6wke - Revision history

OCA at 14:29, 18 October 2023

OCA — Wed, 18 Oct 2023 14:29:01 GMT

←Older revision		Revision as of 14:29, 18 October 2023
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	<StructureSection load='6wke' size='340' side='right'caption='[[6wke]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6wke' size='340' side='right'caption='[[6wke]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wke]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chainia_sp~~. ~~Chainia~~ sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WKE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wke]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WKE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>penA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1931 Chainia sp.])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Pentalenene_synthase Pentalenene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.7 4.2.3.7]~~ </~~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=6wke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wke OCA], [https://pdbe.org/6wke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wke RCSB], [https://www.ebi.ac.uk/pdbsum/6wke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wke ProSAT]</span></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=6wke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wke OCA], [~~http~~://pdbe.org/6wke PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wke RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wke PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wke ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PENA_STREX PENA_STREX]] Catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene, which is the hydrocarbon precursor of the pentalenolactone family of antibiotics produced by a variety of Streptomyces species.<ref>PMID:8180213</ref>	+	[https://www.uniprot.org/uniprot/PENA_STREX PENA_STREX] Catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene, which is the hydrocarbon precursor of the pentalenolactone family of antibiotics produced by a variety of Streptomyces species.<ref>PMID:8180213</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: Chainia sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pentalenene synthase]]~~	+	[[Category: Streptomyces sp]]
-	~~[[Category: Kumar, R Prem~~]]	+	[[Category: Matos JO]]
-	[[Category: Matos~~, J O~~]]	+	[[Category: Oprian DD]]
-	[[Category: Oprian~~, D D~~]]	+	[[Category: Prem Kumar R]]
-	[[Category: ~~Fluoro analog]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metal binding]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Sesquiterpene]]~~	+
-	~~[[Category: Terpene synthase]]~~	+
-	~~[[Category: Terpene synthase fold~~]]	+

OCA at 10:15, 16 September 2020

OCA — Wed, 16 Sep 2020 10:15:59 GMT

←Older revision		Revision as of 10:15, 16 September 2020
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	==Crystal structure of pentalenene synthase mutant F76Y==		==Crystal structure of pentalenene synthase mutant F76Y==
-	<StructureSection load='6wke' size='340' side='right'caption='[[6wke]]' scene=''>	+	<StructureSection load='6wke' size='340' side='right'caption='[[6wke]], [[Resolution\|resolution]] 2.40Å' 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=6WKE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WKE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wke]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chainia_sp. Chainia sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WKE 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=6wke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wke OCA], [http://pdbe.org/6wke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wke RCSB], [http://www.ebi.ac.uk/pdbsum/6wke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wke ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">penA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1931 Chainia sp.])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenene_synthase Pentalenene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.7 4.2.3.7] </span></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=6wke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wke OCA], [http://pdbe.org/6wke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wke RCSB], [http://www.ebi.ac.uk/pdbsum/6wke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wke ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PENA_STREX PENA_STREX]] Catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene, which is the hydrocarbon precursor of the pentalenolactone family of antibiotics produced by a variety of Streptomyces species.<ref>PMID:8180213</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most terpene synthase reactions follow Markovnikov rules for formation of high-energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 atom of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide the regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the nonreactive substrate analogue 12,13-difluorofarnesyl diphosphate, and determined the X-ray structure of the resulting complex at 2.2 A resolution. The most striking feature of the active site structure is that C9 is perfectly positioned to make a C-H...pi interaction with the side chain benzene ring of residue F76; this would enhance hyperconjugation to stabilize a developing cation at C10 and thus support the anti-Markovnikov regioselectivity of the cyclization. The benzene ring is also positioned to catalyze the migration of H to C10 and stabilize a C9 carbocation. On the opposite face of C9, further cation stabilization is possible via interactions with the main chain carbonyl of I177 and the neighboring intramolecular C6 horizontal lineC7 bond. Mutagenesis experiments also support a role for residue 76 in these interactions, but most interesting is the F76W mutant, whose crystal structure clearly shows C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases from Streptomyces that catalyze similar anti-Markovnikov addition reactions.
		+
		+	Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase.,Matos JO, Kumar RP, Ma AC, Patterson M, Krauss IJ, Oprian DD Biochemistry. 2020 Aug 18. doi: 10.1021/acs.biochem.0c00518. PMID:32786410<ref>PMID:32786410</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wke" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chainia sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Matos JO]]	+	[[Category: Pentalenene synthase]]
-	[[Category: Oprian DD]]	+	[[Category: Kumar, R Prem]]
-	[[Category: ~~Prem Kumar R~~]]	+	[[Category: Matos, J O]]
		+	[[Category: Oprian, D D]]
		+	[[Category: Fluoro analog]]
		+	[[Category: Lyase]]
		+	[[Category: Metal binding]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Sesquiterpene]]
		+	[[Category: Terpene synthase]]
		+	[[Category: Terpene synthase fold]]

OCA at 11:17, 26 August 2020

OCA — Wed, 26 Aug 2020 11:17:09 GMT

←Older revision		Revision as of 11:17, 26 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6wke is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of pentalenene synthase mutant F76Y==
-		+	<StructureSection load='6wke' size='340' side='right'caption='[[6wke]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WKE FirstGlance]. <br>
-	~~Description~~:	+	</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=6wke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wke OCA], [http://pdbe.org/6wke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wke RCSB], [http://www.ebi.ac.uk/pdbsum/6wke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wke ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Matos JO]]
		+	[[Category: Oprian DD]]
		+	[[Category: Prem Kumar R]]

OCA at 04:13, 20 May 2020

OCA — Wed, 20 May 2020 04:13:08 GMT

←Older revision		Revision as of 04:13, 20 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 22 Apr 2020 04:20:09 GMT

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

←Older revision

Revision as of 04:20, 22 April 2020

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

OCA — Wed, 22 Apr 2020 04:20:07 GMT

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

New page

'''Unreleased structure'''

The entry 6wke is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]