component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport [
]. Mutations in the WDR35 gene cause diseases such as cranioectodermal dysplasia 2 [] and short-rib thoracic dysplasia 7 with or without polydactyly [].
Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions [
]. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [
,
].Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [
,
]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [
,
]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK [
]. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain.This entry represents signal transduction histidine kinases involved in nitrogen fixation and metabolism regulation, such as NtrY [
,
].
This domain can be found in the tip attachment protein J from Enterobacteria phage lambda. J is a tail fibre protein that attaches the virion to the host receptor LamB, inducing viral DNA ejection [
].
The function of this family is unknown. These proteins are from 222 to 233 residues in length, lack hydrophobic stretches, and are found predominantly in thermophiles.
This entry represents the antigenic membrane protein (also known as Phyto-Amp) from Candidatus Phytoplasma [
]. The bacteria are limited to the phloem and pose a major threat to agriculture worldwide. They are transmitted in a persistent, propagative manner by phloem-sucking Hemipteran insects. Phytoplasma membrane proteins are in direct contact with hosts and are assumed to be involved in determining vector specificity. Phyto-Amp is thought to be one family of proteins that mediates such specificity. The proteins appear to be encoded by circular extrachromosomal elements, at least one of which is a plasmid [].
