Conserved Protein Domain Family
PBP2_LysR

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cd08456: PBP2_LysR 
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold.
LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. 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: 176145
View PSSM: cd08456
Aligned: 7 rows
Threshold Bit Score: 305.497
Threshold Setting Gi: 187921186
Created: 26-Jan-2010
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                       ## ##  #   # #######                                             
CAQ33165      95 ELSIACLpvFSQSFLPQLLQPFLARYPdVSLNIVPqesplLEEWLSAQRHDLGLTEtlht--pagTERTELLSlDEVCVL 172 Escherichia col...
NP_883232     92 RLHIAVApaLSHGFLASAVTAFTQRHPrVTLSIRTcnsymVEQLVNSQLCDLGLAAfighvtepgLETERIASiRGVCLL 171 Bordetella para...
YP_001890218  96 QLTVGVLqaLSGSFINRVVKSFLRIHPdVMITIHTrdspfLAEWLSTQQIDVGLISsivd--npyIERDTLIEhPLICVL 173 Burkholderia ph...
YP_617457     93 TLRIAALpaLAVSFLPRVIAAFRETHPgVTVQLQTrssstVRQWMANQQFDIGLATpare--lpgIRMERFLRcPGACVL 170 Sphingopyxis al...
NP_311723     95 ELSIACLpvFSQSFLPQLLQPFLVRYPdVSLNIVPqesplLEEWLSAQRHDLGLTEtlht--pagTERTELLSlDELCVL 172 Escherichia col...
YP_002008530  92 TLRIGTVpsIAMSVMPQAILAFRERYPdVPIAVHTndsptVAKWTAARFCDIGLVSymae--ttgIRSELLRReDGVCIV 169 Cupriavidus tai...
YP_551196     93 ELRIAAVstIAFGLLPRAIKRFAQDHPeVGISIHMghssvISQWVDSHFCDLGIVSqlsr-qdisTEPDVLYRiDGVCLM 171 Polaromonas sp....
Feature 1                                                        ######     ## ##                
CAQ33165     173 PPGHPLavkkvltpddFQGENYISLSrtdsYRQLLDQLFtehqvkrrmIVETHSaaSVCAMVRAGvGVSVVNPLtaldya 252 Escherichia col...
NP_883232    172 PQAHRLasrdvihardLEGEPFVSIArqngSREHVDSLFekakvtrkiEVEAENasTICHLVAQGlGVSVLNAViaedfr 251 Bordetella para...
YP_001890218 174 PPGHHLcskpvidisdLNEEDFITFPestlTRQRVDALFeqnavrpriVMQASTapTICEAVAAGiGVSLVHPLftdg-v 252 Burkholderia ph...
YP_617457    171 PAGHRLavkdvirpadLEGEPFISLAledgVRHRIDRIFedagvhremVIETQYamTICALVMQGvGCSILNPVtaadya 250 Sphingopyxis al...
NP_311723    173 PPGHPLavkkvltpddFQGENYISLSrtdsYRQLLDQLFtehqvkrrmIVETHSaaSVCAMVRAGvGVSVVNPLtaldya 252 Escherichia col...
YP_002008530 170 PATHRLarkrrlhasdLDGERFISLThgdgTRATVDAAFvpad-rrvlTLETPYaaTICTMVGMGlGVSVVNPLvvrslk 248 Cupriavidus tai...
YP_551196    172 PENHRLaekkrltpmdLEGETFISSAkpdeLRKSVDRIFdqagvkriiNIETSYssIIWSLVGLGmGISIVNPLavqdyr 251 Polaromonas sp....
Feature 1                                              
CAQ33165     253 asGLVVRRFSiavPFTVSLIRPLhrpssaLVQAFSGHL 290 Escherichia coli BL21(DE3)
NP_883232    252 chGLVVREFRpaiHFPITLLRSShrprslLVAAFIDCL 289 Bordetella parapertussis 12822
YP_001890218 253 keRLVLRRFTpstPFSFQLCRNRssnnvqLVDDFLREA 290 Burkholderia phytofirmans PsJN
YP_617457    251 erGLTVRDFApevHFEYMLFTPKlrpmsqVAAAFIAVL 288 Sphingopyxis alaskensis RB2256
NP_311723    253 asGLVVRRFSiavPFTVSLIRPLhrpssaLVQAFSEHL 290 Escherichia coli O157:H7 str. Sakai
YP_002008530 249 paGVKAIPFEpviAFESHILFNPqrpvpaLAQWFLACL 286 Cupriavidus taiwanensis
YP_551196    252 saPVVTRPFDpalPYEGILIIPKgrpanrLVAKFSEVL 289 Polaromonas sp. JS666

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