Conserved Protein Domain Family
PBP2_NocR

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cd08458: PBP2_NocR 
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold.
This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147
View PSSM: cd08458
Aligned: 3 rows
Threshold Bit Score: 141.387
Threshold Setting Gi: 552033
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                    ## ##  #   # #######                                             
AAA50519  104 SLRVACYtapalSFMSGVIQTFIADRPdVSVYLDTvpsqtVLELVSLQHYDLGISIla-gdYPGLTTEPVPSfRAVCLLP 182 Agrobacterium tume...
P35112     93 SLRVACYtapalSFMSGVIQTFIADRPdVSVYLDTvpsqtVLELVSLQHYDLGISIla-gdYPGLTTEPVPSfRAVCLLP 171 Agrobacterium tume...
YP_551181  94 TLRIASMhtlglSLLSEGVRRFSLARPgVVISLDVrnslgILELTAAHQIDIGFVQmmgteYPGVDVFPLPSvPAVCVLP 173 Polaromonas sp. JS666
Feature 1                                                    ######     ## ##                 
AAA50519  183 PGHRLedketvhatdLEGESLICLSpvslLRMQTDAALDscgvhCNRRIESSLalNLCDLVSRGmGVGIVDPFtadyysa 262 Agrobacterium tume...
P35112    172 PGHRLedketvhatdLEGESLICLSpvslLRMQTDAALDscgvhCNRRIESSLalNLCDLVSRGmGVGIVDPFtadyysa 251 Agrobacterium tume...
YP_551181 174 RGHALarkkavqitdLQGESLISLSrnspMRMRLEMALEaagvtCRRSVDTTLahLACSMVAGGlGLTVVDPFtagrmra 253 Polaromonas sp. JS666
Feature 1                                          
AAA50519  263 nPVIQRSFDpvvPYHFAIVLPTdsppprLVSEFRAAL 299 Agrobacterium tumefaciens
P35112    252 nPVIQRSFDpvvPYHFAIVLPTdsppprLVSEFRAAL 288 Agrobacterium tumefaciens (strain T37)
YP_551181 254 pSVVYRPLLptvPCEFSMVLPAhqprskVVDDFIRVM 290 Polaromonas sp. JS666

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