2wyb: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2wyb.jpg|left|200px]]


<!--
==The quorum quenching N-acyl homoserine lactone acylase PvdQ with a covalently bound dodecanoic acid==
The line below this paragraph, containing "STRUCTURE_2wyb", creates the "Structure Box" on the page.
<StructureSection load='2wyb' size='340' side='right'caption='[[2wyb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2wyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WYB FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
{{STRUCTURE_2wyb|  PDB=2wyb  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wyb OCA], [https://pdbe.org/2wyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wyb RCSB], [https://www.ebi.ac.uk/pdbsum/2wyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wyb ProSAT]</span></td></tr>
</table>
== 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/wy/2wyb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2wyb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In many Gram-negative pathogens, their virulent behavior is regulated by quorum sensing, in which diffusible signals such as N-acyl homoserine lactones (AHLs) act as chemical messaging compounds. Enzymatic degradation of these diffusible signals by, e.g., lactonases or amidohydrolases abolishes AHL regulated virulence, a process known as quorum quenching. Here we report the first crystal structure of an AHL amidohydrolase, the AHL acylase PvdQ from Pseudomonas aeruginosa. PvdQ has a typical alpha/beta heterodimeric Ntn-hydrolase fold, similar to penicillin G acylase and cephalosporin acylase. However, it has a distinct, unusually large, hydrophobic binding pocket, ideally suited to recognize C12 fatty acid-like chains of AHLs. Binding of a C12 fatty acid or a 3-oxo-C12 fatty acid induces subtle conformational changes to accommodate the aliphatic chain. Furthermore, the structure of a covalent ester intermediate identifies Serbeta1 as the nucleophile and Asnbeta269 and Valbeta70 as the oxyanion hole residues in the AHL degradation process. Our structures show the versatility of the Ntn-hydrolase scaffold and can serve as a structural paradigm for Ntn-hydrolases with similar substrate preference. Finally, the quorum-quenching capabilities of PvdQ may be utilized to suppress the quorum-sensing machinery of pathogens.


===THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ WITH A COVALENTLY BOUND DODECANOIC ACID===
The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket.,Bokhove M, Jimenez PN, Quax WJ, Dijkstra BW Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):686-91. Epub 2009 Dec 22. PMID:20080736<ref>PMID:20080736</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
2WYB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYB OCA].
<div class="pdbe-citations 2wyb" style="background-color:#fffaf0;"></div>
[[Category: Acyl-homoserine-lactone acylase]]
== References ==
[[Category: Pseudomonas aeruginosa]]
<references/>
[[Category: Bokhove, M.]]
__TOC__
[[Category: Dijkstra, B W.]]
</StructureSection>
[[Category: Jimenez, P Nadal.]]
[[Category: Large Structures]]
[[Category: Quax, W J.]]
[[Category: Pseudomonas aeruginosa PAO1]]
[[Category: Hydrolase]]
[[Category: Bokhove M]]
[[Category: Periplasm]]
[[Category: Dijkstra BW]]
[[Category: Zymogen]]
[[Category: Nadal Jimenez P]]
 
[[Category: Quax WJ]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 30 14:41:26 2009''
Retrieved from "https://proteopedia.org/2wyb"