Conserved Protein Domain Family
PBP2_CbbR_RubisCO_like

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cd08419: PBP2_CbbR_RubisCO_like 
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold.
CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The 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: 176111
View PSSM: cd08419
Aligned: 59 rows
Threshold Bit Score: 267.836
Threshold Setting Gi: 152997924
Created: 25-Sep-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on sequence similarity to the known structures of LysR-type transcriptional regulators.
  • Comment:Most members of the LysR family of transcriptional regulators are tetrameric, while CrgA assembles into octameric rings

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                      ## ##  #   # #######                                              
P42722        99 SITIGLiSTSKYFAPKLLAGFTALHPgVDLRIAEGNRetLLRLLQDNaiDLALMGRPPreldAVSEPIAAHPHVLVASPR 178 Ralstonia eutro...
YP_002296500  94 PLRLAVaTTAKYFTPHLLGRFVADHPaVVPRLVVTNRarLIQRLGENldDFVIMGQVPddlpLVAHPIIENRLVVVAHPH 173 Rhodospirillum ...
YP_001342759 103 ELTLVAvSTAQYVVPYLLRAYTSLHPnVTINVKVMNRaaAIERLNENhdELAIMGMVQndkpMFSIPFLNNELIAVVPQN 182 Marinomonas sp....
BAD15306      97 ELTMAVvTPAKYFMPYILKSFLNRYPnVIPRITVVNRrrILDELKQNqyDLAIMGRVPeeykMEAFPFFKSDLVVIAPPK 176 Hydrogenovibrio...
YP_001021970  96 TLRVGAvTTAEYLLPPLLVSFANEHPnVKVKLRVGNRdeIVRMLAAQevDLVIMGRPPgelkTVATAFAKHPMAFIASPR 175 Methylibium pet...
YP_003166222  95 RIAVAVaSTAEYFAPGLLAEFRKVQAdVRIRLLIDNRdtVTRLLVGNevDLAIMGRPPaeldATAVAFAPHPLVIVASAA 174 Candidatus Accu...
BAA95688      95 ELKIGMvSTAQYFVPQMLGDFRREHPgISLSLRVGNRaqVVAMLESReiDIAVMGRPPegfaVRAEAFAGHPSGFVAPPD 174 Hydrogenophilus...
YP_573606    101 ELNLAAvSTAQYVVPHILARFRARYPeVQVRLRVCNRgqALERLAERrdDLVIMGMVPedanLAFMPILDNEMIPVVWPG 180 Chromohalobacte...
YP_549604     95 KLNVAViSAGDYFFPRLLVEFARRHSgVTLNFGVCNReeLLDQLANNvtDLAIMVRPPldmdTVSEPFAPHPYVIVAPPD 174 Polaromonas sp....
YP_568688     98 PLRLSVvTSTKYFLPHLLGSFIVDHPaVLPRLIVTNRerVIERLVENldDFVIMGQAPddlaVEAHPFYENLIVVAAHTQ 177 Rhodopseudomona...
Feature 1                                                      ######     ## ##                  
P42722       179 HPLhdakgfd-lqelrheTFLLREPGSGTRtvaeYMFRDHLftpakVITLGSNETIKQAVMAGmGISLLSLHTlglelrt 257 Ralstonia eutro...
YP_002296500 174 HPGadqagla-lpdlageRWLMREPGSGTRtsfeRELAGQGltiepYMELGSTEAIKQAVMAGlGLSVLPMHSielelaa 252 Rhodospirillum ...
YP_001342759 183 HPLlaledis-lstflehNLLLREAGSGSRlaleLHCQKQRirlhaEMEIGSNDAIKHAVIAGlGVAVLPKLGilseltl 261 Marinomonas sp....
BAD15306     177 HPLakvknit-qdqianeNFILREKGSGIRiateELFAKNGvqiepYMELGSTESIKQAVMAGlGISVIPQHAirieskh 255 Hydrogenovibrio...
YP_001021970 176 HPLmaqrrlt-ladlegaSLLARERGSGTRttleRLFKDEAitlriGSELSSNEAIKQMCVAGfGVAFLSLHTcrlelda 254 Methylibium pet...
YP_003166222 175 HPLagqanva-vedlageTLIVRETGSGTRsameEFFQERSikpriGMEMGSNEAIKQAVVAGlGISFISQHTlglelsa 253 Candidatus Accu...
BAA95688     175 HPLadetrsidpkvirrePLIVREAGSGTRaamdLFFAERRvtptvAMQMESNEAIKQAVIAGlGVAFLSLHTvggelar 254 Hydrogenophilus...
YP_573606    181 HPLltadapt-ledftryYVLMREPGSGTRtafeDFVARERvslrhTLELGTNEAIKQGVMAHlGVAVLPRLAvqlelas 259 Chromohalobacte...
YP_549604    175 HPLaskkrip-vsrlarePFVVREKGSDTWnsmeEGFRGHLadlniAMEIKSTETIKQALIAGmGVSFLSAHTvsrelqa 253 Polaromonas sp....
YP_568688    178 HPLsavrsip-plqiareRWLVREAGSGTRsafdRYLIENDlaitpYMELGSTEAIKQGVMAGlGVSVLPISSmqleltn 256 Rhodopseudomona...
Feature 1                                              
P42722       258 gEIGLLDVaGTPIERIWHVAHMSskrlspaSESCRAYL 295 Ralstonia eutropha H16
YP_002296500 253 hRLVILDIaGFPLCRRWNAVHLQgktlsraARSFLQFL 290 Rhodospirillum centenum SW
YP_001342759 262 gTLIEVPIkDFPLRRSWCLIHPQgrhptptMRSFIDYI 299 Marinomonas sp. MWYL1
BAD15306     256 gHLEILDVeGFPLNRDWYVVKLEqktppppAQAFLEFL 293 Hydrogenovibrio marinus
YP_001021970 255 dLLQLLPLdSNPVEREWFVLHLAsrqlpqvAVAFEQFL 292 Methylibium petroleiphilum PM1
YP_003166222 254 aRLVILKVeGTPVIRRWHIVRHKnkhltpaLGAFWDFV 291 Candidatus Accumulibacter phosphatis clade IIA str. UW-1
BAA95688     255 gELKVIPVrGTPVVRSWYVVHRTsqfvaptVEAFRYFL 292 Hydrogenophilus thermoluteolus
YP_573606    260 gLLASPTLpGFPLRRSWCTVHPKdryptpvTELFLRFV 297 Chromohalobacter salexigens DSM 3043
YP_549604    254 gSLAVLDVqGFPLMLHWYVVHRKhkrlppvAQAFKSFL 291 Polaromonas sp. JS666
YP_568688    257 gCLAVLDVqGFPLCRRWNAVWLKgktlspvARAFVDFL 294 Rhodopseudomonas palustris BisB5

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