6e2v: Difference between revisions
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==MDDEF in complex with MVAPP, ADPBeF3 and magnesium== | |||
<StructureSection load='6e2v' size='340' side='right'caption='[[6e2v]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6e2v]] 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=6E2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2V 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]] 2.1Å</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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=DP6:(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC+ACID'>DP6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6e2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2v OCA], [https://pdbe.org/6e2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2v RCSB], [https://www.ebi.ac.uk/pdbsum/6e2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2v 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6e2v" style="background-color:#fffaf0;"></div> | ||
[[Category: Chen | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Enterococcus faecalis]] | |||
[[Category: Large Structures]] | |||
[[Category: Chen C-L]] | |||
[[Category: Stauffacher CV]] | |||
Latest revision as of 09:17, 11 October 2023
MDDEF in complex with MVAPP, ADPBeF3 and magnesiumMDDEF in complex with MVAPP, ADPBeF3 and magnesium
Structural highlights
FunctionPublication Abstract from PubMedMevalonate 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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