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Search results 1 to 100 out of 143 for Pbp2

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Type Details Score
Gene
Type: gene
Organism: Rattus norvegicus
Gene
Type: gene
Organism: Saccharomyces cerevisiae
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus caroli
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus musculus
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus pahari
Protein Coding Gene
Type: protein_coding_gene
Organism: Mus spretus
Publication
First Author: Okazaki Y
Year: 2002
Journal: Nature
Title: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Volume: 420
Issue: 6915
Pages: 563-73
Publication
First Author: Hickox DM
Year: 2002
Journal: Biol Reprod
Title: Identification of a novel testis-specific member of the phosphatidylethanolamine binding protein family, pebp-2.
Volume: 67
Issue: 3
Pages: 917-27
Publication
First Author: Kawai J
Year: 2001
Journal: Nature
Title: Functional annotation of a full-length mouse cDNA collection.
Volume: 409
Issue: 6821
Pages: 685-90
Publication      
First Author: Helmholtz Zentrum Muenchen GmbH
Year: 2010
Journal: MGI Direct Data Submission
Title: Alleles produced for the EUCOMM and EUCOMMTools projects by the Helmholtz Zentrum Muenchen GmbH (Hmgu)
Publication
First Author: Gaudet P
Year: 2011
Journal: Brief Bioinform
Title: Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Volume: 12
Issue: 5
Pages: 449-62
Publication        
First Author: Mouse Genome Informatics Scientific Curators
Year: 2010
Title: Human to Mouse ISO GO annotation transfer
Publication        
First Author: Mouse Genome Informatics Scientific Curators
Year: 2000
Title: Gene Ontology Annotation by electronic association of SwissProt Keywords with GO terms
Publication
First Author: Kazuki Y
Year: 2004
Journal: Biochem Biophys Res Commun
Title: Human chromosome 21q22.2-qter carries a gene(s) responsible for downregulation of mlc2a and PEBP in Down syndrome model mice.
Volume: 317
Issue: 2
Pages: 491-9
Publication      
First Author: MGI Genome Annotation Group and UniGene Staff
Year: 2015
Journal: Database Download
Title: MGI-UniGene Interconnection Effort
Publication      
First Author: Mouse Genome Database and National Center for Biotechnology Information
Year: 2000
Journal: Database Release
Title: Entrez Gene Load
Publication      
First Author: Mouse Genome Informatics Group
Year: 2003
Journal: Database Procedure
Title: Automatic Encodes (AutoE) Reference
Publication      
First Author: Allen Institute for Brain Science
Year: 2004
Journal: Allen Institute
Title: Allen Brain Atlas: mouse riboprobes
Publication        
First Author: Mouse Genome Informatics Scientific Curators
Year: 2005
Title: Obtaining and loading genome assembly coordinates from NCBI annotations
Publication      
First Author: Mouse Genome Informatics (MGI) and The National Center for Biotechnology Information (NCBI)
Year: 2010
Journal: Database Download
Title: Consensus CDS project
Publication      
First Author: Lennon G
Year: 1999
Journal: Database Download
Title: WashU-HHMI Mouse EST Project
Publication      
First Author: The Jackson Laboratory Mouse Radiation Hybrid Database
Year: 2004
Journal: Database Release
Title: Mouse T31 Radiation Hybrid Data Load
Publication        
First Author: Mouse Genome Informatics Scientific Curators
Year: 2005
Title: Obtaining and Loading Genome Assembly Coordinates from Ensembl Annotations
Publication      
First Author: Mouse Genome Informatics Scientific Curators
Year: 2009
Journal: Database Download
Title: Mouse Microarray Data Integration in Mouse Genome Informatics, the Affymetrix GeneChip Mouse Gene 1.0 ST Array Platform
Publication      
First Author: Mouse Genome Informatics Scientific Curators
Year: 2009
Journal: Database Download
Title: Mouse Microarray Data Integration in Mouse Genome Informatics, the Affymetrix GeneChip Mouse Genome 430 2.0 Array Platform
Publication      
First Author: Mouse Genome Informatics Scientific Curators
Year: 2010
Journal: Database Download
Title: Mouse Microarray Data Integration in Mouse Genome Informatics, the Affymetrix GeneChip Mouse Genome U74 Array Platform (A, B, C v2).
Publication      
First Author: Bairoch A
Year: 1999
Journal: Database Release
Title: SWISS-PROT Annotated protein sequence database
Publication        
First Author: Mouse Genome Informatics Scientific Curators
Year: 2002
Title: Mouse Genome Informatics Computational Sequence to Gene Associations
Publication      
First Author: Mouse Genome Informatics
Year: 2010
Journal: Database Release
Title: Protein Ontology Association Load.
Publication      
First Author: Elliott R
Year: 2000
Journal: Personal Communication
Title: Chromosome Locations Based on RH mapping
Publication
First Author: Fisher RF
Year: 1993
Journal: J Mol Biol
Title: Interactions of NodD at the nod Box: NodD binds to two distinct sites on the same face of the helix and induces a bend in the DNA.
Volume: 233
Issue: 3
Pages: 336-48
Publication
First Author: Peck MC
Year: 2006
Journal: J Bacteriol
Title: Diverse flavonoids stimulate NodD1 binding to nod gene promoters in Sinorhizobium meliloti.
Volume: 188
Issue: 15
Pages: 5417-27
Publication
First Author: Hou B
Year: 2009
Journal: Acta Biochim Biophys Sin (Shanghai)
Title: The properties of NodD were affected by mere variation in length within its hinge region.
Volume: 41
Issue: 11
Pages: 963-71
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Publication
First Author: Olekhnovich I
Year: 1998
Journal: Gene
Title: Recognition of binding sites I and II by the TrpI activator protein of pseudomonas aeruginosa: efficient binding to both sites requires InGP even when site II is replaced by site I.
Volume: 223
Issue: 1-2
Pages: 247-55
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Publication
First Author: Lodge J
Year: 1993
Journal: FEMS Microbiol Lett
Title: Investigation of the Pseudomonas aeruginosa ampR gene and its role at the chromosomal ampC beta-lactamase promoter.
Volume: 111
Issue: 2-3
Pages: 315-20
Publication
First Author: Balasubramanian D
Year: 2015
Journal: Pathog Dis
Title: Pseudomonas aeruginosa AmpR: an acute-chronic switch regulator.
Volume: 73
Issue: 2
Pages: 1-14
Publication
First Author: von Lintig J
Year: 1994
Journal: J Bacteriol
Title: Opine-regulated promoters and LysR-type regulators in the nopaline (noc) and octopine (occ) catabolic regions of Ti plasmids of Agrobacterium tumefaciens.
Volume: 176
Issue: 2
Pages: 495-503
Publication
First Author: Marincs F
Year: 1993
Journal: Mol Gen Genet
Title: Nopaline causes a conformational change in the NocR regulatory protein-nocR promoter complex of Agrobacterium tumefaciens Ti plasmid pTiT37.
Volume: 241
Issue: 1-2
Pages: 65-72
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: 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 [, , ].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) [].
Protein Domain
Type: Domain
Description: 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 [, , ].This entry represents the C-terminal substrate binding domain of LysR-type transcriptional regulator YidZ, which is involved in anaerobic NO protection []. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).
Publication
First Author: Peng HL
Year: 1999
Journal: J Bacteriol
Title: Characterization of mdcR, a regulatory gene of the malonate catabolic system in Klebsiella pneumoniae.
Volume: 181
Issue: 7
Pages: 2302-6
Publication
First Author: Knapp GS
Year: 2009
Journal: Protein Sci
Title: The oligomerization of CynR in Escherichia coli.
Volume: 18
Issue: 11
Pages: 2307-15
Publication
First Author: Lamblin AF
Year: 1994
Journal: J Bacteriol
Title: Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation.
Volume: 176
Issue: 21
Pages: 6613-22
Publication
First Author: Opel ML
Year: 2001
Journal: Mol Microbiol
Title: DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths.
Volume: 39
Issue: 1
Pages: 191-8
Publication
First Author: Rhee KY
Year: 1999
Journal: Proc Natl Acad Sci U S A
Title: Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli.
Volume: 96
Issue: 25
Pages: 14294-9
Publication
First Author: Peng WT
Year: 1998
Journal: J Bacteriol
Title: The phenolic recognition profiles of the Agrobacterium tumefaciens VirA protein are broadened by a high level of the sugar binding protein ChvE.
Volume: 180
Issue: 21
Pages: 5632-8
Publication
First Author: Doty SL
Year: 1993
Journal: J Bacteriol
Title: The chromosomal virulence gene, chvE, of Agrobacterium tumefaciens is regulated by a LysR family member.
Volume: 175
Issue: 24
Pages: 7880-6
Publication
First Author: Mayer D
Year: 1995
Journal: J Bacteriol
Title: Identification of the transcriptional activator controlling the butanediol fermentation pathway in Klebsiella terrigena.
Volume: 177
Issue: 18
Pages: 5261-9
Publication
First Author: Renna MC
Year: 1993
Journal: J Bacteriol
Title: Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin.
Volume: 175
Issue: 12
Pages: 3863-75
Publication
First Author: Fr├Ądrich C
Year: 2012
Journal: J Bacteriol
Title: The transcription factor AlsR binds and regulates the promoter of the alsSD operon responsible for acetoin formation in Bacillus subtilis.
Volume: 194
Issue: 5
Pages: 1100-12
Publication
First Author: Johnson DI
Year: 1984
Journal: Mol Gen Genet
Title: New regulatory genes involved in the control of transcription initiation at the thr and ilv promoters of Escherichia coli K-12.
Volume: 195
Issue: 1-2
Pages: 70-6
Publication
First Author: Malakooti J
Year: 1994
Journal: J Bacteriol
Title: Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus.
Volume: 176
Issue: 5
Pages: 1275-81
Publication
First Author: Demont N
Year: 1994
Journal: EMBO J
Title: The Rhizobium meliloti regulatory nodD3 and syrM genes control the synthesis of a particular class of nodulation factors N-acylated by (omega-1)-hydroxylated fatty acids.
Volume: 13
Issue: 9
Pages: 2139-49
Publication
First Author: Coco WM
Year: 1993
Journal: J Bacteriol
Title: Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida.
Volume: 175
Issue: 2
Pages: 417-27
Publication
First Author: Ishiguro K
Year: 1996
Journal: J Biochem
Title: Purification and characterization of the Proteus vulgaris BlaA protein, the activator of the beta-lactamase gene.
Volume: 120
Issue: 1
Pages: 98-103
Protein Domain
Type: Domain
Description: 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 [, , ].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 catalyzes 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 []. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: 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 [, , ].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).
Protein Domain
Type: Domain
Description: This entry represents the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes []. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: 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 (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 [, , ].
Protein Domain
Type: Domain
Description: 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 [, , ].CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function) []. CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. CynR, as other LysR-type transcriptional regulators, is composed of two functional domains joined by a linker helix involved in oligomerization: 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 (PBP2) [].
Protein Domain
Type: Domain
Description: 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 [, , ].In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids []. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA []. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner []. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2).
Protein Domain
Type: Domain
Description: 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 [, , ].Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE []. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression []. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2).
Protein Domain
Type: Domain
Description: 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 [, , ].In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins []. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).
Protein Domain
Type: Domain
Description: 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 [, , ].This entry represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway []. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2).
Publication
First Author: Sperandio B
Year: 2007
Journal: J Bacteriol
Title: Control of methionine synthesis and uptake by MetR and homocysteine in Streptococcus mutans.
Volume: 189
Issue: 19
Pages: 7032-44
Publication
First Author: Maxon ME
Year: 1989
Journal: Proc Natl Acad Sci U S A
Title: Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes.
Volume: 86
Issue: 1
Pages: 85-9
Publication
First Author: Plamann LS
Year: 1987
Journal: J Bacteriol
Title: Nucleotide sequence of the Salmonella typhimurium metR gene and the metR-metE control region.
Volume: 169
Issue: 9
Pages: 3932-7
Publication
First Author: Wu WF
Year: 1995
Journal: J Bacteriol
Title: Characterization of a second MetR-binding site in the metE metR regulatory region of Salmonella typhimurium.
Volume: 177
Issue: 7
Pages: 1834-9
Publication
First Author: Lochowska A
Year: 2004
Journal: Mol Microbiol
Title: Identification of activating region (AR) of Escherichia coli LysR-type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter.
Volume: 53
Issue: 3
Pages: 791-806
Publication
First Author: Kouzuma A
Year: 2008
Journal: J Bacteriol
Title: Transcription factors CysB and SfnR constitute the hierarchical regulatory system for the sulfate starvation response in Pseudomonas putida.
Volume: 190
Issue: 13
Pages: 4521-31
Protein Domain
Type: Domain
Description: 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 [, , ].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 utilization 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 utilization 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 oligomerization: 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).
Protein Domain
Type: Domain
Description: 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 [, , ].MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes []. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes []. The MetJ repressor negatively regulates the E. coli met genes, except for metH []. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).
Publication
First Author: Stec E
Year: 2006
Journal: J Mol Biol
Title: Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactor-binding domain of the Cbl transcriptional regulator.
Volume: 364
Issue: 3
Pages: 309-22
Protein Domain
Type: Domain
Description: 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 [, , ].Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis []. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine []. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: 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).
Publication
First Author: Habeeb LF
Year: 1991
Journal: Mol Plant Microbe Interact
Title: Transcription of the octopine catabolism operon of the Agrobacterium tumor-inducing plasmid pTiA6 is activated by a LysR-type regulatory protein.
Volume: 4
Issue: 4
Pages: 379-85
Publication
First Author: Akakura R
Year: 2002
Journal: J Biol Chem
Title: Mutations in the occQ operator that decrease OccR-induced DNA bending do not cause constitutive promoter activity.
Volume: 277
Issue: 18
Pages: 15773-80
Protein Domain
Type: Domain
Description: 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 [, , ].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 Tiplasmid []. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2).
Publication
First Author: Soriani M
Year: 2010
Journal: J Biol Chem
Title: Exploiting antigenic diversity for vaccine design: the chlamydia ArtJ paradigm.
Volume: 285
Issue: 39
Pages: 30126-38