6e2y: Difference between revisions

New page: '''Unreleased structure''' The entry 6e2y is ON HOLD Authors: Stauffacher, C.V., Chen, C.-L. Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data [[Categor...
 
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'''Unreleased structure'''


The entry 6e2y is ON HOLD
==MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data==
<StructureSection load='6e2y' size='340' side='right'caption='[[6e2y]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6e2y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2Y 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]] 2.34&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6e2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2y OCA], [https://pdbe.org/6e2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2y RCSB], [https://www.ebi.ac.uk/pdbsum/6e2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9FD68_ENTFL Q9FD68_ENTFL]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg(2+)-decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg(2+) ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of gamma-phosphate from ATP to MVAPP, followed by the production of IPP.


Authors: Stauffacher, C.V., Chen, C.-L.
Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.,Chen CL, Paul LN, Mermoud JC, Steussy CN, Stauffacher CV Nat Commun. 2020 Aug 7;11(1):3969. doi: 10.1038/s41467-020-17733-0. PMID:32769976<ref>PMID:32769976</ref>


Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Chen, C.-L]]
<div class="pdbe-citations 6e2y" style="background-color:#fffaf0;"></div>
[[Category: Stauffacher, C.V]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Enterococcus faecalis]]
[[Category: Large Structures]]
[[Category: Chen C-L]]
[[Category: Stauffacher CV]]

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