Conserved Protein Domain Family
PBP2_LTTR_like_1

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cd08421: PBP2_LTTR_like_1 
The 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: 176113
View PSSM: cd08421
Aligned: 49 rows
Threshold Bit Score: 208.915
Threshold Setting Gi: 33598033
Created: 7-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                       ## ##  #   # #######                                             
NP_522826     94 HVRLLsntaAMTEFLPETLSAFLAQHPeVDIDLEElvsheivEAVAQGrADIGIvndav--dlsgLETFPFRHDRLVLVT 171 Ralstonia solan...
YP_001862289  94 VVRLYanasAIVGFLPERLKAFQARYPlVEIALSEhisdevvRACIDDrADVGIssggr--apgvLESWHFADDPLLVVM 171 Burkholderia ph...
YP_001888385  99 RVRVVanlsSIVQFLPEDVAAFGRAFPeVSIELEEensadvlRIVGEHaADFGIcnava--gaeaFEQVPYRQDRLAVLV 176 Burkholderia ph...
YP_287276    121 QVTVFantnAINCFLPEDLGDFLREHPhIRVSLEEqpspaiiQAVAAGqVEIGVvaseg--glagVETRPYRQDRLVLIV 198 Dechloromonas a...
YP_002942813  98 HLRLCanpsAFGGFLPSVLAEYARRYPqVVIDMEDalsedgiRAVQKGtAELAVigdnv--phdgLETLVCNVDQLVLLV 175 Variovorax para...
YP_001117809  94 HVTVFannnAISSHLPDDLARFFAAFPsVRITLEErlshdivGAVVAGrADVGVvales--ehsaLRFVPYKKDQLVLLA 171 Burkholderia vi...
YP_366962    104 HIRISststIIVHFLAREIAEFTRDFPlVEIELQEdtnanviGSVVTGkADVAMfyatadidrdaLDIIEFRTDRLVAVV 183 Burkholderia sp...
YP_001353268  94 TLRLAgttvANSTFLPAALGPFLADYPeIDLQLVEhksadvlLAVQSGeVEVGVldgnl--atsdVIPLPFRHDKLVLLV 171 Janthinobacteri...
YP_299632     98 QLVLYanssAIASFLPGDLQGFLQSHPkARITLEEhlsrdvlVAVVEGrADIGIltkde--phpdLVYFPYHEDEIVLLL 175 Ralstonia eutro...
NP_885676    104 SLTVAttgsLIVQYVAKEIGEFSRNYPqIDLALEQhlnpdaiRAVVSGgADLAIylvgmdvheegLDVTPYRTDRLVALA 183 Bordetella para...
Feature 1                                                        ######     ## ##                
NP_522826    172 ARDHPLaarreiaFVDALQEDFVGLtgdnalqaylaghaaraGHRLKYRVRLRSFdaVCRMVERSVGVGVIPehaairlq 251 Ralstonia solan...
YP_001862289 172 PVGHELaaletpaFADVLRFPLVALqaggsldlvlreravaaSTPLRFSVTVNSFdaQCRMVEAGLGIGIMPtsaasafa 251 Burkholderia ph...
YP_001888385 177 PGGHRLagalrvsFNDLLDDSFVGLrsesaltqlltqqaagaGRQLDVKIRVSSLdaLCRMVHAGLGIAIVPeqvgllyl 256 Burkholderia ph...
YP_287276    199 APGHALaekcelaFADVLAEPFVCLhagsaihtfmmnhaarlGGRLDVRIQVRSFnaVCRMVAAGVGIGMVPrssi---g 275 Dechloromonas a...
YP_002942813 176 PAGHALdgrqnacLADVLDHDLVTLarsasltrkvmaaadaaKRTPRIRVQVRSFdsMCRMVSFGLGLAILPraaaalya 255 Variovorax para...
YP_001117809 172 PVTHALarqsevsFAACLGQPFISLqsgaalhtflvnhaaalDGRLDIRVQVSGYraIARLVSSGAGIGIVPrtaie-ss 250 Burkholderia vi...
YP_366962    184 PHGHRLgacasvtTQDLVDENIIGLapttllmtqlhdaasalGRELRVKYRVSSIeaARSLVKAGLGVMIHPesmlp-ae 262 Burkholderia sp...
YP_001353268 172 PSGHALaerpsvqLKDALGFAFVCLpperamqrfieemavqnSRPLRVRVRAPSFyaIAQLVAEQAGIAMLPeaaalrhi 251 Janthinobacteri...
YP_299632    176 AETQPWtktepvaFLDCLSFPFVSQqngsaihsfllakaseqGRRVDVRIQVAGFaaVASMVRSGVGVAIVPrsala-ai 254 Ralstonia eutro...
NP_885676    184 PAGHPLaekagvtLADLLGHAFISVepstammadiskaakssGLAVKPKFHVTSVeaARSLVEEGLGVTIQPecmlp-va 262 Bordetella para...
Feature 1                                                 
NP_522826    252 rsmGIRRVgLTDAWATRLLRICVRRfd-dLPAYARQLIEHL 291 Ralstonia solanacearum GMI1000
YP_001862289 252 gshGFVRRpLDEPWAKTRTLQLHALrkkpRPRAVQALIDLL 292 Burkholderia phymatum STM815
YP_001888385 257 nalDVSLLsLSDAWAVRRLIMIFKArd-qLSASAAALVGFL 296 Burkholderia phytofirmans PsJN
YP_287276    276 aadAVKTIeITDSWAPRDLQLCIRSrv-aLAPAAAALFDHL 315 Dechloromonas aromatica RCB
YP_002942813 256 qalGLVQVgLEGIEMERVLLLAMRSra-eLSTPAAALVDMI 295 Variovorax paradoxus S110
YP_001117809 251 degKVAVIpLIEPWSQRNLHVCVQRnpaeKNLYRDKLISML 291 Burkholderia vietnamiensis G4
YP_366962    263 dvnKVTLVaLDEPWALRRLCIGTRRgd-aLTAATRAFVAQL 302 Burkholderia sp. 383
YP_001353268 252 relPVHMVaLEDAWATRELRICIRAwd-tLSTHARQLVDYL 291 Janthinobacterium sp. Marseille
YP_299632    255 nveGLRVVaLSDAWARRTLSLCVRRdvlgSRNYVTALVDVL 295 Ralstonia eutropha JMP134
NP_885676    263 yqrRVSVLrLDEAWALRKVHIGTRRgr-aPTAATRLLIEQL 302 Bordetella parapertussis 12822

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