Conserved Protein Domain Family
PBP2_NodD

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cd08462: PBP2_NodD 
The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold.
The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has 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: 176151
View PSSM: cd08462
Aligned: 20 rows
Threshold Bit Score: 257.558
Threshold Setting Gi: 222106523
Created: 30-Sep-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              # ##   #                                                         #        
AAA26190      98 VFRIISSDYSTSIFIRGVISAASTSLPlLRFELISpdd-nchDLLNKSevDALIMPEIFmssaHPFVPLFEEKMVCVGCa 176 Azorhizobium ca...
YP_660448     98 CYRIAASELTTMVLMPTVISRLAQDAPnIRLNLSTig---etDLLDKGdiDLMIIPKQFtqdgHPFDEIYQEGYKCICWq 174 Pseudoalteromon...
YP_002547314  98 SINLIVSDYTLNTIMPPFLRQVTALAPgVQIHFQPqqn-yphLLLERGeaDLLVAPSDFcstnHPSEPFLEDQICCVVDv 176 Agrobacterium v...
NP_773069     99 CFKILASDYTMATLVPALLARCEAAAPgIRFDFLQqvq-apeRALERGdvDLLIIPREFssklHPSEVIVEEDFCAIAWs 177 Bradyrhizobium ...
YP_002871578  98 KFVLMASDYVCTVLLPQVSRRLNELAPmASLEMIPpnd-tprETLERGnvDLLVLPATHlgddHPSLTIFEDRFVCMTCq 176 Pseudomonas flu...
YP_001341902  98 EFRICVSDYMLHTLIPYVIEMTQEQGCtVKLNFLPqvs-dpkNELDRGeaDLLILPEIFcsdyHLSEPLITDEFVCVVWd 176 Marinomonas sp....
YP_496506     98 RFRIIGSDYIMVAVLVPLIERFARTAPgVRIEIIQpne-hsvAELEAGraDLLVTPEPFlaswHPSEVLFDEEQVVVGWa 176 Novosphingobium...
YP_001341992  98 IFSIFCSDYTQTVLVPHALEIVGKQKStARFQLLAqvannphEQLEQGkaDLLIIPSDFmsteHPCDILYEEEFVCVVWk 177 Marinomonas sp....
YP_001262036  98 EFTIVASDYVQAVLLEPFMRKAAHHAPgMRFRILPisq-qgiDEFKRGviDLIIVADSVilpeHPSQKLFEDEAKLICSa 176 Sphingomonas wi...
YP_660428     98 HFVVSVSDYAYTILLADVVAKAASLAPsVTFEIVPpne-qvnERFERAeiDLLLTVDRFalpgHAFTELWRDEEVIISWq 176 Pseudoalteromon...
Feature 1                                    #                                                   
AAA26190     177 rnhedrnissiqeYLSMRHVVAkfgrgMRPSLEEWFmaengmrRRIDIVVQSFSMIPPVIQGtERIAIMPYRLVEHfsk- 255 Azorhizobium ca...
YP_660448    175 entsigekitfedYQSAGHVVVsygknNAPAFDSWFmshygisRRVEIMTSNLLAPPSLIIGtQRIATVHSRLAQIvsq- 253 Pseudoalteromon...
YP_002547314 177 ngplaegpmtekdFLEAGHVVMqp-pnGGETFAQRAcdrlglkIKVEASTFSFSSLPFLIRGsKRIAMVQRSLAECmln- 254 Agrobacterium v...
NP_773069    178 kgkfargklsrsdYTKASHVVMrp-aiATQSLETRYleqggvtRNEAISTYAFTAIPHLVVGtNRIATLHRRLAKLaqr- 255 Bradyrhizobium ...
YP_002871578 177 dnplvgdslsfeqYKQMGHVLVrwgmqRVPSMDEWFlnrynfeRRVEVITNAFSNVPTFLPGtLRIATMHLRLAQQcar- 255 Pseudomonas flu...
YP_001341902 177 qselskkgmtmdaFMSAGHICMqp-pnSNPSFETHAykikgvsRRIDVRTYSFSCIPSLVVGtNLIATLQKRLVDKsisq 255 Marinomonas sp....
YP_496506    177 qnpifargvtaddFYAAGHVTVafganRTPAFADSAlsrmgreRRVEVTVGSFASAPWFIEGtSRLAVLHERLVRQiar- 255 Novosphingobium...
YP_001341992 178 hskiasgeltaekYAAAGHVLMrpeatKKDFFGTLFtqkygikRHVIATTFSFASLPALVIGsENIATIHARLATKmak- 256 Marinomonas sp....
YP_001262036 177 dhptigdeismeqFGTVGHVTTslhhhRPGSLFDLMllersiaRRIEIQVPAFSMMAGAVVGtERVAILHARLATSyar- 255 Sphingomonas wi...
YP_660428    177 ganfd--tidadtFFACGHAVAsfgleRRPSIADNHinqagwkRRVEVQLPDFGALCQAVVGtKRLATMHRRYALHfak- 253 Pseudoalteromon...
Feature 1                         #                        
AAA26190     256 fmPLKVFALPFPLPRFTECLQWPSiatpDLGNRWLRAYLADH 297 Azorhizobium caulinodans
YP_660448    254 slPIRVLQPPIEIPPLTQSMQYHRnrenDVGLSWLRQLIIDV 295 Pseudoalteromonas atlantica T6c
YP_002547314 255 lgGIRIMDPPFPLPPLLQCLQWHSyrtrDPALVWFRSQMHEA 296 Agrobacterium vitis S4
NP_773069    256 slPIRIIELPVSLPIMQQCVQWHRyrsnDAGLIWLRDTMRAA 297 Bradyrhizobium japonicum USDA 110
YP_002871578 256 elPLKILPVPWDAPTLVMAIQWNRhqqhDPGLSWLRSLIVES 297 Pseudomonas fluorescens SBW25
YP_001341902 256 gmALKSFATPVKLPLLRESMQWHKyqhaDLGIIWLRQLMLAA 297 Marinomonas sp. MWYL1
YP_496506    256 rfNLAWARMPFDFPTMQEMMQFHEaraeDAGLAWLRQQMREV 297 Novosphingobium aromaticivorans DSM 12444
YP_001341992 257 vwPLKILPLPFDIPPMKQCVQWHQyrnnDEGLIWLRNTLKEA 298 Marinomonas sp. MWYL1
YP_001262036 256 ilPIKLLSLPFALPPIREVIQWHAlrqrDRGLQWLLEALTSE 297 Sphingomonas wittichii RW1
YP_660428    254 lyPIKLHSTWEPFPKIVEGMQWHKvrnlDPGLQWLAGLIKDG 295 Pseudoalteromonas atlantica T6c

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