3HHG,3HHF


Conserved Protein Domain Family
PBP2_CrgA_like

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cd08422: PBP2_CrgA_like 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain.
This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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: 176114
View PSSM: cd08422
Aligned: 1043 rows
Threshold Bit Score: 128.712
Threshold Setting Gi: 187923681
Created: 22-Sep-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                   ##   ## ##  #   # #######                                            
3HHG_A        93 GVLSVDsampMVLHLLAPLAAKFNERYPhIRLSLVSsegyINLIERkvDIALRAGelddsgLRARHLFDSRFRVIASPEY 172 Neisseria menin...
NP_518364     92 GKLRIRmlpgYALHHFAQPLARFGAQYPdLQLDVVVddgvVDPIAEgfDVVFQIFppindsLIEKRLFILRRLFCATPDY 171 Ralstonia solan...
YP_001021313  86 GTLRINstqgFAKHQLLEFMAEFQGRYPrLTLELQItgqaVDLIDEgvDLAIRLGelrdtsLVGRKLGESQRLVCASPQY 165 Methylibium pet...
ACD38713      92 GKLRVQmlpgFAIDHFGPLLAEFTALYPdIEVDVIVndrlTDPIEEgfDIAFQMFppqaetLIERKLFSVRRLFLASPEY 171 Pseudomonas aer...
YP_001326291  96 GRLKIAssvaFGRHVIAPLVPSFAARYPdVSIELVVtdrsIDHIGEgiDISVRFAqqlepgLITRKLGSVPLVICAAPSY 175 Sinorhizobium m...
YP_003048654  92 GRLKIAtsvaFGRHVLSTIIPSFTAMYPkLSIELILtdqnIDHVKEdiDISIRFKqqlelgLVAKRIAVVPVLFCASPTY 171 Methylotenera m...
YP_001566080  92 GRLRIAcmaaFGRHVLAPLLPVFAAQHPrLELELLVvdrqVDVLKEdvDISVRYRdvlepgMAVRQLAAVPRVLCASPAY 171 Delftia acidovo...
YP_002947957  92 GTLRVHaltgFVLGHFATLLRAFQSSFPdIHLELIVsdavVDPVKAgvDCALQIFpaasteLVSRSLFPVRRVFCATPEY 171 Variovorax para...
YP_556104    116 GRLKVKapsaLTYLHLAKVINRFLIRHPkVTLELLLidrpVNPATEgfDLVITGLppsydqIDEIPLFPIQRMLFASPEY 195 Burkholderia xe...
NP_766755     92 DHLRIKaptsLTVARLADAFSAFQTQNPrLKLEIVLidrpVDPVTEgfDIAIGAFphsfggVVDEPLCALKRLLCASPAY 171 Bradyrhizobium ...
Feature 1                        #                               #####      ##  #                
3HHG_A       173 LAKHgtpqsteELAGHQCLGFtep--gslNTWAVldaqgn--pykisPHFTASSGeiLRSLCLSGcGIVCLSdflvDNDI 248 Neisseria menin...
NP_518364    172 VEEYgmpqqpaDLQRHALALYsgy--ptrKHWVFsrsgevaaeldlpEQVRSNSVhlLRDYALTGaGIACLPtlvaSDDL 249 Ralstonia solan...
YP_001021313 166 LNARgrptrpsDLLDHDCLRLsts--dvfNQWHFsgatgp-elvnvqGHFVTDNVdvLHEYARLGgGIVRLSafmvAKDI 242 Methylibium pet...
ACD38713     172 LQRHpaperpaDLLEHRIGLYegy--psrNRWQFqhgdet-velslaGQVRSNSVhlLRDYALAGtALVCLPtlvaHADL 248 Pseudomonas aer...
YP_001326291 176 IARRgrpetpeDLRHHDCLIYrfaghgrlFRWAFvrdglr-fepelrPTIVSNDIdtLAQMAIAGaGITRLGtfiaNQFF 254 Sinorhizobium m...
YP_003048654 172 ISRKgephtpeGLQRHDCLMFrmptsgrlLNWGFlrdelr-fepelkPSIISNDInsLAELAIAGaGIVRLAafiaNPLI 250 Methylotenera m...
YP_001566080 172 LQAHgrprtaqDLLDHACLLYrreadgrfMRWPFsrdgkr-vdpqlrVTAIASDVdaLTEMAVAGgGIVWIGsfiaHRYM 250 Delftia acidovo...
YP_002947957 172 LRAHgrpasprELHKHTLGLYsgy--ptrDRWTFhhggeq-vtmymsAALLTNSVhlLREYAMEHaGIVCLPtlvaGEAI 248 Variovorax para...
YP_556104    196 LAEMgtplqpeDLAHHRCLQYsyl--sagMTWTLngrhgq-vdvhvnSTFQTNDIqvMHQAVTDGlGIGILPgyaaQKAL 272 Burkholderia xe...
NP_766755    172 LKKHgtpkhprDLVEHRCLSFlp----tgPEWIFdgprgr-isiqvsPLLSSNEGhvLARSAIAGnGIALIShylvADAL 246 Bradyrhizobium ...
Feature 1                                                         
3HHG_A       249 AEGKLIPLlaeq------tsdkTHPFNAVYYSdkav--nlrLRVFLDFL 289 Neisseria meningitidis serogroup B
NP_518364    250 LAGRLVPVlpdy-------dlaPFHFSAVYPAtqrq--avkVCALIDCL 289 Ralstonia solanacearum GMI1000
YP_001021313 243 AAGRLEPLltny-------hieKQLIYAVYPHrrhl--pakVRVLLEYL 282 Methylibium petroleiphilum PM1
ACD38713     249 ESGRLLPLlidy-------plsSFNFSAVFPAtqrr--alkVRSLIDFL 288 Pseudomonas aeruginosa
YP_001326291 255 EQGLLVPLfgeaaae-dgtrvdHEPLDFYACFldrqaetpkVRSFIDHA 302 Sinorhizobium medicae WSM419
YP_003048654 251 KNGQLIPLfqrdtnnpsimhadNEPLEFYACFrdhhamtlkVKTFINHL 299 Methylotenera mobilis JLW8
YP_001566080 251 REGLLQPLtlgpark-gqlhfeDTTLDFFACFrdrqyvptkVRALVDYL 298 Delftia acidovorans SPH-1
YP_002947957 249 LRGELEVVlpah-------qlsSFSLSAVYAGtsrn--afkLRLFIEHL 288 Variovorax paradoxus S110
YP_556104    273 ENGRLIAVlenf-------alpEFWFRAQFAKshrq--rrlLMALIDHI 312 Burkholderia xenovorans LB400
NP_766755    247 RDGTLKPVlrdf-------pipELWVKAAIPErrrn--aaaVQALLTLL 286 Bradyrhizobium japonicum USDA 110

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