Conserved Protein Domain Family
PBP2_MdcR

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cd08416: PBP2_MdcR 
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold.
This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 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. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 176108
View PSSM: cd08416
Aligned: 9 rows
Threshold Bit Score: 322.373
Threshold Setting Gi: 119947262
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                       ## ##  #   # #######                                             
YP_002384235  97 TLRLGLLYSlvmKTAPQIVQGLKNRRPeLTIEFIMNSNkkLLEALNEGkVDAVLvstpde-yntqlFETWTIFSDSIFLA 175 Escherichia fer...
AAC45461     100 RLRIGTLYSltlETVPRIIMGMKLRRPeLELDLTMGSNqmLLDMLEDDaLDAILiatnegefnntaFDVVPLFEDDIFLA 179 Klebsiella pneu...
NP_794810     98 RFRLGALYSltvKTVPQLIMGLKIRRSeLNIDLILGSNidLLYKLKNMeVDAMLvsldes-tndpdCEHLALFSDDIFLA 176 Pseudomonas syr...
YP_001155408  97 QIRLGSMYSltaNIIPRLIMGTKIRRPdLDIDLYLGSNedLMKKLSEGqIDAVViatpsg-klpedIQVVPLFEDQLFFA 175 Polynucleobacte...
YP_001893447  98 TLKIGGLYSmtvGTLPRIFAGLKTRRSaLDIELTLGSNrsLLAKLEDGqLDAIVialgep-lrnpdLLTVPMFDDEILFA 176 Ralstonia picke...
YP_944942     97 HFKLGSIYSltfNSIPALITSMKKQDKkLEIELTTSSNkyLFKKLTALeLDVIVvsldap-lldpsLIFFPLFEDHLALA 175 Psychromonas in...
YP_046423     98 VLHLGSLYSltvNTIPNVISRLKLRRGeLDIQLLLSSNldLVKKLKSTeLDAIIvalnet-trdpdFESLPMFEDNIYLA 176 Acinetobacter s...
P52684       100 RLRIGTLYSltlETVPRIIMGMKLRRPeLELDLTMGSNqmLLDMLEDDaLDAILiatnegefnntaFDVVPLFEDDIFLA 179 Klebsiella pneu...
YP_299116    100 HLKIGSLYSltaHTVPQIVIGLKARRPdLQTELVLGSNadLLQMLKQGsIDATLmatpe---pdpeIESIPLFEDEIFFA 176 Ralstonia eutro...
Feature 1                                                         ######     ## ##               
YP_002384235 176 VPvtdvdllespvdlcqlqNKKFIALSeGFATWRGFQEAFKiAGFEPEITVRVHDIFsLMSMVNAGvGYSLIPGRmrdlf 255 Escherichia fer...
AAC45461     180 APaterldasrladlrdyaDRKFVSLAeGFATYAGFREAFHiAGFEPEIVTRVNDIFsMISLVQAGvGFALLPGRmkkvy 259 Klebsiella pneu...
NP_794810    177 VPtdspfaehhevdlidlrEATFITLTqGFATHRDGVRVFQqAGFEPKVAMQVNDIFtLLSMVSSGvGYALLPGRiaavy 256 Pseudomonas syr...
YP_001155408 176 SSksskplsg-aidlldyrDEKFVTLQdGFATTSGFDDAFAlAGFKPNVVMKVGDIFsLMNMVSGDmGRSLLPGRvrslm 254 Polynucleobacte...
YP_001893447 177 APlgspyaasaeidlqtvhGEKFVALGdDFATYHDFMAAFDkAGFAPQIALRVGDIFsLMNLVSGGiGYALLPRRvad-f 255 Ralstonia picke...
YP_944942    176 VPvndplasyssialadikNCPFVMLSkGFATAQDVLRTFEkAQIKPNVVMEVNDIFsLISMVSTGlGYSLLPNRiaril 255 Psychromonas in...
YP_046423    177 VNkhsplasldeidlstlkDETFLTLSkGFATRNDSDLVFEkAGIDPKVFLQVSDIFtLVSMVSTGvGLALLPGRistiy 256 Acinetobacter s...
P52684       180 APaterldasrladlrdyaDRKFVSLAeGFATYAGFREAFHiAGFEPEIVTRVNDIFsMISLVQAGvGFALLPGRmkkvy 259 Klebsiella pneu...
YP_299116    177 APadspyaampavdlracqDEPFVSLSeGFATSRGFAEAFKiADFQPNLVMKVGDIFsLMNLVGGGvGYTLLPGRvkavh 256 Ralstonia eutro...
Feature 1                                                 
YP_002384235 256 tsGIRLLPLQIPYr-mEQEISLVFPRsqetHPSILSLLAEC 295 Escherichia fergusonii ATCC 35469
AAC45461     260 ekDVQLLKLAEPYq-mRQLISIVYSHhrerDADLLALAAEG 299 Klebsiella pneumoniae
NP_794810    257 enRVRLIPLQSRYr-mQQHIGVVFLKskerDPNLLALLAEC 296 Pseudomonas syringae pv. tomato str. DC3000
YP_001155408 255 gdAIDFIPLAPKYq-vVQRIALMYLQanesNPNILALAAEG 294 Polynucleobacter sp. QLW-P1DMWA-1
YP_001893447 256 spKVQLIPLAARYa-iSQHIVLVIQRnrerDPNLLALSAEC 295 Ralstonia pickettii 12J
YP_944942    256 ndKVKLIPLHEQDk-iKQTITMVCLAsrskEPKILAFTKQC 295 Psychromonas ingrahamii 37
YP_046423    257 esSVKLIPLQGSYq-iKQEIGLVFLKskerDPNLLALVAEC 296 Acinetobacter sp. ADP1
P52684       260 ekDVQLLKLAEPYq-mRQLISIVYSHhrerDADLLALAAEG 299 Klebsiella pneumoniae
YP_299116    257 srNVAFVPLTSDYdniRQTIGLSFLRrrerDPNLLALAAVC 297 Ralstonia eutropha JMP134

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