Conserved Protein Domain Family
PBP2_CrgA_like_8

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cd08477: PBP2_CrgA_like_8 
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 8. 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: 176166
View PSSM: cd08477
Aligned: 23 rows
Threshold Bit Score: 284.123
Threshold Setting Gi: 145301009
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                   ##   ## ##  #   # #######                                            
NP_900786     92 GVLRVNASiTFGTLRLAPLLAEFMARWPdIGVELELsdqlADLVADGYDAVFRIGrla-dsgMVARRLRPYRMMIAASPA 170 Chromobacterium...
YP_002800242  92 GKLKISAPvTFGSYSLMPFVTEFLRQHPeVEIDLHLtdrfVDLVEEGYEVTFRIGpla-assLTAKPLAPYRLVACAAPS 170 Azotobacter vin...
YP_190956     92 GTLRVTAPvTYGTQSVTPCLARYLAENPsVDVDLVLtersVDLTHEKFDIAIRLGvpe-pssLMCRRLTDYRMTLCASPE 170 Gluconobacter o...
NP_792426     92 GTLRITAPlTFGSELLAPALVGFSQRFPdVKLDLVLtnqrLDMIDNGFDVAIRLGnlaqsspLIARPLQDYTLTICAAPD 171 Pseudomonas syr...
YP_001972870  92 GRLRISAPvTFGVHALGPAVVAYMQQYPdVQVDLNLsnslVDIVEDGYDLVFRTGdla-dsgLVARRLGPYPLVLCASPD 170 Stenotrophomona...
YP_002892836  92 GKLRINASvTFGVHALTPKIAEYMQLYPeVSVELCLsnryIDLIDEGFDAIFRIGels-dsgLIARQLRPYRLILCASPR 170 Tolumonas auens...
NP_102086     92 GLLRVNAAvSFGAHCVTPVVARYLSSHPsVDVDLVLndrfVDLIDDGFEAVFRIGplg-esnLGAIELAPFQTIACGSPA 170 Mesorhizobium l...
YP_002546082  92 GRLRVSAPvTFGINALAPKLPEYLKAYPeVSIDLSLsnrlVDLIDEGYDAIFRVGels-dsgLIARRLDPYRLIICAAPR 170 Agrobacterium r...
YP_002238652  92 GKLRVGCPvSFGVHALSPVTAQFLIEWTdMAVDLVLsdksMDMADEGLDVMIKIGellhvntLVARPIAPYRSVMCASPA 171 Klebsiella pneu...
YP_003066510  92 GELRINAPfSFGVHSLSPLLPIYMAENPeVSVRLTLsdrvVDLVDEGYDCVFRAGvlh-dsaLIARGLRPLRLIACASPT 170 Methylobacteriu...
Feature 1                         #                                   #####      ##  #           
NP_900786    171 YLAARGTPatPADLADHDCLGFsrw------rrDDGWEAlaqlhg--vrmraSRFQCNQGqaLRQLALSGaGIALQAeaL 242 Chromobacterium...
YP_002800242 171 YLTDRGVPqiPGDLKNHECLGYayws----rpaDREWVFckgsav-ervqvvGRLQVNESkaLLSAALDGfGIVLGPedF 245 Azotobacter vin...
YP_190956    171 YLDRREELlvPQQLATHDALAFaytssspwhwaRHEWHFespkgr-vtvemrRRGLFNSTqaMRRAALGGlGIAMLPtdL 249 Gluconobacter o...
NP_792426    172 YLARHSAPtrPEDLRAHNCLAFaypagdewrtaGTQWRMtgpege-vlvdvdGSMVANTSagLYQAARAGmGVVMLPdaL 250 Pseudomonas syr...
YP_001972870 171 YLASRPAIthPNDLSRHECLGFahs------iiRTRWSFrdadgsvltvpvsSRFMVNQAepLLTAAVGGlGLILQPyeM 244 Stenotrophomona...
YP_002892836 171 YMETHEPLltPDDLTRHECLGFsht------elRTTWTFdgpdgh-ktvqvkGRLMSDSGeaIVCAGLCGaGIMLQPseL 243 Tolumonas auens...
NP_102086    171 YLKERGMPsiVSDLVNHECLLFgnwp----eptFSDWLFvrdglt-skasvhGRLKVNNPasLLEAALAGfGLALIGeeA 245 Mesorhizobium l...
YP_002546082 171 YLESRGTPrtPGDLVDHECLIFsht------rlRTHWAFegpdgy-vdvpisGRLTVDSGeaLLQAAVAGlGIIFQPleL 243 Agrobacterium r...
YP_002238652 172 YIKRAGEPitPEELCHHRCLGFahp------iaANEWTLqregkp-vrapvnITMTCNNGeaLRRAALNGlGIIMQPeiL 244 Klebsiella pneu...
YP_003066510 171 YLAHHTQPkcPDDLARHTCLGFags------alEERWTFygdgge-tivpivSRFSTNSGeaLRQAALAGlGIVLHAeeL 243 Methylobacteriu...
Feature 1                                                     
NP_900786    243 LAEDVAAGRLVSLLdgylpdPKPMHLIYPAdrqplpkLRVFVDFI 287 Chromobacterium violaceum ATCC 12472
YP_002800242 246 LEPALRSGELVRLLadyeapSRQMHLLYTAnrqktakLRRFIDAA 290 Azotobacter vinelandii AvOP
YP_190956    250 VQDDLKAGTLQALLpdytlpSRPIYLLYHKerysaptLHSFIRFI 294 Gluconobacter oxydans 621H
NP_792426    251 VQRDLQEGRLVALLpdyhlpRRPMNLLYVQdryrlpkLRSFVEFA 295 Pseudomonas syringae pv. tomato str. DC3000
YP_001972870 245 LAAALARGELVEVLpdhvpvSTWINLVYPRdrqltpkLRSFLDFC 289 Stenotrophomonas maltophilia K279a
YP_002892836 244 VTPYLQSGQLVEILpeykapTRPMHLVHTPdrrmtpkLRSFVDFI 288 Tolumonas auensis DSM 9187
NP_102086    246 VRTHLATGRLVRVLpnyetpPRPIHLLFHPdrrqtpkLKTFIEMV 290 Mesorhizobium loti MAFF303099
YP_002546082 244 IRASIESGQLVPILpeyripTRPLHVLYAPdrritpkLRSFLDYV 288 Agrobacterium radiobacter K84
YP_002238652 245 LAEDLQHGRLLPLMsefqplAKPVHILTFAnrqqlpkIRLYVDFL 289 Klebsiella pneumoniae 342
YP_003066510 244 LADDVATGRLVHILpew-rsERPLHVLYSPdrritpkLRSFLDFA 287 Methylobacterium extorquens DM4

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