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Conserved domains on  [gi|15595486|ref|NP_248980|]
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transcriptional activator GpuR [Pseudomonas aeruginosa PAO1]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-301 1.07e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.40  E-value: 1.07e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  92 QVRGLGGRDREALHLGCVDGVIGQHclpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYY 171
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 172 QPLFREEQNLYCGSAHPFfarADDEPTLGeicaadyvgrgymaenhrphdlrfnqgtdayTMEAIATLVFSGTYIGYLPT 251
Cdd:COG0583 158 RPLGEERLVLVASPDHPL---ARRAPLVN-------------------------------SLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 15595486 252 HYAATWVAEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSLFEA 301
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-301 1.07e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.40  E-value: 1.07e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  92 QVRGLGGRDREALHLGCVDGVIGQHclpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYY 171
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 172 QPLFREEQNLYCGSAHPFfarADDEPTLGeicaadyvgrgymaenhrphdlrfnqgtdayTMEAIATLVFSGTYIGYLPT 251
Cdd:COG0583 158 RPLGEERLVLVASPDHPL---ARRAPLVN-------------------------------SLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 15595486 252 HYAATWVAEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSLFEA 301
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-301 1.16e-24

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: 98.90  E-value: 1.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   104 LHLGCVDGVIGQHclpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYC 183
Cdd:pfam03466   4 LRIGAPPTLASYL---LPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   184 GSAHPFFARADDEPT--LGEICA---ADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPTHYAATWV 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEdlADEPLIllpPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 15595486   259 AEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSLFEA 301
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-298 6.78e-13

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: 66.47  E-value: 6.78e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 104 LHLGCVDgVIGQHCLPlPLaIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYC 183
Cdd:cd05466   2 LRIGASP-SIAAYLLP-PL-LAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 184 GSAHPF-------FARADDEPTLgeICAADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPtHYAAT 256
Cdd:cd05466  79 PPDHPLakrksvtLADLADEPLI--LFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLP-ESAVE 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595486 257 WVAEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSL 298
Cdd:cd05466 156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
12-177 5.93e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.05  E-value: 5.93e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGRDREALHLGCVDGVIGQHCLPlplAIRLFRQRAPEVLLKLHTRRPdELEHAVLEERlQLAVG----AFHHRLS 167
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRP---AMRHFLKENPNVEWLLRELSP-SMQMAALERR-ELDAGiwrmADLEPNP 161

                        170
                 ....*....|
gi 15595486  168 GLYYQPLFRE 177
Cdd:PRK09986 162 GFTSRRLHES 171
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
12-301 1.07e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.40  E-value: 1.07e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:COG0583   1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  92 QVRGLGGRDREALHLGCVDGVIGQHclpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYY 171
Cdd:COG0583  81 ELRALRGGPRGTLRIGAPPSLARYL---LPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 172 QPLFREEQNLYCGSAHPFfarADDEPTLGeicaadyvgrgymaenhrphdlrfnqgtdayTMEAIATLVFSGTYIGYLPT 251
Cdd:COG0583 158 RPLGEERLVLVASPDHPL---ARRAPLVN-------------------------------SLEALLAAVAAGLGIALLPR 203

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 15595486 252 HYAATWVAEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSLFEA 301
Cdd:COG0583 204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-301 1.16e-24

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: 98.90  E-value: 1.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   104 LHLGCVDGVIGQHclpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYC 183
Cdd:pfam03466   4 LRIGAPPTLASYL---LPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   184 GSAHPFFARADDEPT--LGEICA---ADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPTHYAATWV 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEdlADEPLIllpPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 15595486   259 AEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSLFEA 301
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
14-73 4.53e-14

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 65.87  E-value: 4.53e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486    14 LRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQ 73
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-298 6.78e-13

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: 66.47  E-value: 6.78e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 104 LHLGCVDgVIGQHCLPlPLaIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYC 183
Cdd:cd05466   2 LRIGASP-SIAAYLLP-PL-LAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 184 GSAHPF-------FARADDEPTLgeICAADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPtHYAAT 256
Cdd:cd05466  79 PPDHPLakrksvtLADLADEPLI--LFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLP-ESAVE 155

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15595486 257 WVAEGRMRAIRPRQLAYDSEFHCITRQGHEERPTLTLFLRSL 298
Cdd:cd05466 156 ELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09986 PRK09986
LysR family transcriptional regulator;
12-177 5.93e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 62.05  E-value: 5.93e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGRDREALHLGCVDGVIGQHCLPlplAIRLFRQRAPEVLLKLHTRRPdELEHAVLEERlQLAVG----AFHHRLS 167
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTALWGRLRP---AMRHFLKENPNVEWLLRELSP-SMQMAALERR-ELDAGiwrmADLEPNP 161

                        170
                 ....*....|
gi 15595486  168 GLYYQPLFRE 177
Cdd:PRK09986 162 GFTSRRLHES 171
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
12-197 2.09e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.80  E-value: 2.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARfRE 91
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ-AL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGRDREALHLGCvdgvigQHCLP-LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLY 170
Cdd:PRK15421  81 QACNEPQQTRLRIAIEC------HSCIQwLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH 154

                        170       180
                 ....*....|....*....|....*..
gi 15595486  171 YQPLFREEQNLYCGSAHPFFARADDEP 197
Cdd:PRK15421 155 YSPMFDYEVRLVLAPDHPLAAKTRITP 181
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 120-296 4.37e-09

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: 55.58  E-value: 4.37e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAV--GAFHHrlSGLYYQPLFREEQNLYCGSAHPFFARadDEP 197
Cdd:cd08420  15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLveGPVDH--PDLIVEPFAEDELVLVVPPDHPLAGR--KEV 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 198 TLGEICAADYVGR--G---------YMAEnHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPTHYAATWVAEGRMRAI 266
Cdd:cd08420  91 TAEELAAEPWILRepGsgtrevferALAE-AGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVAL 169

                       170       180       190
                ....*....|....*....|....*....|
gi 15595486 267 RPRQLAYDSEFHCITRQGHEERPTLTLFLR 296
Cdd:cd08420 170 PVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 12-261 4.81e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 56.23  E-value: 4.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGrdreALHLGcVDGVIGQHCLPLPLAirLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAV--GAFHHrlSGL 169
Cdd:PRK10837  83 LFREDNG----ALRIY-ASSTIGNYILPAMIA--RYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLieGPCHS--PEL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  170 YYQPLFREEQNLYCGSAHPFFARaddEPTLGEICAADYV----GRG------YMAENHRPHdlrFNQGTDAYTMEAIATL 239
Cdd:PRK10837 154 ISEPWLEDELVVFAAPDSPLARG---PVTLEQLAAAPWIlrerGSGtreivdYLLLSHLPR---FELAMELGNSEAIKHA 227

                        250       260
                 ....*....|....*....|..
gi 15595486  240 VFSGTYIGYLPTHYAATWVAEG 261
Cdd:PRK10837 228 VRHGLGISCLSRRVIADQLQAG 249
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 13-144 5.48e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 56.54  E-value: 5.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   13 DLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFREQ 92
Cdd:PRK14997   3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15595486   93 VRGLGGRDREALHLGCVDGVIGQHCLPLplaIRLFRQRAPEVLLKLH--TRRPD 144
Cdd:PRK14997  83 IAALQVEPRGIVKLTCPVTLLHVHIGPM---LAKFMARYPDVSLQLEatNRRVD 133
rbcR CHL00180
LysR transcriptional regulator; Provisional
 14-189 5.48e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.18  E-value: 5.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   14 LRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAA---LGLFSDIARFR 90
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnriLALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   91 EQVRGLggrDREALHLGcVDGVIGQHCLPLPLAirLFRQRAPEVLLKLH---TRRpdeLEHAVLEERLQLAV--GAFHHR 165
Cdd:CHL00180  87 EDLKNL---QRGTLIIG-ASQTTGTYLMPRLIG--LFRQRYPQINVQLQvhsTRR---IAWNVANGQIDIAIvgGEVPTE 157

                        170       180
                 ....*....|....*....|....*
gi 15595486  166 LSG-LYYQPLFREEQNLYCGSAHPF 189
Cdd:CHL00180 158 LKKiLEITPYVEDELALIIPKSHPF 182
PRK09801 PRK09801
LysR family transcriptional regulator;
17-206 1.33e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 55.43  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   17 LRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFREQVRGL 96
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   97 GGRDREALHLGCVDGVIGQHCLPlplAIRLFRQRAPE--VLLKLHTRRPDELEHAV-LEERLQLAVGAFhhrlsglYYQP 173
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAP---AITELMRNYPElqVHFELFDRQIDLVQDNIdLDIRINDEIPDY-------YIAH 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 15595486  174 LFREEQNLYCgsAHPFFARADDEP-TLGEICAAD 206
Cdd:PRK09801 161 LLTKNKRILC--AAPEYLQKYPQPqSLQELSRHD 192
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 120-208 4.27e-08

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: 52.60  E-value: 4.27e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPffaRADDEPTL 199
Cdd:cd08417  15 LPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHP---LAGGPLTL 91


                ....*....
gi 15595486 200 GEICAADYV 208
Cdd:cd08417  92 EDYLAAPHV 100
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 12-188 1.54e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.99  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGRDREALHLGCVDGVIGQHcLPLPLaIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYY 171
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPGTAASS-LTMPL-LQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSS 158

                        170
                 ....*....|....*..
gi 15595486  172 QPLFREEQNLYCGSAHP 188
Cdd:PRK11233 159 QPLLKEDLFLVGTQDCP 175
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 14-255 1.75e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 51.88  E-value: 1.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   14 LRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFREQV 93
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   94 RGLGGRDREALHLGCVDG----VIGqhclplPLaIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGL 169
Cdd:PRK11242  83 HDVADLSRGSLRLAMTPTftayLIG------PL-IDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEI 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  170 YYQPLFREEQNLYCGSAHPFFAR--------ADDEPTLgeICAADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVF 241
Cdd:PRK11242 156 EAQPLFTETLALVVGRHHPLAARrkaltldeLADEPLV--LLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVR 233

                        250
                 ....*....|....
gi 15595486  242 SGTYIGYLPTHYAA 255
Cdd:PRK11242 234 RGRLATLLPAAIAR 247
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 120-208 2.93e-07

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; 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), 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 49.96  E-value: 2.93e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAF--HHRLSGLYYQPLFREEQNLYCGSAHPFFARAddEP 197
Cdd:cd08435  15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLadDEQPPDLASEELADEPLVVVARPGHPLARRA--RL 92

                        90
                ....*....|.
gi 15595486 198 TLGEICAADYV 208
Cdd:cd08435  93 TLADLADYPWV 103
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-158 9.94e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 49.38  E-value: 9.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15595486   92 QVRGLGGRDREaLHLGCVDGVIGQhclPLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLA 158
Cdd:PRK09906  81 RARKIVQEDRQ-LTIGFVPSAEVN---LLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG 143
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 120-194 1.47e-06

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: 47.90  E-value: 1.47e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPFFARAD 194
Cdd:cd08411  16 LPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKS 90
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-298 5.16e-06

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: 46.36  E-value: 5.16e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPFFARadDEPTL 199
Cdd:cd08440  15 LPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARR--RSVTW 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 200 GEICAADYVG-------RGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPThYAATWVAEGRMRAIRPRQLA 272
Cdd:cd08440  93 AELAGYPLIAlgrgsgvRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPA-LALPLADHPGLVARPLTEPV 171

                       170       180
                ....*....|....*....|....*.
gi 15595486 273 YDSEFHCITRQGHEERPTLTLFLRSL 298
Cdd:cd08440 172 VTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 120-298 6.55e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 45.96  E-value: 6.55e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEqnLYCG--SAHPFFARadDEP 197
Cdd:cd08414  15 LPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREP--LVVAlpADHPLAAR--ESV 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 198 TLGE------ICAADYVGRGY---MAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPTHYAATWVAEGRMRAIRP 268
Cdd:cd08414  91 SLADladepfVLFPREPGPGLydqILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQRPGVVYRPLAD 170

                       170       180       190
                ....*....|....*....|....*....|
gi 15595486 269 RQLAydSEFHCITRQgHEERPTLTLFLRSL 298
Cdd:cd08414 171 PPPR--SELALAWRR-DNASPALRAFLELA 197
PRK10341 PRK10341
transcriptional regulator TdcA;
9-178 9.95e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 46.39  E-value: 9.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486    9 INDIDL---RMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSD 85
Cdd:PRK10341   1 MSTILLpktQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   86 IARFREQVRGLGGRDREALHLGcVDGVIGQHClpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAF--H 163
Cdd:PRK10341  81 MKNMVNEINGMSSEAVVDVSFG-FPSLIGFTF--MSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLsnE 157

                        170
                 ....*....|....*
gi 15595486  164 HRLSGLYYQPLFREE 178
Cdd:PRK10341 158 MKLQDLHVEPLFESE 172
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 108-217 1.27e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 45.32  E-value: 1.27e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 108 CVDGVIGQHCLPlPLAIRLfRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAH 187
Cdd:cd08466   5 AANETLDLLLLP-RLLARL-KQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDH 82

                        90       100       110
                ....*....|....*....|....*....|
gi 15595486 188 PffaRADDEPTLGEicaadyvgrgYMAENH 217
Cdd:cd08466  83 P---RIQGSLSLEQ----------YLAEKH 99
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
12-76 1.31e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 46.12  E-value: 1.31e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNgGFQLTEEGQELY 76
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLL 65
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 113-208 5.13e-05

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: 43.33  E-value: 5.13e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 113 IGQHCLpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPffaR 192
Cdd:cd08459   9 IGEMYF-LPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHP---R 84

                        90
                ....*....|....*.
gi 15595486 193 ADDEPTLGEICAADYV 208
Cdd:cd08459  85 IGSTLTLEQFLAARHV 100
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-75 9.73e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.22  E-value: 9.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15595486   11 DIDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNgGFQLTEEGQEL 75
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRL 64
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
14-108 2.19e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.44  E-value: 2.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   14 LRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFREQV 93
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90
                 ....*....|....*
gi 15595486   94 RGLGGRDREALHLGC 108
Cdd:PRK10632  84 YAFNNTPIGTLRIGC 98
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 30-202 3.40e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.57  E-value: 3.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   30 TAAQARLNTSLSRLSVLVRDLEVRLGYSL-CRRGNGGFQLTEEGQELydaaLGLFSDIARFREQVRGLGG--RDREALHL 106
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIfIRRGKRLTGLTEPGKEL----LQIVERMLLDAENLRRLAEqfADRDSGHL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486  107 gCVDGVIGQHCLPLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVL--EERLQLAVGAFhHRLSGLYYQPLFREEQNLYCG 184
Cdd:PRK12683  96 -TVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLngEADIGIATEAL-DREPDLVSFPYYSWHHVVVVP 173

                        170
                 ....*....|....*...
gi 15595486  185 SAHPFFARadDEPTLGEI 202
Cdd:PRK12683 174 KGHPLTGR--ENLTLEAI 189
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 30-153 3.53e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 41.52  E-value: 3.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   30 TAAQARLNTSLSRLSVLVRDLEVRLGYSL-CRRGNGGFQLTEEGQELYDAALGLFSDIARFREQVRGLGGRDREALHLGC 108
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIfIRHGKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 15595486  109 VDGvigQHCLPLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEE 153
Cdd:PRK12682 100 THT---QARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISG 141
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-267 5.27e-04

The 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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 40.28  E-value: 5.27e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLA-VGAFHHRLSGLYYQPLFREEQNLYCGSAHPFFARAddEPT 198
Cdd:cd08436  15 LPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAfVGLPERRPPGLASRELAREPLVAVVAPDHPLAGRR--RVA 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15595486 199 LGEICAADYVGRGYMAENHRPHDLRFNQG----------TDAYTMEAiatLVFSGTYIGYLPTHYAATWvaeGRMRAIR 267
Cdd:cd08436  93 LADLADEPFVDFPPGTGARRQVDRAFAAAgvrrrvafevSDVDLLLD---LVARGLGVALLPASVAARL---PGLAALP 165
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-75 5.29e-04

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 41.33  E-value: 5.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQEL 75
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHL 65
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 112-267 1.89e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 38.90  E-value: 1.89e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 112 VIGQHCLPLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHP--- 188
Cdd:cd08450   7 LPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRlag 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 189 -------------FFARADDEPTLGEICAAdyvgrgYMAEnhrpHDLRFNQGTDAYTMEAIATLVFSGTYIGYLPThYAA 255
Cdd:cd08450  87 rekippqdlagenFISPAPTAPVLQQVIEN------YAAQ----HNIQPNIIQEADNLLSAMSLVASTLGCALLPL-YAN 155

                       170
                ....*....|...
gi 15595486 256 TWVAEG-RMRAIR 267
Cdd:cd08450 156 NLLPPSvVARPLS 168
cbl PRK12679
HTH-type transcriptional regulator Cbl;
36-147 2.33e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.02  E-value: 2.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   36 LNTSLSRLSVLVRDLEVRLGYSL-CRRGNGGFQLTEEGQELYDAALGLFSDIARFREQVRGLGGRDREALHLGCVDGvig 114
Cdd:PRK12679  26 LFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHT--- 102

                         90       100       110
                 ....*....|....*....|....*....|...
gi 15595486  115 QHCLPLPLAIRLFRQRAPEVLLKLHTRRPDELE 147
Cdd:PRK12679 103 QARYSLPEVIKAFRELFPEVRLELIQGTPQEIA 135
PRK09791 PRK09791
LysR family transcriptional regulator;
12-188 2.38e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.97  E-value: 2.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   12 IDLRMLRTFCAIVEAGGFTAAQARLNTSLSRLSVLVRDLEVRLGYSLCRRGNGGFQLTEEGQELYDAALGLFSDIARFRE 91
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486   92 QVRGLGGRDREALHLGcVDGVIGQHClpLPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAV-----GAFHHRL 166
Cdd:PRK09791  85 DIRQRQGQLAGQINIG-MGASIARSL--MPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyyqGPYDHEF 161

                        170       180
                 ....*....|....*....|..
gi 15595486  167 SglyYQPLFREEQNLYCGSAHP 188
Cdd:PRK09791 162 T---FEKLLEKQFAVFCRPGHP 180
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 120-176 3.12e-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: 3.12e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFR 176
Cdd:cd08415  15 LPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLAS 71
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 121-250 3.50e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; 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. The CynR 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 (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.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 38.08  E-value: 3.50e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 121 PLaIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPFfARADDEPTLG 200
Cdd:cd08425  18 PL-IDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPL-AQRRTALTLD 95

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15595486 201 EICA-------ADYVGRGYMAENHRPHDLRFNQGTDAYTMEAIATLVFSGTYIGYLP 250
Cdd:cd08425  96 DLAAeplallsPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILP 152
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 120-208 5.90e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 37.14  E-value: 5.90e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15595486 120 LPLAIRLFRQRAPEVLLKLHTRRPDELEHAVLEERLQLAVGAFHHRLSGLYYQPLFREEQNLYCGSAHPFFARadDEPTL 199
Cdd:cd08412  15 LPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHPLAGK--DEVSL 92


                ....*....
gi 15595486 200 GEICAADYV 208
Cdd:cd08412  93 ADLAAEPLI 101
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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