2avx

From Proteopedia

(Difference between revisions)

Current revision

solution structure of E coli SdiA1-171

Structural highlights

2avx is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDIA_ECOLI Activates cell division by specifically increasing transcription from one of the two promoters that lie immediately upstream of the ftsQAZ gene cluster. Activates ydiV expression in response to extracellular autoinducer AI-1 (Vibrio fischeri autoinducer oxoC6).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The three-dimensional structure of a complex between the N-terminal domain of the quorum sensing protein SdiA of Escherichia coli and a candidate autoinducer N-octanoyl-L-homoserine lactone (C8-HSL) has been calculated in solution from NMR data. The SdiA-HSL system shows the "folding switch" behavior that has been seen for quorum-sensing factors produced by other bacterial species. In the presence of C8-HSL, a significant proportion of the SdiA protein is produced in a folded, soluble form in an E.coli expression system, whereas in the absence of acyl homoserine lactones, the protein is expressed into insoluble inclusion bodies. In the three-dimensional structure, the autoinducer molecule is sequestered in a deep pocket in the hydrophobic core, forming an integral part of the core packing of the folded SdiA. The NMR spectra of the complex show that the bound C8-HSL is conformationally heterogeneous, either due to motion within the pocket or to heterogeneity of the bound structure. The C8-HSL conformation is defined by NOEs to the protein only at the terminal methyl group of the octanoyl chain. Unlike other well-studied bacterial quorum sensing systems such as LuxR of Vibrio fischeri and TraR of Agrobacterium tumefaciens, there is no endogenous autoinducer for SdiA in E.coli: the E.coli genome does not contain a gene analogous to the LuxI and TraI autoinducer synthetases. We show that two other homoserine lactone derivatives are also capable of acting as a folding-switch autoinducers for SdiA. The observed structural heterogeneity of the bound C8-HSL in the complex, together with the variety of autoinducer-type molecules that can apparently act as folding switches in this system, are consistent with the postulated biological function of the SdiA protein as a detector of the presence of other species of bacteria.

Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones.,Yao Y, Martinez-Yamout MA, Dickerson TJ, Brogan AP, Wright PE, Dyson HJ J Mol Biol. 2006 Jan 13;355(2):262-73. Epub 2005 Nov 8. PMID:16307757^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang XD, de Boer PA, Rothfield LI. A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli. EMBO J. 1991 Nov;10(11):3363-72. PMID:1915297
↑ Zhou X, Meng X, Sun B. An EAL domain protein and cyclic AMP contribute to the interaction between the two quorum sensing systems in Escherichia coli. Cell Res. 2008 Sep;18(9):937-48. doi: 10.1038/cr.2008.67. PMID:18560382 doi:http://dx.doi.org/10.1038/cr.2008.67
↑ Yao Y, Martinez-Yamout MA, Dickerson TJ, Brogan AP, Wright PE, Dyson HJ. Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones. J Mol Biol. 2006 Jan 13;355(2):262-73. Epub 2005 Nov 8. PMID:16307757 doi:10.1016/j.jmb.2005.10.041

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2avx"

@@ Line 1: / Line 1: @@
 ==solution structure of E coli SdiA1-171==
-<StructureSection load='2avx' size='340' side='right' caption='[[2avx]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2avx' size='340' side='right'caption='[[2avx]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2avx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2avx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVX FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HTF:N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE'>HTF</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sdiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HTF:N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE'>HTF</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2avx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2avx RCSB], [http://www.ebi.ac.uk/pdbsum/2avx PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2avx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avx OCA], [https://pdbe.org/2avx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avx RCSB], [https://www.ebi.ac.uk/pdbsum/2avx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avx ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SDIA_ECOLI SDIA_ECOLI] Activates cell division by specifically increasing transcription from one of the two promoters that lie immediately upstream of the ftsQAZ gene cluster. Activates ydiV expression in response to extracellular autoinducer AI-1 (Vibrio fischeri autoinducer oxoC6).<ref>PMID:1915297</ref> <ref>PMID:18560382</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/av/2avx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/av/2avx_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2avx ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2avx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 30: / Line 34: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Brogan, A P.]]
+[[Category: Large Structures]]
-[[Category: Dickerson, T J.]]
+[[Category: Brogan AP]]
-[[Category: Dyson, H J.]]
+[[Category: Dickerson TJ]]
-[[Category: Martinez-Yamout, M A.]]
+[[Category: Dyson HJ]]
-[[Category: Wright, P E.]]
+[[Category: Martinez-Yamout MA]]
-[[Category: Yao, Y.]]
+[[Category: Wright PE]]
-[[Category: Homoserine lactone]]
+[[Category: Yao Y]]
-[[Category: Quorum sensing]]
-[[Category: Transcription]]

2avx

From Proteopedia

Current revision

solution structure of E coli SdiA1-171

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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