2F6G,3GLB,2H99,2F6P,2H98,2F7B


Conserved Protein Domain Family
PBP2_BenM_CatM_CatR

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cd08445: PBP2_BenM_CatM_CatR 
Click on image for an interactive view with Cn3D
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold.
This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136
View PSSM: cd08445
Aligned: 24 rows
Threshold Bit Score: 274.875
Threshold Setting Gi: 226943019
Created: 22-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 9 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 A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1               #                              #                 ##                      
2F6G_A        10 KTIRIGFVgSLLFGLLPRIIHLYRQAHPnLRIELYEmgTKAQTEALKEGRIDAGFGRLkisDPAIKRTLLRNERLMVAVH 89  Acinetobacter b...
3GLB_A         2 QTLRIGYVsSLLYGLLPEIIYLFRQQNPeIHIELIEcgTKDQINALKQGKIDLGFGRLkitDPAIRHIVLHKEQLKLAIH 81  Acinetobacter s...
YP_001416037  91 SLFVVGCVaSTLYGGMPDLARRMRRLWPdMEIELKEmsSTQQVAALKEGRIDLGFGRVrvtDPAIERITLREERLVLALP 170 Xanthobacter au...
BAA61956      91 EKLTIGFVaSALYAALPTVIRRLRRVRPdLDFKWVEmtSGEQIIALQEGKIDVGFGRVyteTTEVCRTVLREERLLAAFP 170 Pseudomonas putida
YP_580536     90 NSLSIGFVsSILYGILPKVIARFREVYPnIEIKLYElnSWQQTQSLVEGKIDVGYGRLlfeDASIRRLLLREESLVVAVP 169 Psychrobacter c...
YP_001768273  91 NRFRVGFVaSTLYGRLPEILRGYRLKRPdVDLTLLEllTLEQIAALKEGRIDVGFGRIeieDPAIARVLLRNETMIVAVP 170 Methylobacteriu...
BAA75209      90 ERIVIGFVpSTLYGALPAVIRAFREAAPhIELSLIEmfTIEQLGALKGGRIDVGFGRLrfdDAQLAREVLVEERMIAALP 169 Frateuria sp. A...
BAC16778      90 RTLSIGFVgSTLYGMLPKIIRRFRDENTtVELSLHEmsTMDQIRALKSGQIDVGFGRIrheEANIRRVILREEKMIVALP 169 Burkholderia sp...
YP_495818     91 RRFTIGFVaSTIYARLPELIRAFRKRAPdVELTLVEssTLEQLAALKDGRIDVGFGRIrfeDPAIKRIILRNERLAVALP 170 Novosphingobium...
YP_001630007 105 QTLSIGFVaSTLYGGLPMLVRKLRQRYPeVDIQLVEltSMQQFAALKSGRIDVGFGRIrsnDSSVERIVLREERLVLALP 184 Bordetella petr...
Feature 1                                 ##     ##                       #                      
2F6G_A        90 ASHplnqmkdkgvhlndLIDEKILLYPsspkPNFSTHVMNIFSDhGLEPtkINEVREVQLALGLVAAGeGISLVPAStqs 169 Acinetobacter b...
3GLB_A        82 KHHhlnqfaatgvhlsqIIDEPMLLYPvsqkPNFATFIQSLFTElGLVPskLTEIREIQLALGLVAAGeGVCIVPASamd 161 Acinetobacter s...
YP_001416037 171 LDHpklahkg-plplatLEDEMLVLYPseprPSFADEVLVLLGDrNVRPraIREVRELQMALGLVAADdGVTIVPASaqr 249 Xanthobacter au...
BAA61956     171 STFalaaeas-pislseFGDLPVIVYPahihPSFADQVTKLLQAhGSVAseIHAVGDLQTALGLASAEsGYCIIPASarh 249 Pseudomonas putida
YP_580536    170 VKHrlaqekqksirlmdLTNENLLLYPmaprPSFIDYVLELFEArNLKAnyFTEVRELHIALGLVAAGeGLTIVPKTleh 249 Psychrobacter c...
YP_001768273 171 TAWdaarppg-plrlrdLADTPLIIYPksarPNNADRILALFRDhAVRPpvIHEVRELQTALGLVAAEaGVCVVPASver 249 Methylobacteriu...
BAA75209     170 QDHplarqkk-pltlaaLAQETLIVYPstprPSYADQQLSAMHDhALEPraVHEVRELQTALGLVAAQvGVCLVPESveg 248 Frateuria sp. A...
BAC16778     170 EGHslslvkp-vlalsdLVNETLIIFPkaprPSYADQVLSAFKDrGLKPrrIYEVRELQIALGLVAAGeGISVVPSSvyg 248 Burkholderia sp...
YP_495818    171 RDHplalddr-pltlkqVAAEPQILYPraprPSYADQVISLFRDhGLEPriAHEARELQIAIGLVAAEeGLAIIPESisr 249 Novosphingobium...
YP_001630007 185 PGSpltegde-qvtlkaLEGQKLIVYPkeprPSFADHILSLLNDqAIRPseIHEVREIQTALGLVAAEsGICLIPASarl 263 Bordetella petr...
Feature 1                                                    
2F6G_A       170 iqlfNLSYVPLLdpdaITPIYIAVRNmeestyIYSLYETIRQIY 213 Acinetobacter baylyi
3GLB_A       162 igvkNLLYIPILdddaYSPISLAVRNmdhsnyIPKILACVQEVF 205 Acinetobacter sp. ADP1
YP_001416037 250 lrsyDVAYRHFDdpklVSPIIMSYRAndasgrIEAIKQLIREMY 293 Xanthobacter autotrophicus Py2
BAA61956     250 -lrpELTYRLISepeaVSPLIMSYRPedesgiVATIKQLTRELY 292 Pseudomonas putida
YP_580536    250 lrsqEVTYIPFEdgllTSPIVMSVRHfdkselLKTLLDVTYQIY 293 Psychrobacter cryohalolentis K5
YP_001768273 250 lrrdGVAYRPLNeeraLIPVIMSYRKddpspeIPLILQCVREDY 293 Methylobacterium sp. 4-46
BAA75209     249 lrahGVVYRPVPaaniASPIIMSRRLqdesptTTLLCSLARELF 292 Frateuria sp. ANA-18
BAC16778     249 lkrdDVSYKELDdptlVSPIIMSMRAldesrdIREMLELIYRLY 292 Burkholderia sp. TH2
YP_495818    250 srshDVVYRELAea-aTSPIIMSHRMndssaeLRLMAQVIASEY 292 Novosphingobium aromaticivorans DSM 12444
YP_001630007 264 --rnDLHYRLIDdtraTSPIILTHRIndngwyIDAVKQVVADMY 305 Bordetella petrii DSM 12804

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