Cep290 and similar centrosomal proteins carry a number of coiled-coil regions, and this is the fifth along the length of the protein. It is thought that the proteins are involved in cilia biosynthesis [
].
This entry represents a group of plant zinc finger proteins, including STOP1/STOP2 from Arabidopsis and their homologues, Os01g0871200/STAR3 from rice. They are putative transcription factors that regulate gene expression associated with multiple stress tolerances in plant roots [
,
,
]. STOP1 (sensitive to proton rhizotoxicity 1) regulates transcription of multiple genes critical for tolerance to aluminum (Al) and low pH in Arabidopsis []. STOP2 is a physiologically minor isoform of STOP1, but it can activate expression of some genes regulated by STOP1 []. In rice, ART1 regulates multiple genes implicated in aluminum tolerance [].
Spindle assembly abnormal protein 6 (SAS-6) is the centre of the cartwheel assembly that scaffolds centrioles early in their biogenesis. Structural studies have shown that SAS-6 self-associates in vitro into assemblies that resemble cartwheel centres through the formation of a parallel coiled-coil dimer [
].This entry represents the N-terminal domain of the SAS-6 , both in C.elegans and in humans. The N-terminal domain is the region through which the 9 rod-shaped homodimers that SAS-6 forms on oligomerisation interact with each other. Proper functioning of the centriole requires this correct oligomerisation [
].
Non-structural protein 3, SUD-N macrodomain, SARS-CoV
Type:
Domain
Description:
This entry represents a macrodomain referred to as SUD-N (N-terminal subdomain) of the SARS-unique domain (SUD) which binds G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). It is found in the non-structural protein 3 (NSP3) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and highly related coronaviruses [
].SUD consists of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C [
]. Among these, SUD-N and SUD-M are macrodomains. The SUD-N domain is a related macrodomain which also binds G-quadruplexes []. While SUD-N is specific to the NSP3 of SARS and betacoronaviruses of the sarbecovirus subgenera (B lineage), SUD-M is present in most NSP3 proteins except the NSP3 from betacoronaviruses of the embecovirus subgenera (A lineage). SUD-M, despite its name, is not specific to SARS. SUD-C adopts a frataxin-like fold, has structural similarity to DNA-binding domains of DNA-modifying enzymes, binds single-stranded RNA, and regulates the RNA binding behavior of the SUD-M macrodomain. SARS-CoV Nsp3 contains a third macrodomain (the X-domain). The X-domain may function as a module binding poly(ADP-ribose); however, SUD-N and SUD-M do not bind ADP-ribose, as the triple glycine sequence involved in its binding is not conserved in these [].
This entry represents the middle region of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures. FlgT is composed of three domains, the N-terminal domain (FlgT-N), the middle domain (FlgT-M), and the C-terminal domain (FlgT-C). FlgT-N and FlgT-M are thought to be involved in the H-ring and the T-ring formation, respectively, and FlgT-M is also required for the stable association of FlgT with the basal body [
].
Intracellular hyaluronan-binding protein 4, N-terminal domain
Type:
Domain
Description:
This is the N-terminal region of intracellular hyaluronan-binding protein 4 and SERPINE1 mRNA-binding protein 1-like proteins. This region carries nuclear localisation sites, and may also be involved in the binding to some of the partners in the translational machinery [
,
,
].
GspB is an accessory component of the type II secretion system (T2SS). Together with GspA, it contribute to GspD assembly and transport to the outer membrane possibly by increasing the pore size of the peptidoglycan or anchoring it to this structural meshwork [
]. The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space [
]. T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK [
]. GspD has been shown to interact with the inner membrane component GspC []. The T2SS pseudopilus is a periplasmic filament composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. Pseudopilus is assembled by the polymerization of GspG (also known as PulG) subunits. Pseudopilin proteins have a conserved N-terminal hydrophobic segment followed by a more variable C-terminal periplasmic and globular domain [
].
Nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) feature the most complex genetic organization among plus-strand RNA viruses. Their replicase genes encode an exceptionally large replicase polyprotein 1a/ab which is then proteolytically processed to release different nonstructural proteins (NSPs) that mediate the key functions required for replication and transcription. One of these NSPs, called NSP10 in arteriviruses (Av) and NSP13 in coronaviruses (CoV) functions as a helicase [
,
]. It is a multidomain protein consisting of a N-terminal Cys/His rich zinc-binding domain (ZBD) and a helicase core that belongs to the superfamily SF1 of helicases. The helicase core contains two RecA1 and RecA2 domains and a 1B domain [].This entry represents the 1B domain, which has a regulatory role modulating the nucleic acid substrate binding. Based on the structures from the Equine arteritis virus (EAV) NSP10, 1B domain undergoes large conformational change upon substrate binding, and forms a channel together with 1A and 2A domains that accommodates the single stranded nucleic acids [
,
].
Helicase nonstructural protein 13 (NSP13) is encoded by the replicase polyprotein 1a/ab of coronaviruses and released after a proteolytic process. It plays a vital role in catalysing the unwinding of duplex oligonucleotides into single strands in an NTP-dependent manner. It is a multidomain protein which includes an N-terminal Cys/His rich zinc-binding domain (ZBD), followed by a stalk and 1B domains, and a helicase core that belongs to the superfamily SF1 of helicases, containing two RecA1 and RecA2 domains [
,
]. The stalk region connects the ZBD domain and 1B domain. Nsp13 adopts a triangular pyramid shape in which the two RecA1 and A2 and 1B domain form the triangular base, while N-terminal ZBD and stalk domains are arranged at the apex of the pyramid [,
,
]. Recently, it has been reported that SARS-CoV-2 NSP13 as an interferon antagonist. It is involved in type I interferon (IFN-I) response as it binds and blocks TBK1 phosphorylation to inhibit interferon regulatory factor 3 (IRF3) which results in decreased IRF3 activation [
,
].This entry represents the 1B domain, which has a regulatory role modulating the nucleic acid substrate binding. Based on the structures from the related Equine arteritis virus (EAV) NSP10, it is likely that 1B domain forms a channel together with 1A and 2A domains that accommodates the single stranded nucleic acids [
,
].
Protein quaking, putative nuclear localisation signal
Type:
Domain
Description:
This entry represents the very C-terminal region of quaking proteins that is purported to be the nuclear localisation signal [
,
]. Quaking is a RNA-binding protein that plays a central role in myelinisation [].
Non-structural protein 2, bat coronavirus HKU9-like
Type:
Domain
Description:
The functions of NSP2 remain unclear. SARS-CoV NSP2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of NSP2 from the SARS-CoV genome results in only a modest reduction in viral titers, and it has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2 which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis [,
]. MHV NSP2, also known as p65, different from SARS-CoV NSP2, may play an important role in the viral life cycle [].This entry includes NSP2 from Rousettus bat coronavirus HKU9 and betacoronaviruses in the nobecovirus subgenera (D lineage).
Protein N-terminal and lysine N-methyltransferase EFM7
Type:
Family
Description:
This entry includes N-terminal and lysine N-methyltransferase EFM7 that trimethylates the N-terminal glycine of elongation factor 1-alpha (TEF1 and TEF2) and then the adjacent lysine [
]. It may be involved in rDNA silencing and in lifespan determination [].
Toxin coregulated pilus biosynthesis protein S (TcpS) is part of an operon associated with biosynthesis of the toxin coregulated pilus (TCP) of Vibrio cholerae [
]. TCP is essential for successful colonisation of the bacteria in the small intestine. The genes tcpR, tcpD, tcpS, tcpT, tcpE and tcpF are organised to permit translational coupling and are followed by an inverted repeat structure which is likely to act as a strong Rho-independent terminator []. TcpS possesses an N-terminal signal sequence, suggesting that it is localised to the periplasm.
This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
DNA-dependent protein kinase catalytic subunit, CC1/2
Type:
Domain
Description:
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ) which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand break (DSB) repair. It folds into three well-defined large structural units, consisting of a N-terminal region, the Circular Cradle (consisting of five supersecondary α-helical structures CC1 to CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The N-terminal and CCs regions resemble HEAT repeats, and thus, they are also referred to as N-HEAT and M-HEAT ('middle'), respectively. The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. This entry represents CC1 and CC2, which contain the Highly conserved region I (HCR-I) [
,
,
,
].
Protein of unknown function DUF2227, metal-binding
Type:
Family
Description:
This entry represents a family of hypothetical bacterial proteins that may possess metal binding properties; however, their exact function has not yet been determined.
Protein of unknown function DUF2178, transmembrane
Type:
Family
Description:
This entry, found in various hypothetical bacterial and archaeal proteins, has no known function, but contains several predicted transmembrane helices.
The stage IV sporulation protein A (
) is an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore [
,
,
]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane [].This entry represents the C-terminal domain of SpoIVA, which plays a key role in targeting the protein to the outer forespore membrane, in particular the five hydrophobic residues at the extreme C-terminal are essential for this function [
,
]. Structure predictions suggest that it has three conserved α-helices followed by a β-hairpin [].
Heavy metal-associated isoprenylated plant protein 9-like
Type:
Family
Description:
Heavy-metal-associated (HMA) isoprenylated plant proteins (HIPPs) only exist in vascular plants. They contain a metal binding domain (HMA) and a C-terminal isoprenylation motif. They play important roles in responses to biotic/abiotic stresses, heavy-metal homeostasis, and detoxification. This entry includes AtHIP09, which may act as a metallochaperone [
].
Menaquinone biosynthesis protein MenD, middle domain
Type:
Domain
Description:
This entry represents the middle domain of menaquinone biosynthesis protein MenD, an enzyme that belongs to the thiamine pyrophosphate (TPP) enzyme family, but is not captured by
. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [
].
LYR motif-containing protein Cup1-like, N-terminal domain
Type:
Domain
Description:
This entry represents a domain found at the N-terminal end of fungal LYR domain-containing proteins, including Cup1 (caffeine unstable phenotype 1, previously known as uncharacterised protein C17G9.13c) from S. pombe [
]. Cup1 is a mitochondrial protein whose silencing by heterochromatin island formation results in caffeine resistance. LYR-motif containing proteins are basic polypeptides carrying a conserved tripeptide L-Y-R (leucine/tyrosine/arginine) sequence close to the N terminus in addition to some basic arginine/lysine residues and a highly-conserved phenylalanine downstream of the LYR motif [,
].
Heavy metal-associated isoprenylated plant protein 16/46
Type:
Family
Description:
This entry represents a group of plant putative heavy metal binding proteins, including HIPP16/46. They contain an apparent HMA-like domain but lacks the core conserved Cys-X-X-Cys motif [
].
This entry represents a group of plant proteins, including Protein SUPPRESSOR OF GENE SILENCING 3 (SGS3) from Arabidopsis. Post-transcriptional gene silencing (PTGS) in plants requires at least two proteins-SGS3 and MET1 (a DNA-methyltransferase) [
,
]. SGS3 is required for juvenile development and the production of trans-acting siRNAs []. SGS3 is also involved in a mechanism for plant resistance to viruses [,
].
Cytoplasmic polyadenylation element-binding protein 1, N-terminal
Type:
Domain
Description:
This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1 (CPEB1), a sequence-specific RNA-binding protein that regulates mRNA translation and cell differentiation [
,
].
This entry includes ClpS from bacteria and chloroplastic CLPS1/2 from plants. ClpS binds directly to N-terminal destabilising residues through its substrate-binding site distal to the ClpS-ClpA interface, and targets these substrates to the ClpAP protease for degradation [
,
].ClpS is a small alpha/beta protein that consists of three α-helices connected to three antiparallel β-strands [
]. The protein has a globular shape, with a curved layer of three antiparallel α-helices over a twisted antiparallel β-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue β-strand, which is flanked by two other β-strands in a small β-sheet.
Rhizobial nodulation (Nod) factors are signalling molecules secreted by root-nodulating rhizobia in response to flavanoids excreted by the host plant. They induce various symbiotic responses on the roots of the leguminous host plant at low concentrations, and are required for successful infection [
]. Nodulation factors are lipo-chitooligosaccharides made by bacterial nitrogen-fixing bacteria as a signal to plant hosts. Nod factors differ slightly from system to system and serve as host range determinants.This signature pattern identifies a conserved region in the first third of the protein.
BTB/POZ and TAZ domain-containing protein 1/2/3/4/5
Type:
Family
Description:
This entry represents a group of plant BTB/POZ and TAZ domain-containing proteins, including BT1-5 from Arabidopsis. They are scaffold proteins that play roles in both male and female gametophyte development [
]. BT2 can activate telomerase expression in mature Arabidopsis leaves []. It mediates multiple responses to nutrients, stresses, and hormones in Arabidopsis [].
ProlycopenC2 and GRAM domain-containing protein At1g03370/At5g50170-like
Type:
Family
Description:
This entry represents the C2 and GRAM domain-containing proteins from plants, including At1g03370 and At5g50170 from Arabidopsis. At1g03370 and At5g50170 contain two VASt domains, two C2 domains and a GRAM domain. Their function is not clear.
Uncharacterised protein family UPF0021, conserved site
Type:
Conserved_site
Description:
The following uncharacterised proteins have been shown to share regions of similarities, yeast chromosome VII hypothetical protein YGL211w; Dictyostelium discoideum (Slime mold) protein veg136; and Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical proteins MJ1157 and MJ1478.The signature in this entry recognises a conserved pattern in the N-terminal domain of the proteins.
Cytochrome c-type biogenesis protein CcmF, C-terminal
Type:
Domain
Description:
This entry represents the C-terminal region of CcmF, one of the cytochrome c-type biogenesis proteins. This domain may deliver reductant to haem on CcmE [
,
,
].
Heavy metal-associated isoprenylated plant protein 1/3/5/6
Type:
Family
Description:
This entry represents a group of heavy metal-associated isoprenylated plant proteins, including HIPP1/3/5/6 from Arabidopsis [
]. HIPP3 acts as an upstream regulator of the salicylate-dependent plant immunity pathway and of flowering time []. HIPP6, also known as CdI19, plays an important role in the maintenance of heavy metal homeostasis and/or in detoxification by endowing plasma membranes with the capacity to serve as an initial barrier against inflow of free heavy metal ions into cells [].
GspF is the inner membrane component of the type II secretion system (T2SS). It interacts with GspE, a cytoplasmic hexameric ATPase of the T2SS [
]. Note, some genes from Xylella and Xanthomonas strains do not match this entry due to excessive divergence.The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space [
]. T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK []. GspD has been shown to interact with the inner membrane component GspC []. The T2SS pseudopilus is a periplasmic filament composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. Pseudopilus is assembled by the polymerization of GspG (also known as PulG) subunits. Pseudopilin proteins have a conserved N-terminal hydrophobic segment followed by a more variable C-terminal periplasmic and globular domain [
].
Bacterial binding protein-dependent transport systems [
,
] are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown [,
] that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems to be located in a cytoplasmic loop between two transmembrane domains []. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices.This entry describes a subfamily of both CysT and CysW, paralogous and generally tandemly encoded permease proteins of the sulphate ABC transporter [
,
].
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These 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.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [
].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [,
,
].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [
,
,
,
,
,
].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [
]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [,
]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [,
,
].This entry represents CysT, one of two homologous, tandem permeases in the sulphate ABC transporter system; the other is CysW (
). The sulphate transporter has been described in Escherichia coli as transporting sulphate, thiosulphate, selenate, and selenite. Sulphate transporters may also transport molybdate ion if a specific molybdate transporter is not present.
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These 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.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [
].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [,
,
].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [,
,
,
,
,
].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [
]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [,
]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [,
,
].This entry represents CysW, one of two homologous, tandem permeases in the sulphate ABC transporter system; the other is CysT (
). The sulphate transporter has been described in Escherichia coli as transporting sulphate, thiosulphate, selenate, and selenite. Sulphate transporters may also transport molybdate ion if a specific molybdate transporter is not present.
Outer membrane protein (OMP) assembly factor BamB is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involved in assembly and insertion of β-barrel proteins into the outer membrane [
,
,
,
,
]. Although BamB is not essential in E. coli, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. It was suggested that BamB serves as a scaffolding protein in the Bam complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones [].
This entry describes PtsA, one of a pair of permease proteins in the ABC (high affinity) phosphate transporter [
]. In a number of species, this permease is fused with the PtsC protein (). In Escherichia coli, this transport system is induced when the concentration of extrallular inorganic phosphate is low. A constitutive, lower affinity transporter operates otherwise.
This is a family of phosphate transport system permease proteins. They are membrane transport proteins that use the hydrolysis of ATP to function. They contain ABC (ATP-binding cassette-type) transporter domains.Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space [
]. PstA and PstC are hydrophobic and they form the transmembrane portion of the Pst system []. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD) [].
Proteins in this family are known as RTC4 (restriction of telomere capping protein 4) as deletion of RTC4 in Saccharomyces cerevisiae affects the cell response to telomere uncapping [
].
PKB (also called Akt) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase which alters the activity of the targeted protein [
]. Among its many roles, Akt appears to be common to signaling pathways that mediate the metabolic effects of insulin in several physiologically important target tissues[]. Human Akt has three isoforms derived for distinct genes: Akt1/PKBalpha, Akt2/PKBbeta, and Akt3/PKBgamma. All Akts have an N-terminal PH domain with an activating Thr phosphorylation site, a kinase domain, and a short C-terminal regulatory tail with an activating Ser phosphorylation site []. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. The phosphorylation of Akt at its Thr and Ser phosphorylation sites leads to increased Akt activity toward forkhead transcription factors, the mammalian target of rapamycin (mTOR), and the Bcl-xL/Bcl-2-associated death promoter (BAD), all of which possess a consensus motif R-X-R-XX-ST-B (X = amino acid, B = bulky hydrophobic residue) for Akt phosphorylation [,
].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized [
].
PATE proteins are secreted, small, cysteine-rich proteins selectively expressed in male reproductive tissues (prostate, testis, epididymis, seminal vesicle).This proteins include 10 cysteine residues conforms to a consensus cysteine pattern found in a well-conserved large family of three-fingered proteins (TFPs), characterised by a distinct disulfide bonding pattern between 8 and 10 cysteine residues []. Critical roles of the PATE (Pate)-like proteins in activities related not only to fertility and reproduction but also to neuronal activity. Neurons and sperm share many common "neuron specific"receptors. Nicotinic acetylcholine receptors (nACHR) subunits alpha7, 9, 3, 5 and beta 4 have all been demonstrated to be present in human sperm and the alpha-7 subunit likely exists as a homomer in the posterior post-acrosomal and neck regions of sperm. Human acrosome reaction initiated by acetylcholine involves the alpha-7 nAChR [
]. Common functionality of nAChR in both reproductive and neuronal tissues thus reconciles the neuro-modulatory activity of the PATE (Pate)-like proteins.Prostate and testis expressed protein 2 (PATE2, also known as PATE-M) belongs to the PATE family and is expressed in prostate and testis [
].
Reversion-inducing cysteine-rich protein with Kazal motifs
Type:
Family
Description:
Reck is a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity [
]. It also regulates two other MMPs, MMP-2 and MT1-MMP, known to be involved in cancer progression [,
]. Reck and the orphan receptor Gpr124 interact to activate Wnt7a/Wnt7b signaling in CNS vascular development [,
].
This group of functionally uncharacterised bacterial proteins includes TM1506 from Thermotoga maritima (
), which has a cytidine deaminase-like fold. It binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate [
].
CDK2-associated and cullin domain-containing protein 1
Type:
Family
Description:
CDK2-associated and cullin domain-containing protein 1 (CACUL1) interacts with cyclin-dependent kinase 2 (CDK2), which regulates cell proliferation and allows progression from the G1 to S phase of the cell cycle [
]. It has been linked to the proliferation of colorectal carcinoma, lung and gastric cancers [].
Nickel ABC transporter, substrate-binding protein NikA
Type:
Family
Description:
The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor [
,
]. This entry represents NikA, which contains a pocket rich in aromatic and arginine residues that lodged a Ni-(H2O)5 2+ species. It has been shown that NikA is able to bind nickel and Fe(III)EDTA in the same pocket [
] and that His416 is the only direct metal-protein contact []. This entry also includes metal-staphylopine-binding protein CntA from Staphylococcus aureus [,
]. CntA is involved in the import of divalent metals ions such as nickel, cobalt and zinc. It binds the metal via the metallophore StP, and transfers the StP-metal complex to the membrane-bound permease [,
].Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins [
,
].
The surface presentation of antigens protein SpaK (also known as InvB) from Salmonella typhimurium is involved in a secretory pathway responsible for the surface presentation of determinants needed for the entry of Salmonella species into mammalian cells [
,
]. Other Spa genes in the cluster are related to invasion (Inv) genes in similar Salmonella and Shigella species [], and to flagella biosynthesis genes in Helicobacter pylori [
]. A further analogous gene in Yersinia (Spa15 homologue) has also been found [
]. The SpaK/InvB protein has a molecular mass of 15kDa, and is believed to play a part in the sec-independent type III protein secretion system of
S. typhimurium and Shigella flexneri []. In the organisation of the Spa/Inv locus, the SpaK/InvB gene is found adjacent to SpaL/InvC [
], and may play a part in the ATPase activity possessed by the latter.
This domain is found at the C terminus of bacteriophage PRD1 spike protein P5. The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. The C-terminal fragment of P5 appears to contain the residues responsible for the trimerization of the protein, whereas the smaller N-terminal part mediates the interaction with protein P31 [
,
].
The SMC5-SMC6 complex localization factor protein 1 plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance [
]. The RAD18-SLF1-SLF2 complex suppresses the genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions [].
Photosynthetic complex assembly protein 2, putative
Type:
Family
Description:
This uncharacterised protein family was identified, by the method of partial phylogenetic profiling, as having a matching phylogenetic distribution to that of the photosynthetic reaction centre of the alpha-proteobacterial type. It is nearly always encoded near other photosynthesis-related genes, including puhA.
The proteins in this family are poorly characterised, but an investigation [
] has indicated that the immediate early protein is required for the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90.
This entry represents a set of repeats named ALF (Alanine-rich, AL - conserved Phenylalanine, F), which are found in a small family of secreted proteins of no known function. They may be involved in signal transduction [
].
Conserved hypothetical protein CHP03076, glycine cleavage
Type:
Family
Description:
The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia lack the P and T proteins, and have a single homologue of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The proteins in this entry are only found in the Chlamydiae, and always are part of a two-gene operon, upstream of the homologue of GcvH. Its function is unknown.
Members of this family are related to RctB. RctB is often is encoded near RNA cyclase and therefore is suggested to be a tRNA or mRNA processing enzyme. This family of RctB-like proteins in encoded upstream of, and apparently is translationally coupled to, the putative peptide chain release factor RF-H (
), product of the prfH gene. Note that a large deletion at the junction between this gene and the prfH gene in Escherichia coli (strain K12) marks both as probable pseudogenes.
CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4 [
].
Zinc finger CCHC domain-containing protein 3 (ZCCHC3) is a zinc-finger protein that acts as a co-sensor of cGAS in innate immune response to cytosolic dsDNA and DNA virus [
]. It has been shown to bind DNA and RNA in the cytoplasm and acts by promoting recognition of viral nucleic acids by virus sensors, such as DDX58/RIG-I, IFIH1/MDA5 and CGAS [,
].
Members of this protein family are the Fe-S protein, NrfC, of the cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family
) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of polysulphide reductase.
Retinoic acid receptor responder protein 2 (also known as chemerin or TIG2) is an immunomodulating protein secreted predominantly by adipose tissue and skin. It is secreted in an inactive form and further processed to an active form through cleavage of its carboxyl terminus [
]. It regulates adipogenesis, metabolism and inflammation through activation of the chemokine-like receptor 1 (CMKLR1) []. It also binds to G protein-coupled receptor 1 (GPR1) and C-C chemokine receptor-like 2 (CCRL2) []. Chemerin has been linked to obesity and inflammation. It also possesses antimicrobiological functions and may serve as a tumorsuppressor in skin [].
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 [].Atg5 comprises two ubiquitin-like domains that flank a helix-rich domain. The N- and C-terminal ubiquitin-like domains are called UblA and UblB, respectively, and the helix-rich domain between UblA and UblB, is called HR. Both UblA and UblB comprise a five-stranded -sheet and two-helices, which is a conserved feature in all ubiquitin superfamily proteins. The HR domain consists of three alpha helices [
].This superfamily represents the helix rich domain (HR) found in Atg5.
Putative selenium-dependent hydroxylase accessory protein YqeC
Type:
Family
Description:
This uncharacterised protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis [
]. Instead, this family appears to mark a selenium-dependent molybdenum hydroxylase maturation system.
ER membrane protein complex subunit 7 (EMC7) is a component of the endoplasmic reticulum membrane protein complex (EMC). This complex was first found to interact with the degradation of misfolded proteins by the ubiquitin- and proteasome-dependent process known as ER-associated degradation (ERAD) [
], thus suggesting a role in the biosynthesis of transmembrane proteins. More recently, it was shown that EMC acts as a conserved co- and post-translational insertase at the endoplasmic reticulum in an energy-independent manner [,
]. EMC7 has been misnamed C11orf3, but is more correctly named C15orf24 because the gene is actually on human chromosome 15.
Fetal and adult testis-expressed transcript protein
Type:
Family
Description:
FATE1 is a member of the Miff protein family, whose members are involved in the control of mitochondrial and peroxisomal fission. It is localized in mitochondria associated ER membranes (MAM) and is implicated in the regulation of Ca2+ and drug-dependent apoptosis in cancer cells by modulating ER-mitochondria distance [
]. Homologues are found only in chordates.
Proteins in this entry contain an armadillo-type fold, and a BP28, C-terminal domain. This entry includes U3 small nucleolar RNA-associated protein 10 (Utp10), which is a HEAT-repeat containing protein involved in nucleolar processing of pre-18S ribosomal RNA [
]. Utp10 is also involved in 40S ribosome maturation []. This entry also includes HEAT repeat-containing protein 1 (HEATR1) from humans. HEATR1 is required for optimal pre-ribosomal RNA transcription by RNA polymerase I [].
N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein
Type:
Family
Description:
N-acetylmuramic acid 6-phosphate etherase (MurQ) is an enzyme involved in peptidoglycan recycling in Escherichia coli. In cyanobacteria MurQ may promote low-light adaptation through peptidoglycan recycling [
]. MurQ contains a sugar isomerase (SIS) domain with similarity to the glucokinase regulatory protein (GKRP) in humans [].GCKR regulates glucokinase (GK), an enzyme responsible for regulating the uptake and storage of dietary glucose [
]. In the liver, GKRP forms an inhibitory complex with glucokinase (GCK). The disruption and reformation of this complex occurs in response to direct binding of glucose to GCK, and fructose 1-phosphate (F1P) and fructose 6-phosphate (F6P) to GKRP [].
This entry describes a domain found as a C-terminal extension to the cell division protein FtsZ in many, but not all, members of the alphaproteobacteria.
Nuclear speckles are subnuclear storage sites containing pre-mRNA splicing machinery. Nuclear speckle splicing regulatory protein 1 (Nsrp1), also known as NSRP70, is a nuclear speckle-related protein that mediates alternative splice site selection, targeting several pre-mRNAs [
]. It contains an N-terminal coiled-coil domain that is critical not only for self-oligomerization but also for splicing activity. It interacts physically with two SR (serine/arginine) proteins, SRSF1 and SRSF2, and reverses their splicing activity in terms of CD44 exon v5 as exon exclusion [].
Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein
Type:
Family
Description:
This family includes the periplasmic binding protein component of ABC transporters for phosphonates [
] as well as other related binding components for closely related substances such as phosphate [] and phosphite []. A number of members of this family are found in genomic contexts with components of selenium metabolic processes, suggestive of a role in selenate or other selenium-compound transport.Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates [
] as well as other, related binding components for closely related substances such as phosphate [] and phosphite. A subset of this entry in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232, []) is shown in (). Nevertheless, there are members of this subfamily which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
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 the RING zinc finger domain of 'RING finger protein Z', a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [
,
]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication [].The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [
,
,
]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [,
]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is:C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C
Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second.
The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) [
].
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-13
Type:
Family
Description:
A guanine nucleotide-binding protein (G protein) is involved in transmembrane signaling systems and is a complex of alpha, beta and gamma subunits. The beta and gamma subunits are required for GTPase activity. The entry includes the G protein gamma subunit GNG13. GNG13 associates with the alpha subunit of gustducin, a transducin-like G protein selectively expressed in taste receptor cells [
]. The equivalent subunit in Drosophila melanogasteris known as guanine nucleotide-binding protein subunit gamma-e (Ggamma30A).
Salmonella typhimurium contains a 90kb plasmid that is associated with
virulence []. This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the70kDa mkaA protein [
], a recognised virulence factor, and more recently described, four spv genes under the control of a regulator []. The spv genes are induced under carbon-poor conditions at a stationary phase of growth, and their expression is under the control of both the spvR regulator, and the katF locus in Salmonella. It has been proposed that individual spv proteins may be required at different time points during infection [
].SpvB is a 65kDa protein that has been localised to the bacterial cytoplasm
[]. Its expression peaks during early stationary phase, but declines as the latent phase of the infection is reached, suggesting a role in initiating virulence.
Kinase non-catalytic C-lobe domain-containing protein 1
Type:
Family
Description:
Kinase noncatalytic C-lobe domain containing 1 (KNDC1), also known as very-KIND, is a brain-specific Ras guanine nucleotide exchange factor (RasGEF) that regulates microtubule-associated protein 2 (MAP2) during dendrite morphogenesis [
,
]. It contains two kinase noncatalytic C-lobe domains (KIND1 and KIND2), a RasGEF N-terminal domain (RasN) and a putative RasGEF domain []. The KIND2 domain regulates dendrite complexity via targeting of v-KIND to MAP2 associated with the dendritic microtubule cytoskeleton [].
Autonomous transposable element EN-1 mosaic protein
Type:
Family
Description:
This entry represents a group of plant proteins, including EN-1 (also known as SPM) from maize. EN-1 is a autonomous transposable element controlled by interacting epigenetic and autoregulatory mechanisms [
].
This entry represents a group of plant proteins including, protein GRAVITROPIC IN THE LIGHT 1 (GIL1) from Arabidopsis. GIL1 is essential for light-dependent randomization of hypocotyl growth orientation [
].
Lung surfactant protein D coiled-coil trimerisation
Type:
Domain
Description:
This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein [
].
This entry represents a zinc finger found in ZNF750 and related proteins. ZNF750 is a transcription factor that controls epithelial homeostasis by inhibiting progenitor genes while inducing differentiation genes [
]. Proteins containing this domain also include proline-rich protein 35. Its function is not clear.
Proline-serine-threonine phosphatase-interacting protein 2, F-BAR domain
Type:
Domain
Description:
F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization [
]. Proline-Serine-Threonine Phosphatase-Interacting Protein 2 (PSTPIP2) is mostly expressed in hematopoietic cells but is also expressed in the brain. It is involved in regulating cell adhesion and motility [
]. Mutations in the gene encoding murine PSTPIP2 can cause autoinflammatory disorders such as chronic multifocal osteomyelitis and macrophage autoinflammatory disease []. PSTPIP2 contains an N-terminal F-BAR domain and lacks the PEST motifs and SH3 domain that are found in PSTPIP1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules [].
Members of this family are the downstream member (B) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown.
This entry includes TssE1, which is a baseplate component of the bacterial type VI secretion system (T6SS). It shares structural homology with T4 inner baseplate protein gp25 [
]. The type VI secretion system (T6SS) is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath [
]. Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA [].
This entry includes TssM1, which is a component of the bacterial type VI secretion system (T6SS) [
].The type VI secretion system (T6SS) is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath [
]. Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA [].
This entry represents one of two related families in type VI secretion systems (T6SS) that contain an ImpA-related N-terminal domain (
). This group includes Rhizobium leguminosarum ImpA [
], thought to be an T6SS homologue [].This entry also includes TssA, which is a T6SS component forming dodecameric ring structures positioned at one end of the TssB/TssC sheath. [
]. The type VI secretion system (T6SS) is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath [
]. Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA [].
