6n10 - Revision history

OCA at 06:43, 11 October 2023

2023-10-11T06:43:01Z

←Older revision		Revision as of 06:43, 11 October 2023
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	<StructureSection load='6n10' size='340' side='right'caption='[[6n10]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6n10' size='340' side='right'caption='[[6n10]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n10]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N10 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N10 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n10]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N10 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N10 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MVD1, MDD1, MVD, At2g38700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3702 ARATH])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class="sblockDat"><span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33]~~ </~~span~~></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=6n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n10 OCA], [https://pdbe.org/6n10 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n10 RCSB], [https://www.ebi.ac.uk/pdbsum/6n10 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n10 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n10 OCA], [~~http~~://pdbe.org/6n10 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n10 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n10 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n10 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MVD1_ARATH MVD1_ARATH]] Performs the first committed step in the biosynthesis of isoprene-containing compounds such as sterols and terpenoids (PubMed:10344201, PubMed:26216978). Is specific for (R)-5-diphosphomevalonate (MVAPP). The catalytic efficiency with (R)-5-phosphomevalonate (MVAP) as substrate is 10000-fold lower than for MVAPP (PubMed:26216978). Can complement a yeast mutant defective in MVD activity (PubMed:10344201).<ref>PMID:10344201</ref> <ref>PMID:26216978</ref>	+	[https://www.uniprot.org/uniprot/MVD1_ARATH MVD1_ARATH] Performs the first committed step in the biosynthesis of isoprene-containing compounds such as sterols and terpenoids (PubMed:10344201, PubMed:26216978). Is specific for (R)-5-diphosphomevalonate (MVAPP). The catalytic efficiency with (R)-5-phosphomevalonate (MVAP) as substrate is 10000-fold lower than for MVAPP (PubMed:26216978). Can complement a yeast mutant defective in MVD activity (PubMed:10344201).<ref>PMID:10344201</ref> <ref>PMID:26216978</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath]]~~	+	[[Category: Arabidopsis thaliana]]
-	~~[[Category: Diphosphomevalonate decarboxylase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Louie~~, G V~~]]	+	[[Category: Louie GV]]
-	[[Category: Noel~~, J P~~]]	+	[[Category: Noel JP]]
-	[[Category: Thomas~~, S T]]~~	+	[[Category: Thomas ST]]
-	~~[[Category: Lyase~~]]	+

OCA at 15:59, 28 August 2019

2019-08-28T15:59:09Z

←Older revision		Revision as of 15:59, 28 August 2019
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	<StructureSection load='6n10' size='340' side='right'caption='[[6n10]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6n10' size='340' side='right'caption='[[6n10]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n10]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N10 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N10 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n10]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N10 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N10 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MVD1, MDD1, MVD, At2g38700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n10 OCA], [http://pdbe.org/6n10 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n10 RCSB], [http://www.ebi.ac.uk/pdbsum/6n10 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n10 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n10 OCA], [http://pdbe.org/6n10 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n10 RCSB], [http://www.ebi.ac.uk/pdbsum/6n10 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n10 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Diphosphomevalonate decarboxylase]]		[[Category: Diphosphomevalonate decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 10:45, 17 July 2019

2019-07-17T10:45:35Z

←Older revision		Revision as of 10:45, 17 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6n10 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Arabidopsis thaliana mevalonate 5-diphosphate decarboxylase 1 complexed with (R)-MVAPP==
		+	<StructureSection load='6n10' size='340' side='right'caption='[[6n10]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n10]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N10 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N10 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphomevalonate_decarboxylase Diphosphomevalonate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.33 4.1.1.33] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6n10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n10 OCA], [http://pdbe.org/6n10 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n10 RCSB], [http://www.ebi.ac.uk/pdbsum/6n10 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n10 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MVD1_ARATH MVD1_ARATH]] Performs the first committed step in the biosynthesis of isoprene-containing compounds such as sterols and terpenoids (PubMed:10344201, PubMed:26216978). Is specific for (R)-5-diphosphomevalonate (MVAPP). The catalytic efficiency with (R)-5-phosphomevalonate (MVAP) as substrate is 10000-fold lower than for MVAPP (PubMed:26216978). Can complement a yeast mutant defective in MVD activity (PubMed:10344201).<ref>PMID:10344201</ref> <ref>PMID:26216978</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A bifurcation of the mevalonate (MVA) pathway was recently discovered in bacteria of the Chloroflexi phylum. In this alternative route for the biosynthesis of isopentenylpyrophosphate (IPP), the penultimate step is the decarboxylation of (R)-mevalonate 5-phosphate ((R)-MVAP) to isopentenyl phosphate (IP), which is followed by the ATP-dependent phosphorylation of IP to IPP catalyzed by isopentenyl phosphate kinase (IPK). Notably, the decarboxylation reaction is catalyzed by mevalonate 5-phosphate decarboxylase (MPD), which shares considerable sequence similarity with mevalonate diphosphate decarboxylase (MDD) of the classical MVA pathway. We show that an enzyme originally annotated as an MDD from the Chloroflexi bacterium Anaerolinea thermophila possesses equal catalytic efficiency for (R)-MVAP and (R)-mevalonate 5-diphosphate ((R)-MVAPP). Further, the molecular basis for this dual specificity is revealed by near atomic-resolution X-ray crystal structures of A. thermophila MPD/MDD bound to (R)-MVAP or (R)-MVAPP. These findings, when combined with sequence and structural comparisons of this bacterial enzyme, functional MDDs, and several putative MPDs, delineate key active-site residues that confer substrate specificity and functionally distinguish MPD and MDD enzyme-classes. Extensive sequence analyses identified functional MPDs in the halobacteria class of archaea that had been annotated as MDDs. Finally, no eukaryotic MPD candidates were identified, suggesting the absence of the alternative MVA (altMVA) pathway in all eukaryotes, including, paradoxically plants, which universally encode a structural and functional homolog of IPK. Additionally, we have developed a viable engineered strain of Saccharomyces cerevisiae as an in vivo metabolic model and a synthetic biology platform for enzyme engineering and terpene biosynthesis in which the classical MVA pathway has been replaced with the altMVA pathway.

-	~~Authors~~:	+	Substrate specificity and engineering of mevalonate 5-phosphate decarboxylase.,Thomas ST, Louie GV, Lubin JW, Lundblad V, Noel JP ACS Chem Biol. 2019 Jul 3. doi: 10.1021/acschembio.9b00322. PMID:31268677<ref>PMID:31268677</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6n10" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Diphosphomevalonate decarboxylase]]
		+	[[Category: Large Structures]]
		+	[[Category: Louie, G V]]
		+	[[Category: Noel, J P]]
		+	[[Category: Thomas, S T]]
		+	[[Category: Lyase]]

OCA at 05:18, 12 December 2018

2018-12-12T05:18:14Z

←Older revision		Revision as of 05:18, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n10 is ON HOLD	+	The entry 6n10 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6n10" [edit=sysop:move=sysop]

2018-11-14T06:47:32Z

Protected "6n10" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:47, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6n10 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-11-14T06:47:31Z

New page: '''Unreleased structure''' The entry 6n10 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6n10 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]