Conserved Protein Domain Family
PBP2_LysR_opines_like

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cd08415: PBP2_LysR_opines_like 
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.
Statistics
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PSSM-Id: 176107
View PSSM: cd08415
Aligned: 45 rows
Threshold Bit Score: 173.517
Threshold Setting Gi: 13475849
Created: 21-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on sequence similarity to the known structures of LysR-type transcriptional regulators.
  • Comment:most members of the LysR family of transcriptional regulators are tetrameric, while CrgA assembles into octameric rings

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                    ## ##  #   # #######                                             
P35112     93 SLRVACYtapalSFMSGVIQTFIADRPdVSVYLDTvpsqtVLELVSLQHYDLGISIlagdypgLTTEPVPSfRAVCLLPP 172 Agrobacterium tume...
YP_996215  94 TLNIASSpclsrGLIPQAITRFVWRYPnIRVNYHTtllnsMAQEVLSNQVDLAISVlplahpnLTMQPFAEgRMVCVVPF 173 Verminephrobacter ...
NP_891252  94 ILNLVASpslgqMLIPAAIAQYRQAHPqVKLSFHHltqapLTERLLKRQADLALTIlpaghpnLEQEEIGAaRMVLICPP 173 Bordetella bronchi...
YP_373768  94 HLRIACSpnlgqSLLPRAIAAFYERFPdVRIILHTmipsvLLQAVLTQQVELGIAFlqdthpnVESQRLYEnRMVAAVPA 173 Burkholderia sp. 383
YP_725897  94 SLRLTCSpnlgqTVLPRAIASFRAAHPaVRVVVRTqipgnMLRALLSGQVDLAVSNmplvhpnLEARLLVKnAIVALVPV 173 Ralstonia eutropha...
YP_582854  92 RLRVAATpslanPLLVPAVRRFCARHPeTQVQVLThhtseIVEALLANQIDVGFAFspprheaITSEPVAAgRMLLAVPR 171 Ralstonia metallid...
YP_918728 108 LLRLGASlpvawSVLPPALARFRASHPeVRIHLHTlpkqeIAEALRTGAIDLAVTLspilaptVRTQTLAPiPLAVLMPQ 187 Paracoccus denitri...
NP_438034  94 ELALGSVpsianAMMPQAIAGLMRRYPdIRINFDIlrieeAIDYLLLGKGELVAMSyhlthpsITFEPLSKgHLVCIAAR 173 Sinorhizobium meli...
NP_879945  94 ELKLCSSpslalNFLPPVIARYVNEHPrVRLKYHTtllsdMAHELLGRKVELAVSVlpidnpnLVVEPFATgHMVCILPQ 173 Bordetella pertuss...
NP_886952  98 VLRLTSIpslaqYLVPRAVARFQRTHAdILLRLNAtalphLINDVLHGEAELGLVVmqadhpfLTSLPLHTgRMVAAIPR 177 Bordetella bronchi...
Feature 1                                                      ######     ## ##               
P35112    173 GHRLedket---vhatdLEGESLICLSpvslLRMQTDAALdscgvhcnrRIESSLalNLCDLVSRGmGVGIVDPFtadyy 249 Agrobacterium tume...
YP_996215 174 GHELaqlat---vsiadLARYTLIVHHptipFGQLVSAAFrkagvtlesRIDIHQtdVACSLVRSGaGIAMVDQFtvegi 250 Verminephrobacter ...
NP_891252 174 GHPLagrep---vgaeaLAPYPLVAYErgsaFGQKLQAWFdaqsvaarpVIEVGSpqNACALVQAGaGVALVDEFsarsw 250 Bordetella bronchi...
YP_373768 174 SHPFarrkt---lavrdLADQPLIGYGsdipLGQLVRRLFsdeglvpqvKIEVQQahVACALAQAGtGIALIDELtvagp 250 Burkholderia sp. 383
YP_725897 174 DHRLatrtw---vrpaeLVGEDLIGYGpdvpFGLLVREMFgsegnqpdmRVQVEQahVARALAQAGaGIALVDAMtvfgq 250 Ralstonia eutropha...
YP_582854 172 PQALpsggrrgivsirkLMERPFIGYDddssLGLLVRQTLarhalephsTLEVQTysLALALVDAGlGVTLLDQYtalsa 251 Ralstonia metallid...
YP_918728 188 GHALaglda---vapgdLAGQPLISYGshaeIGPALDQAFraeglvrqvAIQVASsvAAVPLVRAGlGVALVDGLvdwa- 263 Paracoccus denitri...
NP_438034 174 EHPIagrsr---isareIAEHPLIGIDprdpYGAIMAGIFerekleyrtPIRARFgtTVCALVKRNlGIAVIDAFtvggm 250 Sinorhizobium meli...
NP_879945 174 GHALarqds---vglaeLARNRLVLYSrnipFGQLVAAAFqranvpwraTVDIVRaeLACALVRSGvGVAIVDEFsvagg 250 Bordetella pertuss...
NP_886952 178 SHPLaergq---vtladLSPHPHIVVGtrmpYGMLVQSAFeqaglpcrmCADVPWsqLACALVNAGaGIAIVDEFtvmqn 254 Bordetella bronchi...
Feature 1                                            
P35112    250 sanPVIQRSFDpvvPYHFAIVLPTdsppprLVSEFRAAL 288 Agrobacterium tumefaciens (strain T37)
YP_996215 251 awtDLQVLPLAdeiRLVPSIVRSVfdtrktHADKFIELL 289 Verminephrobacter eiseniae EF01-2
NP_891252 251 pgaGFVMRPVRdlaPLTAYLLRLReepashLMQSFIETL 289 Bordetella bronchiseptica RB50
YP_373768 251 vwpQIVVKPIVptiAAPVSVLHPVlaplsrLAHEFIDTL 289 Burkholderia sp. 383
YP_725897 251 swpNIVAVPIRtkvNASVQIFHVQteplsrLSLEFVDTL 289 Ralstonia eutropha H16
YP_582854 252 npaNVALHDVQpelPFEIQMLRAThrgkssLVDDMRTQF 290 Ralstonia metallidurans CH34
YP_918728 264 dmaGLAMRPFRprlAMGLALATDGarpiprLAQALIALL 302 Paracoccus denitrificans PD1222
NP_438034 251 adqGLAVIPISedtEFQTYVAYRAdaalssYAERLVTTL 289 Sinorhizobium meliloti 1021
NP_879945 251 gwpGIEVRPLRepiPLALSLVRSRferpgrQAQRFVKLL 289 Bordetella pertussis Tohama I
NP_886952 255 iwpEIAIVPLAediPLHISAVHANnrplsrIAAEFIPHL 293 Bordetella bronchiseptica RB50

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