Conserved Protein Domain Family
PBP2_PnbR

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cd08469: PBP2_PnbR 
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold.
PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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.
Statistics
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PSSM-Id: 176158
View PSSM: cd08469
Aligned: 9 rows
Threshold Bit Score: 265.038
Threshold Setting Gi: 167646649
Created: 13-Jan-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Burkholderia sp. DntR structure (1UTH_A)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                         #        
AAF01443      97 RFVIAANDHVTEVIVAPLSRALRKVAPgVDLVIRPstrldlaEQIDLGrIDIAIGIFsqvpprLNSRTLMDQGESILMCq 176 Ralstonia picke...
YP_001863029  97 KFVVAANDYITSLLLGRLSQRLHAEAPlVDLVVRPstrldlaGQIDVGrIDMAIGIFadvptrLRGTTLWEQTDVVLLHr 176 Burkholderia ph...
AAF01447     103 SFVIAANDYVSATLLPQLNRQLSTAAPgIDLSITPatrldlaEQIDLGrIDVAIGTFrsaperFSTRPVMSQDEVFICSg 182 Pseudomonas sp....
YP_001264124 100 RFSIACGDYVTAVLMPEVIARFRKAAPlAELRIQPvga--vmKELDAGrIDLAMGGFeriperLASEPLFADDMVWVMRa 177 Sphingomonas wi...
YP_002495070 106 QFRLAATDHITAVVAPALMRTFETEAPlASILIRPatridltMQVDLGqIDIVVGIFsqiphrLHARTLFEDRDVLVTAp 185 Methylobacteriu...
YP_001473463 100 HFRIQTHDFILASYLSKAFKRINHEAPnILIDIKIlde-tayDKLDDGeLEMIIGAGlqakprFMQKRLTDENLVCLLDk 178 Shewanella sedi...
YP_001372522  98 SFVVATSDFYIGTLFPAVMERLEKEAPgIRLWLRLfndlnlvEELDRGtLHLVVGAFgripsrFRRETLVSVDNVWIMRk 177 Ochrobactrum an...
YP_002362988  98 TFRIAATDYVAVAILPQLVGRLAEVAPqIDLRIFPfnrtdvvRHLDEGrIDFVMGWFgdlpdrMRRATIVVEKEAMVVRt 177 Methylocella si...
YP_001684312 100 VFHVGASAYLCSVLMPGVVRRIQTEAPgVKLRIRGveg-alaEDLDHGrLDLVIGGFehvaprFAYTPLFKETGVWVIRa 178 Caulobacter sp....
Feature 1                                        #                                               
AAF01443     177 ghpasr----rklkiedLTKYPLVTLsvggqEEGAVGGFIVERGlarqsemfdrraleeallasgeaprlRITVPH-ALA 251 Ralstonia picke...
YP_001863029 177 dhpiag----ravtrddMLAHPLIAIsqggeEEGAVGGFIVERGlarqsemfnrdalnrafddpaetprmRMSVAH-SLA 251 Burkholderia ph...
AAF01447     183 thpign----kalqledLARYPLAVVslggeGEGMLSGFILERGlarqaqmydrnalenalteaglsvrrQIVLPH-FLA 257 Pseudomonas sp....
YP_001264124 178 dspfan----rqptlegLAALPHLAIas-pdNDRAVSGIVSDAGlerrvvrddprildqyfeerglrrtvAMTAPN-PIV 251 Sphingomonas wi...
YP_002495070 186 dhpeag----gatdirtLARDPLMVVtvggtEDGLPDGRLSERGltrqtemfdrdalnrafraaglvprlSVLQPH-FLA 260 Methylobacteriu...
YP_001473463 179 gnpvlk-----nwtpetIFRYPHIKSsllddRDDPVSKYGKAMGlpk---------------------rkIGFLAEtLNF 232 Shewanella sedi...
YP_001372522 178 dhpass----gpltietLGHYPHIDVllsgrAAMEAAGMQEQEGlerafvtsnppflegllrevglsrriGATVSL-ILA 252 Ochrobactrum an...
YP_002362988 178 ghplte----gpltkerLFSFPHIVVeligtEEAAVDGFFDDRGvwrrvwierlli--eadadqgevgrvAVSVPH-YAA 250 Methylocella si...
YP_001684312 179 dhpaaraagageitpriLAGIPCLVVsagheVEEARRGSRRELGlrritswsddy-----alsstggldgPVTVPD-ASS 252 Caulobacter sp....
Feature 1                                                 #                        
AAF01443     252 IPALLREtDMLSIVPASLALAlanrgGLARRAPPYQSRTEIMQAVWHGrdddDVGHAWLREMIAKT 317 Ralstonia pickettii
YP_001863029 252 LPALLRHsDMLALVPSSLGRElqrygELKMCATPYACPDVAVRAVWHErndaDPALQWLRQQLADV 317 Burkholderia phymatum STM815
AAF01447     258 LPMLLEGsELLAIVPHPLARTfartlGFMIKPLPYPVARQQLDMIWHSsndnDSAQRWLRGQISAA 323 Pseudomonas sp. YH102
YP_001264124 252 AMAIVAEcDLAAMMPRNLAEAfadryKLALWKPPHPSALFQISTVWHRwhgdQPAVDWLRAMIRSV 317 Sphingomonas wittichii RW1
YP_002495070 261 VPSLLADsRRVAIVPASLAHGfeaagVARVSMPPWEPRTMAVQMVWHErwrqDPAHAWLREALFRA 326 Methylobacterium nodulans ORS...
YP_001473463 233 QLPLLSDsDLIAFLPDSIAKKgsqvyGLVVKECPFPLPPLTIRAMWHErhqnDVVHQWIREKIEDV 298 Shewanella sediminis HAW-EB3
YP_001372522 253 VPPLVAAtNMIALLPRSVAETykdtyGLVLHEAPYPLPATQINMLSHNtfgaHPAVAWLRSVLREA 318 Ochrobactrum anthropi ATCC 49188
YP_002362988 251 VPPMVRVsDMVATLPSALARAaveqgSLVMLDLPYEPLAVPVEMVWHQrterDEGSQWLLGELISA 316 Methylocella silvestris BL2
YP_001684312 253 ALVMVSQtDMAALLPRRLATLaaergAVVMVEPGRHPEPAQFGAVIRGgeseAGPVAWLLRLVTEV 318 Caulobacter sp. K31

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