Conserved Protein Domain Family
PBP2_MetR

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cd08441: PBP2_MetR 
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold.
MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132
View PSSM: cd08441
Aligned: 32 rows
Threshold Bit Score: 252.487
Threshold Setting Gi: 145299295
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                       ## ##  #   # #######                                             
P0A9F9        90 RLRIAIECHsCIQWLTPALENFHKNWPqVEMDFKSgvtfdpqPALQQGelDLVMtsdilprsgLHYSPMFDYEVRLVLAP 169 Escherichia col...
AAF33428      90 RLRIAIECHsCIQWLTPALENFRASWPqVEMDFTSgvtfdpqPALQQGelDLVMtsdilprsgLHYSPMFDFEVRLVLAP 169 Salmonella ente...
YP_928500     93 LLKVGIECHsCFRWLMPVIETFRAEYPdADLDLSSrhlfdslNALESGelDIVLtsdpvpghqLAYQHLFDFEVRLVVAK 172 Shewanella amaz...
NP_231342     93 RLHMAIECHsCFQWLMPALREYQVSWPnVALDFSSgfgfeplPALLAGelDLVItsdilprseVHYEPLFDFEMRLITAT 172 Vibrio cholerae...
YP_001142136 100 RLHLALDCHsCIQWLLPLLPDFRRQWPgVDLEVESvpgfdaiNALLGGqlDLLLtsdvqargdLHFEPLFAFDLTLVMAP 179 Aeromonas salmo...
CAC81937      93 SLRIGMECHpCYQWLLRVIEPYLEHWPdIDIDVKQefqfgalGALLSYeiDVLItpdplfkpkISYIPVFNYEHRLVVAK 172 Aliivibrio salm...
YP_002894118  91 QLRINVECHsCIRWLTPALQQLQQRYPdLELTFASqldftpqQALLQGelDMVLtadllpengIYYAPLFDFEMRLVLPV 170 Tolumonas auens...
YP_526111     93 QLRLGMECHpCYEWLMTVVAPFLTRWPdVDLDVIQqfrfdglAALREHkiDILItsdpmdapeLAHCPVLDYELLLVVAA 172 Saccharophagus ...
YP_001352439  93 ALRIGMECHpCYQWLLKIVSPYLSAWPdVDVDVKQkfqfggiGALFAYeiDLLVtpdplykpgLKFEPVFDYEQVLVVAR 172 Janthinobacteri...
YP_002127146  93 ILRIGMECYpCFEWLLKVVAPFLKAFPdVDVDVRRafsfgglQALHGYdiDILLtpdplsldtIAYTPVFEYEQVLAMDK 172 Alteromonas mac...
Feature 1                                                      ######     ## ##                  
P0A9F9       170 DHPLaaktritpedlaseTLLIYPvqrsRLDVWRhFLQPAGVSp-sLKSVDNTllLIQMVAArmGIAALPHWvvesferq 248 Escherichia col...
AAF33428     170 DHPLasktqitpedlaseTLLIYPvqrsRLDVWRhFLQPAGISp-lLKSVDNTllLIQMVAArmGIAALPHWvvesverq 248 Salmonella ente...
YP_928500    173 EHPLaskslvlpkdlaglPIISYPvpleRLDLFRlFLEPAGIEpgvQKSCDLTsvLFQRIACqdGIAALPSWsiseaqgl 252 Shewanella amaz...
NP_231342    173 NHPLadkagiepqdladqTMLTYPvqkqRLDVVKhFLQPAGVEparWKQADNTlmLVQMVSAglGVAALPNWaisefsrq 252 Vibrio cholerae...
YP_001142136 180 DHPLchqgritpedlkqeVLLVYPveraRMDVFSrFLQPAGVEparCKLVDNTsvMLQMAAAglGVAALPRWaseefvrq 259 Aeromonas salmo...
CAC81937     173 SHKLatqefvlpeqlseeVLFSYPveplRLDIFSqFLNPAKCSvkkHKTIETTeiMLQMVAAgrGICALPGWlvdeyskt 252 Aliivibrio salm...
YP_002894118 171 THPLasaelitaenlsdeVLLTYPvvpqRLDVLRhFMQPAGLKpkqIKTLENTlmLTQMVAAgwGITVLPDWvcrefeqq 250 Tolumonas auens...
YP_526111    173 NTPQakltsinagdlqqqTLITFPveraRLDVFThFLIPAAIEpkrQHAVETIevMLQLVSSnrGVCTLPNWlvekyqhh 252 Saccharophagus ...
YP_001352439 173 DHALakvkyvkpeqlmneVLITYPvatdRLDVYNqFLLPAGVTpkrHKTIETTdiMLQMVASgrGVAALPRWlvqeyagk 252 Janthinobacteri...
YP_002127146 173 HHPLadkpfikpqdlsneTLITYPvelsRLDIFThFLTPANCTvrqHKTIETTeiILQMVAAgrGVTALPKWlidesker 252 Alteromonas mac...
Feature 1                                              
P0A9F9       249 GLVVTktl-geGLWSRLYAAVRDgeqrqpvTEAFIRSA 285 Escherichia coli K-12
AAF33428     249 GLVVTktl-gdGLWSRLYAAVRDgdqrqavTEAFIRST 285 Salmonella enterica subsp. enterica serovar Typhimurium s...
YP_928500    253 SLTSLrlg-aeGVKRPLFGAYRRgsansrqLQRYLELV 289 Shewanella amazonensis SB2B
NP_231342    253 GLITSkpl-gkGLWRRLFAATRHsekdkryLQAFFATA 289 Vibrio cholerae O1 biovar eltor str. N16961
YP_001142136 260 GLLEArpl-gnGVRRHMYGAVRAadkdqpcLQSLFERI 296 Aeromonas salmonicida subsp. salmonicida A449
CAC81937     253 MPIKSlrfgeqGINKRIFVGIRNneqhidyLNDFIAQA 290 Aliivibrio salmonicida
YP_002894118 251 QLIISkal-gdGLWRRLHAAVRVgerqqpaIRTLIKAL 287 Tolumonas auensis DSM 9187
YP_526111    253 HPISGvrlgqsGVHKTLYLVYRRddskldyINDFLTTA 290 Saccharophagus degradans 2-40
YP_001352439 253 VDVVPvrlgpdGIAKQIFLGAREadldtdyLQAFIALA 290 Janthinobacterium sp. Marseille
YP_002127146 253 DLLTYrslgevGVSKTLYLGHRKaqdvlgfVDDFIALS 290 Alteromonas macleodii 'Deep ecotype'

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