Conserved Protein Domain Family
PBP2_XapR

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cd08449: PBP2_XapR 
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold.
In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), 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: 176140
View PSSM: cd08449
Aligned: 16 rows
Threshold Bit Score: 241.792
Threshold Setting Gi: 148260160
Created: 13-Oct-2009
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 sequeuce similarity to CatM from Acinetobacter baylyi ADP1

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              #                                                #                        
YP_001473733 103 TINIGLMSSiFWAGFGAALREFKKSYPeYTFNFIELAPqkQKQALIEHrIDIGLARFadtqnihpLSAKLLYAePMCVLV 182 Shewanella sedi...
NP_992364    101 HLNIGIIGSaLWHQLLEKFKHYKTVNPkTTWSLHELPPskQYEALLNKkLDIGFWRCadleqnpaLIYRRVEKqRVAVAV 180 Yersinia pestis...
YP_001480478  82 HMVIGMVGTsVWGGLIPALKRFTWQTAnVTWALNELTPsqQIAALQKRhIDIGVWREakeqvlpgLASQLLAReNIALVL 161 Serratia protea...
YP_918127     92 LLEIGATGSiLRGGLSELLAHFARLHPrITLRVHEQTPaaQITEVLSRrTDVSFNRSvpr--deeLAHEYGWReEMVALV 169 Paracoccus deni...
NP_416900     98 RIELGVVGTaMWGRMRPVMRRFLRENPnVDVLFREKMPamQMALLERReLDAGIWRMatep-ptgFTSLRLHEsAFLVAM 176 Escherichia col...
NP_936260     96 QLDIGLMSSiFWAGFGPAFHALQQLMPhATLNLLELSPekQVRQLLMHqIDLGLVRFadtrdvapLLSECLYQeSMVVAL 175 Vibrio vulnific...
YP_001766584  96 ILNIGMTSSvLAGPAGCLIRAFEQRFRaVDVRIHEMAPtdQIAALKANrTDLSFLRSppe--dpdLVAHMAWPeRLCVAV 173 Methylobacteriu...
NP_437930     92 TLNIATTGSvLLGPLSNLIARFRGAWPgVFVRIHEMDPeaQEAALLSHrTDLSFVRRprn--npdLVAHVAWHeKVGVAL 169 Sinorhizobium m...
NP_945904     92 ILNVGLTGSvLTGPLGRAIQQFALNYPnVDLRIHEMSPdrQVAALKSGqTDVSFLRCppq--daeIASELAWReSVRLVL 169 Rhodopseudomona...
YP_001234287  97 TLDIGMTGAvLLGGLGGLVAAFQIFAPgVQVRLHEMPPgeQEAALGAGrLDLCFLRTpga--dpaLRVEPAWHeGVSAVL 174 Acidiphilium cr...
Feature 1                                ##     #                                                
YP_001473733 183 SDEHPLkrkqslsldeLINEEFVFIDrtnSASTDMIIEVLlesGFYPKVTQEVIEptTLMAVVATStmVSIVPQSyrqhq 262 Shewanella sedi...
NP_992364    181 SNESLLvnkkiltlkdLSGQTLIFLTfnhSGYSKNLYNSClnaGCTPQAIYQFDEpqTQLAFVNSNlgIALVPESmqeip 260 Yersinia pestis...
YP_001480478 162 PQGHPLaqaeslplaaLRHEKFIVLPpheASLGLYLHNLClqqGFKPDIAYQVNEpqTLMALVAEGygITLLPDSygrip 241 Serratia protea...
YP_918127    170 RSDHRLagrtcvsiddLREDQHVVLRpdsSDFAAYVMACIvaaGYRPRVSQQVVDaqSIPSLIVAGfgVSIVPAGiarlt 249 Paracoccus deni...
NP_416900    177 PEEHHLssfstvpleaLRDEYFVTMPp-vYTDWDFLQRVCqqvGFSPVVIREVNEpqTVLAMVSMGigITLIADSyaqmn 255 Escherichia col...
NP_936260    176 PSEHPLaqrgqltlsdLKSADFVMLKqenSSSTRFIVEYCakaGYRPNIVQEVVEpnTLLAVISARqaVSIVPQSyanls 255 Vibrio vulnific...
YP_001766584 174 PREHALaagrsvaidvFRSEPLISLGlesSRFAADIYHACiqrGFTPSISQQVNEasSLINLVAAGfgLAIIPEFvgrar 253 Methylobacteriu...
NP_437930    170 PEHHRMagsetielgdLRKENFVFLRladSRFARYLHDCCvaaGFVPDITNEVVEsySLTSLVAAGlgVALVPECistls 249 Sinorhizobium m...
NP_945904    170 PKGHALsarkv-tladLRDESFVFLRledSLFAKYLWQCCfeaGYAPRVTHQAIEstSLTSLVAAGlgVAIIPEFvskla 248 Rhodopseudomona...
YP_001234287 175 PRDHPLavrrrlaladLRDEPFVFFRradSRFADHLWTCCieaGFAPRIVQEVVEahAVMALVADGfgIALLPDSarrla 254 Acidiphilium cr...
Feature 1                                              
YP_001473733 263 WQNVCFIPLKet-iSADIYAIYHSgsaresVNAFLTAI 299 Shewanella sediminis HAW-EB3
NP_992364    261 WPNIKFIPLKed-lSADLFAVYHPdsvtpaLNKLLALF 297 Yersinia pestis biovar Microtus str. 91001
YP_001480478 242 WPGVRFCPLQqa-pSADLYAIYHAdsatpvVQAFLEML 278 Serratia proteamaculans 568
YP_918127    250 AGPLTFLPIRpnppVSEVFIVYHHrdpapaLQLFLAEI 287 Paracoccus denitrificans PD1222
NP_416900    256 WPGVIFRPLKqr-iPADLYIVYETqqvtpaMVKLLAAL 292 Escherichia coli str. K12 substr. MG1655
NP_936260    256 WPQVRFIPLKqr-iPAGVYALYHPetq-snIKRMLDEL 291 Vibrio vulnificus YJ016
YP_001766584 254 HPDVVVLPIKpsflSADVYALHHTrrn-pvIDNFLALI 290 Methylobacterium radiotolerans JCM 2831
NP_437930    250 RPGVVYRPLAepapEADVYVISRPnpg-pvIAAFLEAA 286 Sinorhizobium meliloti 1021
NP_945904    249 HPDVVYRPIAgppiSADVHALTTAann-plASQFIALV 285 Rhodopseudomonas palustris CGA009
YP_001234287 255 PSGLGFRPLAgnpaRADVSLVYPRehs-avVGEFIGFA 291 Acidiphilium cryptum JF-5

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