Conserved Protein Domain Family
PBP2_OccR

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cd08457: PBP2_OccR 
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold.
This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146
View PSSM: cd08457
Aligned: 6 rows
Threshold Bit Score: 251.64
Threshold Setting Gi: 86360499
Created: 19-Oct-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on sequence similarity to the known structures of LysR-type transcriptional regulators.
  • Comment:most members of the LysR family of transcriptional regulators are tetrameric, while CrgA assembles into octameric rings

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                       ## ##  #   # #######                                             
P0A4T4        92 TLRIAAMPalanGLLPRFLAQFIRDRPnLQVSLMGlpssmVMEAVASGRADIGYADgpq--erqGFLIETRSlPAVVAVP 169 Agrobacterium t...
P72294        92 TLRIAAMPalanGFLPRFLAQFLHKPK-LQVSLMGlpssmVMEAVASGRADIGYADgps--erqGFLIETRSlPAMVAVP 168 Sinorhizobium m...
ZP_04681602   92 MLRIAAMPalanGIMPRFLARFLRERPnIHASLNGissalVVEAVASGQVDLGFADgpl--drpGFDIETRAiPAVVAVP 169 Ochrobactrum in...
YP_001672311  98 RLRIGVMPicsnSFMPDVIAAFLSLHPnVSIELESasriqLLEMVRSHRIDIAITTnveadedeFSCRFLRRhRAVVLLH 177 Shewanella hali...
YP_002987413 101 PLVVAATPamsvGLLPQALARLTLTAPlQLLSQSAe---qTLQAVIAGHADLAISSlple-hqnVNRHWIGQsRCVVVLN 176 Dickeya dadanti...
YP_472387    100 TLTIAATPslaaGILPQALAALSPGLIpRHLHVQAlaaenVVQAVLARSADLGISSlple-hpgLDIHWIAEaPCVIAIG 178 Rhizobium etli ...
Feature 1                                                       ######     ## ##                 
P0A4T4       170 MGHRLagldrvtpqdLAGERIIKQEtgtlFAMRVEVAIggiq--rrpSIEVSLshTALSLVREGaGIAIIDPAaaie-ft 246 Agrobacterium t...
P72294       169 MGHRLagldritpqePGGERIIKQEtgtlFAMRVEVAIgsil--rrpSLEVSLshTALSLVREAaGIAIIDPTaaie-fk 245 Sinorhizobium m...
ZP_04681602  170 LGHRLadysevspedLANERMITLEpgslFAMRVEVALarip--rsaTIETRLshTALTLVAEGvGITIIDPSsatdfrg 247 Ochrobactrum in...
YP_001672311 178 EGHPLaqksslspidLKHERFMTLAygspFRTRVEDAFlkqsvkrniILEAREqsTLFQLVRKGvGIAILDPFvlhs-ga 256 Shewanella hali...
YP_002987413 177 DNDPLaqapvvalqaLASRRLITLYnpyrLRNRFEQVLkkagikpryVIETNSsaTILSCVRAGlGAAITEPVtayglpl 256 Dickeya dadanti...
YP_472387    179 ADDPLaandvvrladLAEHRIITLAnpyrLRHRVDEAMeragvapdrIIDVNAslTALSLVRAGlGIAIVEPAtvcgvpl 258 Rhizobium etli ...
Feature 1                                             
P0A4T4       247 dRIVLRPFSifiDAGFLEVRSAigapstIVDRFTTEF 283 Agrobacterium tumefaciens (strain Ach5)
P72294       246 dSIALRPFSifiDAGFLEVRSAngapstVVDRFATEF 282 Sinorhizobium meliloti
ZP_04681602  248 rGVAIRPFTtfvDAGFLVIRRSngpdnsLAQRFIDEF 284 Ochrobactrum intermedium LMG 3301
YP_001672311 257 dGIVSRPFEpvtEWEYHVVQAKgiqtprMVNAFLDIL 293 Shewanella halifaxensis HAW-EB4
YP_002987413 257 dGLAIRELDtdiPYHFGVVTPQsrtprtPVLQLIDAL 293 Dickeya dadantii Ech703
YP_472387    259 dGIVMRALDqaiPFLFGAISAAalplapTVAAAIDAA 295 Rhizobium etli CFN 42

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