3HHF,3HHG


Conserved Protein Domain Family
PBP2_CrgA

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cd08478: PBP2_CrgA 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain.
This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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 further 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: 176167
View PSSM: cd08478
Aligned: 10 rows
Threshold Bit Score: 328.914
Threshold Setting Gi: 34496154
Created: 14-Oct-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
dimerizationputative
Conserved site includes 24 residues -Click on image for an interactive view with Cn3D
Feature 1:dimerization interface [polypeptide binding site]
Evidence:
  • Comment:CrgA shows the assembly of the protein into an octameric ring-like structure.
  • Structure:3HHG_A; interface at a dimeric unit of Neisseria meningitidis CrgA, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                     ##   ## ##  #   # #######                                          
3HHF_B         5 PQGVLSVDsaxPXVLHLLAPLAAKFNERYPhIRLSLVSsegyINLIERkvDIALRAGelddsgLRARHLFDSRFRVIASP 84  Neisseria menin...
3HHG_A        91 PQGVLSVDsamPMVLHLLAPLAAKFNERYPhIRLSLVSsegyINLIERkvDIALRAGelddsgLRARHLFDSRFRVIASP 170 Neisseria menin...
YP_001474440  80 PSGTLRVNgasPVLVHLVCPIIKKYLQLYPdVNIELQNseeiIDIIESkaDIALRVApitessYHVTHIGSSKRRLLASS 159 Shewanella sedi...
YP_001280080  91 PSGKLRIDaatPFMLHVIAPLMTKYSQAYPqIDIELVSnenlVDLLEErtDVAIRIGelkdstLNATPLGLSQIRILASP 170 Psychrobacter s...
NP_718045     91 PRGRLRVDaasPFVFHQLVPLIRPFKQTYPdIELELTSnegfVDLLEKktDLAIRIGnltdstLHARPLGKSLLYIVASP 170 Shewanella onei...
ABO13827      91 TAGLIRVDsatPFVLHVIAPLMHKFRECYPdIEIELNSndqvIDLLQHktDVAFRFGelndssLHAKLVCKSRLYIVASP 170 Acinetobacter b...
NP_900369     90 PSGLVRVNaaiPVLDHLLAPHLAGFQARYPdIRLELAGaeavVDLIEEraDLAIRVGpladstLNARLLCESPLRIVAAP 169 Chromobacterium...
NP_414744     91 PRGLLRIDaatPVVLHFLMPLIKPFRERYPeVTLSLVSsetiINLIERkvDVAIRAGtltdssLRARPLFNSYRKIIASP 170 Escherichia col...
NP_885165     95 PAGRLRVDaatPFMLHVLVPLIAGFHARYPeVELELNSnegiVDLIEKrtDVAFRIGvlkdstLHARAVGTSRLRVLASP 174 Bordetella para...
NP_250550     91 PAGRLRINaasPFMLHAVVPHIGEFRRLYPdIQLELNTndliIDLLEQrtDVAIRIGalsdstLHARPLGASRLHILASP 170 Pseudomonas aer...
Feature 1                          #                           #####      ##  #                  
3HHF_B        85 EYLAKHGTPqsteELAGHQCLGFtePGSLNTWAVldaqgnpykisPHFTASSGEILRSLCLSGcGIVCLSDFlvDNDIAE 164 Neisseria menin...
3HHG_A       171 EYLAKHGTPqsteELAGHQCLGFtePGSLNTWAVldaqgnpykisPHFTASSGEILRSLCLSGcGIVCLSDFlvDNDIAE 250 Neisseria menin...
YP_001474440 160 EYLRRYGFPssieDLKNHILLGLegPSILNTWPIedgkgkklkicPRVVASSGEVLRKLTLSGaGIACISDFmtKSDRNN 239 Shewanella sedi...
YP_001280080 171 AYLQRQGTPqsveDLAHHQLLGFnaLPKLNDWPIydafnnlfhaqTNIKADSGETLRQLALCGtGIVCLSDFmtQQDIKE 250 Psychrobacter s...
NP_718045    171 DYLSRRGFPnkssDLIHHDSLGFstPKTLNDWPLkgft----rltPTLTSSNGETLRQLALTGnGIACLSGFmvKKDIAE 246 Shewanella onei...
ABO13827     171 DYLALKGTPtqpeELEQHDLIGFtkPTYINSWPIkvgde-yffaqSKIKASSGETVRQLTIRGhGIARLSEFeiWKDMEE 249 Acinetobacter b...
NP_900369    170 DYLRRHGRPrtaaDLQAHRQLGFtsPASLNLWPLgang---lkvnPSPAASSGATLRALALHGcGIACLADFlvGPDIAA 246 Chromobacterium...
NP_414744    171 DYISRYGKPetidDLKQHICLGFtePASLNTWPIarsdgqlhevkYGLSSNSGETLKQLCLSGnGIACLSDYmiDKEIAR 250 Escherichia col...
NP_885165    175 AYLERRGAPtrtaQLAQHALLGFtqPETLNDWPLrdadgtvlrirPTIASSSGETLRHMALAGlGIVCLSDFmtGEDRRA 254 Bordetella para...
NP_250550    171 EYLARHGTPasieGLRGHTLLGFtqPEHLNRWPVvhadgdrleiqPDISASSGETLRQLALSHqGIACLASFmtDRDIQD 250 Pseudomonas aer...
Feature 1                                                 
3HHF_B       165 GKLIPLLaeqt--sdkTHPFNAVYYSdkavnlRLRVFLDFL 203 Neisseria meningitidis serogroup B
3HHG_A       251 GKLIPLLaeqt--sdkTHPFNAVYYSdkavnlRLRVFLDFL 289 Neisseria meningitidis serogroup B
YP_001474440 240 GKLIEVLkeqt--vhdKRDISAVCYRgtspsaKVSTFIDFL 278 Shewanella sediminis HAW-EB3
YP_001280080 251 GRLIELFasst--ikmQQPINLVYYKnrklsqRVSSFIDFM 289 Psychrobacter sp. PRwf-1
NP_718045    247 GRLIPLLesekisnsgREHINAVYYKsstvakRISAFIDFI 287 Shewanella oneidensis MR-1
ABO13827     250 GRLIALFedki--ehqYQSIHAVYYQqehlpkRIRLFIEFL 288 Acinetobacter baumannii ATCC 17978
NP_900369    247 GRLEAVRlpeq--rdwKQPIWAVFYKqgrplpRIACLVDYL 285 Chromobacterium violaceum ATCC 12472
NP_414744    251 GELVELMadkv--lpvEMPFSAVYYSdravstRIRAFIDFL 289 Escherichia coli str. K12 substr. MG1655
NP_885165    255 GALVQLFarqt--ldvRQPVNAVYYRntalaaRITCFVDHV 293 Bordetella parapertussis 12822
NP_250550    251 GRLVPLFaeqm--seyRQPIHAVYYRnsqlalRIQCFLDFI 289 Pseudomonas aeruginosa PAO1

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