2v8j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:56, 9 May 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2v8j.png|left|200px]]
 
-
<!--
+
==Structure of a Family 2 Pectate Lyase in Complex with a Transition Metal==
-
The line below this paragraph, containing "STRUCTURE_2v8j", creates the "Structure Box" on the page.
+
<StructureSection load='2v8j' size='340' side='right'caption='[[2v8j]], [[Resolution|resolution]] 2.01&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'>[[2v8j]] 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=2V8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V8J 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]] 2.01&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_2v8j| PDB=2v8j | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v8j OCA], [https://pdbe.org/2v8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v8j RCSB], [https://www.ebi.ac.uk/pdbsum/2v8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v8j 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/v8/2v8j_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=2v8j 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 A TRANSITION METAL===
+
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>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_17881361}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2v8j" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 17881361 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17881361}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
2V8J is a [[Single protein]] structure of 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=2V8J OCA].
+
-
 
+
-
==Reference==
+
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/17881361 17881361]
+
-
[[Category: Pectate lyase]]
+
-
[[Category: Single protein]]
+
[[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]]
+
-
[[Category: Periplasm]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:39:41 2008''
+

Current revision

Structure of a Family 2 Pectate Lyase in Complex with a Transition Metal

PDB ID 2v8j

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/2v8j"
Personal tools