LysR family transcriptional regulator [Hydrogenophaga sp. PBC]
LysR family transcriptional regulator( domain architecture ID 10444297)
LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes
List of domain hits
Name | Accession | Description | Interval | E-value | ||||
Periplasmic_Binding_Protein_Type_2 super family | cl21456 | Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ... |
102-300 | 9.97e-60 | ||||
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences. The actual alignment was detected with superfamily member cd08431: Pssm-ID: 473866 [Multi-domain] Cd Length: 195 Bit Score: 189.40 E-value: 9.97e-60
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HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
16-72 | 4.34e-14 | ||||
Bacterial regulatory helix-turn-helix protein, lysR family; : Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 65.87 E-value: 4.34e-14
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Name | Accession | Description | Interval | E-value | |||||
PBP2_HupR | cd08431 | The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ... |
102-300 | 9.97e-60 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176122 [Multi-domain] Cd Length: 195 Bit Score: 189.40 E-value: 9.97e-60
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PRK11074 | PRK11074 | putative DNA-binding transcriptional regulator; Provisional |
11-300 | 3.76e-56 | |||||
putative DNA-binding transcriptional regulator; Provisional Pssm-ID: 182948 [Multi-domain] Cd Length: 300 Bit Score: 183.99 E-value: 3.76e-56
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LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
16-306 | 3.93e-40 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 140.77 E-value: 3.93e-40
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LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
102-303 | 1.22e-16 | |||||
LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 460931 [Multi-domain] Cd Length: 205 Bit Score: 76.94 E-value: 1.22e-16
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HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
16-72 | 4.34e-14 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 65.87 E-value: 4.34e-14
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PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
20-77 | 5.02e-10 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 59.63 E-value: 5.02e-10
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argP | TIGR03298 | transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ... |
16-263 | 1.61e-08 | |||||
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions] Pssm-ID: 274509 [Multi-domain] Cd Length: 292 Bit Score: 54.92 E-value: 1.61e-08
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ModE | COG2005 | DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription]; |
1-91 | 6.49e-06 | |||||
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription]; Pssm-ID: 441608 [Multi-domain] Cd Length: 118 Bit Score: 44.43 E-value: 6.49e-06
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Name | Accession | Description | Interval | E-value | |||||
PBP2_HupR | cd08431 | The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ... |
102-300 | 9.97e-60 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176122 [Multi-domain] Cd Length: 195 Bit Score: 189.40 E-value: 9.97e-60
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PRK11074 | PRK11074 | putative DNA-binding transcriptional regulator; Provisional |
11-300 | 3.76e-56 | |||||
putative DNA-binding transcriptional regulator; Provisional Pssm-ID: 182948 [Multi-domain] Cd Length: 300 Bit Score: 183.99 E-value: 3.76e-56
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PRK10094 | PRK10094 | HTH-type transcriptional activator AllS; |
11-282 | 7.13e-46 | |||||
HTH-type transcriptional activator AllS; Pssm-ID: 182237 [Multi-domain] Cd Length: 308 Bit Score: 157.66 E-value: 7.13e-46
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LysR | COG0583 | DNA-binding transcriptional regulator, LysR family [Transcription]; |
16-306 | 3.93e-40 | |||||
DNA-binding transcriptional regulator, LysR family [Transcription]; Pssm-ID: 440348 [Multi-domain] Cd Length: 256 Bit Score: 140.77 E-value: 3.93e-40
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LysR_substrate | pfam03466 | LysR substrate binding domain; The structure of this domain is known and is similar to the ... |
102-303 | 1.22e-16 | |||||
LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Pssm-ID: 460931 [Multi-domain] Cd Length: 205 Bit Score: 76.94 E-value: 1.22e-16
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HTH_1 | pfam00126 | Bacterial regulatory helix-turn-helix protein, lysR family; |
16-72 | 4.34e-14 | |||||
Bacterial regulatory helix-turn-helix protein, lysR family; Pssm-ID: 459683 [Multi-domain] Cd Length: 60 Bit Score: 65.87 E-value: 4.34e-14
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PRK13348 | PRK13348 | HTH-type transcriptional regulator ArgP; |
13-263 | 2.74e-11 | |||||
HTH-type transcriptional regulator ArgP; Pssm-ID: 237357 [Multi-domain] Cd Length: 294 Bit Score: 63.07 E-value: 2.74e-11
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PBP2_LTTR_substrate | cd05466 | The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ... |
104-300 | 8.49e-11 | |||||
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are 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 genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176102 [Multi-domain] Cd Length: 197 Bit Score: 60.31 E-value: 8.49e-11
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PRK11242 | PRK11242 | DNA-binding transcriptional regulator CynR; Provisional |
21-194 | 2.45e-10 | |||||
DNA-binding transcriptional regulator CynR; Provisional Pssm-ID: 183051 [Multi-domain] Cd Length: 296 Bit Score: 60.36 E-value: 2.45e-10
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PRK10341 | PRK10341 | transcriptional regulator TdcA; |
14-177 | 2.91e-10 | |||||
transcriptional regulator TdcA; Pssm-ID: 182391 [Multi-domain] Cd Length: 312 Bit Score: 60.26 E-value: 2.91e-10
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PRK10086 | PRK10086 | DNA-binding transcriptional regulator DsdC; |
20-77 | 5.02e-10 | |||||
DNA-binding transcriptional regulator DsdC; Pssm-ID: 182231 [Multi-domain] Cd Length: 311 Bit Score: 59.63 E-value: 5.02e-10
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argP | TIGR03298 | transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ... |
16-263 | 1.61e-08 | |||||
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions] Pssm-ID: 274509 [Multi-domain] Cd Length: 292 Bit Score: 54.92 E-value: 1.61e-08
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rbcR | CHL00180 | LysR transcriptional regulator; Provisional |
14-82 | 5.77e-08 | |||||
LysR transcriptional regulator; Provisional Pssm-ID: 177082 [Multi-domain] Cd Length: 305 Bit Score: 53.10 E-value: 5.77e-08
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PRK09791 | PRK09791 | LysR family transcriptional regulator; |
17-152 | 3.44e-07 | |||||
LysR family transcriptional regulator; Pssm-ID: 182077 [Multi-domain] Cd Length: 302 Bit Score: 50.92 E-value: 3.44e-07
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PRK09801 | PRK09801 | LysR family transcriptional regulator; |
13-97 | 1.16e-06 | |||||
LysR family transcriptional regulator; Pssm-ID: 182085 [Multi-domain] Cd Length: 310 Bit Score: 49.26 E-value: 1.16e-06
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PRK09986 | PRK09986 | LysR family transcriptional regulator; |
30-188 | 1.81e-06 | |||||
LysR family transcriptional regulator; Pssm-ID: 182183 [Multi-domain] Cd Length: 294 Bit Score: 48.57 E-value: 1.81e-06
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PRK12683 | PRK12683 | transcriptional regulator CysB-like protein; Reviewed |
18-190 | 2.38e-06 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 237172 [Multi-domain] Cd Length: 309 Bit Score: 48.50 E-value: 2.38e-06
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PRK03635 | PRK03635 | ArgP/LysG family DNA-binding transcriptional regulator; |
16-263 | 3.19e-06 | |||||
ArgP/LysG family DNA-binding transcriptional regulator; Pssm-ID: 235144 [Multi-domain] Cd Length: 294 Bit Score: 47.85 E-value: 3.19e-06
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PBP2_Nitroaromatics_like | cd08417 | The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ... |
102-295 | 4.60e-06 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176109 [Multi-domain] Cd Length: 200 Bit Score: 46.44 E-value: 4.60e-06
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PRK15421 | PRK15421 | HTH-type transcriptional regulator MetR; |
14-187 | 4.97e-06 | |||||
HTH-type transcriptional regulator MetR; Pssm-ID: 185319 [Multi-domain] Cd Length: 317 Bit Score: 47.32 E-value: 4.97e-06
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ModE | COG2005 | DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription]; |
1-91 | 6.49e-06 | |||||
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription]; Pssm-ID: 441608 [Multi-domain] Cd Length: 118 Bit Score: 44.43 E-value: 6.49e-06
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cbl | PRK12679 | HTH-type transcriptional regulator Cbl; |
40-189 | 1.34e-05 | |||||
HTH-type transcriptional regulator Cbl; Pssm-ID: 183676 [Multi-domain] Cd Length: 316 Bit Score: 45.96 E-value: 1.34e-05
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PRK10632 | PRK10632 | HTH-type transcriptional activator AaeR; |
22-71 | 1.47e-05 | |||||
HTH-type transcriptional activator AaeR; Pssm-ID: 182601 [Multi-domain] Cd Length: 309 Bit Score: 45.91 E-value: 1.47e-05
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PRK03601 | PRK03601 | HTH-type transcriptional regulator HdfR; |
31-135 | 1.96e-05 | |||||
HTH-type transcriptional regulator HdfR; Pssm-ID: 235137 [Multi-domain] Cd Length: 275 Bit Score: 45.39 E-value: 1.96e-05
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PBP2_HvrB | cd08483 | The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ... |
140-297 | 3.18e-05 | |||||
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176172 [Multi-domain] Cd Length: 190 Bit Score: 43.87 E-value: 3.18e-05
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PBP2_OxyR | cd08411 | The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ... |
131-285 | 5.21e-05 | |||||
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176103 [Multi-domain] Cd Length: 200 Bit Score: 43.28 E-value: 5.21e-05
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PBP2_LTTR_like_4 | cd08440 | TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
131-267 | 1.01e-04 | |||||
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are 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 genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176131 [Multi-domain] Cd Length: 197 Bit Score: 42.51 E-value: 1.01e-04
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PBP2_TdcA | cd08418 | The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ... |
102-285 | 1.14e-04 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176110 [Multi-domain] Cd Length: 201 Bit Score: 42.34 E-value: 1.14e-04
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PRK12682 | PRK12682 | transcriptional regulator CysB-like protein; Reviewed |
20-190 | 2.14e-04 | |||||
transcriptional regulator CysB-like protein; Reviewed Pssm-ID: 183679 [Multi-domain] Cd Length: 309 Bit Score: 42.29 E-value: 2.14e-04
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PBP2_CysL_like | cd08420 | C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ... |
143-278 | 2.17e-04 | |||||
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176112 [Multi-domain] Cd Length: 201 Bit Score: 41.71 E-value: 2.17e-04
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PRK11716 | PRK11716 | HTH-type transcriptional activator IlvY; |
37-76 | 3.18e-04 | |||||
HTH-type transcriptional activator IlvY; Pssm-ID: 236961 [Multi-domain] Cd Length: 269 Bit Score: 41.73 E-value: 3.18e-04
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PRK12684 | PRK12684 | CysB family HTH-type transcriptional regulator; |
45-201 | 7.28e-04 | |||||
CysB family HTH-type transcriptional regulator; Pssm-ID: 237173 [Multi-domain] Cd Length: 313 Bit Score: 40.73 E-value: 7.28e-04
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PBP2_LysR_opines_like | cd08415 | The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ... |
122-190 | 4.01e-03 | |||||
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors 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 and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. 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. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176107 [Multi-domain] Cd Length: 196 Bit Score: 37.93 E-value: 4.01e-03
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PBP2_DntR_NahR_LinR_like | cd08459 | The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ... |
128-221 | 6.52e-03 | |||||
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176148 [Multi-domain] Cd Length: 201 Bit Score: 37.17 E-value: 6.52e-03
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PBP2_CrgA_like_6 | cd08475 | The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ... |
152-284 | 7.36e-03 | |||||
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which 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. Pssm-ID: 176164 [Multi-domain] Cd Length: 199 Bit Score: 37.15 E-value: 7.36e-03
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