Conserved Protein Domain Family
PBP2_Nac

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cd08433: PBP2_Nac 
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold.
The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to 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: 176124
View PSSM: cd08433
Aligned: 32 rows
Threshold Bit Score: 189.343
Threshold Setting Gi: 83591670
Created: 21-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                        ## ##  #   # #######                                            
EAP72558      92 AVSVGlapgtaasTLALPLLRAVRARHPgIVLYLNEtygstlsELIMNGrMDMAVLYggmtvvhgLSFLPLLREQLYVVG 171 Ralstonia solan...
YP_585972     92 TVAIGlptt-aaaAFGMALIRTVRQRYPqVRLQLFEsmsgyisELLNQNrLDFAILFrdtp-sraVEPEPLASEPLYLIG 169 Ralstonia metal...
YP_001479357  92 QVSVGlapgslasQLALPLLQAVRDQHPgILLSLNEnigstlaGQVANQnLDMAVIYgakm-pagLQATALMREDLYLVA 170 Serratia protea...
YP_002486552  92 RVSIAiapysmasSLTPRIISEVNRRYPdIVLHLTEiyggvlsEAIKNGrLDMALIYepgp-irgVQFTTLIVEDLYLIV 170 Arthrobacter ch...
NP_770260     97 RVSIGlatysassTLSLPILKEMSTLHPqIIVHINDsfghvlsELIMTGrMDMAMIYgsgp-ikgVKLQPLFREELFLVS 175 Bradyrhizobium ...
YP_002979364  92 RVSVGlvpfssaaTLSVDLLAETRKRHPgILLHLTEsvgqtysQMIMNGrLEMALLHgtgp-ikgVRFEPILSEEFFLVA 170 Rhizobium legum...
YP_299950     94 SVRLSiags-iagAVIAPLLGAVAREYPgIEVTVREsmsfesrALVESGqAHLALMPspse-iqgMASIPLYEERFMLYG 171 Ralstonia eutro...
YP_001342693  90 YVSIGmppt-tatVLALPLIRAMRERYPhIHLHIVEmlsghleNMLNARqLDLSILFhket-vhrWSTRVLLDEELFLIS 167 Marinomonas sp....
YP_586342     90 TVSVGlapt-tasVIGVPLIRAMRERYPdVRLHIVEslsghltAMLNARqLDLAVLFdtha-arrWTVMPLLEETLFLIQ 167 Ralstonia metal...
YP_587407     90 HVSVGmaps-tlaVLGPPFMVAMRERYPdIRLHLVEslsgnlaSMIGARqLDLAVLFqlea-gqrWSTTPLLEERLFLIA 167 Ralstonia metal...
Feature 1                                                                ######     ## ##        
EAP72558     172 Pasmpapp---------eevplamLGEIDLYLArpyNVVRRLVDeafsaigmapkvSAEIESagtLKAIVADGlGATILP 242 Ralstonia solan...
YP_585972    170 TppvtaprpgkrgsatadtvplkaLDGIPLVLPsgsQGLREVVErtfakagmnlnvVADLDSlpfLLASAREGlACTILP 249 Ralstonia metal...
YP_001479357 171 Travpnpg---------nsvelldVARLNLFLPregDVVRSQVDeamairkltanvIGEIESpgtLSAAIASGlGATILP 241 Serratia protea...
YP_002486552 171 Nagrelpvgp-----dagtitleeASTLGLFLPeqiHTLRQVVQagiegkglklhlVGEVESvpsLTRLLRSDlGATILP 245 Arthrobacter ch...
NP_770260    176 Pagpgakkpa------deplplsaLANVKLLLPsqgHFLRRLIDeslararvapnvVSEIESvsaLGAAVTEGlGSTILP 249 Bradyrhizobium ...
YP_002979364 171 Hrdfaiead-------akpvpvnsLDGMPLLLPpayNFVRRAVDtaftrtrtnlkvVAEVEIvrtLARAVGSGlGATIMP 243 Rhizobium legum...
YP_299950    172 Traamrrkp--------etmtfaeVAELPLAAPdgaHDLRKIIEraanaigrsldvRYELNSpqmLIALARDGlAYVVMP 243 Ralstonia eutro...
YP_001342693 168 Sptdleapag------ssslyikdLANVNLIMPsrlHGLRNNLMaaferhnihpniIMEIDGltlLMDTVHQGfGATIQP 241 Marinomonas sp....
YP_586342    168 Srnalpqgkae----pptrltmadLSEVPLIMPtgvHGLRSTLDaafsrakvvphvTQEIDSlamLMDAVDMGfGTTLQP 243 Ralstonia metal...
YP_587407    168 Rpdqpglpa-------anavrledIGDIPLILPssaHGLRAVLNaaaarhqralnvVAEIDGlavLMDAVRAGiGATIQP 240 Ralstonia metal...
Feature 1                                                         
EAP72558     243 asmake-vatscDAWQCRIvdPVIEAPLALCQSGhqplsepAQAIKEIL 290 Ralstonia solanacearum UW551
YP_585972    250 assl----gdgdATVPRRLivPELRRTLSLCWPRalprsnaAEAVADVL 294 Ralstonia metallidurans CH34
YP_001479357 242 esvara-migpaKAWMARInaPSLSVPLSLCISGqqslsapALVVKEIL 289 Serratia proteamaculans 568
YP_002486552 246 ksaada-lfheeDFRVLRIvdPALQCKIALCTPDheplseaGSAVLLVL 293 Arthrobacter chlorophenolicus A6
NP_770260    250 asvaas-assfgGVEVRRLvrPAIEATVSLCISDhlplsepALATRSVL 297 Bradyrhizobium japonicum USDA 110
YP_002979364 244 kaiadrivsessEPLICRLvsPRIEETLSLCVSDqnplsepALAVRDIL 292 Rhizobium leguminosarum bv. trifolii WSM1325
YP_299950    244 psacle-avaakSIVGRPVtePDLTRIQALVWPGdrplspaAAAIRDLI 291 Ralstonia eutropha JMP134
YP_001342693 242 gaaaa--rfgesGLCIRRIedDQLIRRNYLVSLPdddlspsALATRVMI 288 Marinomonas sp. MWYL1
YP_586342    244 waavgrypdaetRFHLAHIddPQVGRQNLLCSLSddelspaALALRVVL 292 Ralstonia metallidurans CH34
YP_587407    241 gaava--rhlgdPLALIEIadASVRRPNLLVSLSddelspaGLAARGVL 287 Ralstonia metallidurans CH34

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