2v8k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2v8k" [edit=sysop:move=sysop])
Current revision (09:56, 9 May 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2v8k.png|left|200px]]
 
-
{{STRUCTURE_2v8k| PDB=2v8k | SCENE= }}
+
==Structure of a Family 2 Pectate Lyase in Complex with Trigalacturonic Acid==
 +
<StructureSection load='2v8k' size='340' side='right'caption='[[2v8k]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2v8k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V8K FirstGlance]. <br>
 +
</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=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</scene></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=2v8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v8k OCA], [https://pdbe.org/2v8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v8k RCSB], [https://www.ebi.ac.uk/pdbsum/2v8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v8k ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/A1JSS8_YERE8 A1JSS8_YERE8]
 +
== 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/v8/2v8k_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/main_output.php?pdb_ID=2v8k ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5A, reveals it to be the first prokaryotic protein reported to display the rare (alpha/alpha)(7) barrel fold. In addition to its apo form, we have also determined the structure of a metal-bound form of YePL2A (to 2.0A) and a trigalacturonic acid-bound substrate complex (to 2.1A) Although its fold is rare, the catalytic center of YePL2A can be superimposed with structurally unrelated families, underlining the conserved catalytic amino acid architecture of the beta-elimination mechanism. In addition to its overall structure, YePL2A also has two other unique features: 1) it utilizes a metal atom other than calcium for catalysis, and 2) its Bronstead base is in an alternate conformation and directly interacts with the uronate group of the substrate.
-
===STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH TRIGALACTURONIC ACID===
+
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.,Abbott DW, Boraston AB J Biol Chem. 2007 Nov 30;282(48):35328-36. Epub 2007 Sep 19. PMID:17881361<ref>PMID:17881361</ref>
-
{{ABSTRACT_PUBMED_17881361}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2v8k" style="background-color:#fffaf0;"></div>
-
[[2v8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V8K OCA].
+
== References ==
-
 
+
<references/>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:017881361</ref><references group="xtra"/>
+
</StructureSection>
-
[[Category: Pectate lyase]]
+
[[Category: Large Structures]]
[[Category: Yersinia enterocolitica]]
[[Category: Yersinia enterocolitica]]
-
[[Category: Abbott, D W.]]
+
[[Category: Abbott DW]]
-
[[Category: Boraston, A B.]]
+
[[Category: Boraston AB]]
-
[[Category: Beta-elimination]]
+
-
[[Category: Lyase]]
+
-
[[Category: Pectate lyase]]
+
-
[[Category: Pectin degradation]]
+

Current revision

Structure of a Family 2 Pectate Lyase in Complex with Trigalacturonic Acid

PDB ID 2v8k

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v8k"
Personal tools