6e2w - Revision history

OCA at 06:17, 11 October 2023

OCA — Wed, 11 Oct 2023 06:17:52 GMT

←Older revision		Revision as of 06:17, 11 October 2023
Line 1:		Line 1:

	==MDDEF in complex with MVAPP, ADP, sulfate and cobalt==		==MDDEF in complex with MVAPP, ADP, sulfate and cobalt==
-	<StructureSection load='6e2w' size='340' side='right'caption='[[6e2w]]' scene=''>	+	<StructureSection load='6e2w' size='340' side='right'caption='[[6e2w]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6E2W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e2w]] 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=6E2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2W FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6e2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2w OCA], [~~http~~://pdbe.org/6e2w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e2w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e2w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2w ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</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=6e2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2w OCA], [https://pdbe.org/6e2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2w RCSB], [https://www.ebi.ac.uk/pdbsum/6e2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2w ProSAT]</span></td></tr>
	</table>		</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>
		+	</div>
		+	<div class="pdbe-citations 6e2w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterococcus faecalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen C-L]]		[[Category: Chen C-L]]
	[[Category: Stauffacher CV]]		[[Category: Stauffacher CV]]

OCA at 06:28, 19 August 2020

OCA — Wed, 19 Aug 2020 06:28:17 GMT

←Older revision		Revision as of 06:28, 19 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6e2w ~~is ON HOLD until Paper Publication~~	+	==MDDEF in complex with MVAPP, ADP, sulfate and cobalt==
-		+	<StructureSection load='6e2w' size='340' side='right'caption='[[6e2w]]' scene=''>
-	~~Authors~~: ~~Stauffacher~~, C.V., ~~Chen~~, C.-L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6E2W FirstGlance]. <br>
-	~~Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6e2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2w OCA], [http://pdbe.org/6e2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e2w RCSB], [http://www.ebi.ac.uk/pdbsum/6e2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2w ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Stauffacher,~~ C.V]]	+	__TOC__
-	[[Category: ~~Chen, C.-L~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen C-L]]
		+	[[Category: Stauffacher CV]]

OCA at 05:52, 25 July 2018

OCA — Wed, 25 Jul 2018 05:52:44 GMT

←Older revision		Revision as of 05:52, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6e2w is ON HOLD	+	The entry 6e2w is ON HOLD until Paper Publication

	Authors: Stauffacher, C.V., Chen, C.-L.		Authors: Stauffacher, C.V., Chen, C.-L.
Line 7:		Line 7:
	Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt		Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chen, C.-L]]
	[[Category: Stauffacher, C.V]]		[[Category: Stauffacher, C.V]]
		+	[[Category: Chen, C.-L]]

OCA: Protected "6e2w" [edit=sysop:move=sysop]

OCA — Wed, 18 Jul 2018 05:43:54 GMT

Protected "6e2w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:43, 18 July 2018

OCA: New page: '''Unreleased structure''' The entry 6e2w is ON HOLD Authors: Stauffacher, C.V., Chen, C.-L. Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt [[Category: Unreleased St...

OCA — Wed, 18 Jul 2018 05:43:52 GMT

New page: '''Unreleased structure''' The entry 6e2w is ON HOLD Authors: Stauffacher, C.V., Chen, C.-L. Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6e2w is ON HOLD

Authors: Stauffacher, C.V., Chen, C.-L.

Description: MDDEF in complex with MVAPP, ADP, sulfate and cobalt
[[Category: Unreleased Structures]]
[[Category: Chen, C.-L]]
[[Category: Stauffacher, C.V]]