1TM2,1TJY


Conserved Protein Domain Family
PBP1_LsrB_Quorum_Sensing

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cd06302: PBP1_LsrB_Quorum_Sensing 
Click on image for an interactive view with Cn3D
Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs
Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.
Statistics
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PSSM-Id: 107297
View PSSM: cd06302
Aligned: 46 rows
Threshold Bit Score: 321.074
Threshold Setting Gi: 162149492
Created: 21-Jul-2006
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand binding
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:1TJY_A; Salmonella typhimurium LsrB binds R-ThmF (autoinducer-2), contacts calculated at 3.5 A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              #                                                                         
1TM2_A         5 RIAFIPKlvgvgFFTSGGNGAQEAGka-lGIDVTYDGptepsvSGQVQLVNNFVNqGYDAIIVSAVSPDGLCPALKRAmq 83  Salmonella typh...
1TJY_A         5 RIAFIPKlvgvgFFTSGGNGAQEAGka-lGIDVTYDGptepsvSGQVQLVNNFVNqGYDAIIVSAVSPDGLCPALKRAmq 83  Salmonella typh...
NP_416033     29 RIAFIPKlvgvgFFTSGGNGAQQAGke-lGVDVTYDGptepsvSGQVQLINNFVNqGYNAIIVSAVSPDGLCPALKRAmq 107 Escherichia col...
YP_001178776  25 KIALVAKslgngFFEAANVGAQEAAkelgDVKVIYTGpttttaEAQIEVLNGLIAqGVDAIAISANDPDALVPVLKKAmq 104 Enterobacter sp...
BAB52104      28 KIALVVKslgngFFDAANKGAEEAAkelgDVDIIYTGptkataEAQIEVVNSLIAqKVNAIAISANDADALVPVLKKAme 107 Mesorhizobium l...
YP_996885     37 KIAVVVKslgngFFDAVNQGAQEAAkeikNIEIIYTGpakstaEGQIEIINALISqKVAAIVISANDPDALAPSLKRAmg 116 Verminephrobact...
YP_001603953  33 RLMMTPKwtgfpYFEAAAHGARRAAke-lGDTLVYAGpdradaSLQVETLENFLTqRPNGVILSAVDLNAVAPVLKRArk 111 Gluconacetobact...
AAT64000      35 KFAFIPKltgvgFFTSGGEGAKEMGdk-lGVQVKYDGpseasvSGQVKYINNFINqNYDALMVSSTSVDGLSQSLQRAkk 113 Bacillus thurin...
ABA81104      25 EIAFIPKlvgvgFFTSGGNGAMKMGee-lGVKVTYDGptepsvSGQVQFVNNFVNqGYGAIVLSSVSPDGLCPALKQAma 103 Rhodobacter sph...
ZP_01440478   66 TVVDIPKlvgvgYFASTASGMQQAVeelgNITINTDGptraniDEQITFVDNYITsGVDGILFAANDPVAIAPVLKRAld 145 Fulvimarina pel...
Feature 1                #             #                                      ##  #              
1TM2_A        84 rGVKILTWDsdtkpecrsyYINQGTPKQLGSMLVEMAAhqv---dkEKAKVAFFYSsptvtDQNQWVKEAKAKisqe--h 158 Salmonella typh...
1TJY_A        84 rGVKILTWDsdtkpecrsyYINQGTPKQLGSMLVEMAAhqv---dkEKAKVAFFYSsptvtDQNQWVKEAKAKisqe--h 158 Salmonella typh...
NP_416033    108 rGVRVLTWDsdtkpecrsyYINQGTPAQLGGMLVDMAArqv---nkDKAKVAFFYSsptvtDQNQWVKEAKAKiake--h 182 Escherichia col...
YP_001178776 105 rGIKVVSWDsgvakagrqiHLNPSNNALIGETNVKLAAdalkalnvEKGDVAVLSAtptstNQNTWIAEMKKVlpky--- 181 Enterobacter sp...
BAB52104     108 rGITVISWDsgvakegrqlHLNPSDTGLIGETIIKLAAdy----lpEGGDVAILSAsstatNQNAWIDAAKKVlpek--f 181 Mesorhizobium l...
YP_996885    117 rGIKVLSFDsgvrkdgrmmHLSPSSNALIGEKLVQLTQqa----igDSGEIAVVSStaqatNQNIWIEEIRKVlarpa-y 191 Verminephrobact...
YP_001603953 112 rGVVVTTFDsdaalpardmFVNQLSYEQAARTMLDAALid----apQGGEIAFISAsptapNHVAHMRIMTQLtqtdpky 187 Gluconacetobact...
AAT64000     114 kGMTVLTWDsdvnpkdrsfYISQGTPDQLANLLIEMTSkq----igDKGKVAFFYSsptvtDQNQWVTKAKEIikek--y 187 Bacillus thurin...
ABA81104     104 rDVLVMTWDsdvnpdcrsyYINQGTPEQLGGLLVDMANdgl--egkEKAKVAFFYSsptvtDQNAWAEAAKARiaad--h 179 Rhodobacter sph...
ZP_01440478  146 aGINVVGYDadaeadarqwFVNQALPNGVAKSMMDQLAse----igEEGSFAIVTStfttpNQARWISEMQAYtekc--y 219 Fulvimarina pel...
Feature 1                                              ###                                       
1TM2_A       159 pgwEIVTTQFGYNDaTKSLQTAEGIIKAYP-DLDAIIAPDANALPAAAQAAENLkr-nnLAIVGFSTPnvmrpyvqrGTV 236 Salmonella typh...
1TJY_A       159 pgwEIVTTQFGYNDaTKSLQTAEGIIKAYP-DLDAIIAPDANALPAAAQAAENLkr-nnLAIVGFSTPnvmrpyvqrGTV 236 Salmonella typh...
NP_416033    183 pgwEIVTTQFGYNDaTKSLQTAEGILKAYS-DLDAIIAPDANALPAAAQAAENLkn-dkVAIVGFSTPnvmrpyverGTV 260 Escherichia col...
YP_001178776 182 psvNLVTVAYGDDLsDKSYREAVGLLKTYP-DLKVIVSPSSVGIVAAAQAVKDQgkigkVYVTGLGLPsemagavksGAS 260 Enterobacter sp...
BAB52104     182 pkiKLVATVYGDDDsAKSTDEAKGLLKSYP-NLKAIIAPTTVGVVAAAQVVTDEkligkVNVTGLALPsefkkfidnGAS 260 Mesorhizobium l...
YP_996885    192 kglKLVSVAYGDDQiDKSYRETQGLFKSYP-NLKAIIAPTTIGVAAAAKAVQDEkkvgsVYVTGLGLPsemaghvknGAV 270 Verminephrobact...
YP_001603953 188 kvfTVVDRQYAQDDdAKSYDVAINLMQAHP-NLKVIISSSAVSAPAAARAIDASghagkVFATGFALPsaiknylqdGSE 266 Gluconacetobact...
AAT64000     188 pnwEIVTTQYGENNaQKSLSVGENILKTYP-DINAVICPDATALPAMAQAAENLkmdkkVVVTGFSTPnvmrdyvkrGTV 266 Bacillus thurin...
ABA81104     180 pgwEIVTTQYGYNDaQKSLQTAESILSAYP-DLDAIIAPDANALPASAQAAENLgrageVTIVGFSTPnvmrpyvkrGTV 258 Rhodobacter sph...
ZP_01440478  220 pnlTFLETVEAQEDnILSFNQAQTLINKYGdELNGILGMTSVATPAASEAVQQNglcgkVSVVGLALPnamkpyingDCI 299 Fulvimarina pel...
Feature 1             #                                                                       
1TM2_A       237 KEFGLWDVVQQGKISVYVANallknmpmnvgdsldipgig-kvtvspnseqgyhyeakgnGIVLLPeRVIFNKDNID 312 Salmonella typhimu...
1TJY_A       237 KEFGLWDVVQQGKISVYVANallknmpmnvgdsldipgig-kvtvspnseqgyhyeakgnGIVLLPeRVIFNKDNID 312 Salmonella typhimu...
NP_416033    261 KEFGLWDVVQQGKISVYVADallkkgsmktgdkldikgvg-qvevspnsvqgydyeadgnGIVLLPeRVIFNKENIG 336 Escherichia coli K12
YP_001178776 261 KSFAIWNPIDLGYAATYLADdlvkgtatkdeasm------------gklgkvkldadgsgAMAEPFvYDASNIDKFS 325 Enterobacter sp. 638
BAB52104     261 QAVALWNPIDLGYSAVYLAHdlavkkeeakpgatl-----------sigrvgkvtlddsnSAAMAP-PFQFDKTNIE 325 Mesorhizobium loti...
YP_996885    271 KSFAIWNPIDLGYSSIQAASqliagkftgkpgdkv-----------slgrvgsvvldansEAAMAE-PFTYDASNVE 335 Verminephrobacter ...
YP_001603953 267 KAFALWNPEELGYLATYVTHlrlagkldlkpgts------------fvagtagtykvgedGEIDYGkPLIFTKDNIE 331 Gluconacetobacter ...
AAT64000     267 QQFGLWDVKQQGALATYVANeivvkgkklkvgdsfevkgigkvkvepnsiqgydyeaegnGIIVLPeRVVFTKDNID 343 Bacillus thuringie...
ABA81104     259 ERFGLWDVTQQGAISVAVAAhvlkdgplnvgdslevpgig-svevspnsvqgydyeaegnGIILLPeRTVFTAENID 334 Rhodobacter sphaer...
ZP_01440478  300 KSTILWNTVDLGYAAAQVMRqvadgtlepgattv-------------nagrlgelqvvnqSQVLLGaPKVFTKEDIN 363 Fulvimarina pelagi...

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