Conserved Protein Domain Family
PBP2_YofA_SoxR_like

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cd08442: PBP2_YofA_SoxR_like 
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold.
YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133
View PSSM: cd08442
Aligned: 23 rows
Threshold Bit Score: 203.223
Threshold Setting Gi: 154248484
Created: 27-Oct-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                       ## ##  #   # #######                                             
O34685        91 PLRIGsletmavTHLPEHAASFLRRFPeVDLSVNTadthhliQQVLDHkVDGAFVygpvehaaVRQLHVSHdELVLISSr 170 Bacillus subtilis
YP_002796279  90 TLRLGsmettaaIRLPQVLPAFHRRHPaVQLVLDTlptrqavSAVLEYrLDAAFVcgpvtepgLEGCPVWCeAPCLIAEa 169 Laribacter hong...
NP_250104     90 DFALGsmystaaIHLPPRLAEYHRRYPaVNLQLQTapsgelvESLLGGrLDAVLVdgpldfdgLEGLPMFEeRMVLVTEn 169 Pseudomonas aer...
NP_981989     90 IFTLGaiestaaVRLPPLIARYHQSWPqVGLDLSTgpsgdmvDGVLAGrYSAAFVdgppkhprLEGIPVFAeELVLITAl 169 Erwinia amylovora
YP_001907225  90 HFAFGsmestaaTRLPLLLTEFHQRYPaVTLALVTgtsgeliERVRAGtLAAALVdgpvnveeLNGCVAFHeEMVLISSr 169 Erwinia tasmani...
NP_310160     90 LFSLGslestaaVRIPATLAEFNRRYPkIQFSLSTgpsgtmlEGVLEGkLNAAFIdgpinhtaIDGIPVYReELMIVTPq 169 Escherichia col...
YP_002353816  93 SLRLGslesaasVRLPPILSRYHAAHPrTHVELQTgttaallRRLDNHqIDAAFVsepfdkgsLSAVAVFAeELVLITAr 172 Thauera sp. MZ1T
YP_001992652  90 VLRLGslesaagVRLPPLLSRFHARYPdVAIQMTTdttgallRQLERFeIDAAFVsepfepgsFASVAAFNeELVLITAk 169 Rhodopseudomona...
NP_899731     90 RLRLGamestaaARLAPVLADYHARYPaVRLELQTgesrgltAAVLDGrLDAALVsgplddvrLDQTVVAVeEIMLVAAa 169 Chromobacterium...
YP_001628752  93 LLRVGtmestaaARLPPILAAYHQTWPqVRIELVSgtsgalvNQVHRGdIEAAFVarpyaedgLDAAPAFTeELALISPl 172 Bordetella petr...
Feature 1                                                  ######     ## ##                      
O34685       171 egtae----dmlqqPMLFFGAGCSHRdrvkrlleeagihnqkIIEFGTleaIIKGVSAGmGTALLPksavdg-sehrtNV 245 Bacillus subtilis
YP_002796279 170 glsla---eatvapVLLTFGAGCAYRdrledwcrvrgivpatVLEFRSfqaILGCVAAGmGIALLPrsvlddpasahlGL 246 Laribacter hong...
NP_250104    170 ghppvrgpedvagsAVIAFRPRCSYRllleswfasarvsmgrVMEIESyhsMLACVVAGgGVALMPvsmlqs-lpgreSV 248 Pseudomonas aer...
NP_981989    170 nhppvsaasavsgsTIYTFRENCSYRrlfenwfarthavpgkIFEMESyhgILACVSAGaGLALIPasmles-mpgrdSV 248 Erwinia amylovora
YP_001907225 170 dhsaisrpteaagsTLFTFSSGCSYRarfenwfraagvqpgnVMEVSSyhaMLACVASGgGLALLPaavlvq-lpgheRV 248 Erwinia tasmani...
NP_310160    170 ghapvirasqvngsNIYAFRANCSYRrhfeswfhadgaapgtIHEMESyhgMLACVVAGaGIALIPrsmles-mpghhQV 248 Escherichia col...
YP_002353816 173 ggpriggaqdladqTVVAFPHGCSYRrllvdwfaaagvtprrFLDLGSyhaIVACVAAGtGVAIMPasvldn-avmgdSI 251 Thauera sp. MZ1T
YP_001992652 170 gdrplrrsadlggkTVVAFPHGCSYRrrlmewlasegvspdrILDLGSyhaIVACVAAGsGIAIVPagvldh-aalgtAV 248 Rhodopseudomona...
NP_899731    170 tlgrps-levladtTLLAFGSGCSYRqrleqwlqrqgvqprrVVELSSyhaMLSCVACGmGLALLPqalldtmpqmaaQV 248 Chromobacterium...
YP_001628752 173 arppveraqdlrgaTLIAFSTGCSYRriletwlaqenvapgsIMEFASyhaIVACVAAGtGVAIVPrsvlgv-lqaeaSL 251 Bordetella petr...
Feature 1                                           
O34685       246 WIHqlppsyqDLEIVFIYRKdffitsaFQTFLDEI 280 Bacillus subtilis
YP_002796279 247 AVHdlp-aeaAPMQTWLVWRrgwqspaLRALCASL 280 Laribacter hongkongensis HLHK9
NP_250104    249 AVHala-epfARANTWLVWRkgmvganLKAWIGLL 282 Pseudomonas aeruginosa PAO1
NP_981989    249 KAWplr-eamGQIAIWLVWRkgtrsanLQAMKTLL 282 Erwinia amylovora
YP_001907225 249 QQHplp-samRDTDTLLIWRrdafsanIKALKYLI 282 Erwinia tasmaniensis Et1/99
NP_310160    249 EAWpla-eqwCWLTTWLVWRrgaktrpLEAFIQLL 282 Escherichia coli O157:H7 str. Sakai
YP_002353816 252 QRHelp-eamRTNRTNLVWAgep-ggpLSALLELL 284 Thauera sp. MZ1T
YP_001992652 249 DRHplp-aklRNNRTHLVWPgdp-gspLQALMALL 281 Rhodopseudomonas palustris TIE-1
NP_899731    249 SAHalp-ddlARAPTLLIRRrqsrqpaLKALEEML 282 Chromobacterium violaceum ATCC 12472
YP_001628752 252 RVCalp-qpfAQAPTMLVWRrghqspaLDALRAGL 285 Bordetella petrii DSM 12804

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