1IZ1,1IXC


Conserved Protein Domain Family
PBP2_Chlorocatechol

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cd08446: PBP2_Chlorocatechol 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold.
This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137
View PSSM: cd08446
Aligned: 21 rows
Threshold Bit Score: 254.128
Threshold Setting Gi: 44937741
Created: 23-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putativedimerization
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Acinetobacter baylyi CatM structure (3GLB_A)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1               #                                                #                       
1IZ1_A        91 GELSVAYFGtPIYRSLPLLLRAFLTSTPtATVSLTHmtkdEQVEGLLAGtIHVGFSRFFPrhpgIEIVNIAQeDLYLAVH 170 Cupriavidus nec...
CAD60253      27 GQLDVAFFGsPVYLAVPVALRAFQRALPeTEISLTRmgkqEQINALRDGrIHIGFARFYPvepdITVEKVADeRLFAAIP 106 Defluvibacter l...
YP_002894072  91 GILDVGVYGsASLNTIPALLSIFSEKHPdVEIRLHNahrsIQLEALRQRrVLIAFDRYRPedtdLAVELVSQePLIVAFK 170 Tolumonas auens...
BAB62046      91 GQLDVGLFGsGVLDVIPRILARFHEERPeVKIVLHNltkdAQLQALRERrISVGFNRLVPqeadISIETVLHePLVVALA 170 Pseudomonas putida
YP_002800224  91 GRLDIATFGsGILDTIPKLLLAFRKNYPdVKVVLHTmnknEQIEALLQRrISLGFNRLLTptpgIASELVTNeSLLLAIN 170 Azotobacter vin...
YP_001564149  91 GDLDIGIFGsGMLNVIPRLIGSFHTQRPeVRIRLHNltkgEQIQALREHrIQVGFHRLPPaepdLAVRLVLRePMYVGMH 170 Delftia acidovo...
AAX47248      91 GQLDVGLFGsGVLDVIPRILARFHEERPeVKIVLHNltkdAQLQALRERrISVGFNRLVPqeadISIETVLHePLVVALA 170 Delftia tsuruha...
AAC38250      94 GALAVGYFGsTIFGLVPRLLRLFLDTRPeVRIVIERatrdMQAQAIRDGrMHIGFSRQYPaepdLAVRNIASePLYVALP 173 Rhodococcus opacus
YP_933339     91 GRLDVAIFGsAILDRIPKLILNFRNEYPdVNVVLHTmtkaEQISALRQNrITVGFNRMLAplpdIRSEVIATeSLLLAVN 170 Azoarcus sp. BH72
YP_002798075  91 GSLVIGIFGsSILDFIPRVLLEFGRTHPaVEISLHPmdkdAQIQALRERrLTIGFNRLVPgepdIEQELVRReALMLALP 170 Azotobacter vin...
Feature 1                               ##      #                                                
1IZ1_A       171 RSQsgkfgKTCKLadLRAVELTLFPrggrPSFADEVIGLFkhaGIEPRIARVVEDAt-AALALTMAGaASSIVPASvaaI 249 Cupriavidus nec...
CAD60253     107 QDLalasgSEVTMadVATLPLVLFPsgdrPSFADAVLAAFaemAITPPVHSTAVDTt-AGLALTASGkRCSIVPESvaaL 185 Defluvibacter l...
YP_002894072 171 QNHplaakEIVSIedLRNEPMSMPAal-nTLTVNAALNLCrahGFEPRLVNEATDVitGLVTLASSQhGVALIPASvatL 249 Tolumonas auens...
BAB62046     171 ASHplavrPSLRLsdLEGMPLILYPnvplRGLAQEVTDAFraeGIPPRVEQEVQDVv-TAVALVAGGfGCCITTRSatsL 249 Pseudomonas putida
YP_002800224 171 KNDplskaSEVSLqsLADHPFILFPtgsrPSFIDKTVGLCqqaGFTPQVSQEVEDVv-TAISLVASGfGICLVSETtsvL 249 Azotobacter vin...
YP_001564149 171 EGHplstrAGISIrdLERQPMILYPntplAGLAQEVVAAFrreKVQIEVMQEVEDVt-TCIALVSAGlGLCITPESgtmL 249 Delftia acidovo...
AAX47248     171 ASHplavrPSLRLsdLEGMPLILYPnvplRGLAQEVTDAFraeGIPPRVEQEVQDVv-TAVALVAGGfGCCITTRSatsL 249 Delftia tsuruha...
AAC38250     174 ETHpllskQKVLLadIQNEPLVLFPsaprPGFADEVVQLLmrtGGEPRIEAEASDVv-TALAYVAIAqLCAVVPRSasnI 252 Rhodococcus opacus
YP_933339    171 LNDplaaqPALPFdvLARRPVILFPsgarPNFVDKVLALCearGFLPEVAQEVGDAv-TGVALVASGfGVCMVPESattL 249 Azoarcus sp. BH72
YP_002798075 171 AKHplaarDAIELgeVLQEPFILYPrgvrRGLTTHVRRLFadyDALPRVAQEVTDVt-TSIALVAGGlGLCVVPRSavnL 249 Azotobacter vin...
Feature 1                                                  
1IZ1_A       250 RWPDIAFARIVgt--rvKVPISCIFRKek-qpPILARFVEHV 288 Cupriavidus necator
CAD60253     186 RFPTLRFLPIAdc--piRAQIACAYSSer-kaPILEHFLNCL 224 Defluvibacter lusatiensis
YP_002894072 250 QIPGLVFRPLKetr-eiFMELNCFYLKde-asPLLRELLQVV 289 Tolumonas auensis DSM 9187
BAB62046     250 RLPGVTYRPLRsrh-lsDIELSCLYRSdvgagARPAVFAGLP 290 Pseudomonas putida
YP_002800224 250 AFPGVVYRPLAhlpenaHIDLSCIFRAdd-gsPLLAAFLNEI 290 Azotobacter vinelandii AvOP
YP_001564149 250 RLPGVVFRPLRsrf-lkDIELSCVHRRdd-tsALLAAFMEVV 289 Delftia acidovorans SPH-1
AAX47248     250 RLPGVTYRPLRsrh-lsDIELSCLYRSdd-psPVLGAFLDVV 289 Delftia tsuruhatensis
AAC38250     253 ALPGVVYVPLAda---pPESLSCIYRAie-tpTLVRAFLDHL 290 Rhodococcus opacus
YP_933339    250 QYPGVVYLPFEdapaeaRVDLSCIYRAdd-hsPILSTFLASI 290 Azoarcus sp. BH72
YP_002798075 250 RLPGVEYRALRcrg-kaEIELACLYRKgd-gsPLLRAFLATV 289 Azotobacter vinelandii AvOP

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