5dw7 - Revision history

OCA at 22:02, 28 June 2023

OCA — Wed, 28 Jun 2023 22:02:24 GMT

←Older revision		Revision as of 22:02, 28 June 2023
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	<StructureSection load='5dw7' size='340' side='right'caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5dw7' size='340' side='right'caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strco Strco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5dz2\|5dz2]]</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]] 3.202Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">cyc2, SCO6073, SC9B1~~.~~20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=100226 STRCO])~~</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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [https://pdbe.org/5dw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [https://www.ebi.ac.uk/pdbsum/5dw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dw7 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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [~~http~~://pdbe.org/5dw7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dw7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dw7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CYC2_STRCO CYC2_STRCO]] Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.<ref>PMID:12556563</ref> <ref>PMID:12563033</ref> <ref>PMID:14995166</ref> <ref>PMID:16787064</ref>	+	[https://www.uniprot.org/uniprot/CYC2_STRCO CYC2_STRCO] Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.<ref>PMID:12556563</ref> <ref>PMID:12563033</ref> <ref>PMID:14995166</ref> <ref>PMID:16787064</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Strco]]~~	+	[[Category: Cane DE]]
-	[[Category: Cane~~, D E~~]]	+	[[Category: Chou WK]]
-	[[Category: Chou~~, W K~~]]	+	[[Category: Christianson DW]]
-	[[Category: Christianson~~, D W~~]]	+	[[Category: Cole KE]]
-	[[Category: Cole~~, K E~~]]	+	[[Category: Harris GG]]
-	[[Category: Harris~~, G G~~]]	+	[[Category: Koksal M]]
-	[[Category: Koksal, M]]	+	[[Category: Lombardi PM]]
-	[[Category: Lombardi~~, P M~~]]	+	[[Category: Matsui T]]
-	[[Category: Matsui, T]]	+	[[Category: Murphy FV]]
-	[[Category: Murphy~~, F V~~]]	+	[[Category: Pemberton TA]]
-	[[Category: Pemberton~~, T A~~]]	+	[[Category: Vedula LS]]
-	[[Category: Vedula~~, L S~~]]	+	[[Category: Weiss TM]]
-	[[Category: Weiss~~, T M]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Terpene cyclase~~]]	+

OCA at 11:28, 25 December 2019

OCA — Wed, 25 Dec 2019 11:28:26 GMT

←Older revision		Revision as of 11:28, 25 December 2019
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	==Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor==		==Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor==
-	<StructureSection load='5dw7' size='340' side='right' caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='5dw7' size='340' side='right'caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dz2\|5dz2]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dz2\|5dz2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cyc2, SCO6073, SC9B1.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [http://pdbe.org/5dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/5dw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dw7 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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [http://pdbe.org/5dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/5dw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dw7 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Strco]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]
	[[Category: Chou, W K]]		[[Category: Chou, W K]]

OCA at 06:41, 6 October 2017

OCA — Fri, 06 Oct 2017 06:41:47 GMT

←Older revision		Revision as of 06:41, 6 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor==		==Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor==
	<StructureSection load='5dw7' size='340' side='right' caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5dw7' size='340' side='right' caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dz2\|5dz2]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dz2\|5dz2]]</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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [http://pdbe.org/5dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/5dw7 PDBsum]</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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [http://pdbe.org/5dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/5dw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dw7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:15, 9 December 2015

OCA — Wed, 09 Dec 2015 07:15:27 GMT

←Older revision		Revision as of 07:15, 9 December 2015
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CYC2_STRCO CYC2_STRCO]] Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.<ref>PMID:12556563</ref> <ref>PMID:12563033</ref> <ref>PMID:14995166</ref> <ref>PMID:16787064</ref>		[[http://www.uniprot.org/uniprot/CYC2_STRCO CYC2_STRCO]] Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.<ref>PMID:12556563</ref> <ref>PMID:12563033</ref> <ref>PMID:14995166</ref> <ref>PMID:16787064</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique alphaalpha domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of approximately 36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible alphaalpha domain architectures as frameworks for bifunctional catalysis.
		+
		+	Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with alphaalpha Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.,Harris GG, Lombardi PM, Pemberton TA, Matsui T, Weiss TM, Cole KE, Koksal M, Murphy FV 4th, Vedula LS, Chou WK, Cane DE, Christianson DW Biochemistry. 2015 Dec 8;54(48):7142-7155. Epub 2015 Nov 24. PMID:26598179<ref>PMID:26598179</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dw7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:45, 1 December 2015

OCA — Tue, 01 Dec 2015 04:45:40 GMT

←Older revision		Revision as of 04:45, 1 December 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor==
-		+	<StructureSection load='5dw7' size='340' side='right' caption='[[5dw7]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~The entry~~ 5dw7 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dw7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DW7 FirstGlance]. <br>
-	~~Authors~~: ~~Lombardi~~, P.M., ~~Christianson~~, D.W.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dz2\|5dz2]]</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=5dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dw7 OCA], [http://pdbe.org/5dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/5dw7 PDBsum]</span></td></tr>
-	~~Description~~:	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	== Function ==
-	[[Category: Lombardi, P.M]]	+	[[http://www.uniprot.org/uniprot/CYC2_STRCO CYC2_STRCO]] Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.<ref>PMID:12556563</ref> <ref>PMID:12563033</ref> <ref>PMID:14995166</ref> <ref>PMID:16787064</ref>
-	[[Category: ~~Christianson~~, ~~D.W~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cane, D E]]
		+	[[Category: Chou, W K]]
		+	[[Category: Christianson, D W]]
		+	[[Category: Cole, K E]]
		+	[[Category: Harris, G G]]
		+	[[Category: Koksal, M]]
		+	[[Category: Lombardi, P M]]
		+	[[Category: Matsui, T]]
		+	[[Category: Murphy, F V]]
		+	[[Category: Pemberton, T A]]
		+	[[Category: Vedula, L S]]
		+	[[Category: Weiss, T M]]
		+	[[Category: Lyase]]
		+	[[Category: Terpene cyclase]]

OCA at 12:38, 7 October 2015

OCA — Wed, 07 Oct 2015 12:38:48 GMT

←Older revision		Revision as of 12:38, 7 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dw7 is ON HOLD	+	The entry 5dw7 is ON HOLD until Paper Publication

	Authors: Lombardi, P.M., Christianson, D.W.		Authors: Lombardi, P.M., Christianson, D.W.

OCA: Protected "5dw7" [edit=sysop:move=sysop]

OCA — Wed, 30 Sep 2015 13:36:39 GMT

Protected "5dw7" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:36, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dw7 is ON HOLD Authors: Lombardi, P.M., Christianson, D.W. Description: Category: Unreleased Structures Category: Lombardi, P.M [[Categor...

OCA — Wed, 30 Sep 2015 13:36:38 GMT

New page: '''Unreleased structure''' The entry 5dw7 is ON HOLD Authors: Lombardi, P.M., Christianson, D.W. Description: Category: Unreleased Structures Category: Lombardi, P.M [[Categor...

New page

'''Unreleased structure'''

The entry 5dw7 is ON HOLD

Authors: Lombardi, P.M., Christianson, D.W.

Description:
[[Category: Unreleased Structures]]
[[Category: Lombardi, P.M]]
[[Category: Christianson, D.W]]