Conserved Protein Domain Family
PBP2_CrgA_like_4

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cd08473: PBP2_CrgA_like_4 
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 4. 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: 176162
View PSSM: cd08473
Aligned: 31 rows
Threshold Bit Score: 256.714
Threshold Setting Gi: 167621768
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                     ##   ## ##  #   # #######                                          
CAM74539      90 PQGLIRLScpvALAQSKVGPIIARFLADHPrVRVHLEAtnrrVDVIEEgfDLAIRVRmppledsgLIIKVLERHQGYLVG 169 Magnetospirillu...
YP_573832     90 PQGTVRLScspSVLHYLITPLLVRFMARCPkVEVQVEAtsrrVDVIKEgfDLAIRVRfppledsdLTMKVLASSPQRLMA 169 Chromohalobacte...
YP_348093    103 PGGVLRVTcptTLLEECVGGIITRFMAMHPrVEMHLEAsdrqVDVVAEgvDLALRVRppplqdseLVSRVLSQRPQCLVA 182 Pseudomonas flu...
NP_251107     95 PCGMVRLTcstPLLHFELAPMLARFMAQYPnVELYVKTfnrrVDVIAEgyDISLSLRfppledsdLVMKVLARSPQVLVA 174 Pseudomonas aer...
YP_002288796  90 PRGVIRVScpvALLSFQFGDLIARFMAKHPaVEVHLEStnrhVDVIAEgfDIAIRVRfpplnptdLVMRKLDESTQCLVA 169 Oligotropha car...
YP_002490381  90 PTGTLRVScpiALAQARVSEIVARFMIAHPgVSVRFIAtnrtVDLIEEgiDVALRVRfppleesdLVMRVLSDSTQAIVG 169 Methylobacteriu...
NP_455441     92 PRGIVKLTcpvTLLHVHIGPMLAKFMARYPdVSLQLEAtnrrVDVVGEgvDVAIRVRprpfedsdLVMRVLADRGHRLFA 171 Salmonella ente...
YP_001713639  91 PCGVIRVScppAWLYDHIADMISKFMRLYPqVNIHLEVtnknIDLLNDgiDIALRIRfppledsdQVMKIFAKNPQCIVG 170 Acinetobacter b...
NP_747350     90 PRGLVRIScptTLLNSWVGPMLTRYMLKYPqVELFIEStnrrVDLLHEgfDIALRVRfpplentdMVMKVLSNSTQCLVG 169 Pseudomonas put...
NP_522223     90 PQGTVRMScptALLEYRIAGLVAQFMVEYPrVQVHLEAtnrrVDVMGErlDLALRVRfppledsdLVMRVLSDSQQRLVA 169 Ralstonia solan...
Feature 1                            #                               #####      ##  #            
CAM74539     170 APDLLDRLgrpqspdQLSALPSLGMtragdRHSWQLvdaageg--ievahqPRLVTDDMvaLRHAARAGiGIVQLPslmV 247 Magnetospirillu...
YP_573832    170 APSLFAERprprspaDLVELPSLDFeqydhRHCWDLvgpngas--aqvphwPRLVTDSAetLHAAALEGlGVVKLGllvG 247 Chromohalobacte...
YP_348093    183 SPALLSRLgepsepeDLSRFPSAHHgspqqVYSWTLfhqdgse--ftlqhrPQLITKGLpmLRCAAIDSvGVAQMPmslV 260 Pseudomonas flu...
NP_251107    175 SPELLARYrppelpaDLSAMPYVGWersrlDGSLRLvgadgss--aalnlrPQLLSDDLgtLRQAVLEGvGIGGLPlcvV 252 Pseudomonas aer...
YP_002288796 170 SPGLISASlqs--paDLHGLPSLDLgpayeGHHWQLeaadgqt--asvphrPRLVTDDMavLRQAAIEGvGIVQLPtmmI 245 Oligotropha car...
YP_002490381 170 APALLDRLgrpsapeALAGMDALDLirqdrNHVWHLthqdgrs--vaipfaPRLVSDDMltLRQAAREGvGVVRLPtylV 247 Methylobacteriu...
NP_455441    172 SPDLIARMgipsapaELSHWPGLSLasgkhIHRWELygpqgar--aevhftPRMITTDMlaLREAAMAGvGLVQLPvlmV 249 Salmonella ente...
YP_001713639 171 HCELVQQHgmpetplDLCGYPSIGLgnseqKSIWTLysrengk-iekvihtPRLIVNDMigVRDAVLRGvGIAQLPfalI 249 Acinetobacter b...
NP_747350    170 QPQYLAQLpkgfdpqLLGTLPSVHWgsaqrEYQWELfqgednsrsiviphtPRMVTDDLfaLRHFVVAGvGIAHLPrvaV 249 Pseudomonas put...
NP_522223    170 CPAFLEGRalpkhpaDLAGMPTLDWgp-prDHVWHLvgpqgme--aqvrhqPRYVTDDMtaLRRAAQQGvGIVQLPcmvV 246 Ralstonia solan...
Feature 1                                                    
CAM74539     248 AEDLRAGVLEKILTAWtppRGLIHAVYPSRRGlvPAVRLFLDAL 291 Magnetospirillum gryphiswaldense MSR-1
YP_573832    248 ARDIQEGRLIDVLPGWeprGGILHAAFPSRRGllPAVRALLDFL 291 Chromohalobacter salexigens DSM 3043
YP_348093    261 HDFIERGQLAVVLPDWaprTEMIYAVFASRQGmlPSLRMLIDFM 304 Pseudomonas fluorescens PfO-1
NP_251107    253 SRDLAERRLVRVLPEWtpvEGMVVAMFPSRRGllPSVRALIDFL 296 Pseudomonas aeruginosa PAO1
YP_002288796 246 WQDIEAGRLVPVLPQWrprAGIIHAVFPSRRGllPSVRAFLDFL 289 Oligotropha carboxidovorans OM5
YP_002490381 248 QAALDKGDLEAVLPAWtprSGIIHAVLPSRRGlaRATRLFVDSL 291 Methylobacterium nodulans ORS 2060
NP_455441    250 KEQLAAGELVAVLEEWeprREVIHAVFPSRRGllPSVRALVDFL 293 Salmonella enterica subsp. enterica serovar Typhi s...
YP_001713639 250 YKEIERGELINLMPNWelkNSIMHAVYPSRKGllPSVRALLDFL 293 Acinetobacter baumannii AYE
NP_747350    250 REDLAAGRLVELIPDWhprCGIVHAIFPSRRGllPSVRALIDHL 293 Pseudomonas putida KT2440
NP_522223    247 EADLRNGTLVDILPGWapkGGIIHAVFPSRRGlvPKVRLLIDYL 290 Ralstonia solanacearum GMI1000

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