Conserved Protein Domain Family
PBP2_CrgA_like_3

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cd08472: PBP2_CrgA_like_3 
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 3. 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: 176161
View PSSM: cd08472
Aligned: 52 rows
Threshold Bit Score: 234.714
Threshold Setting Gi: 226939161
Created: 13-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                   ##   ## ##  #   # #######                                            
NP_251567     91 GRLKVDvpsRVARLLIAPALPEFFRQHPdIELELGSsdrsVDLVQEgvDCVLRVGqlgnssLVARRLGEMQLINCASPAY 170 Pseudomonas aer...
NP_887755     94 GRVAVEmptPVGIHLVIPALHGFTERYPhIHLDIGCservVGLMQEgiDCAIRGGdiadqdLIARRVGQMRFCLCAAPAY 173 Bordetella bron...
NP_644068     92 GRLRVDvpsPLALLILMPALPAFHARYPqIQLDMGVsdrrVDLIGEnvDCVIRGGtitdqsLIARHVGDLQAGVYAAPDY 171 Xanthomonas axo...
NP_396146     92 GKLRVDigsVLANQILIPALPDFQHQYPdIDLMLGVsdrpADLISEgiDCVIRGGalgdssMKARKLCELDYVICASPTY 171 Agrobacterium t...
YP_001524913  92 GRLRVDisaALATMLLIPALPDFHARYPdIQIDLGVtddvVDLLGEnvDCVIRAGqladqsLVARRIGEMHSVLVAAPGY 171 Azorhizobium ca...
ACB13019      92 GRLRVDvpsPLARFVLVPALSGFHARYPdIQIDMGVsdriMDLISDsvDCVIRGGeitdpsLIARLVGELPIKAYAAPGY 171 Hydrogenophaga ...
YP_002239098  92 GHLRIAiggSTACDVLIPLLADFMTAWPdIRIDLQVadkpADLISGniDCAIRGGpmddstLIARKIGEATLVTCATPGY 171 Klebsiella pneu...
NP_670844     92 GKLRVEalvSVARWVIAPSLHEFQARYPnISVRLGGsdriSHLLDNgiDCAIRGGhledssQIARHVCDVHLGLYAAPAY 171 Yersinia pestis...
YP_002281180  92 GKLRVDiggTFANAILIPRLPEFYALYPeIELHLGVterqADIVEEgiDCVIRAGdlssasIVARKLCSVEIVTCATPGY 171 Rhizobium legum...
YP_001676566  92 GRITVDasaWVANAILIPALPRFYDDYPdIQIDLGVsdrpVHLIREnaDCVIRGGhladqtLVGRSLGASRWVTAASPSY 171 Caulobacter sp....
Feature 1                          #                               #####      ##  #              
NP_251567    171 LEEHGEPrtpaDLDRH--WAVNYaspssgrVLPWEYredgrt-ltralrSRVTVNNAesYIACCLSGLGLIQIPaydvRE 247 Pseudomonas aer...
NP_887755    174 LDAHPAIthpaQLARH--RHLGFrfpgtgkRFVATLrkqrds-hpldhpPHVYFNNGtaVTAGAAAGLGIAALPraevRH 250 Bordetella bron...
NP_644068    172 LQRLGTPthptELENTrhRCVGFmrwgsstTVPYVMqrgdea-vrvhgrHVVAADDGnaYLAAGLAGMGVLWLPvymaNA 250 Xanthomonas axo...
NP_396146    172 LDGLQLPerpdDIEKF--RIVSYfsassgkRFPLRFqrgaerseyfptsGGVSVNEStaHLNALLSGLGIGQSFgflaRP 249 Agrobacterium t...
YP_001524913 172 LEAHGTPahplDLETSh-RAVGYfkprmgrSLSLTLskdadeavevngrYMLAVSDSnaYITAAMAGIGIAMMPvfmaRP 250 Azorhizobium ca...
ACB13019     172 LQRHGTPehpkDLEHShhRVVGFlstrngrVPPFSMqlgdgeridvrghHVVAIDDGnaYLAAGLAGLGVLRLPtymaRD 251 Hydrogenophaga ...
YP_002239098 172 LQRCGTPaspdELHHGh-QLISYlspasgrAFPFRFtrhgvs-telktePHLGINESnaHIAAGEAGLGIVQTFtyslKP 249 Klebsiella pneu...
NP_670844    172 LEAAGAVthpqELSVH--RRISWftg-qrnPFIWSLqsasda-felpaeEGLLFDDPdvALASCMAGSGICPGApfavES 247 Yersinia pestis...
YP_002281180 172 LEKYGVPaspsDLQRDh-IFVQYffarslkAAPVRLmkgeek-ieiyspIKLSTSDAtaHLQGILAGLGIGQTFeflaRP 249 Rhizobium legum...
YP_001676566 172 LERYGTPshpsDLGEGh-QLISHqla-sgrTTQFRFerdgke-vkvdgvSRLSVNESnaHLAAGLAGLGVLQSFewklRP 248 Caulobacter sp....
Feature 1                                                     
NP_251567    248 HLQRGELREVlpqwraeAMPAYALYPHrrhlsrrVRAFVDWLEQL 292 Pseudomonas aeruginosa PAO1
NP_887755    251 LLEAGALREIlpdwtltSMPMSVVYPQthqlsarVQVFVQWVAEL 295 Bordetella bronchiseptica RB50
NP_644068    251 HVASGELVPIfqdwqleAMPLSIAFPPnrhvsakLRVFIDWVIAL 295 Xanthomonas axonopodis pv. citri str. 306
NP_396146    250 HFKSGALVELlpdwtpdNHPLHLVYPAdrfpnprLRAFTEWAAKI 294 Agrobacterium tumefaciens str. C58
YP_001524913 251 HIESGALVPVltewrapAKPIYAVFPPsrhlsnrLRVFVDWVAAL 295 Azorhizobium caulinodans ORS 571
ACB13019     252 HVARGELVTLfdewsfePMPLYLAYPPnryvsakLRVFVDWVVSV 296 Hydrogenophaga sp. PL2G6
YP_002239098 250 ALASGKLVEIlaawrpaPYPFHVVYARhrhvpprLRVFIEWLAAV 294 Klebsiella pneumoniae 342
NP_670844    248 WVRAGALVPVlphwrfkARPIHIIYPSnrhlsarVRCFVDWSLEM 292 Yersinia pestis KIM
YP_002281180 250 HIARGTLVPImndwappRYPVHILRPAgrfpsvkYQVFADWVAGV 294 Rhizobium leguminosarum bv. trifolii WSM2304
YP_001676566 249 ALRSGQLVSIlddwrpsTYPFHVLYPPnrfmntrLRVFIDWLVTI 293 Caulobacter sp. K31

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