1AL3,1I69,2HXR,2QL3,3HHG,1IXC,1UTH,2QSX


Conserved Protein Domain Family
PBP2_LTTR_substrate

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cd05466: PBP2_LTTR_substrate 
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The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily.
This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form 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, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of 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. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 176102
View PSSM: cd05466
Aligned: 350 rows
Threshold Bit Score: 48.3653
Threshold Setting Gi: 2582482
Created: 26-Apr-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
dimerization
Conserved site includes 23 residues -Click on image for an interactive view with Cn3D
Feature 1:dimerization interface [polypeptide binding site]
Evidence:
  • Comment:most members of the LysR family of transcriptional regulators are tetrameric, while CrgA assembles into octameric rings .
  • Structure:1I69; interface at dimeric unit of the tetrameric OxyR from Escherichia coli , contacts at 4 A.
    View structure with Cn3D
  • Structure:2HXR; interface at a dimeric unit of the tetrameric CynR from Escherichia coli, contacts at 4 A.
    View structure with Cn3D
  • Structure:3HHG; interface at a dimeric unit of the octameric CrgA from Neisseria Meningitidis, contacts at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                        ## ##  #   #  #######                                           
1AL3_A        94 SLYVAttht-qarYALPGVIKGFIERYPr-VSLHMHQgsptqiaEAVSKGn--aDFAIateal--hlyddLVMLPCYHwN 167 Klebsiella aero...
1I69_A         6 PLHIGlipt-vgpYLLPHIIPMLHQTFPk-LEMYLHEaqthqllAQLDSGk--lDAVIlalvk---eseaFIEVPLFDeP 78  Escherichia coli
YP_002239149  92 RLHLGyvssamydSKLPGLLRELRADWPg-IELSLVQgdvqmlyEALLDLr--lDIAIirapla-sppdaLVVRPFVReK 167 Klebsiella pneu...
NP_883222     92 LVHIGcsta-aslFIVPRVMEDLAAEGLe-IVLHVHEgeigymlQQLRERs--lDLTIcrsqh---mapdLESQVIMEeP 164 Bordetella para...
NP_720608     90 HYSTLgcpp-iiiNYLLSLLKETNQDLAflKRIRSIRggsvellEQLLQGd--lDLSLigtiep-fyhdeLVIKKILHrK 165 Streptococcus m...
NP_249694     94 NLRVLldta-ippSFCDTVSSVLLDDFNm-VSLIRTSpad--slATIKQDnaeiDIAItidee--lkisrFNQCVLGYtK 167 Pseudomonas aer...
CAW29077      94 NLRVLldta-ippSFCDTVSSVLLDDFNm-VSLIRTSpad--slATIKQDnaeiDIAItidee--lkisrFNQCVLGYtK 167 Pseudomonas aer...
YP_574725    108 ELTVQvhna-farGWFSQQMENFVADHPg-VRLDLQTrl---tpPTGPEDe---ALCVwlgtv---decgLRQETLGHmR 176 Chromohalobacte...
AAK91496      96 DISIAydgi-igiHHFFSLVDALGNVSK--TRVRLQEeilagcwESLQSGr--aDLLVcpkle--vlphdVKADTIGKmS 168 Vibrio vulnificus
AAA24221      96 LFDVGvada-lskRLVSSVLNAAVVEGEp-IHLRCFEsthemllEQLSQHk--lEMIIsdcpidstqqegLFSVRIGEcG 171 Escherichia coli
Feature 1                                                                ######     ## ##        
1AL3_A       168 RSIVVTpehplatkgs-vsieelaqyPLVTYtfgftgrseldt--afnragltpriVFTATDadvIKTYVRLglgVGVIA 244 Klebsiella aero...
1I69_A        79 MLLAIYedhpwanrea-vpmadlageKLLMLedghslrdqamg--fcfeagadedtHFRATSletLRNMVAAgsgITLLP 155 Escherichia coli
YP_002239149 168 LCLALYqqhplagvga-lnlaslrtdNWISLddpqgtgleqvfidacrvagftpqvVQRINDvtsMISLVSAgvgVALVP 246 Klebsiella pneu...
NP_883222    165 LFVALPpghplagrar-vrladlrdeRFLLHrsplgtgisdmvlracrnagfapnvVYWGGEtlpMLLMARRglgIAFAP 243 Bordetella para...
NP_720608    166 LYLIVSkdhllakrkkaiafadvlkeNFILLdehnihlkafdy--lnqthqnqaqiFFKSDDvtlIKQMVSHnmgVSLLT 243 Streptococcus m...
NP_249694    168 AFVVAHpqhplcnasl-hsiaslanyRQISLgsrsgqhsn--------llrpvsdkVLFVENfddMLRLVEAgvgWGIAP 238 Pseudomonas aer...
CAW29077     168 AFVVAHpqhplcnasl-hsiaslanyRQISLgsrsgqhsn--------llrpvsdkVLFVENfddMLRLVEAgvgWGIAP 238 Pseudomonas aer...
YP_574725    177 RGLYAHpdylrrhgap-rhprdlaehAWVDLlgtsehgvtlhharegewdltlppsRLRVDQyvlHIDAIARgggLGLLP 255 Chromohalobacte...
AAK91496     169 MTWVAApnhyvhkrsgefndsarekyRIIAIadtareqpai------tvniiqkqpRLTVTNlqaKVDALVTglgIGTLP 242 Vibrio vulnificus
AAA24221     172 VSFWCTnpppekpf-----pacleerRLLIPgrrsmlgrklln--wfnsqglnveiLGEFDDaalMKAFGAMhnaIFVAP 244 Escherichia coli
Feature 1                                                                
1AL3_A       245 smavd---pvsdpDLVKLdang-ifsHSTTKIGFRRstfl-----rsyMYDFIQRF 291 Klebsiella aerogenes
1I69_A       156 alavpp--erkrdGVVYLpaik-pepRRTIGLVYRPgspl-----rsrYEQLAEAI 203 Escherichia coli
YP_002239149 247 vsara----lrldNVVYIdlqd-rlaESELSMVYHRhfr------savVRKVISLL 291 Klebsiella pneumoniae 342
NP_883222    244 qsfaq---lglqgLAALVpvad-aefRTHLNMVWPRqqal-----spiASWVRELI 290 Bordetella parapertussis 12822
NP_720608    244 dislt----kqdhHLVKIpfkennklGFYVNYAYLKsstl-----tpdIRHLVDLL 290 Streptococcus mutans UA159
NP_249694    239 hyfveerlrngtlAVLSElyep-ggiDTKVYCYYNTal--------esERSFLRFL 285 Pseudomonas aeruginosa PAO1
CAW29077     239 hyfveerlrngtlAVLSElyep-ggiDTKVYCYYNTal--------esERSFLRFL 285 Pseudomonas aeruginosa LESB58
YP_574725    256 hwmaekrlqhhpgSLTPCleew-apsSLPITLLYPFgrl------prkTVTLLERI 304 Chromohalobacter salexigens DSM 3043
AAK91496     243 tdiatp--lieagKLKEIega--eqqHLEIILAWKRnqm------geaKSWCIQYL 288 Vibrio vulnificus
AAA24221     245 tlyayd--fyadkTVVEIgrv--envMEEYHAIFAErmiqhpavqricNTDYSALF 296 Escherichia coli

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