SII-SWORD/CoKE huggingface dataset:
HTH-type transcriptional regulator AlsR, PBP2 domain (AlsR_PBP2)
Type: Domain

This entry represents the substrate-binding domain of the HTH-type transcriptional regulator AlsR from Bacillus subtilis and similar proteins from Bacillales. It shows significant homology to the type 2 periplasmic binding proteins (PBP2).

AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon . The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyses the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources .

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator IlvR, PBP2 domain (IlvR_PBP2)
Type: Domain

The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product . This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
Mucosal addressin cell adhesion molecule 1 (MADCAM1)
Type: Family

Mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) proteins are cell adhesion molecules expressed on the endothelium in mucosa that guide the specific homing of lymphocytes into mucosal tissues . MAdCAM-1 belongs to a subclass of the immunoglobulin superfamily (IgSF), whose members are ligands for integrins . MAdCAM-1 is the major ligand for alpha4beta7 integrin and the ligand for L-selectin .
Transcriptional activator protein LysR, PBP2 domain (LysR_PBP2)
Type: Domain

LysR is the transcriptional activator of lysA, a diaminopimelate decarboxylase that catalyses the decarboxylation of diaminopimelate to produce lysine. The C-terminal substrate-binding domain of LysR shows significant homology to the type 2 periplasmic binding proteins (PBP2) .

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
Octopine catabolism/uptake operon regulatory protein OccR, PBP2 domain (OccR_PBP2)
Type: Domain

This entry represents the C-terminal substrate-domain of OccR, which is a LysR-type transcriptional regulator of Agrobacterium tumefaciens that positively regulates the octopine catabolism operon of the Ti plasmid . This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
Nodulation protein D, PBP2 (NodD_PBP2)
Type: Domain

The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD negatively auto-regulates expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots . This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator SyrM, PBP2 domain (SyrM_PBP2)
Type: Domain

Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis . This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator TrpI, PBP2 (TrpI_PBP2)
Type: Domain

TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase . This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional activator AmpR, PBP2 (AmpR_PBP2)
Type: Domain

This entry represents the C-terminal substrate binding domain of LysR-type transcriptional regulator AmpR, whichis involved in control of the expression of beta-lactamase genes . Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other Gram-negative bacilli. AmpR is a key player in the intricate network of regulators that is responsible for mediating virulence and antibiotic resistance in P. aeruginosa . The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator ClcR, PBP2 domain (ClcR_PBP2)
Type: Domain

In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation . The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator BlaA, PBP2 domain (BlaA_PBP2)
Type: Domain

This entry represents the C-terminal substrate binding domain of LysR-type transcriptional regulator BlaA, which is involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase . The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
HTH-type transcriptional regulator CysB, PBP2 domain (CysB_PBP2)
Type: Domain

This entry represents the PBP2 domain of Cys2 and similar proteins from preoteobacteria.

CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl . CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilisation of sulfur from aliphatic sulfonates, in the presence of cysteine . Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilisation of taurine as sulfur source for growth . Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerisation: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins . As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor . The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
Regulatory protein NocR, PBP2 domain (NocR_PBP2)
Type: Domain

This entry represents the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of opines. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumours that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR positively regulates the catabolism of nopaline. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region . This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).

The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction .
Sorting nexin-9, BAR domain (SNX9_BAR)
Type: Domain

Sorting nexin 9 (SNX9) has been suggested to be involved in the endocytic process as an accessory factor . SNX9 has binding sites for both clathrin and adaptor protein AP-2 in a low complexity region, and binds dynamin-2 (Dyn2) by its SH3 domain. SNX9 has its own membrane-binding activity, mediated by a carboxyl-terminal region containing the PX domain and the BAR domain . Endogenous SNX9 partially co-localizes with AP-2 and Dyn2 at the plasma membrane, and over expression in K562 and HeLa cells of truncated versions of SNX9 inhibits the uptake of transferrin . Moreover, SNX9 is required for efficient clathrin-mediated endocytosis, which suggests that it functions to regulate dynamin activity .

SNXs are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNX9 also contains a BAR and a SH3 domain. This entry represents the BAR domain of sorting nexin-9. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions .
Sorting nexin-9, PX domain (SNX9_PX)
Type: Domain

Sorting nexin 9 (SNX9) has been suggested to be involved in the endocytic process as an accessory factor . SNX9 has binding sites for both clathrin and adaptor protein AP-2 in a low complexity region, and binds dynamin-2 (Dyn2) by its SH3 domain. SNX9 has its own membrane-binding activity, mediated by a carboxyl-terminal region containing the PX domain and the BAR domain . Endogenous SNX9 partially co-localizes with AP-2 and Dyn2 at the plasma membrane, and over expression in K562 and HeLa cells of truncated versions of SNX9 inhibits the uptake of transferrin . Moreover, SNX9 is required for efficient clathrin-mediated endocytosis, which suggests that it functions to regulate dynamin activity .

SNXs are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNX9 also contains a BAR and a SH3 domain. This entry represents the PX domain of sorting nexin-9. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions .
Sorting nexin-33, BAR domain (SNX33_BAR)
Type: Domain

Sorting nexins are a large family of evolutionarily conserved phosphoinositide-binding proteins that have roles in cargo sorting through the endosomal netwrok . Sorting nexins contain at least a PX domain (a phospholipid-binding motif). Some nexins contain a few additional domains.

SNX33 plays a role in maintaining cell shape and cell cycle progression through its interaction with WASp (Wiskott-Aldrich syndrome protein) . It interferes with cellular prion protein (PrP) formation by modulation of its shedding . It may also promote the formation of macropinosomes (large endocytic organelles) .
Bridging integrator 3, BAR domain (Bin3_BAR)
Type: Domain

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions . Bridging integrator 3 (Bin3) is widely expressed in many tissues except in the brain. It plays roles in regulating filamentous actin localization and in cell division. In humans, the Bin3 gene is located in chromosome 8p21.3, a region that is implicated in cancer suppression. Homozygous inactivation of the Bin3 gene in mice led to the development of cataracts and an increased likelihood of lymphomas during aging, suggesting a role for Bin3 in lens development and cancer suppression . BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions .
Rvs161/Hob3, BAR domain (Rvs161/Hob3_BAR)
Type: Domain

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions . This entry represents the BAR domain found in fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 161 (Rvs161p) and Schizosaccharomyces pombe Hob3 (homologue of Bin3). S. cerevisiae Rvs161p plays a role in regulating cell polarity, actin cytoskeleton polarization, vesicle trafficking, endocytosis, bud formation, and the mating response. It forms a heterodimer with another BAR domain protein Rvs167p. Rvs161p and Rvs167p share common functions but are not interchangeable . Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. S. pombe Hob3 is important in regulating filamentous actin localization and may be required in activating Cdc42 and recruiting it to cell division sites . BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions .