Conserved Protein Domain Family
PBP2_LTTR_like_6

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cd08423: PBP2_LTTR_like_6 
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: 176115
View PSSM: cd08423
Aligned: 43 rows
Threshold Bit Score: 150.056
Threshold Setting Gi: 148272066
Created: 5-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                       ## ##  #   # #######                                             
CAJ88838      93 TVTVASFatGIALVVAPALGRLAESAPgIRIRVQDaegdaslPMVLDRrVDVAVaveyrgappaddprLTHVPLYAePFD 172 Streptomyces am...
YP_002776843  96 TVRLGSFptVSASLLSDALKDYHAHWPgIDVRVQSavrprllEMLHSSeVEMALlwsydwt-eeteksLALVPLMEdETV 174 Rhodococcus opa...
YP_001362556 102 HLSLAYIssVGSTWLPEVARRLTQAHPeVDLDLQLled-stlEGTERPdVQLVVgpgtpv---ragagFDVHRLAEdPYR 177 Kineococcus rad...
YP_001828426 112 PLHTGAFatASIALLPAALRALKDARPeIEVVAAEsptgtlmRQLADGtLDLAVvsdypyg-lpsaegITTTVLCEdELL 190 Streptomyces gr...
YP_003118532  92 GLRVGAIptADMALIPRAVAAFRRAHPaVAVSHVEgltrglvVDVREGdLDLAVigtahp--epafegVRLRKLMDdPLS 169 Catenulispora a...
YP_001108783  93 LLRVRFFhtASVALIPPAVAKFRAERPeVRLDLKMvdddgglGEVASGaADIAVivvgre--apelrgVRVLELVRePYH 170 Saccharopolyspo...
YP_001108373  94 RLRLGAFptAGLALLPDVLAALRHRHPdAELSVVDlgpvegmALVGSHeLDLALvgeygtp-ldappgVRLAPLIDdPVH 172 Saccharopolyspo...
YP_002782518  93 MLAIGTFptAGSSLLPLVVKEFKTHHPgIDLRVLSgrfaqlvESLRRReTELSLlwdyewn-riddplLTCHHLMNdPTL 171 Rhodococcus opa...
NP_827151     93 RLAVRYFatAGAPLVAPALARMRAEHPgVRVEVKLidpedplPDVKEGrADLALvvrsge---aghegIRLVHLLDdPYR 169 Streptomyces av...
YP_831498     93 SLTVGTFptLAGSFLPVVIRTFKKRYPaISLSVRSarfdelvADLQSGvTGLCLlwdypwn-pfrddsIRVTEVFReSTV 171 Arthrobacter sp...
Feature 1                                                             ######     ## ##           
CAJ88838     173 AVVPVAHRladadevpLAELAKDPWIGPypgnpchdv--vvlacesaGFQPRMEHSSDDFraVVSLAAADvGVALVPRSa 250 Streptomyces am...
YP_002776843 175 LLVPLDGPyad--dvaVASLRSAKWIIRntnhpaaev--lyrscetaGFTPNVVYEAHDYqeIEAMVAAGvGIAMVPRLa 250 Rhodococcus opa...
YP_001362556 178 VLLPATHPlsgrreveLAELATDRWIDSepragwcrg-nlleactaaGFAPAFHVQAHDYamSAAFVGAGlGITVLPALa 256 Kineococcus rad...
YP_001828426 191 VALPRRHPlagaeavdLYELRDETWIQSaygdrptm---ladacaraGFTPRSVMRIGGWagKFGYAVAGlGVALVPSLa 267 Streptomyces gr...
YP_003118532 170 VALPLDHRladrdllsLADLEGENWIAGqprsqdtl----iagvldgEFQPRIPYVVLEWsaKQGFVAAGlGVTLVPALa 245 Catenulispora a...
YP_001108783 171 VVLPKGHPmcgeeridLARLQDEEWVDTvmnstgpcgeslddafasaGFKPKIALCTDGGysAQGFVAAGlGIALLPRFa 250 Saccharopolyspo...
YP_001108373 173 AVLPTDHRladhpavrLADFADEPWAAAprtlpnrrq--leeatraqGFLPNVPFESESYavAEAVVSAGvAVAFIPRLa 250 Saccharopolyspo...
YP_002782518 172 LLVSEKHRladresirITELRDESWVVRaddhpvaht--lerlcqqgGFTPRTSFLAHDYgeVQAMVGVElGVAIAPRLa 249 Rhodococcus opa...
NP_827151    170 VVLPEGHRladrevveLSELAEEPWVGSewpgpclda--qldacaaaGFRPGFVVESGDYltAQGFVAAGlGVSLIPRLg 247 Streptomyces av...
YP_831498    172 ILVARGHRladreqvsMEDLRNESWIVRaeahpvvev--lqrsahdaGFEPEIAFLANDYqeAQAMVSVGmGVAMVPKTa 249 Arthrobacter sp...
Feature 1                                                      
CAJ88838     251 lhgtdltGVVVRPVDgv--apTRRVFAAVRRgaeehPLIRPVLDAL 294 Streptomyces ambofaciens ATCC 23877
YP_002776843 251 vth-hrpDVYAVRFRptdrvpTRSIYIASLArrqytPGMHAVSRAL 295 Rhodococcus opacus B4
YP_001362556 257 aht-lpdGVRSVPVVrp--tpTRTIYVVVRKtiaqwPPALLVVDTL 299 Kineococcus radiotolerans SRS30216
YP_001828426 268 apa-vpgELVLRPLTdp--alRRTVHVAMPDtp--lAAALVLREFL 308 Streptomyces griseus subsp. griseus NBRC 13350
YP_003118532 246 aaa-vrpDVVVVALDqse-vaPRSVFAATPEgvadsAAVTAFLELL 289 Catenulispora acidiphila DSM 44928
YP_001108783 251 ldv-vhpGVVVRSVGrp--epVRKVYVAVREavaeqPTTRTMLAAL 293 Saccharopolyspora erythraea NRRL 2338
YP_001108373 251 is--gtsGTVHRPLAep--glFRRIHAVVPAsaghaPLTEVCLRLL 292 Saccharopolyspora erythraea NRRL 2338
YP_002782518 250 vln-prpDVRSIPLAtr--spQRRILIAHLTerrlsPAAQEAITQC 292 Rhodococcus opacus B4
NP_827151    248 lgg-rpaGVVVREVRgp--epVRRIYAAVREtappqPALRGLLEAL 290 Streptomyces avermitilis MA-4680
YP_831498    250 val-qhpDVKVLSLGea--apLRRVLLAQREdkvyaPAEVAFHSTL 292 Arthrobacter sp. FB24

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