1UTH,1UTB,1UTB,2UYE,2UYF,1UTH,2ESN


Conserved Protein Domain Family
PBP2_Nitroaromatics_like

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cd08417: PBP2_Nitroaromatics_like 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold.
This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows 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: 176109
View PSSM: cd08417
Aligned: 383 rows
Threshold Bit Score: 104.989
Threshold Setting Gi: 34496534
Created: 27-Mar-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
substratedimerization
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding pocket [chemical binding site]
Evidence:
  • Structure:1UTB; Burkholderia sp. DntR binds acetic acid, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                            #     
1UTH_A       106 TFNLAMTDIGEMYFMPPLMEALAQRAPhIQISTLRpnag--nlkEDMESGavDLALGLLpel-qtgFFQRRLFRHRYVCM 182 Burkholderia sp.
1UTB_B       106 TFNLAMTDIGEMYFMPPLMEALAQRAPhIQISTLRpnag--nlsEDMESGavDLALGLLpel-qtgFFQRRLFRHRYVCM 182 Burkholderia sp.
YP_001250875  97 FLKTASVGTGEYFILPRLCAHLAKNAPkFVLKISSlsey--lslEYLLMSelDFAIGPGfvetgnnIIRELLFEEEAVCV 174 Legionella pneu...
YP_268025     96 QFVISSLSVFGFTILPPLSALMSQHAPlASVKIEPlnnh--dftNMLRSQhfDLVIDAHsnq-ypqLRSKVIMEDTLCVM 172 Colwellia psych...
NP_230430     99 EFIIGGQGYFDLVVLPPLLQKISDIAPhITVNLKSyeddhftpsQVLSEReaDLFLAALpis-hpsIVTTQVAEEALVVV 177 Vibrio cholerae...
YP_001502603  98 HFSLMGPEEYNAKLLSAFAGEQNNGLT-YSLMQQAstde--eaiASLRTRmtDLVIDSVvla-dssIESELLFEDRIVLI 173 Shewanella peal...
YP_269732    100 NFHINILGVGNNDFLTKLSQRLAHVAPnISLTVSTemlv--daeKSLRDKeyDLHLDYLtid-eigCHHQELFNDQLFII 176 Colwellia psych...
YP_002313609  93 KFRVSSHKDLDLMLIPSLVRYRQKKAPhTKFIADIehdseesrqDDLRMRkvDIIISTVqle-ehgYHNQLLFKQDLVVA 171 Shewanella piez...
NP_762143     96 IFSIACVSVASYELMPQLLKQIRQHAPnISLEVHPlfte--dyeSDLRLQryDLIIDMAprg-wttLKVEPIFSERLMVV 172 Vibrio vulnific...
YP_204802    100 IFSIAVVSTVNYSLIPKLVKQLRSSAPnISLEIHPqfte--dleSDLRLQryDLVIDMAirg-rtiLKSEVVYTERLRVV 176 Vibrio fischeri...
Feature 1                                           #                                            
1UTH_A       183 FRkdhpsak--spmslkqFSELEHVGVval--ntGHGEVDGLLeragi--krrmRLVVPHFIAIGPILHStDLIATVPQR 256 Burkholderia sp.
1UTB_B       183 FRkdhpsak--spmslkqFSELEHVGVval--ntGHGEVDGLLeragi--krrmRLVVPHFIAIGPILHStDLIATVPER 256 Burkholderia sp.
YP_001250875 175 MHkshplan--qeltqdmYLQAEHVDIqfs--ymGNENILYKAlqgyh--qrniKVIVPNIISALEVVYHtNFITTVPRT 248 Legionella pneu...
YP_268025    173 CRidhprlsg-dsisideFLAEKHVTHsql-dqkGGYLSGKGLkedeilnqrkiAWQAASIMEMLPVIECcDYIALLPQR 250 Colwellia psych...
NP_230430    178 YAknhprlg--stlsfeqFFAEKHTALts---rrFGNYLFSSLvdqvl-parrvHYQSESMLNLMATASVtDLLCFTPKR 251 Vibrio cholerae...
YP_001502603 174 AAksnstid--enltfeqYQELPQSVLsl---rrSGKLALEMFledklevrrniSHEASSIMANILIVSQtMLFCHVPLR 248 Shewanella peal...
YP_269732    177 ARkghpnlnnktnlllseYLAEKHAVLap---rkGNVYPLSLAlqdfs-ynreiKYTSTSIENILEIVSAtDLICIMPGT 252 Colwellia psych...
YP_002313609 172 LSsehpriq--grmsedaFFAEEHILWqtk--rmDRYTLNSVAtkhlp--srrvAYSTGSAMTGLNLVADtEWLCVSSRW 245 Shewanella piez...
NP_762143    173 CCadhpria--dacsvaqFLAEEHVVVsrwharkSLMSEEDIAdlaq----rkiAYRASGALEMLPVIHGsEYIGMLPES 246 Vibrio vulnific...
YP_204802    177 CSkdhprig--dsisleqFLSEEHVAAsrwhsrsSLLNAEDIGelea----rniVIRAAGAFEMMPIIGStEMIGMLPQS 250 Vibrio fischeri...
Feature 1                                #                        
1UTH_A       257 FAVrcevpfGLTTSPHPAKLPDIAINLFWHAkynrDPGNMWLRQLFVEL 305 Burkholderia sp.
1UTB_B       257 FAVrcevpfGLTTSPHPAKLPDIAINLFWHAkynrDPGNMWLRQLFVEL 305 Burkholderia sp.
YP_001250875 249 LAVtfkdryQIELHPLPFPKKTFLVNFYYHKrlsnHKPLQWVLDVIKKY 297 Legionella pneumophila str. Corby
YP_268025    251 LVDkyrhiyQLKQLHSNFLLDPIKVAMYWHSsrtnDPSHKWLREQIVKV 299 Colwellia psychrerythraea 34H
NP_230430    252 LADmwaeklGLQIQPLPFEIRSVPTFMCWHKakqqDKGLIWLREQIEAI 300 Vibrio cholerae O1 biovar eltor str. N16961
YP_001502603 249 LAIhyqeqlSLKIIEPPISLKPVPVIMQWHKsnsiDPSHIWLRNRIKQI 297 Shewanella pealeana ATCC 700345
YP_269732    253 VLQsmhnvnDYIWFNPPFKTKQMIAYMNWHWsmehVKSHRWLRTIIIDI 301 Colwellia psychrerythraea 34H
YP_002313609 246 HSNqvavtgRIQVLELPFATQQVPVYMTWHHsqhkDAGHQWFREAIMTT 294 Shewanella piezotolerans WP3
NP_762143    247 TINafagtyNIKAVSLPFDHDVYDLCAIWHPsrssESAHQWLRNQLKAA 295 Vibrio vulnificus CMCP6
YP_204802    251 SIDdlgdyyNLKSLDLPLNRQQHDLCSIWHPsrsnDSGHRWLRQQIQKA 299 Vibrio fischeri ES114

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