Conserved Protein Domain Family
PBP2_LTTR_like_3

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cd08436: PBP2_LTTR_like_3 
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: 176127
View PSSM: cd08436
Aligned: 29 rows
Threshold Bit Score: 173.171
Threshold Setting Gi: 256374543
Created: 21-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                        ## ##  #   # #######                                            
ACG70961      92 RLAVGaipt-vaaVDLPVLLRDYRRRHPrVRITLTSagsq--dliERVRRGgVDVAFlglpprtepkgVRSLRLGGgELV 168 Planobispora rosea
NP_822338     92 TLSLGteqc-iagVHVARLLAGFRRQHPdVEIRLRQagsg--alaEEVAAGrLDLAFavrte-tdtdqLRSVPLTGePMT 167 Streptomyces av...
NP_828411     92 TVNVGamas-vevVDLPALLGQLHARHPaIDVRLRLattgsaglaHALLSGdLDVAFlslpe-hkpagIDARELATvPLV 169 Streptomyces av...
YP_001105282  92 ELSIGtlqc-lhvVDLPPVLAGFVTAHPgIEVRLRQggsg--dlaEQVRAGrLDLAFavrpa-rcpdgVLVHSLDTePLV 167 Saccharopolyspo...
YP_001106986  92 RVAIGtiqt-lteVDLPGELGTFQRRHPgVRIHVRQglvp--dlmAAVGNGeLDLAYlapeg-plaeeLVSFAQWRqKLV 167 Saccharopolyspo...
YP_003101126  95 TVRLGtisf-tgpLDLAGLLRSFAARHPrVEVHLRQttsgtatslDDLRSGaLDLALvstpa-dglpgVALTEIHRePLV 172 Actinosynnema m...
YP_001363106  92 TLRVGaeqc-lgvVDVSTLLERFHRRFPqVEIHFEQagsh--dllGRLREGeLDLVFvatte--hlgaLPASELGRePLV 166 Kineococcus rad...
YP_001235939  92 TLKIGtvqslpafLDLPLLLARFHQRHPgIEIRLIQgsss--alaDRTRAGgIDAAFfpvgt--hltdLVTTMIACdEVV 167 Acidiphilium cr...
YP_002907909  92 KLSIGtvqslpqfLELPALLSRFYHAHPgVEVRLVQggaa--elnEKVDAReLDLAIlpiee--rnerLASHVIACdEMV 167 Burkholderia gl...
YP_001363771  96 PVAVGvvtt-mhpVDLPRLLQRFTAEHPrVSVSMRVfadgsrgllRALVEGeLDAAFlswpf-rppgaVALRPLVRaPLR 173 Kineococcus rad...
Feature 1                                                           ######     ## ##             
ACG70961     169 AVVAPDYHLaer-eveLRSLADEPFIDFRAGTAgraqsDEAFAVAGvrrevPFEVSSadfMVDLVRQglgVGMLPaaya- 246 Planobispora rosea
NP_822338    168 VLCHPTHPLatagavmPEDLGGEAFVDFHPDWGprritDAAFAAAGvrrtvALEVNDvhsLLDLVEEglgVAVVPrhfr- 246 Streptomyces av...
NP_828411    170 LVVSADHPLaqrgevaLADLAAEPFVDFPPGYGnrevvDRAFAGAGvvrrvALEVPDidmGAALVRHglgIAFLPafav- 248 Streptomyces av...
YP_001105282 168 LACAGDHPMaerdrvdPRELGEQPFVDFHPDWGtrdvvDRVLAETGverrvALEVTDvhsLLELVACglgIALVPrsfs- 246 Saccharopolyspo...
YP_001106986 168 LLGYPGHRLaqrrrvrLAELDGEPFVDFSGSGLqd-miGRRFADAGvrrdrVCEATHvplLVELVAAglgVSIVPepva- 245 Saccharopolyspo...
YP_003101126 173 LVCGRDHPLasaervgIGQLAGEPFIDFPTGWGnraviDHAFASAGvtraiRTEVTDfalARTLVEHglgLSIFPagavd 252 Actinosynnema m...
YP_001363106 167 LLTPPEHPLagrphapWAELAAHPFIDFVPSWGvrpitDAACAAHGvhrrvRFSVGDvhaLLDLVGRglgIAIVPrhvaa 246 Kineococcus rad...
YP_001235939 168 LACPRGHPLegltgvtLEAIKDFPFVDFETGWGtrrlvDGRFGDAGigrhtAFEVSDldtMLKLVSLglgIALLPetvvv 247 Acidiphilium cr...
YP_002907909 168 LACRRDHPLaasgqvpLSRLTKQAFVDFVPGQGtrrlvDRGFAEAGlqrrvAFEIGDldtLLELVRQglgVALLPedivv 247 Burkholderia gl...
YP_001363771 174 LLLPAGHPLaspgpveLADLAGERWIDGPPGFGnrlqvDAVFERAGarrhvVLEVPDvstFPRYVAAglgPAFVPgsvp- 252 Kineococcus rad...
Feature 1                                                         
ACG70961     247 -prfpDLRVIrlr--gapARVEHLVWDNrps--------saTRAFLELV 284 Planobispora rosea
NP_822338    247 -hkreALTALplkgtgetVYETVAILPPsaat------spaARALMTLL 288 Streptomyces avermitilis MA-4680
NP_828411    249 -artpGLHVLdvhg-tmlRWSMHLGTSStrrp------ssaLRALLDLV 289 Streptomyces avermitilis MA-4680
YP_001105282 247 -akngQVRFVplas-papTWETVAITSDpts--------taAAALLRDV 285 Saccharopolyspora erythraea NRRL 2338
YP_001106986 246 --arsGLPHArieq-pslSRPIHLAGRGaepv------npaARALLQHL 285 Saccharopolyspora erythraea NRRL 2338
YP_003101126 253 gpadgPVARVpir--espEWTIKLARPAprre------gtaATALARAV 293 Actinosynnema mirum DSM 43827
YP_001363106 247 kpqaaRLAVVpmpp-gtpEWVVSVVTSAgss--------paPQLLELLE 286 Kineococcus radiotolerans SRS30216
YP_001235939 248 -ardpDIGMArlss-pelCWELVVAHLPvagp------gtpVAAFLSLL 288 Acidiphilium cryptum JF-5
YP_002907909 248 -rrpdMLACVrleq-tqlCWELVVTHAAsaagdapdpldpaPVAFLDML 294 Burkholderia glumae BGR1
YP_001363771 253 --vppGCHEQavtg-eqpGWTLSLATARpspe------rpaRRAVTAFV 292 Kineococcus radiotolerans SRS30216

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