Conserved Protein Domain Family
PBP2_LTTR_like_5

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cd08426: PBP2_LTTR_like_5 
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: 176117
View PSSM: cd08426
Aligned: 9 rows
Threshold Bit Score: 232.584
Threshold Setting Gi: 27378884
Created: 2-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_356218     92 RVTVYangatvaNLLAPVLAQFSLKYPkLRFEVHItsarqamEALGAAeaDLVVslfapklsgVKVRSRTRiSYDVIFPA 171 Agrobacterium t...
YP_994988     97 QVRLAtsdafanELVPRLCVEFQRTHTgIQFSVISlptaqvpGAVRSGaaDIGLcfsraphqdIEVAYRQTaPVRALVPP 176 Verminephrobact...
YP_002545384  50 KVRIVttvglaaGPLPEIIARFLSEHPrVFIQLRNdsgsttvAPVLSGevDIGLgfnipatpgIRSLGNFDiPIGVVLPP 129 Agrobacterium r...
YP_841818     97 RVRVAssagfaiEFLPRIIAEFRQRYPgLQFHVRVaspaevtGIVLHGdaDIGItysraaeqgIRVEHRQPaPVIAIMRP 176 Ralstonia eutro...
YP_002500644 102 HIDVVlgegfvgDLMSGVLQGFWSRYPdLTMTLDLaatndviRRVIEDeaHVGLvynpppeprIRTHLAMPhPIRVVVRP 181 Methylobacteriu...
YP_002005309  92 EVTVAvtaglagSLMPSLVHDFRQRYPgIVVRVNDlpvadivAAVEQGdaDLGLgydlpelpaFRALASSDwQIGAVVPP 171 Cupriavidus tai...
YP_002240648  93 TISVRiggglvtTFIESVMSTFSQSWPnVFVDISVgnmqemlNDIASGeaDMAVafgpignpeLKRHSFQWgPICAVVSP 172 Klebsiella pneu...
YP_295866    112 RVRLAsvegiahEFLPTLAARFREQHTgIRFDLDVclqgdvaRRIRDGeaDIGVtlsglpereIEVELRHPaPVLAIMAP 191 Ralstonia eutro...
NP_770413     94 TVSIAcieslteSVLPDLIASHRGRARrVSFTTEVkgssdvlEALSRGeaDIGIamalrhppdLRQVALKRfRLGAVVSR 173 Bradyrhizobium ...
Feature 1                                                       ######     ## ##                 
NP_356218    172 GHALaaqpevs-lkelagmPLALPdksfaarqafdtlfadagieldpVFITSSlemLKELVLGn-aAATLLPalsvarei 249 Agrobacterium t...
YP_994988    177 GHPLararsvs-laqmarhPLALPppettvrqmidivcsrqglqmapVLISNHaktVLNFVAHg-gGLSVASeiaarhlv 254 Verminephrobact...
YP_002545384 130 GHPLiepgpin-ladvveeRLLLAqpgtslrdiinltlarlsvqvepVLESNAsemLKQLVKCg-aGLTLLNpldvitdc 207 Agrobacterium r...
YP_841818    177 DHPLarfrsvt-laqmqpyPLALPegdntvrqlfdiacgergvvfepVLVTNHfetLTSFVLHg-gGLSISGavtvgdrl 254 Ralstonia eutro...
YP_002500644 182 DHPLaaspgplslrdlaghRLGMMhpaygirqiiagaertegvrlgaALITSSisvLKQFVAAa-dGVTLLPafcaapei 260 Methylobacteriu...
YP_002005309 172 GHALaarpsvl-lsecvgyPLILParalsirgildaafarnaievspVAESTStvlIRQLVLLg-tGIALLNpldvmeer 249 Cupriavidus tai...
YP_002240648 173 QHPIarqsmvt-ideltqyRLIALtesfglqrhmnamfktagrqfhpAYRCNLfstAMSLSQAg-lGISFMTefaareai 250 Klebsiella pneu...
YP_295866    192 DHPLagqrqvs-lsqviayPLALPpkgsslrqlldtscsrqdlhyqtVFSSNHldaLVSFVVAgggAISFYGelsirgrl 270 Ralstonia eutro...
NP_770413    174 EHPLarrktvt-leqclafPVINAlpelsiyhllqpliaqlsetpepAIQANSidlMRELAARg-vGVAFQTqlgigrls 251 Bradyrhizobium ...
Feature 1                                                  
NP_356218    250 rsGQMVAVPLagk-kgiHTQIDLCVAPdrqLSFAASKLADFI 290 Agrobacterium tumefaciens str. C58
YP_994988    255 aaGAIVALPIsdp-gmdLRDLEVQTLAgrsLPVAVQAFLDLL 295 Verminephrobacter eiseniae EF01-2
YP_002545384 208 rrGELVFRPIaep-hsrHQPLKLFARArapLDAATSLFVEYL 248 Agrobacterium radiobacter K84
YP_841818    255 rrGELHAASIrer-gmrSRAVELQTLAgrtLPEGVRAFLGFI 295 Ralstonia eutropha H16
YP_002500644 261 aaGTLCALPLadp-dlnAVEAQIVTRLgrqLPTAAARFLQHL 301 Methylobacterium nodulans ORS 2060
YP_002005309 250 arQALVYVPLrdr-hlqGQTLTLVARAggqLSAAAGLMAERI 290 Cupriavidus taiwanensis
YP_002240648 251 ahGILKAVPIdhp-iasSAQCHLLRNSnrrFPPAAHHMWRLL 291 Klebsiella pneumoniae 342
YP_295866    271 esGTIAAVPLrdr-emnERYIEIQTLAkrsLPPAARAFVQQL 311 Ralstonia eutropha JMP134
NP_770413    252 reSQLVFLPLdnagspvWSDLGIYVRAertLPAYTESFLQEL 293 Bradyrhizobium japonicum USDA 110

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