Conserved Protein Domain Family
PBP2_DntR_like_2

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cd08464: PBP2_DntR_like_2 
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold.
This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. 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: 176153
View PSSM: cd08464
Aligned: 27 rows
Threshold Bit Score: 207.471
Threshold Setting Gi: 251789889
Created: 13-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putativeputative
Feature 1:putative substrate binding pocket [chemical binding site]
Evidence:
  • Comment:based on the sequence-structure comparison with Burkholderia sp. DntR structure (1UTH_A)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              # ##   #                                                          #       
CAB91105     101 VFRIGLSDDAEFALLPQLLKRIRAEAPgIVLVVRRvnyllmpTLLASGeISVGVSYTsel-panAKRKVLRRSMPKLLRA 179 Pseudomonas putida
YP_001348385 104 VFNIALSDDIESYLAPCIVNAAAAEGLgVSFAFHQsnsslwkQSLLDPdMDLVICSEpkdfntsYSSQVLFSSSYSCLFR 183 Pseudomonas aer...
YP_946152    104 TFHIAMSDDLEAVFVPKIVTEAIRSNWnVKFSFHQtnsvlwqEALDDPrMDLVMCATppqvpaaYHHSVLFASSYTCLYD 183 Arthrobacter au...
YP_260014    101 SVTLGLSDDFEIAYGRQMIEAVARRAPkLRLIFRQshsqivaEALLQRsVDLAISAGgfa-erlLSRQVLGEGHYLCLAD 179 Pseudomonas flu...
YP_002910063 101 AVSVAMSDDFEIAFGGRLIECAARLAPgLRVIFRQthsqivgDALANReVDLAIAAGgfa-trgLGHMALGHGRYACLVD 179 Burkholderia gl...
YP_002989275 101 TVTMGWSDDYEIALARTLTNQVAAEYPgIRLIFRQthsrvaaDMLMERaVDLAISTEgfs-ssiLGRQVLGGGSYACLLD 179 Dickeya dadanti...
ACV74679     105 HFSIGMSDDFQLALGSEISKQIQAIAPeASVVYRQtnrytaqQMLENNdIDLAIVTAslp-rrgLWQQVIGEGGYACLCD 183 Zymomonas mobil...
YP_001203964 104 VFRIGAMDYVQAVIADPLLAVLQAQAPgCKLILTTtdcdtagRSLARGeIDLAIGAFpqi-kagSHQELLYRERYECVFD 182 Bradyrhizobium ...
YP_003004610 101 TVTLGLSDDFELALGQMLIARLHQRAPgLRLVFRQahsqiaaDLLLRHeLDLALTAGgfs-yrsLSKVQVASGGYACLVS 179 Dickeya zeae Ec...
YP_001520387 104 DFRIATNDYVEATLSANLLQQLTQQAPgIQIRVKGlnkdavlAALDDNsIDLFIGAGldl-krwHVQESLYQEEFVCVLQ 182 Acaryochloris m...
Feature 1                                      #                                                 
CAB91105     180 dsvpgs----itlddFCARPHALVsfagdLSGFIDEALeeigrkrhvVLAVPQFNGLGSLLAGtDIVATVPDYTADAlta 255 Pseudomonas putida
YP_001348385 184 prgsmag-aaiglddYFAANHVRIsy-dgRRGFIDDLFesagyarrvTASFTHFAGALSTLMSgEVIATLPTFAAETysr 261 Pseudomonas aer...
YP_946152    184 gqrmkls-eplsledYAGSGHLRVsy-daQRGFVDEILesqgyerkaVASISHFAGAVAVLRAaDLIATIPTYTAKAfsd 261 Arthrobacter au...
YP_260014    180 paslapgqqqisleeFVAREHLLVss-qgFIGITDEGLanlglsrqvCASTTHFAALPFLLKGsQAVATIPAHAARRiae 258 Pseudomonas flu...
YP_002910063 180 paaapgr-lvltlddFLAREHVLVss-ggVVGIVDEALaeigrrrtvRASTTHFAALPFLLRGtPAVATIPHHAAEAlar 257 Burkholderia gl...
YP_002989275 180 nrpdapd--altleeYIRRRHILVss-ggFIGIVDEALaalglqrriEVSTTHFAAVPYLLKGsESLVTLPAHAAYPiaa 256 Dickeya dadanti...
ACV74679     184 aqscgfs-enptleaYLSLPHILVsy-sgREGLVDEILsimgrsrkiQTALTHFAALPPFLLGsKSIATIPSHAAISlag 261 Zymomonas mobil...
YP_001203964 183 akacrlg-krvtraqWLALPHVIMsvhgdYSGPLDDVLkssgeqrevAVSTPNFLAIPFLLRNkRLIAALPSRMARAfcg 261 Bradyrhizobium ...
YP_003004610 180 rdvtt-----lslerFIHTPHLLIsh-ggHIGLVDEQLaelgfsrriAASTTHFAAIPWLLQDdTLLATLPAHAAQAiaa 253 Dickeya zeae Ec...
YP_001520387 183 sdcplt---elsleqYVERTHILVsfqddFRGIGDLILeqqqqsrqvVWSTPHFMVVPFLLANsDCVALLPKRMAERcak 259 Acaryochloris m...
Feature 1                          #                        
CAB91105     256 -agGLRAEDLPIPVRSFELHMAWRGaqdnDPAERWLRSRIQMF 297 Pseudomonas putida
YP_001348385 262 -mmDLHCCPVPLPVPSFRCFMVWDVakhnKTHHDWLRRFVGEI 303 Pseudomonas aeruginosa PA7
YP_946152    262 -aaGLTMSQPPVPMPRFTISLIWEVpketQPEHVWLRKMMQAC 303 Arthrobacter aurescens TC1
YP_260014    259 -ltGLQLLPCPLALPRYPIELGWRTspqtDPLLVKVREAIVES 300 Pseudomonas fluorescens Pf-5
YP_002910063 258 -mtGLGLVACPLAMPAYPVALGWRVstlrDAAVAKLRQAIVDS 299 Burkholderia glumae BGR1
YP_002989275 257 -iaDLRVLPCPLVLPGYAIELGWRLdalrDPAVVAVRQAVQCV 298 Dickeya dadantii Ech703
ACV74679     262 -ytGLTIFEAPLELTAYPIIATMRLssqkDTALLWLFQIIKQA 303 Zymomonas mobilis subsp. mobilis NCIB 11163
YP_001203964 262 -rlGLSTCPLPFTAPTFDVTMIWHArtgdEPGAAWLRDQITAI 303 Bradyrhizobium sp. ORS278
YP_003004610 254 rtpHLRCLPCPLSMPDYAIELGFRPtiirDGAVRLVRETLSQL 296 Dickeya zeae Ech1591
YP_001520387 260 -emGLKLLPPPIDVTRFTVSMIWHQrhnnRPQHQWLRKQFLIA 301 Acaryochloris marina MBIC11017

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