Conserved Protein Domain Family
PBP2_DntR_like_4

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cd08463: PBP2_DntR_like_4 
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.
This CD includes an uncharacterized LysR-type transcriptional regulator similar to 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. 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: 176152
View PSSM: cd08463
Aligned: 14 rows
Threshold Bit Score: 304.621
Threshold Setting Gi: 78062890
Created: 30-Sep-2009
Updated: 17-Jan-2013
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              # ##   #                                                          #       
NP_520215    101 TFHLGAPDYLDAFFLPNIIERLRKHAPqARLIVHPlnagvdylAALEQGgmDLVIGNWLSPPehLHISPLFDDEVVCMLG 180 Ralstonia solan...
YP_372798    116 TYRIGCPDYLNVLFVPKLVALFRDRAPsAQLVFHPlgdgfddeRALADGelDVVIDNRPARSsrFRQDDLFDDRVVCLMR 195 Burkholderia sp...
YP_002947323 100 TFTIATPDYLAASFMAEVVARFRAEAPqARLLIHPltpgydyeRALAQGelDIVIGNWPLPPerMHLSLLIEDELVCMMS 179 Variovorax para...
ZP_00053030  101 TFRLAANNCLGSVFLPPLVRTIRRAAPgVTVEVGQtppmedllRQMAEGaiDAVIGNWPQPPshLRISTLLSTDIVCVMR 180 Magnetospirillu...
YP_001858640 101 TFRIAAPDYLNDFFMPTVIAQFRETAPhARLEIESlgplfdhtCALDAGelDLVIGNWPKPDlrFERSDLFSDTVVCMMR 180 Burkholderia ph...
YP_002911178 100 CYRIGCPDYLNVLFVPTVVERFRQAAPnATLEFHSlgpafdyeLALEDGklDIVVGNWPEPPeqLHLSNLFVDKIVCLMS 179 Burkholderia gl...
YP_001234295 100 SFRIGSPDYLNILFVPSLVERFRAAAPhARLELHPltsdadyeESLASGtfDLVLGNWPEPPkrLQRRTLFSDEVVCLLA 179 Acidiphilium cr...
YP_001352203 100 TFHIAAPDYMNTQFFTEVIARLRRESPkSHIVIHAlgpdtdyvRLLSDGelDLVIANWDEMPehLHMSKLFDDPIVCLMR 179 Janthinobacteri...
YP_002232199  99 TFTIAMPDYLAPPFFADLARRFRQHAPnAKLVTLPmgtdydyeKALAEGqvDVVIGNWPTPPehLHMNVLLEDEIVCLMS 178 Burkholderia ce...
YP_001792482 108 EFRIAASDYLDPTFLPTLVARIKHEAPmAQLTIHAlsadydyrARLARGevDLVIGNWLEPPgeLHLGRLFSDEIVCLVG 187 Leptothrix chol...
Feature 1                                           #                                            
NP_520215    181 AQHPLarkgl-----slkhYIEMPHLAPapyavmQRSMIDQALaeqglkRRIQVSLPYFGLVPYVLMRtDLVFTTGRQFA 255 Ralstonia solan...
YP_372798    196 ATHPLarrgt----mtaedFAEAPQLCPtpswleASGAIDKQLervglqRRIVVTLPHFELAAHALVRtDMLLTTTYRLA 271 Burkholderia sp...
YP_002947323 180 PGNPLaapga----mtlqrYLAAAHVVPtpfaksHRAVVDSHLaglrqtRDARVFVPYYAMAPYLVAEsDLVFTTARHFA 255 Variovorax para...
ZP_00053030  181 PNHRLarregr---idladFLAEGHLSPtsdrnaQLSPIDGRLielglkRRIAVTVPEYAMVPYMLAQsDLLFTTGRHFA 257 Magnetospirillu...
YP_001858640 181 ADHPLakapl-----trdaYLAAPHLAPahysgaRGGAIDTGFararasRRIVATLPYFGLVPQVLLQsDLIFTTTRRFA 255 Burkholderia ph...
YP_002911178 180 NTHPFakrgg----ltldqYLNAPHLAPtpysvgQRGAIDVHLarerlkRHVVVTLPYFNLAPYVLVKsDLIFTTTRLFA 255 Burkholderia gl...
YP_001234295 180 ADHPLaqrfraggtiseadYLTAAHLAPtpysptQRGPIESHLtrarlkRNVQILVPYFSLAPPLLLKtDLIFTTTRRFA 259 Acidiphilium cr...
YP_001352203 180 SDCAYakrtakd-amtiedYLSLPHAAPsqilpgYHGTIDTFLekqnlrRNIVVESAHFRMLPYMVEKtDLVLTAGQQFT 258 Janthinobacteri...
YP_002232199 179 KDNPLakpgr----ltaesYIDASHLVPlpysssQRGVVESSLatlrlsRGRQMSCPYFSLAPYLVSEsDLILTTARHFA 254 Burkholderia ce...
YP_001792482 188 QDHAAvrnprs---wtldrYLDAEHVAPtalhagARGVIDEHLqrlgksRRIAVRSPHFALVPLMLAQtQLVLTTGRLFC 264 Leptothrix chol...
Feature 1                              #                        
NP_520215    256 AHcaqyLPVRILPAPVAFPKMRFYQLWHErshaAPDVMWLRRMIGEV 302 Ralstonia solanacearum GMI1000
YP_372798    272 RHyaklLPLAAVALPAEPPDIVYRMTWNEsgecTEGVRWLRGLIAEA 318 Burkholderia sp. 383
YP_002947323 256 EQftrsLPVVSVAAPEGFPRMRFYQLWHErsqhQGAHRWLRSLLSTV 302 Variovorax paradoxus S110
ZP_00053030  258 EQiaqsFAFSLVDAPEELGRMSFYMLWHDckhhSPAHAWLRRTIRSV 304 Magnetospirillum magnetotacticum MS-1
YP_001858640 256 LHyaamLPLAVVDVPIPFPRIKCYQMWHPqpdrPSDIAWLRGLMAQV 302 Burkholderia phymatum STM815
YP_002911178 256 DHyakfLPLSVVPAPLDFPPMQYYQLWHErchySDEVRWLRSLVAEA 302 Burkholderia glumae BGR1
YP_001234295 260 EFharhLPLAVVPSPIDFPAVEYYLLWHPrghlSDEVQWLINLVASA 306 Acidiphilium cryptum JF-5
YP_001352203 259 SFyektLSLKSYTVPIKFPPLRFYQLWHErvhqATEHKWLRAQVCAA 305 Janthinobacterium sp. Marseille
YP_002232199 255 AYyarrLPLLIRPAPFNFPLMRFYVLWHPnkhrSNAHAWLRGLLSDS 301 Burkholderia cenocepacia J2315
YP_001792482 265 QRyvdlLPLRIVRCPVNFPSMTYYQLWHDvshsASSLRWLRETVRDV 311 Leptothrix cholodnii SP-6

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