2r2d: Difference between revisions

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[[Image:2r2d.jpg|left|200px]]


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==Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens==
The line below this paragraph, containing "STRUCTURE_2r2d", creates the "Structure Box" on the page.
<StructureSection load='2r2d' size='340' side='right'caption='[[2r2d]], [[Resolution|resolution]] 1.75&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'>[[2r2d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R2D 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]] 1.75&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_2r2d|  PDB=2r2d  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r2d OCA], [https://pdbe.org/2r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r2d RCSB], [https://www.ebi.ac.uk/pdbsum/2r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r2d ProSAT]</span></td></tr>
 
</table>
'''Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens'''
== Function ==
 
[https://www.uniprot.org/uniprot/AHLLB_AGRFC AHLLB_AGRFC]  
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
N-Acyl-l-homoserine lactone (AHL) mediated quorum-sensing regulates virulence factor production in a variety of Gram-negative bacteria. Proteins capable of degrading these autoinducers have been called "quorum-quenching" enzymes, can block many quorum-sensing dependent phenotypes, and represent potentially useful reagents for clinical, agricultural, and industrial applications. The most characterized quorum-quenching enzymes to date are the AHL lactonases, which are metalloproteins that belong to the metallo-beta-lactamase superfamily. Here, we report the cloning, heterologous expression, purification, metal content, substrate specificity, and three-dimensional structure of AiiB, an AHL lactonase from Agrobacterium tumefaciens. Much like a homologous AHL lactonase from Bacillus thuringiensis, AiiB appears to be a metal-dependent AHL lactonase with broad specificity. A phosphate dianion is bound to the dinuclear zinc site and the active-site structure suggests specific mechanistic roles for an active site tyrosine and aspartate. To our knowledge, this is the second representative structure of an AHL lactonase and the first of an AHL lactonase from a microorganism that also produces AHL autoinducers. This work should help elucidate the hydrolytic ring-opening mechanism of this family of enzymes and also facilitate the design of more effective quorum-quenching catalysts.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r2/2r2d_consurf.spt"</scriptWhenChecked>
2R2D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2D OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens., Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, Ringe D, Fast W, Biochemistry. 2007 Oct 23;46(42):11789-99. Epub 2007 Sep 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17900178 17900178]
</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=2r2d ConSurf].
[[Category: Agrobacterium tumefaciens]]
<div style="clear:both"></div>
[[Category: Single protein]]
__TOC__
[[Category: Fast, W.]]
</StructureSection>
[[Category: Hoang, Q.]]
[[Category: Agrobacterium fabrum str. C58]]
[[Category: Liu, D.]]
[[Category: Large Structures]]
[[Category: Momb, J.]]
[[Category: Fast W]]
[[Category: Petsko, G A.]]
[[Category: Hoang Q]]
[[Category: Ringe, D.]]
[[Category: Liu D]]
[[Category: Thomas, P W.]]
[[Category: Momb J]]
[[Category: Agrobacterium tumefacien]]
[[Category: Petsko GA]]
[[Category: Aiib]]
[[Category: Ringe D]]
[[Category: Di-nuclear zinc center]]
[[Category: Thomas PW]]
[[Category: Hydrolase]]
[[Category: Lactonase]]
[[Category: N-acyl hompserine lactone]]
[[Category: Phosphate]]
[[Category: Quorum quenching]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 16:07:15 2008''

Latest revision as of 12:19, 21 February 2024

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciensStructure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens

Structural highlights

2r2d is a 6 chain structure with sequence from Agrobacterium fabrum str. C58. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.75Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AHLLB_AGRFC

Evolutionary Conservation

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

2r2d, resolution 1.75Å

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