View source for 7bbv


==Pectate lyase B from Verticillium dahliae==
<StructureSection load='7bbv' size='340' side='right'caption='[[7bbv]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7bbv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Verticillium_dahliae_VdLs.17 Verticillium dahliae VdLs.17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBV 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]] 1.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7bbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbv OCA], [https://pdbe.org/7bbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbv RCSB], [https://www.ebi.ac.uk/pdbsum/7bbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G2X3Y1_VERDV G2X3Y1_VERDV] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by beta-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae. We first solved the crystal structure of VdPelB at 1.2 A resolution showing that it is a right-handed parallel beta-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. Pectate lyase VdPelB was most active on non-methylesterified pectins, at pH 8.0 in presence of Ca(2+) ions. The VdPelB-G125R mutant was most active at pH 9.0 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.

The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations.,Safran J, Ung V, Bouckaert J, Habrylo O, Molinie R, Fontaine JX, Lemaire A, Voxeur A, Pilard S, Pau-Roblot C, Mercadante D, Pelloux J, Senechal F Int J Biol Macromol. 2023 Mar 15;231:123137. doi: 10.1016/j.ijbiomac.2023.123137. , Epub 2023 Jan 11. PMID:36639075<ref>PMID:36639075</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7bbv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Verticillium dahliae VdLs 17]]
[[Category: Bouckaert J]]
[[Category: Habrylo O]]
[[Category: Pau Roblot C]]
[[Category: Pelloux J]]
[[Category: Safran J]]
[[Category: Senechal F]]