Conserved Protein Domain Family
PBP2_CrgA_like_10

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cd08480: PBP2_CrgA_like_10 
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 10. 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: 176169
View PSSM: cd08480
Aligned: 10 rows
Threshold Bit Score: 313.889
Threshold Setting Gi: 13473471
Created: 15-Jan-2010
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_105038     96 GRLRVNtyvPFGVHRLIPLLPRFLERYSeISVDLVLTdsvIDLMAErADVAIRAGplgesrLVARKLGQSLVVVVAAPSY 175 Mesorhizobium l...
YP_001984768  90 GRLRINttiPFGTMFVAPVIPDFIARNPdLIVDLSFTdgiVDLVAEkTDVAIRMGdlpdsgLIARKLGQSRRVVCASADY 169 Rhizobium etli ...
YP_002944795  96 GRVSINasvSFGHHKLVPLVPRLLELHPqITLDIALTdriVDLMDErADIAIRWGqlppsdLVARRLGETSQSIVASPGY 175 Variovorax para...
NP_744679     94 GRLRVSaalGHARLTVVPLLAAFSARYPqVLVDLTLSdevADILGGqADVALRFGhlpdssLSARAIGETGQVVVASPEY 173 Pseudomonas put...
NP_356363     94 GLLRVNasvGFGERFLLPLIPAFLELYPeVQLDISLTdgiIGLIEErTDIAIRSGamddssLKARKLLESRRVIIASPSY 173 Agrobacterium t...
YP_003067180 104 GRLRVNasvPYGTHVILPVLPRFLAAYPrMSLDLALTdevIDLPATqADVAIRIGplrdtrLRARSLGRSRMVVVAAPSY 183 Methylobacteriu...
YP_551041     96 GRVSVNasmPTGHHLLLPLVPAFHARFPdILLDISLTdrvVDLLDErADVAIRWGalassqLVARRLGDTAQVIVGAPAY 175 Polaromonas sp....
NP_773603     93 GTIRVNttvSFGIFGLEPLLPAFWQAHPeIVVDISLSdeiVDMYLDrTDVAFRVGplqasaMVARRIGVVKRRIVASPDY 172 Bradyrhizobium ...
YP_002798860  93 GTVRVNasvGFGTWGIEPLLPAFWEAHPdILVDLSLSddlVDLYLErTDIAFRVGaladstLRARKIGVAWRRMVAAPAY 172 Azotobacter vin...
NP_251814     96 GRLRVNanvPFGHHFLLPLVPEFLAQHPeVTLDIVLTdevVDILEQrTDVAVRAGplksssLVARKLGSTRMLIVGAPAY 175 Pseudomonas aer...
Feature 1                        #                              #####      ##  #                 
NP_105038    176 LEAHGKPltpaDLDGHNLMGFgfvrhIDGWPFvdaeg-ravmvPITGNTLVSDGeaMRLMTLAGaGISRLARWHvAADIA 254 Mesorhizobium l...
YP_001984768 170 LVRCGSPvkpaDLEHHDCLTFnfrraRPSWPFrcggq--dvaqPVKGSIVVNNGetMKQMALAGaGIARVGLFHvADEIA 247 Rhizobium etli ...
YP_002944795 176 LAKYGTPrtpqELEAHNRLGWsyrrnTPDWPLrvdgr--miavPVAGPVRAGDGetLRQLAIAGaGVARLSLYHvQHDID 253 Variovorax para...
NP_744679    174 LQRYGTPlepeDLARHNCLRFnfrraMPDWPFhrdgh--tfslKVKGNIECSSGeaLAQLARLGaGVARIGTFTvADDLA 251 Pseudomonas put...
NP_356363    174 IKRHGMPqtpaDLAAHNCFSFnfrrsLNEWPFrdpgsteiyrlPVSGNSSVNSGmiMRRLCLAGsGLGRVGQFHvQPDID 253 Agrobacterium t...
YP_003067180 184 LAREGVPdhpdDLARYNCLNFsfrrsLDTWPFragsa--vsqrPIQGNFFGNSGevVRLMALGGaGIARLARFHvAADLS 261 Methylobacteriu...
YP_551041    176 LARHGTPqtmqELAAHQRLGHnykrnAPYWPLrvngq--lqqlPIAGYARVSDGeaLRHLALAGaGLARMSVFHiQADIK 253 Polaromonas sp....
NP_773603    173 INRLGEPkrvqDLSRHNCLGFnfrrsAPVWPLkesgr--iadrAISGSLLANNAqsLRRMAIAGiGLARLADYHvRDDIS 250 Bradyrhizobium ...
YP_002798860 173 LERHGLParieDLDRHNCLGFnfrraSPVWPLrqggr--ivdrMVRGNLLANNGetVRRLAIAGaGVARLADFHvDHDIA 250 Azotobacter vin...
NP_251814    176 LARHGMPatpqALLGHNRLGAnyvrtRSGWPLrdage--elvvPLSGNAQASDGeaLRRLAVAGlGLARLAAFQvREDIA 253 Pseudomonas aer...
Feature 1                                                 
NP_105038    255 AGRLVALLEdfnpgdEEATHAVYVGqgrhLPARVRAFLDFL 295 Mesorhizobium loti MAFF303099
YP_001984768 248 TGRLVPLLEeynpgdLELVHAVYVGgg-pLPHRVRDFIEYM 287 Rhizobium etli CIAT 652
YP_002944795 254 AGRLVPLLEefnpgeVEPIHAVYIGkagtLPARVRAVLDFL 294 Variovorax paradoxus S110
NP_744679    252 NGQLVPLLEaynpgdREPIHAVFVGgp-aMPARVRVFVDFL 291 Pseudomonas putida KT2440
NP_356363    254 AGTLVPVLEdynpddIEEIHAVFAGhe-hLATRIRAFIDFL 293 Agrobacterium tumefaciens str. C58
YP_003067180 262 AGHLVPVLEpfnpgdAEDVHALYVGha-rLALRIRSFVDFL 301 Methylobacterium extorquens DM4
YP_551041    254 AGRLVPVAEhlnpgeREPIHAVFLGkggrLPARVRVFLDFL 294 Polaromonas sp. JS666
NP_773603    251 AGRLVEVLKgta-gdEEQIHALYHGgp-rLPFRVRAFLDFM 289 Bradyrhizobium japonicum USDA 110
YP_002798860 251 AGRLVEVLAesg-hdCEEVHALYPGgr-hPPQRVRVFLDFM 289 Azotobacter vinelandii AvOP
NP_251814    254 AGRLIPVLEaynpgdLEEVHAVYVGqggyLPLRVRAFLDFL 294 Pseudomonas aeruginosa PAO1

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