Conserved Protein Domain Family
PBP2_LTTR_like_4

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cd08440: PBP2_LTTR_like_4 
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are 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. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. 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: 176131
View PSSM: cd08440
Aligned: 83 rows
Threshold Bit Score: 157.687
Threshold Setting Gi: 33598701
Created: 22-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_001972347  96 TVTIAclptaafYFLPSVMARFHEAHPnVRFRILDipateglQAVERGeVEFGInfmga---ndpnLDFDVLAEdPFVLA 172 Stenotrophomona...
YP_001106594  90 AVAVAtlpsvaaVLLPQVISAFRAQRPrVAVHIMDglersvlGRVLSGdADFAIttvge---psdqLEQRPLVRdRFVAV 166 Saccharopolyspo...
YP_705203     98 IVTVAclpslaaTFLPPYVVSFREQHPdVRLQIRDglrqevlDAVYSGtVDLALvttsg---ilpgLQQDVLTSdSFYCA 174 Rhodococcus sp....
YP_003133698  96 SVSIAalpslaaTMLPHVLAKFRTARPdVAVTVLDglsqdvlDHVARGsADMAVtvaat---vpptLHARPIAVdRFVCV 172 Saccharomonospo...
NP_462734     94 LVRVVgapliacAFLPQIIHAFKRQHPhTHVQLIDkpmsqlqKSIMLGeADFGIgperp---lepeIDKQTLFTtEIALY 170 Salmonella typh...
YP_002946970  94 LLRLAapqlmacTLMPRVIALYREAFPdVDVRLADtlpehllAGVTAGdVELAVgqdva---vdgaVERRTLFRdRHWLI 170 Variovorax para...
YP_257939     93 LVRVAavpsfaiTLLPPLLKQFHEQHPqFHLDIRDmdservvQAVLSGdVDIGIgtvpa---sipnIDQDFLFSdAFCVV 169 Pseudomonas flu...
YP_550154     94 VVRVAapqlmacTLMPDAIAAFNSKYPaVQIRLSDcaveavqSKVHSGeVDFAIgpere---vspeIATHSLFEiPFVAV 170 Polaromonas sp....
YP_299693     94 RITVAttpllasTLLPESIAHFLDAYPaITVRIADlpaeqigRRVLSGdVDFGFgvfpe---edpqFDRIPLLRhPLGVM 170 Ralstonia eutro...
YP_580817     94 QVRLAvsq-faaSSMPAVIAQFAKEYPeISVSLLDcsaenvlEHIQNIeVDLGVgtelefmdaeddISADLLYQlPFCVV 172 Psychrobacter c...
Feature 1                                                           ######     ## ##             
YP_001972347 173 CRRDHPLarkr-kveWADLaehQLITVhrtsgnrtlldg-alarenlklswHYEVTHlstSLGMVEAGi-GVSVLPkmat 249 Stenotrophomona...
YP_001106594 167 LPPDHPFteap-evaWEDLagePFLAVgrdssvrrltda-afaqidahaapAAEASSvatVGGLVAAGl-GVSALPalvl 243 Saccharopolyspo...
YP_705203    175 VAPTHPFadrp-alrWSDLagqPFIAFgpessiaapvrr-avedarielgpVMQAQNigaVAGLAAAGl-GVTAVPelvl 251 Rhodococcus sp....
YP_003133698 173 FPPGHRFaehs-eitWNDLdgeEFVAFdptssirayvdr-ilsrhgvrlgsVTQARNvgaVAGLTASGl-GVSAVPglvl 249 Saccharomonospo...
NP_462734    171 CHPDYRLhkk--tvrWEEIqseELIAVgnesipmis------atagvrikpKMTVEHmatAMSLAAQCe-GVVIAGtfsr 241 Salmonella typh...
YP_002946970 171 CPPGHAFakrr-kvrWHELgpyTFIAPtrdfrqrvlpelapaerelmlrpgTQEVSYmttALGMVASGl-GLTVCPtysa 248 Variovorax para...
YP_257939    170 CASDNPLnrlarplrWSDLdgqNFINSglgaeinaa------efrhirdhsTLSVRNttsLLALVAQGm-GVTLLPells 242 Pseudomonas flu...
YP_550154    171 FPPDHPLgklk-rvtWTDIsryPLISLqgeytqrlsadl-qaasgnltlspGMEVTFmttALSMVSAGlgVTTCLPyats 248 Polaromonas sp....
YP_299693    171 VPSSWPLatrkrdlvWSDLegqPLIAMshatgmrtlidq-qlhqagvqvnpRFEVAYlgtAVGLAEAGl-GVTVVPayvg 248 Ralstonia eutro...
YP_580817    173 MPDSHALarks-eivWQDLidtPLITLqgpfieqvtael-derianhiqqaRYKVNFmstALEMTRQGfgITLCLPympe 250 Psychrobacter c...
Feature 1                                                     
YP_001972347 250 p--dgdhpTLVTRtignPVVSRTIGIVRRRgalLSPTAERFLQML 292 Stenotrophomonas maltophilia K279a
YP_001106594 244 p--lvgagPVVTRplvePEVDRRLDIALRAqraRPLAADRFLETL 286 Saccharopolyspora erythraea NRRL 2338
YP_705203    252 p--misfaGLVHIpl-qPTVERTISLVQVAgrpQTASTRGFVNML 293 Rhodococcus sp. RHA1
YP_003133698 250 p--mmtfaEIDSRplvePVVERDICLVHDPtrpLSRTALALMELL 292 Saccharomonospora viridis DSM 43017
NP_462734    242 h--yaksyQLATCsl-tPPLRRNMNLYFHAwraQTPATQRFRDFL 283 Salmonella typhimurium LT2
YP_002946970 249 p--lvrahGLQMVrlesPDFHREVCIYSAArrtLSPAAASFVEIL 291 Variovorax paradoxus S110
YP_257939    243 r--saagdQLNFLrledQRIVRSVSVITAPretLNHASYTFLKAL 285 Pseudomonas fluorescens Pf-5
YP_550154    249 l---lnlyGLQTRllqaPTLRRKFYLLTKKdrpLSPAAQGFSDFL 290 Polaromonas sp. JS666
YP_299693    249 k--lmgsdRVRFRplhkPVVHRQIELIVRAgrsLSPSAAAFRDCL 291 Ralstonia eutropha JMP134
YP_580817    251 vidwvsanGLQMRpltqPVKMRRFFIYQRSsraLSPASIAFKHFL 295 Psychrobacter cryohalolentis K5

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