Conserved Protein Domain Family
PBP2_CrgA_like_9

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cd08479: PBP2_CrgA_like_9 
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 9. 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: 176168
View PSSM: cd08479
Aligned: 25 rows
Threshold Bit Score: 271.778
Threshold Setting Gi: 118472966
Created: 15-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                   ##   ## ##  #   # #######                                            
CAM74068      14 GLLRINagfGFGRRHLGPAMADFVALYPqVEGQLHLsdrpLDLAAEgvDVGIRFGlgp---dsgLLARKIASNRRLLCAA 90  Magnetospirillu...
YP_284362     90 GLLRIHatfGFGRRQLAPAVSEFVRQHPaVDIQLTLsdqpVTPGEQgfDIAIRFGepp---earVVARQIASNQRYLFAS 166 Dechloromonas a...
YP_549880     91 GLIRLAatfGFGRLWLGPALADFQERYPrIEIQLQLteqlPDLAEGgfDGAIWLWevegrqaaqWVSRRLARNQRVLVAS 170 Polaromonas sp....
YP_551590     93 GTLHVRgplGFGRQHLAGALADFHSQHPkLVVALTLsdvpPAADADrfDLIVHIGdla---nssMVAYPIAPNTRILCAS 169 Polaromonas sp....
YP_785200     94 GQLRVLaplGFGQRHIAPLVGRFQQQYPeVTATLMLsdrpQRLDAHhwDVLIHIGelr---dssLIMHRLARNRRILCAA 170 Bordetella aviu...
YP_001166086  92 GHLRVAapyGFGRRHVSPVVEAFAKANPaTTITLDLsdnpVRQVTEswDIVVHIGslp---esdRLVTTLAQNRRILCAS 168 Novosphingobium...
YP_001766711  92 GHLRVVaplGFGRRHVAPVVTAFRLRHPgVRIDLLLsdrlGRIPSEtwDLAIHVGeire-atpsLTVRALAPNDRILCAA 170 Methylobacteriu...
NP_793415     92 GTLRLAapfGYGRQRIAPLLARFAKLHPqLSLHLDLre-tPWPDRHdsDAVIHIGnln---dslWIARPLAQNHRWLCAS 167 Pseudomonas syr...
NP_882798     92 GTLRVAapfGYGRRHIAPVLARLAQRHPeLRVQLDLre-tPWPDHQdaDAVVHIGavr---dssWVTRRLADNERWLCAS 167 Bordetella para...
NP_356690     92 GHLQVAapfGFGRLYIAPAMAQLREQHPeVKLTLSLfedpVSLRSDawNVLIHVGplt---dssLIVHRLAPNRRILCAA 168 Agrobacterium t...
Feature 1                           #                                        #####      ##  #    
CAM74068      91 PAYLRQHPAParpaDLSRHHCIVIRENdr----aFNTWRLvsdsg-------pasiKVTGPLSANHGevAVEWALKGhGV 159 Magnetospirillu...
YP_284362    167 PAYLARRGQPltldELVNHDCIVIREGtg----aFGTWTLcsgkq-------crniKVSGKLSSNHGevAVDWALDGhGI 235 Dechloromonas a...
YP_549880    171 PRYIRQHGAPasleDLQRHTCLIVRENgnatgqrFDVWPLhkerek-----tparvRVRGPLSSNSGelVRDWCVEGrGI 245 Polaromonas sp....
YP_551590    170 PDYLARHAPPqrpeDLTGHQCLVLRENee----dVSLWRFrkgrt-------daavRIAPAMSSNDGdvTRQWALAGkGI 238 Polaromonas sp....
YP_785200    171 PAYLKRQGTPaspeDLHHHDCIALRENde----dVTLWRLgnhdg------rratvRIEPRLASNDGgvALQWALSGlGI 240 Bordetella aviu...
YP_001166086 169 PDYIESHEPIrtpeDLAAHSCLSLRENne----dVTLWRFthask------grvtvRARPAMSSNDGeiVRDWARAGlGI 238 Novosphingobium...
YP_001766711 171 PAYLARHPAPrvpvDLRDHTCIALRENde----dVTLWRFraadg------aearvRVDAGLVSNDGdvVRGWALAGlGV 240 Methylobacteriu...
NP_793415    168 PAYLEQHGVPsmpdELASHRCICIRENde----dVTLWHLskgha-------kktlRIEPALLSNDGsvARRWAEQGlGI 236 Pseudomonas syr...
NP_882798    168 PQYLQDHGMPreprDLLHHRCICIRENde----dASLWRFrradagaagrkaaetvRIAPAYVSNDGnvARAWAEQGlGL 243 Bordetella para...
NP_356690    169 PSYLERHGVPdrpeTLNQHACAVIREDha----dVTLWRFshqek------ppltlRIQPAMSSNDGevIKQWALAGlGI 238 Agrobacterium t...
Feature 1                                                             
CAM74068     160 LLRSEWDiAPYLRSGELVRILPhwsgeEADIHAVYLQrhh-lsaKIRVFIDFL 211 Magnetospirillum gryphiswaldense MSR-1
YP_284362    236 LLRSLWDtATDLRAGRLVRVLPewsgsPADIYALYPQrln-lsaKVRVFLDFL 287 Dechloromonas aromatica RCB
YP_549880    246 MLRSLWDiAPQLASGELVRVLPgyampDADIHWLAPFrpd-sprRIRLLVDFL 297 Polaromonas sp. JS666
YP_551590    239 IMRSEWDvAEHLAAGRLVRLLDgwrlpDADIVALIPQrhg-vsaRVKLFLAFL 290 Polaromonas sp. JS666
YP_785200    241 LARSEWDvAEALRDGKLLEILPgwrlpDADIVALVSSrks-rsaRTERFLEQL 292 Bordetella avium 197N
YP_001166086 239 MVRSEWDvAADIAAGTLREILPdwsapSADVVALLHArhg-rsrRTAVFLELL 290 Novosphingobium aromaticivorans DSM 12444
YP_001766711 241 IVRSEWDvADDLRAGRLTRLLEgyalpSAPVVALLGSqrrsraaRTERFLEAL 293 Methylobacterium radiotolerans JCM 2831
NP_793415    237 VLRSQWDvSDAIASGNLVRVLAdwqlaSAPINLLVPVrkh-rsaRVQALTEFL 288 Pseudomonas syringae pv. tomato str. DC3000
NP_882798    244 VVRSQWDaEGAVARGALVRVMPqwqldSAPVMLLVPGrkg-rsaRVKALLECF 295 Bordetella parapertussis 12822
NP_356690    239 IIRSEWDvAEDLRRGRLVALLPdwqlpDADVVALLDNrsg-rvaRTVCFLQIL 290 Agrobacterium tumefaciens str. C58

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