Conserved Protein Domain Family
PBP2_CrgA_like_6

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cd08475: PBP2_CrgA_like_6 
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold.
This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural 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: 176164
View PSSM: cd08475
Aligned: 34 rows
Threshold Bit Score: 238.609
Threshold Setting Gi: 190572834
Created: 14-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on sequence similarity to Neisseria meningitidis CrgA

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                   ##   ## ##  #   # #######                                            
YP_634909     93 GRLRVSAPvMFGRHCAAPLLRELVLQHPgLELEIAFsDRMVDLVEEgYDLALRVAplad-hagLTARRLGVQTMSVCAAP 171 Myxococcus xant...
YP_788957     95 GRIRLDLPaSYGRLHVLPVVLDFARRHAlLVPHISFsDDFIDPVSQgIDILVRIGgpdiwpetLGHRYLGAQRLVFCAAP 174 Pseudomonas aer...
YP_002873759  95 GRVRIDLPsALGRAQVLPVLLPFLQAHPlLLAHFTFgDGFIEPFEEgVDIVVRIGgtnawpetVGQRVLAHEWHSLYASP 174 Pseudomonas flu...
YP_001750027  95 GRVRIDLPaSYGKLRVLPLLIEFIAEHElLMPHITLtDRFVDPIEHdIDILVRIGgpqtwpqgVERRLIGIQQHIFCAAP 174 Pseudomonas put...
YP_002892842  98 GNIKIDMPaAFGRAVMMPILLGIEEQFPeLKLTLTFnDKIIDPIEEgIDLCIRFGevkd-stdLVAKKLGYQRLVMCASP 176 Tolumonas auens...
NP_992356     95 GRLRVDLPaAFGRQRILPILLDIIRLYPeLALTVTFsERFVDLIEEgIDLVIRIGelad-ssgLVARRLTTQKLVICASP 173 Yersinia pestis...
YP_001973667  94 GRLRIDMPsSFGRLVVLPVLLRLCRQYPdLQLTMTFtDHFVDPIEEgIDLLIRFGglhq-aehLVARRLGRQRLVTCASP 172 Stenotrophomona...
YP_001479359  98 GTVRIDMPaSFGRNLMMPVLIEMMTRYPaLRLALTFnDRLIDPVEEgVDLVLRLGelqs-tdeLIARRLSRQRLILCASP 176 Serratia protea...
YP_236017     95 GRLRIDIPvAFGRRVVAPLLFEIANKYPaLQLNMTFsDHLVDPIEEgIDLLVRFGelkd-tsgLVARRLARQRWAICAAP 173 Pseudomonas syr...
YP_001789865  94 GRLHIDMPvAFGRRVLLPVLIEITRPHPdLSLTLTFtDATSDLLQEdVDLAIRFGaltd-ssdLVARRLVTQERVICASP 172 Leptothrix chol...
Feature 1                           #                               #####      ##  #             
YP_634909    172 GYLKRHGrpktleDLGEH-DAVVYgrn-gvNKPWRFpdgqgg-eqriavQARLRFDDVetIMDAAVQGaGLAWLPRWLiA 248 Myxococcus xant...
YP_788957    175 AYLAAHGeprdveELAAH-DCVLYgqgdglTTPWNFpghqpgelerrvmPTRIAIGDGegVVQALLAShGIGQLPTWLvS 253 Pseudomonas aer...
YP_002873759 175 VYLSRHGtplsehDLEHH-QCIAYgwvdgrTSPWNFadeqga-prrrqiTPQLVVGNGdgLLMAALAGcGIVQLPSWMvQ 252 Pseudomonas flu...
YP_001750027 175 GYLQRRGvpeterDLHEH-GCVLYgrtdggVYPLHFpgahasdseqrvvSGRIAIGNAegQLAMVLAGlGVAQLPSWLvQ 253 Pseudomonas put...
YP_002892842 177 DYLQRFGtpadldDLKKH-RCIMGyrk-gsPLSWLVkdkhgn-dvrfnpTPTHQISDGdaMIQACLAGsGLTQFPESLlT 253 Tolumonas auens...
NP_992356    174 DYLLYHGepvstdELSQH-QCVVGfrr-sqPISWLLkesdgq-isrfapPPTHEFGDGdaMLAATLAGgGLSQLPLWLvG 250 Yersinia pestis...
YP_001973667 173 EYLQAHGvprtveELAQHrSIVGFrh--gqPVWWRIgseede--gtfipNAPYQLNDGdaVIEAAIAGlGICQMPVSLvR 248 Stenotrophomona...
YP_001479359 177 AYLERHGlpadieDLKSH-YCVMGyrr-gaPLAWRLrkager-evkfisATAHQISDGdaMIQACLAGvGIAQFPESMvN 253 Serratia protea...
YP_236017    174 SYLARFGvpdtleDLNRH-HCIVGhrr-gqPLSWRVnedqet--vryapPSAHQIGDGeaMILAAVAGvGLCQMPRCLfK 249 Pseudomonas syr...
YP_001789865 173 EYLRMHGepmtlaDVRAH-RCIVGslk-gpPLVWFVsdggav--erftpPATHRLSDGeaMMDAAIGGlGIVQLPISLvR 248 Leptothrix chol...
Feature 1                                                   
YP_634909    249 EHLSSGRLVEVletqrpyGNEIYAVWPQskhltskVRAAIDLL 291 Myxococcus xanthus DK 1622
YP_788957    254 RHLESGRLREVlpqlasdGLSINLAWQKrrenlpkVGALLDVL 296 Pseudomonas aeruginosa UCBPP-PA14
YP_002873759 253 QPLQEGTLVEVlphlatqGAAITLGWVKsrqalpkVRVVLEAL 295 Pseudomonas fluorescens SBW25
YP_001750027 254 EHLDAGTLVQIlpelstiGLPINVAWLKsrqslpkVGALVDVI 296 Pseudomonas putida W619
YP_002892842 254 QHIKEGKLRIVlkecipaPIELNVIWPKtrhllpnVRYIVDEL 296 Tolumonas auensis DSM 9187
NP_992356    251 KYLESGELREVlpghsggEMPISALWPKnrqllpkIRYVVDTL 293 Yersinia pestis biovar Microtus str. 91001
YP_001973667 249 RHLDSGALRSVldahmqrHIDIHALWPPtrhlrpkVRYVVDEL 291 Stenotrophomonas maltophilia K279a
YP_001479359 254 SHIAAGSLISLmadhapiPVELNVIWPRtrhliprVRLIVDEL 296 Serratia proteamaculans 568
YP_236017    250 DDIDAGRLVEVlagyepePVEVHAVWPRvshlrpkVRYVVDEL 292 Pseudomonas syringae pv. syringae B728a
YP_001789865 249 EPLADGSLRSIlpahsavGVEVHAVWPRqrhlsprVRYVVDQL 291 Leptothrix cholodnii SP-6

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