2QL3,3FZV


Conserved Protein Domain Family
PBP2_PAO1_like

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cd08412: PBP2_PAO1_like 
Click on image for an interactive view with Cn3D
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily.
This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. 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. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 176104
View PSSM: cd08412
Aligned: 34 rows
Threshold Bit Score: 218.182
Threshold Setting Gi: 186475447
Created: 29-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putativedimerization
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on structural analysis of the uncharacterized LysR-type regulators from Rhodococcus jostii RHA1 and Pseudomonas Aeruginosa PAO1.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                #   #                                          #                   #    
2QL3_A         6 PIAVGCYpALGPTILPSXLYAFTAEYPrASVEFREdtqnrLRTQLEGGeLDVAIVYDldl--speWQTVPLXTrEPXVVL 83  Rhodococcus sp....
NP_107760     94 ELVLGCFeDLAPYFAPGLIRAFSERHPdVAVIVRDetfetLGRRLADAaIDLGLSYDlgl--pshFARILLHElRPHALL 171 Mesorhizobium l...
YP_274507     94 ELVLGCYeDLAPYCLPQILRRLQQEHPrVRVDMREggfdyLGKRLAEGtLELALTYDlgl--panMACIELRQlTAYALL 171 Pseudomonas syr...
NP_106051     94 RLQLGVTsLVAGYVLSDLLARYRRAYPgVEVSAIEdngdyLEHLLIGGkLDIAVMVTsnlrdrtaLQSEILEVsAYRLWL 173 Mesorhizobium l...
YP_002870871  93 QLIIGVTsLVAGYYLADLLTRFQRAYPnVEIRVMEderpyIEHLLVSGeIDVGVLILsnledrhaLQTEVLTHsPHRLWL 172 Pseudomonas flu...
YP_611496     91 TINIAATyTVCGYFLPYHLDRLSHRFPnLTINISElnresIEEGLISNrFDVAVILTsnts-npeLATQTLMRsHRRLWV 169 Silicibacter sp...
NP_249182     96 TLKVAASyTVMGYFLPHHLQRLAQWYPeLELQLFEderasIERGLLDGrYDIAVLLTgnlt-epgIAAETLFNsERRLWL 174 Pseudomonas aer...
YP_003188707  94 TLVLGVTpIVAGYVLPDLLTRFRRAFPrVEVILVEdqaeyLDHMLIGGeLDLAIMLRlgdavpsaCGARVMGVsLHNVWL 173 Acetobacter pas...
YP_998058     94 ELSIGAVsPLMGYYLPGLLERFRRSFPrVTVRIIEesgstIEHLIVNGeIDVALTLTshlenhhaFHTLQLVRsPWHLWL 173 Verminephrobact...
YP_858256     94 RLTIGVTtLVAGYYLSEALGRFRRAFPaVQIEVKEdeqpyLEHQIVNGeVDVGILMTnrtirqeaFDTELLTRsPLRVWL 173 Aeromonas hydro...
Feature 1                                      #                       #                #        
2QL3_A        84 GAEHPLagvdgpvrladlaehPXVLLDapPSTNHAXDVCREAGFaprvAYRTANFEtARAFVGRGlGWTLLLQRPrvdvt 163 Rhodococcus sp....
NP_107760    172 PAGHALadhaevs-ladmaayPLITTDqpHSWQHMLDLFRSRGLspvaDRATSSFElQRSMVANGfGVAISYTRPqgdrs 250 Mesorhizobium l...
YP_274507    172 AADHPLanepdvs-lhalsegNLVVTDqvHSWQHVLDLFNMHGLspqsLQRTHSFEfQRSLVANGfGVSLTYTRPfgdrs 250 Pseudomonas syr...
NP_106051    174 PLGHSLvgadiis-igdiagePLIMLTvdEIEENTGKLLAAIGAkphvAFRTRSVEaVRSLVATGaGVALLPDLVyrpws 252 Mesorhizobium l...
YP_002870871 173 PAQHPLlehdsin-ladvarePLIQLNvdEMGHNAQRLWAGAGLqprvTLRTASTEaVRSLVAAGlGVSIQPDMTyrpws 251 Pseudomonas flu...
YP_611496    170 PQNHPLagrefas-fedvaaqDYIMLTvdEAANTSMKYWGPTGLmprvRMRTSSTEaVRSMVANGlGVTILSDMVyrpws 248 Silicibacter sp...
NP_249182    175 PSRHPLgekadlg-ladvagePYIMLTvdEAGQSALRYWQQSGHrpqvILHTSSVEaVRSMVANGsGVAILSDLVyrpws 253 Pseudomonas aer...
YP_003188707 174 PQGHPLaadkqvs-lgqlraePYIALTanVLECRMGAVWERFSFrpniYFRSSSIEaVRSLVGAGhGIALLPQLIyrpws 252 Acetobacter pas...
YP_998058    174 PTGHRLvgakpvt-lrelhneAVIVLRndELERTTGDLWLRESVrpriVAKTRSVEaVRSLVATGnGICVLPEVLfrqws 252 Verminephrobact...
YP_858256    174 AANHPLcaestls-lkalgeePMISLTadQLDQIIGGGLRRYGIapriVLRTASVEaVRSLVASQlGLALLPDFAyrpws 252 Aeromonas hydro...
Feature 1                                                  
2QL3_A       164 yEGLPVVVKPIaepkpaSVAVVVAWHQeatlsrVARAFIRFV 205 Rhodococcus sp. RHA1
NP_107760    251 yDGLPLICKPLsdp-lpMQRIILTYDThqrvsnAALAFVETA 291 Mesorhizobium loti MAFF303099
YP_274507    251 yDGQPLVCRPIret-lpTQRIVLAYDQrypltpPAEAFKNQA 291 Pseudomonas syringae pv. phaseolicola 1448A
NP_106051    253 lEGDRIESRDIsgs-lpVVQVGMVWRRgsslpqAARDFIGLA 293 Mesorhizobium loti MAFF303099
YP_002870871 252 lEGDIIEARPIadl-sqTLDVGLAWRRgtarpaLVDPFLTVA 292 Pseudomonas fluorescens SBW25
YP_611496    249 lEGRRISTVVMdre-ipSMDVGLAWRRnqempnAARHFVDYF 289 Silicibacter sp. TM1040
NP_249182    254 lEGKRIETLSLvdp-vpSMSVGLAWRRdteasaGMRAFREYF 294 Pseudomonas aeruginosa PAO1
YP_003188707 253 lEGEKIECRPVqed-lpTAELLVMWRRglslgvQAQYFMDMA 293 Acetobacter pasteurianus IFO 3283-01
YP_998058    253 sEGLRLIAQPLrne-paTLELGLIWRRgakvsaAISAFTTTA 293 Verminephrobacter eiseniae EF01-2
YP_858256    253 lEQERVEARAIkep-ipAIDIGLVWRRgsrlewTAREFIDIV 293 Aeromonas hydrophila subsp. hydrophila ATCC 7966

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