1IXC,1IZ1,2F6P,2F6G,2H99,2H98,3GLB,2F7B


Conserved Protein Domain Family
PBP2_LTTR_aromatics_like

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cd08414: PBP2_LTTR_aromatics_like 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold.
This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106
View PSSM: cd08414
Aligned: 382 rows
Threshold Bit Score: 89.4887
Threshold Setting Gi: 462725
Created: 27-Mar-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
substratedimerization
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding pocket [chemical binding site]
Evidence:
  • Structure:3GLB_A; CatM from Acinetobacter baylyi ADP1 binds cis, cis-muconic acid (inducer), contacts at 4.5 A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              #                                                 #                       
1IXC_A        92 ELSVAYFgtp-iyRSLPLLLRAFLTSTPtATVSLTHxtkdeQVEGLLAGtIHVGFSRffpr---hpgIEIVNIAQeDLYL 167 Ralstonia eutropha
YP_002992673  92 KLHVSFVyla-lsSTFPQIMGDFIEDYPdVDVSLHEentffQVNAVKEGtRHIGFVTmrmv--diesLESMVVHRcASCA 168 Desulfovibrio s...
YP_569604    112 TVVVGYStfa-amSPMSNIIIDFRRKYPdATVALRLlasseQVTGLDQGaIDVGFMMsnla---aapLRNVAVSKeRLIA 187 Rhodopseudomona...
YP_001611751  92 TVTIGFEsgsayvGPLSTILTRFREQAPrVNVELVPmssaqQWDALRAGqISLGYGNyvpd---dssLQSVVLARhRLGI 168 Sorangium cellu...
NP_053241     99 ELIIGAIspa-tsQLLPLILSRFRQRFPrTRLAIKEvdsieLLRGIERGdFHVGLMRppsn---snlVRFRHLLSeRFVA 174 Agrobacterium t...
YP_001619236 139 TVVVGFDgaladtLLLPEIVQTFRARHPrVEVRLRPlpseeQVAALRDGkISVGYGYhspe--dnplFRFRVLYReRVGV 216 Sorangium cellu...
NP_746578     92 QITIGTIypa-tfGVLPNFVSRINQRFPeARIHIHNgntvgIVREIERGnINLGFIRpven---igsLRWQSIHReKYLL 167 Pseudomonas put...
YP_002979070  92 QIRIGTVypa-ttGVLPAFLGKIARKYPdIRIHISSgntgdIIRGLENGqINLGFIRpven---igsLRFSSIAHeRYLL 167 Rhizobium legum...
3GLB_A         3 TLRIGYVssl-lyGLLPEIIYLFRQQNPeIHIELIEcgtkdQINALKQGkIDLGFGRlkit---dpaIRHIVLHKeQLKL 78  Acinetobacter s...
YP_556263    103 TLSIGLVeyt-nlPFVPPALIRLQALYPdVMIIRREmnarrQWAALGTGeIDVGFGVpveqsgrethIGSEDLLDsGWCV 181 Burkholderia xe...
Feature 1                                    ##      #                                           
1IXC_A       168 AVHRSQsgkfgk--tckladLRAVELTLFPrggrpsFADEVIGLFkhagi-epriARVVEDatAALALTXAGaaSSIVPA 244 Ralstonia eutropha
YP_002992673 169 AVPANHplakkd--vltlrdLSELPYICSAdsfcrmRVKEMQKIFeqqgl-elkiGMKYERkhTGNVFVAAGlgWTVINV 245 Desulfovibrio s...
YP_569604    188 LVPSNHawaadh--aislqqLTTVPIVIGTanrwrgFRKLVDDMFraqgl-tpnvVEEADDvpVLLQLVRSGfgCTILDA 264 Rhodopseudomona...
YP_001611751 169 IVPEQHplatks--mikvkdLANEPMLMDPrksnprLYDDIIAAVrargv-tlnvASEILDgeALLTLVASGfgLTFGAE 245 Sorangium cellu...
NP_053241    175 VMPRQSalarkp--alrlsdFAGHGVFALKrfelscFETVYEQLSgagl--lienDIAVSDtnTALALVTAGvgITFLPE 250 Agrobacterium t...
YP_001619236 217 VMAKSHrlasrr--tlrvadLKQERFLWPPrkegprLQDDIIAAFrahdqplelaHEEASSd-VILMLVASGegLSLFPE 293 Sorangium cellu...
NP_746578    168 AIARENplssks--tvtpddLRKQKIIAFSraynsqTDDNFPEEFkkydl-nqqvVYSCNDtqAMLAMITAGigVGFVPE 244 Pseudomonas put...
YP_002979070 168 AVARSNplaeqa--eigiddLRSEKIIAFNrknlsyTERYFNEKFeeydl-trniAYSCDDtySLVSLVSAGlgIGFAPE 244 Rhizobium legum...
3GLB_A        79 AIHKHHhlnqfaatgvhlsqIIDEPMLLYPvsqkpnFATFIQSLFtelgl-vpskLTEIREiqLALGLVAAGegVCIVPA 157 Acinetobacter s...
YP_556263    182 LMRRDHrfarrt--rlrineLARERLIVPArsvnepLYDSVRARFvstgv-qpniVYETTQsqVGMALVEQGlgSMLGAA 258 Burkholderia xe...
Feature 1                                                      
1IXC_A       245 Svaai-rwpDIAFARIVgtrvKVPISCIFRKekq-ppiLARFVEHV 288 Ralstonia eutropha
YP_002992673 246 Dsagt-ipdGIALKPLEielhPFEIGMIWNPera-tplVRNFIEFY 289 Desulfovibrio salexigens DSM 2638
YP_569604    265 Sfipt-lppGIRSLEIEdasvTLDIVLAWHDdnl-splAAHFVDVA 308 Rhodopseudomonas palustris BisB5
YP_001611751 246 PaapflavgTAIWKPVSdlglEMRNIAMWRPdaq-svlLRPLVDLV 290 Sorangium cellulosum 'So ce 56'
NP_053241    251 Wvsam-apdGVVTRVVDdmsvEISMAVGWNPdcp-vpgILPFVEFA 294 Agrobacterium tumefaciens
YP_001619236 294 Saast-llaGAVFKRVRdldvVILGRSVWRAtddedplVRSLLEIT 338 Sorangium cellulosum 'So ce 56'
NP_746578    245 Wvksi-pgqNFELREVEglerHIGLGLAWSVddp-tvnRDSIIELC 288 Pseudomonas putida KT2440
YP_002979070 245 Wtegl-pnrDFELKAVRgidfRIGLGVAWSKddp-tasRDDIVDIA 288 Rhizobium leguminosarum bv. trifolii WSM1325
3GLB_A       158 Samdi-gvkNLLYIPILdddaYSPISLAVRNmdh-snyIPKILACV 201 Acinetobacter sp. ADP1
YP_556263    259 Yvfas-vpeSLVYCPVSgf-dPLTVKVFFRGder-splVLDFVELA 301 Burkholderia xenovorans LB400

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