Conserved Protein Domain Family
PBP2_SyrM

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cd08467: PBP2_SyrM 
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold.
Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156
View PSSM: cd08467
Aligned: 7 rows
Threshold Bit Score: 245.81
Threshold Setting Gi: 135168
Created: 21-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              # ##   #                                                         #        
CAA80556     132 GATLAIPDHQALAVLPRLLPWLRERAPhLDTLACLpfd-ravRGLEQGdiDLAVGHIdvqlpgYFRRSLYTDRFACLLRH 210 Rhizobium legum...
Q08812       132 GATLAIPDHQALAVLPRLLPWLRERAPhLDTLACLpfd-ravRGLEQGdiDLAVGHIdvqlpgYFRRSLYTDRFACLLRH 210 Rhizobium etli
P18561       122 KVTMAMPDHQAVVLLPHLLPRLHERAPhLDIVTDPllg-galGLLEQGeiDVVVGQMgaaplgYLRRRLYADSFTCVLRH 200 Sinorhizobium m...
YP_001525699  95 LMTIAPNSYAEFALIPTVVARLRAVAPgISLRLTPygsdlseTGVISGttAMAIGRFvevqdnLVVQHLMDDGLACVVRA 174 Azorhizobium ca...
YP_957292     97 HFEIAANDYFEVLILPALASVLREQAPgITLQVRRlsqdmseAGIMSGttDLAFGRQvdppdnLVVREVILEGIECLVGN 176 Marinobacter aq...
YP_613746     95 RFRLLLGPYAEVVLAPDLAEAFAQHAPkAQLELAPigpdldpRKLAAQsfDLAIGRFapppddLVVSDLFSDGFRCIVAP 174 Silicibacter sp...
NP_882961    110 EFSLCMSDSAEFAVIPFVAAEFGRRAPgCRIRGMRihhsqllAMLEKGeaDVALGSLagaapsLRQQRLTDHGMVCLVSG 189 Bordetella para...
Feature 1                                           #                                            
CAA80556     211 GHPAlaqew-----tidnFATLRHAAIstdspdhFGPIYDHLPnlra-drsPILFSSVLTAAVVASAtDLVLLVPRRVAT 284 Rhizobium legum...
Q08812       211 GHPAlaqew-----tidnFATLRHAAIstdspdhFGPIYDHLPnlra-drsPILFSSVLTAAVVASAtDLVLLVPRRVAT 284 Rhizobium etli
P18561       201 NHPAlaqew-----tieaFAALRHVAIasepdelFGQIYDRLTklglqrgdPMVVSTVLTAAVLIAAtDSVLVVPSRVAT 275 Sinorhizobium m...
YP_001525699 175 DHPDvgdvl-----tretYERLRHVNVlpp-grlRAGLFQVLErhglkrdvAVSVTHFLAVPEMIAVtDYCATLPRLICA 248 Azorhizobium ca...
YP_957292    177 EHPLlerlkgngqmtrddFERYAHVLIqph-trlKSGIFKQLEsqnlkrkvALAVTYFMAVPALLEGsSLIASLPTGLCQ 255 Marinobacter aq...
YP_613746    175 AALPegasl-----dldlYETLPHVIVapp-grwRTGVHKLTAasglqrntAVAVSHFLTAAPTVARiNGIATVPARIAA 248 Silicibacter sp...
NP_882961    190 QGRWadtpp-----tlddYAQGRHVAVrrv-sdnLAPVSERLRlngierniMITVSSDFVAAATVVQtDALCTVARAVAR 263 Bordetella para...
Feature 1                             #                        
CAA80556     285 QvsamlPLRVVDPPLEPAPYKVMLIWHErchhDPQHKWLRKEVAAA 330 Rhizobium leguminosarum
Q08812       285 QvsamlPLRVVDPPLEPAPYKVMLIWHErchhDPQHKWLRKEVAAA 330 Rhizobium etli
P18561       276 RvaamlSLAVIPPPVELRPYEVALIWHErchrDPEHRWLRGEIAAA 321 Sinorhizobium meliloti
YP_001525699 249 RlahdtRLKFVPAPVDLGTFPVDMAWHVryrhDPAHRWLRTLIAEV 294 Azorhizobium caulinodans ORS 571
YP_957292    256 HfrrqfAVTPVAPPVAFDAFPFHLSWHHryqkDPAHRWLREQIIAC 301 Marinobacter aquaeolei VT8
YP_613746    249 MvaapyGLRNVAVPRDLGTFPTQIAWHPhqrrDPRHVWLRDLLLSL 294 Silicibacter sp. TM1040
NP_882961    264 QlaaflPVRIQPLPFDVGTLATRMIWHEryqhDASHIWLRKLVRTA 309 Bordetella parapertussis 12822

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