5i1u - Revision history

OCA at 12:33, 6 March 2024

OCA — Wed, 06 Mar 2024 12:33:33 GMT

←Older revision		Revision as of 12:33, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/G5EKM9_9ACTN G5EKM9_9ACTN]		[https://www.uniprot.org/uniprot/G5EKM9_9ACTN G5EKM9_9ACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The sesquiterpene synthase germacradiene-4-ol synthase (GdolS) from Streptomyces citricolor is one of only a few known high-fidelity terpene synthases that convert farnesyl diphosphate (FDP) into a single hydroxylated product. Crystals of unliganded GdolS-E248A diffracted to 1.50 A and revealed a typical class 1 sesquiterpene synthase fold with the active site in an open conformation. The metal binding motifs were identified as D(80)DQFD and N(218)DVRSFAQE. Some bound water molecules were evident in the X-ray crystal structure, but none were obviously positioned to quench a putative final carbocation intermediate. Incubations in H2(18)O generated labeled product, confirming that the alcohol functionality arises from nucleophilic capture of the final carbocation by water originating from solution. Site-directed mutagenesis of amino acid residues from both within the metal binding motifs and without identified by sequence alignment with aristolochene synthase from Aspergillus terreus generated mostly functional germacradien-4-ol synthases. Only GdolS-N218Q generated radically different products ( approximately 50% germacrene A), but no direct evidence of the mechanism of incorporation of water into the active site was obtained. Fluorinated FDP analogues 2F-FDP and 15,15,15-F3-FDP were potent noncompetitive inhibitors of GdolS. 12,13-DiF-FDP generated 12,13-(E)-beta-farnesene upon being incubated with GdolS, suggesting stepwise formation of the germacryl cation during the catalytic cycle. Incubation of GdolS with [1-(2)H2]FDP and (R)-[1-(2)H]FDP demonstrated that following germacryl cation formation a [1,3]-hydride shift generates the final carbocation prior to nucleophilic capture. The stereochemistry of this shift is not defined, and the deuteron in the final product was scrambled. Because no clear candidate residue for binding of a nucleophilic water molecule in the active site and no significant perturbation of product distribution from the replacement of active site residues were observed, the final carbocation may be captured by a water molecule from bulk solvent.
-
-	Mechanism of Germacradien-4-ol Synthase-Controlled Water Capture.,Grundy DJ, Chen M, Gonzalez V, Leoni S, Miller DJ, Christianson DW, Allemann RK Biochemistry. 2016 Apr 12;55(14):2112-21. doi: 10.1021/acs.biochem.6b00115. Epub , 2016 Mar 30. PMID:26998816<ref>PMID:26998816</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5i1u" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:20, 23 August 2023

OCA — Wed, 23 Aug 2023 08:20:24 GMT

←Older revision		Revision as of 08:20, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i1u' size='340' side='right'caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5i1u' size='340' side='right'caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_citricolor"_kusaka_et_al. "streptomyces~~ citricolor~~" kusaka et al.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_citricolor Streptomyces citricolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I1U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~212427~~ "~~Streptomyces citricolor~~" ~~Kusaka et al.])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5i1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1u OCA], [~~http~~://pdbe.org/5i1u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i1u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i1u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1u ProSAT]</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=5i1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1u OCA], [https://pdbe.org/5i1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i1u RCSB], [https://www.ebi.ac.uk/pdbsum/5i1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G5EKM9_9ACTN G5EKM9_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces citricolor kusaka et al]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chen, M~~]]	+	[[Category: Streptomyces citricolor]]
-	[[Category: ~~Christianson, D W~~]]	+	[[Category: Chen M]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Christianson DW]]
-	~~[[Category: Sesquiterpene cyclase~~]]	+

OCA at 11:44, 25 December 2019

OCA — Wed, 25 Dec 2019 11:44:59 GMT

←Older revision		Revision as of 11:44, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of germacradien-4-ol synthase from Streptomyces citricolor==		==Crystal structure of germacradien-4-ol synthase from Streptomyces citricolor==
-	<StructureSection load='5i1u' size='340' side='right' caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5i1u' size='340' side='right'caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_citricolor"_kusaka_et_al. "streptomyces citricolor" kusaka et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1U FirstGlance]. <br>		<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_citricolor"_kusaka_et_al. "streptomyces citricolor" kusaka et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1U FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces citricolor kusaka et al]]		[[Category: Streptomyces citricolor kusaka et al]]
		+	[[Category: Large Structures]]
	[[Category: Chen, M]]		[[Category: Chen, M]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Sesquiterpene cyclase]]		[[Category: Sesquiterpene cyclase]]

OCA at 17:31, 15 November 2017

OCA — Wed, 15 Nov 2017 17:31:57 GMT

←Older revision		Revision as of 17:31, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5i1u' size='340' side='right' caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5i1u' size='340' side='right' caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_citricolor"_kusaka_et_al. "streptomyces citricolor" kusaka et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></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=5i1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1u OCA], [http://pdbe.org/5i1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1u RCSB], [http://www.ebi.ac.uk/pdbsum/5i1u PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212427 "Streptomyces citricolor" Kusaka et al.])</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=5i1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1u OCA], [http://pdbe.org/5i1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1u RCSB], [http://www.ebi.ac.uk/pdbsum/5i1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i1u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces citricolor kusaka et al]]
	[[Category: Chen, M]]		[[Category: Chen, M]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Sesquiterpene cyclase]]		[[Category: Sesquiterpene cyclase]]

OCA at 16:13, 10 May 2016

OCA — Tue, 10 May 2016 16:13:20 GMT

←Older revision		Revision as of 16:13, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i1u is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of germacradien-4-ol synthase from Streptomyces citricolor==
		+	<StructureSection load='5i1u' size='340' side='right' caption='[[5i1u]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i1u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I1U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5i1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i1u OCA], [http://pdbe.org/5i1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i1u RCSB], [http://www.ebi.ac.uk/pdbsum/5i1u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The sesquiterpene synthase germacradiene-4-ol synthase (GdolS) from Streptomyces citricolor is one of only a few known high-fidelity terpene synthases that convert farnesyl diphosphate (FDP) into a single hydroxylated product. Crystals of unliganded GdolS-E248A diffracted to 1.50 A and revealed a typical class 1 sesquiterpene synthase fold with the active site in an open conformation. The metal binding motifs were identified as D(80)DQFD and N(218)DVRSFAQE. Some bound water molecules were evident in the X-ray crystal structure, but none were obviously positioned to quench a putative final carbocation intermediate. Incubations in H2(18)O generated labeled product, confirming that the alcohol functionality arises from nucleophilic capture of the final carbocation by water originating from solution. Site-directed mutagenesis of amino acid residues from both within the metal binding motifs and without identified by sequence alignment with aristolochene synthase from Aspergillus terreus generated mostly functional germacradien-4-ol synthases. Only GdolS-N218Q generated radically different products ( approximately 50% germacrene A), but no direct evidence of the mechanism of incorporation of water into the active site was obtained. Fluorinated FDP analogues 2F-FDP and 15,15,15-F3-FDP were potent noncompetitive inhibitors of GdolS. 12,13-DiF-FDP generated 12,13-(E)-beta-farnesene upon being incubated with GdolS, suggesting stepwise formation of the germacryl cation during the catalytic cycle. Incubation of GdolS with [1-(2)H2]FDP and (R)-[1-(2)H]FDP demonstrated that following germacryl cation formation a [1,3]-hydride shift generates the final carbocation prior to nucleophilic capture. The stereochemistry of this shift is not defined, and the deuteron in the final product was scrambled. Because no clear candidate residue for binding of a nucleophilic water molecule in the active site and no significant perturbation of product distribution from the replacement of active site residues were observed, the final carbocation may be captured by a water molecule from bulk solvent.

-	~~Authors: Chen~~, M., Christianson, D.W.	+	Mechanism of Germacradien-4-ol Synthase-Controlled Water Capture.,Grundy DJ, Chen M, Gonzalez V, Leoni S, Miller DJ, Christianson DW, Allemann RK Biochemistry. 2016 Apr 12;55(14):2112-21. doi: 10.1021/acs.biochem.6b00115. Epub , 2016 Mar 30. PMID:26998816<ref>PMID:26998816</ref>

-	~~Description: Crystal structure~~ of ~~germacradien~~-4-~~ol synthase from Streptomyces citricolor~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5i1u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Chen, M]]		[[Category: Chen, M]]
-	[[Category: Christianson, D.W]]	+	[[Category: Christianson, D W]]
		+	[[Category: Lyase]]
		+	[[Category: Sesquiterpene cyclase]]

OCA at 13:16, 2 March 2016

OCA — Wed, 02 Mar 2016 13:16:09 GMT

←Older revision		Revision as of 13:16, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i1u is ON HOLD	+	The entry 5i1u is ON HOLD until Paper Publication

	Authors: Chen, M., Christianson, D.W.		Authors: Chen, M., Christianson, D.W.

OCA at 16:38, 26 February 2016

OCA — Fri, 26 Feb 2016 16:38:34 GMT

←Older revision		Revision as of 16:38, 26 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i1u is ON HOLD ~~until sometime in the future~~	+	The entry 5i1u is ON HOLD

	Authors: Chen, M., Christianson, D.W.		Authors: Chen, M., Christianson, D.W.

OCA: Protected "5i1u" [edit=sysop:move=sysop]

OCA — Sun, 21 Feb 2016 01:26:39 GMT

Protected "5i1u" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:26, 21 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i1u is ON HOLD until sometime in the future Authors: Chen, M., Christianson, D.W. Description: Crystal structure of germacradien-4-ol synthase fro...

OCA — Sun, 21 Feb 2016 01:26:37 GMT

New page: '''Unreleased structure''' The entry 5i1u is ON HOLD until sometime in the future Authors: Chen, M., Christianson, D.W. Description: Crystal structure of germacradien-4-ol synthase fro...

New page

'''Unreleased structure'''

The entry 5i1u is ON HOLD until sometime in the future

Authors: Chen, M., Christianson, D.W.

Description: Crystal structure of germacradien-4-ol synthase from Streptomyces citricolor
[[Category: Unreleased Structures]]
[[Category: Chen, M]]
[[Category: Christianson, D.W]]