Conserved Protein Domain Family
PBP2_CrgA_like_1

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cd08470: PBP2_CrgA_like_1 
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain.
This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. 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: 176159
View PSSM: cd08470
Aligned: 12 rows
Threshold Bit Score: 342.753
Threshold Setting Gi: 16126756
Created: 30-Sep-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                   ##   ## ##  #   # #######                                            
YP_573040     92 GTLRLTCatTFGERYIAPLVNDFQCRHPqLEIDMHFtnrrVELVEEgFDVAIRMGvlrdssLIARRLCERREYVVGSPAY 171 Chromohalobacte...
YP_001261684  91 GEVRLTCstALGERFVAPIVRRFIETHPrLSVRLELtnrlVDLVSEgFDVAIRTGhptdhrLAARQIASRPAEVCASPAY 170 Sphingomonas wi...
NP_720480     92 GLLKITApvTYGEKTLVPLVNDFIAKYPeLEVKINLtnqkVDLIDDgYDLAIRLGqlkdssIMAKRLGSRTQYVCASPDY 171 Shewanella onei...
NP_900411     92 GQLKLTAplAYGHSHISPLVLDFMQRYPlLEVSLDLsnqvKDLVHEgYDLAIRIGrltdssLMARKLAQRRHHVCASPDY 171 Chromobacterium...
NP_421320     92 GLLRMTCstAYGERFVVPAVNRFMLSHPkLALEIDLddavRDIVSEgFDLAIRFGrltdsrLIAKRLASRTRRLCAAPSY 171 Caulobacter cre...
NP_252320     92 GLLRMTCavAYGERFIVPLVNAFMADYPqLRVDIELsnrqLDLLHEgFDLAIRLGrlsdsrLVATRLAPRVMYLCATPEY 171 Pseudomonas aer...
NP_759343     94 GKLRITApvTYGEQKIAPLLNDFLIRYPkIDLELVLtnqkLDLIEQgVDIAVRLGqledssSMARRLSDRHLHVCATPEY 173 Vibrio vulnific...
YP_935124     99 GLLRMTCavTYGERFIVPLVNDFIERYPeLRVEIELtnamLDIVREgYDLAIRLGrltdssLVATRIAPRVMYLCAAPSY 178 Azoarcus sp. BH72
YP_003061234  91 GELRVTCsmSMGERFIAPILLRYAEQFPnVSVSIHLtnriIDLTSEgFDLAIRTGylddskLVVTRIASRRLILCAAPEY 170 Hirschia baltic...
YP_156153     92 GLIRITApvYYGERFIAPLLNDFLHIYPeCRLDFQLtneqVDLIEGsYDVAIRLGqlgnprLRARKLGSRRHFVVGSPAY 171 Idiomarina loih...
YP_925887     91 GLIRMTApvTYGEQYVMPIVLAYMQQFPqVEVQCELtnqqLDLVQGgFDLAIRLGvlpdssMMARKLAERVQYLVASPDY 170 Shewanella amaz...
YP_496152     92 GQLRITCptALGERFVAPIVRAYVQEYPkLSVDLDMsnrvVELVSEgYDLAIRTGtlpdsrLIRTQIATRGIVTCAAPSY 171 Novosphingobium...
Feature 1                        #                        #####      ##  #                       
YP_573040    172 FERAapphslaELPHHNCLRGsRDSWLFeinghrrevrvdGRWRANSGpaLLDAVLKGlGLAQLPDYYVTPHLARGELVP 251 Chromohalobacte...
YP_001261684 171 LARAghprglaDLDRHECLIGtSVNWHFledgqrrsfvpsGRWRCNSGnaVVDAALAGmGICQLPSFYVRDHIAAGRLVA 250 Sphingomonas wi...
NP_720480    172 VSTFgiphslsELEQHNCLLGtLDYWRFqengktrnvrvkGNLTCNSGyaLVDAAIKGiGIIQLPEYYVLPFLEDGQLVP 251 Shewanella onei...
NP_900411    172 LARCgeprrpqDLQRHQCLQIgNEGWHLqvngrrqsvrvqGRMRCSTAapLAEAAVRGmGLAQLPDYYVSAYLESGALVE 251 Chromobacterium...
NP_421320    172 LTRAgaprsiaDLAAHTCILGaADTWPFrdgereiafkpqGRWRCNSGqaVLDAALLGlGVCQLPNFYVDAAISDGRLVP 251 Caulobacter cre...
NP_252320    172 LRRHgtpqspaELGQFNCLIGsSDLWSFledgretqhrvqGNWRCNSGqaVLDAALRGfGLCQLPDYYVIEHLRSGRLAS 251 Pseudomonas aer...
NP_759343    174 FEQHgmphtlsDLSSHNCLIGtHDHWRFkenhqgrsikvnGRIRCSSGvvLLDAALKGiGLVQLPDYYVDEHLHAGRLIE 253 Vibrio vulnific...
YP_935124    179 LARRgtpqtlaELAGHDCLLGsADTWVFqdqgrehflrvqGNWRCNSGeaVLDAALRGfGLAQLPDYYVLEHLREGRLRA 258 Azoarcus sp. BH72
YP_003061234 171 LEKHgridsiaDLENHNCLAGtSTHWRFkvdgsevswlpkGRWRCNSGvaVRDAALSGmGLCQLPEFYVADYLKSGKLVH 250 Hirschia baltic...
YP_156153    172 FEEFgrpqdinALDAHRCFTGtVRQWRFqvegkletvrpeSYLHCNNGlaLRDAAMKGlGLAMLPDYYVTDSLANGQLEE 251 Idiomarina loih...
YP_925887    171 VSRHgaphslsELSRHQCLLGsLPFWRFqeegklrslkvkGRLSCSSGntLLAAALAGmGIAQLPGYYVDEAIRDGRLLV 250 Shewanella amaz...
YP_496152    172 LEERgtpqtvdDLLGHECIPAtSDVWRYrvdgeqrtirprGRWRCSNGaaVFDAAVAGmGLCQLPAFYVNRAIAAGQLVP 251 Novosphingobium...
Feature 1                                             
YP_573040    252 VLtayqftDTAVWAIYPRhrhLSPKVRQFVDFLVDHL 288 Chromohalobacter salexigens DSM 3043
YP_001261684 251 LLedyrdrPEPVWAVYPQrraLLPKIQQVIAALEAEL 287 Sphingomonas wittichii RW1
NP_720480    252 LLeqnrqpKEGIWALYPHnrhLSPKVRMLLDYLSEAL 288 Shewanella oneidensis MR-1
NP_900411    252 VLadyaepEEGIWALYPHnrqLSPKVRLLVDFLADSL 288 Chromobacterium violaceum ATCC 12472
NP_421320    252 LLeanrpeDEGVWAVYPHlrlLPAKVRLLVEHLEEAL 288 Caulobacter crescentus CB15
NP_252320    252 LLeghqppNTAVWALYPQqrhLSPKVRQLVDYLKEGL 288 Pseudomonas aeruginosa PAO1
NP_759343    254 VLahfrddREGVWALYPHnrhLSPKVRLLVDHLAQHL 290 Vibrio vulnificus CMCP6
YP_935124    259 LLtayqppHTAVWALFPQqryLSPKVRMMVEHLRVAL 295 Azoarcus sp. BH72
YP_003061234 251 VLetesrvFEPIWAVCPErrhLLPKVTRLLDLLKSDK 287 Hirschia baltica ATCC 49814
YP_156153    252 VLadyrqpDDGIWALYPEnrqVIPKVRVLLDYLSGNL 288 Idiomarina loihiensis L2TR
YP_925887    251 LLkpfqepKEGIWGLYPHnrqLSPKIGHLMNMLADKL 287 Shewanella amazonensis SB2B
YP_496152    252 VLdefrpeDDPIWAVYPQrrhLLPKVQRLIEKLRREL 288 Novosphingobium aromaticivorans DSM 12444

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