Conserved Protein Domain Family
PBP2_CrgA_like_7

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cd08476: PBP2_CrgA_like_7 
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 7. 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: 176165
View PSSM: cd08476
Aligned: 21 rows
Threshold Bit Score: 243.691
Threshold Setting Gi: 120611192
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_104042     92 GRLRVSTpiVTYHLLLPVLSEFMSRYPeIELDIDFnDRIVDVIEEGIDVAIRSGelpDSRLVSRPVGPFRMLLCAAPSYL 171 Mesorhizobium l...
YP_556202     91 GRLKVSLp-LVAEPFLSVMAQFKQAYPdVDLDLEFtDRRVDVIDEGFDAVIRSGdapDSRLTARRLGSFSMLLVGSPDYL 169 Burkholderia xe...
YP_367557     92 GRLRVSLpvIGYRFLLPVLPEFRQRYPdVELDLDFnDRMVDVVEGGFDAVIRSGplsDSSLMSRRLGPFAFVLCATPAYL 171 Burkholderia sp...
YP_369147     91 GRLRIGLp-MVGDPFLPVFSAFRQRYPeIELDLDFdNRMADIIEEGYDAVVRSGdvdDSRLTARPLGRFRMMLVGAPDYF 169 Burkholderia sp...
YP_260021     92 GRLRVSLpaIGYRMLLPILPEFSARYPdIELDLDFnDRLIDVIAEGVDAVIRSGelpDSQLKSRNLGPFGFVLVGAPGYF 171 Pseudomonas flu...
YP_001970950  92 GLLRIGLptIGYRFLLPVLPGFQQRYPqVQLELDFnDRIVDVVSEGLDAVIRSGelaDSSLTARRLGGFRFILCAAPGYL 171 Stenotrophomona...
YP_001832581  92 GKLRVSLp-AIGTMLLPVLSEFIQRYPeVELDIDFsDRKVDLIDEGFDAAVRIGetdDTRLLSRQLGVFHRHLVASPDYL 170 Beijerinckia in...
YP_914041     92 GKLRVGLp-QIGIHLMPHLIAFQRTFPeIELELDFsDRLVNLVEEGFDAVMRIGelnDSRLTMRRLDGYHHRLVAAPAYL 170 Paracoccus deni...
YP_002238143  92 GKLRISLpvIGYRLLLPALTAFTRLYPqVELDLDFsDRLVNLIDEGVDVAIRSGelaDSRLIARKLGGFRFVLCASPAYL 171 Klebsiella pneu...
YP_970870     39 GRLRVSV--PAHHLLLPLLPEFLERHPqVELDIDFnVRIVDLIGEGVDIAIRSGdlpDSRLRSQPLRHYRSLLCASPDYL 116 Acidovorax aven...
Feature 1                       #                                                 #####      ##  
NP_104042    172 ERHGTPgepaDLIRHFGINFRFlnsGRLLEWPFitgsa---------------------epqirSKLTCNNMeaLKGATI 230 Mesorhizobium l...
YP_556202    170 ARCGTPetasDLSQHACIQFRYpntGKLQVWPLdqdeit-------------------adlqlsAAIICNNLetRIFFAL 230 Burkholderia xe...
YP_367557    172 AQAGTPrtprDLEAHECVRYCFpttGKLQDWALaaddgt--------------------plklrTALTCNNMeaLRGTVL 231 Burkholderia sp...
YP_369147    170 ARRGTPshprELVEHDCIQFRMpntGKLQTWQLrcdagde------------------pelrlpTAITCNTNeaRMYFAI 231 Burkholderia sp...
YP_260021    172 ARRGTPrtprDLEQHACLRYKFpggSLLQQWSLrlpdga-------------------pplvlgSALTSNNLesLIHAST 232 Pseudomonas flu...
YP_001970950 172 QAHGTPgdvsELRMHTALRFRYpttGKLHPWQLpgiegd-------------------agarlpTAMTCNNMeaVLAAAI 232 Stenotrophomona...
YP_001832581 171 EKVGRPesatELPRHPCLLYRFpttGKIEPWPVpgwesi-------------------lssrelSTVSCNSIetLTYLAL 231 Beijerinckia in...
YP_914041    171 AHRGTPdrpaELMDHACLRYRYpttGKLAPWPLngrgga-------------------psidppQSSVTNSIdsLLEMVQ 231 Paracoccus deni...
YP_002238143 172 AEYGPPdspkELAAHKCIFFRFpstGLIQPWELrdmrlt-------------------gdfraaSVVTVNNIeaAIRLSA 232 Klebsiella pneu...
YP_970870    117 ARRGPPatvgDLADHDGIAFRYpnsGQWLPWPLpgtggatvpeepppplsmssapspsplprlrRVLGFNNMeaVRGAAL 196 Acidovorax aven...
Feature 1        #                                                         
NP_104042    231 AGlGIACMPDFlVREALLDGRLRTVlddh-idgRGQFRMLWPSnrhlsPKVRVFVDFL 287 Mesorhizobium loti MAFF303099
YP_556202    231 QGlGIAYLPDFaIRQHLAAGRLIHVmpsc-seaDTMFRIMWPSgkhfaPRLRVFIDFL 287 Burkholderia xenovorans LB400
YP_367557    232 AGlGIGYMPDFlARDALEHGELVTVlddy-riaPGQFSIVWPSsrqlsPKLRVFVDFL 288 Burkholderia sp. 383
YP_369147    232 TGvGIAYASEFsAKQALEAGQLVTVlddy-taeQNTFQLLWPSgrhvtPRLRAFIDFV 288 Burkholderia sp. 383
YP_260021    233 QGlGIAYVPEFvVCGALADGSLVAVlddy-qqeRGKFSILWPSsrhllPKLRVFVDFL 289 Pseudomonas fluorescens Pf-5
YP_001970950 233 GCmGLAWMPDFlAADALSDGRLQRVlpal-pthQGQFSLLWPGgrhpsARLRVFIDYA 289 Stenotrophomonas maltophilia K279a
YP_001832581 232 EGrGVACLPDFeVKSALADNKLERLlvte-vstPRAMTILWPTskqlaPKLRAFIDLL 288 Beijerinckia indica subsp. indica ATC...
YP_914041    232 AGlGIALLPDFiVADAVAAGRLTVVldrh-gqdRRDFCILWPSsrhtaPKIKAFVDFM 288 Paracoccus denitrificans PD1222
YP_002238143 233 AGmGIAYVPDFvVREAMDEGQLQEVlpgc-cikDGHFSVLWPAsrylsPRIRCFIDFM 289 Klebsiella pneumoniae 342
YP_970870    197 GGlGIGCMPDFlLEGPLREGALRQVlpdpegrpAGRFRAVWPTsrqlsPKVRVFVDFL 254 Acidovorax avenae subsp. citrulli AAC...

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