Conserved Protein Domain Family
PBP2_NhaR

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cd08429: PBP2_NhaR 
The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold.
NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine (PGA) .Thus, it is suggested that NhaR has an extended role in promoting bacterial survival. 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: 176120
View PSSM: cd08429
Aligned: 12 rows
Threshold Bit Score: 308.86
Threshold Setting Gi: 220917050
Created: 19-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                       ## ##  #   #   #######                                           
AAA24221      96 LFDVGVADalsKRLVSSVLNAAVVEGEp--IHLRCFEsthemLLEQLSQHKLEMIISDcpidstqqegLFSVRIGECGVS 173 Escherichia coli
CAL19150      96 LFDVGVADalsKRLVSQVLETAVVEHEk--IHLRCFEsthemLLEQLSQHKLDMILSDcpvdssqqegLFSVKLGECSVS 173 Yersinia pestis...
NP_744592     92 LFRVGVADvvpKSIVYRLLAPTMDLEEv--LRINCREdklerLLADLAIQRLDLVISDspmpnhldikCYSQKLGECGLS 169 Pseudomonas put...
YP_002492354  95 RLVVGVADvipKRMAALLLQPAVDAHPd--LTLVCREgplpqLLAALALHELDVVIADvpapedvkvkAFSHRLGDCGTS 172 Anaeromyxobacte...
YP_065823     95 SLKVGIVDvipKLVARKLLEPTGKLPEk--VRLSCHEgkdeqLLAELALHNLDVVLTDtpirsslsikAYNHLLGECGVS 172 Desulfotalea ps...
YP_821505     95 RLTVGISDlipKLIAYRVLQPAFALKEk--IQLVCYEdrpdqLLLDLSAHRLDLVLSHtpagssvpvrVFSHRLGSCGVT 172 Solibacter usit...
YP_003047452  93 LFRVGISDavpKSIAYHLLAPAMSLAEp--IKIICREgklesLLGELAIHRLDLVLSDrpmpsefdikGRSNALMECGLS 170 Methylotenera m...
YP_524696     93 DFRVGVADsvaKSVVYRLLEPALLVKEp--VKLICSEgkfpdLLAQLALHRLDLVIADeplprrisvkAFSHPLGSSSMS 170 Rhodoferax ferr...
YP_550661     95 PFQVGIADsvtKSVAYRLVEPALKQRQgepMRLVCREgrlpsLLAELAIDRLDMIIADrpmpanlnvrGYSHLLGESGLT 174 Polaromonas sp....
YP_001100752  92 QFRVGVADavpKAIAYLLLEPAMELPEs--LRLVCREgkltnLLADLAVHRLDIVIADspmpanidvrGYNHLLGECGVT 169 Herminiimonas a...
ZP_01116360   93 LLRVGVADavpKTIASRILMPAMDLNEr--IRFICKEstqenLLADLALHRLDCVLADgpipsnlgvrGYNHRLGDSGLS 170 Reinekea sp. ME...
YP_316362     93 PFRVGIADvvpKAIAYQLLAPALTLAEp--VRLVCKEdrleaLAAALSIHRLDMVLADrplpstmdvkGYSHPLGECGIA 170 Thiobacillus de...
Feature 1                                                          ######     ## ##              
AAA24221     174 FWCTnppp---ekpFPACLEERRLLIPgrrsmlGRKLLNWFnsqgLNVEILGEFDDaALMKAFGAMhnAIFVAPtlyayd 250 Escherichia coli
CAL19150     174 FYCRqpvp---dlpFPASLQQKRLLIPgrrsmlGRKLLNWInskgLKVEVLGEFDDaALMNAFAVYhdAIFVAPtiyaad 250 Yersinia pestis...
NP_744592    170 FFATpalaqrlegpFPACLQDAPLLVPgqetvvRSRLLRWLgeqqVQPRIVGEFDDsALMQAFGQSgsGIFVAPsviaee 249 Pseudomonas put...
YP_002492354 173 FLAArplah-lkkgFPRSLQAAPMLLPsegtalRRGLDTWLertgVRPVVAGEFDDsALMQAFGARglGVFAAPrvledd 251 Anaeromyxobacte...
YP_065823    173 FFGVeklakprqsnFPHSLDEAPMLLPmpmsssRGMLDQWFerigVHPVIIGEFDDnALVKVFGQAgdGIFMAPtvieke 252 Desulfotalea ps...
YP_821505    173 LFGSgplvkryrkgFPAQLDGAPFLLPmersssRRALEQWFagqrIRPQIVGEFQDsALLGAFGQAgaGIFAAPsaiere 252 Solibacter usit...
YP_003047452 171 FFAAnsfqasnlasFPHCLNNAPLLVPgedsavRKRLMLWLntlrIQPQIVGEFDDsALMRAFGQAgvGIFCAPsiitde 250 Methylotenera m...
YP_524696    171 FFCAptlksrlqglFPKCLNDMPMLIQggsasvRQQLEGWLtrhqIHPQVIGEFDDaALLKAFGREgrGVFMAPtvleae 250 Rhodoferax ferr...
YP_550661    175 VFGTpslvkelkgsFPAMLDNTAFLLPgedaaiRPKLEQWFkvnnLRPHIVGEFDDsALMKAFGQAgaGLFAAPtaivdq 254 Polaromonas sp....
YP_001100752 170 FFATdelakeyeegFPKSLDGAPFLMPgedaavRPRLIRWFekekVRPRIIGEFDDgALLQAFGGAgkGIFAAPsavadq 249 Herminiimonas a...
ZP_01116360  171 FMAAtsltlassrpFPQMLHEAPMLLTsdvsqiRAPLMTWFtdqqIVPRILGEFDDrALMKAFGQEgvGVFIVPtsiade 250 Reinekea sp. ME...
YP_316362    171 FLAApavaasagsdFPANLHGAPLLVPgedsalHGPLLRWLerrgLQPVVVGEFDDsALMSAFGQAgaGVFPVPlstage 250 Thiobacillus de...
Feature 1                                                       
AAA24221     251 -fyadkTVVEIGrvenvMEEYHAIFAERMIQHPavqricNTDYSALF 296 Escherichia coli
CAL19150     251 tyandsEIIEIGrldnvQEEYYVIFAERMIQHPavqrvcNKDFSALF 297 Yersinia pestis CO92
NP_744592    250 -vcrqyGVQLIGqteavHESFYAISVERKVKHPgivaitEGARRELF 295 Pseudomonas putida KT2440
YP_002492354 252 -irsqlEVGVIGraedvREAYHAITVERRLRHPavvtlaEAARDAIF 297 Anaeromyxobacter dehalogenans 2CP-1
YP_065823    253 -vaqqyQVQVIGrtnkiREKFYAISVERIIKHPavaaisDAAQQKLF 298 Desulfotalea psychrophila LSv54
YP_821505    253 -vrrvyRVSVIGrldsvFEEFYAISAERKINHPavaaitEAARTRLF 298 Solibacter usitatus Ellin6076
YP_003047452 251 -visqhNVTKIGetnevVERFYAISVERRANHPavv-aiNTAPSKIS 295 Methylotenera mobilis JLW8
YP_524696    251 -tvaqfGVDVIGrsdelVEEFFAVSVERRITHPcvlaitDAARDRLF 296 Rhodoferax ferrireducens T118
YP_550661    255 -vceqhQVVEIGridsvVENLYAITTERRLTHPavvtisKTAKEGIF 300 Polaromonas sp. JS666
YP_001100752 250 -iikqyGVTEIGrtslvTEQFYAISVERQLTHPavvaisSAARESLI 295 Herminiimonas arsenicoxydans
ZP_01116360  251 -vaeqyDAREIGritdvTESFYLITSERNPTNPavvtiiEEARRWLG 296 Reinekea sp. MED297
YP_316362    251 -vmrqyAVVDLGrtleiRERFFAISVERRLSHPavvavsEAAHQRFQ 296 Thiobacillus denitrificans ATCC 25259

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