5ika - Revision history

OCA at 13:58, 30 August 2023

2023-08-30T13:58:31Z

←Older revision		Revision as of 13:58, 30 August 2023
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	<StructureSection load='5ika' size='340' side='right'caption='[[5ika]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5ika' size='340' side='right'caption='[[5ika]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ika]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~American_tobacco American tobacco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ika]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IKA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|Related:]]</b></td><td class="sblockDat">[[5ik0\|5ik0]], [[5ik6\|5ik6]], [[5ik9\|5ik9]], [[5ikh\|5ikh]], [[5il3\|5il3]], [[5il8\|5il8]], [[5ild\|5ild]], [[5ilh\|5ilh]], [[5ili\|5ili]], [[5ilj\|5ilj]], [[5ilk\|5ilk]], [[5ily\|5ily]], [[5ilz\|5ilz]], [[5im1\|5im1]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>EAS3, EAS4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4097 American tobacco])</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=5ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ika OCA], [https://pdbe.org/5ika PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ika RCSB], [https://www.ebi.ac.uk/pdbsum/5ika PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ika ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/5-epiaristolochene_synthase 5-epiaristolochene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.61 4.2.3.61]~~ </~~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=5ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ika OCA], [~~http~~://pdbe.org/5ika PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ika RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ika PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ika ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/5EAS_TOBAC 5EAS_TOBAC]] Catalyzes the cyclization of trans,trans-farnesyl diphosphate (FPP) to the bicyclic intermediate 5-epi-aristolochene, initial step in the conversion of FPP to the sesquiterpenoid antifungal phytoalexin capsidiol. Produces germacrene A as an enzyme-bound intermediate that is not released by the enzyme, but is further cyclized to produce the bicyclic 5-epi-aristolochene.	+	[https://www.uniprot.org/uniprot/5EAS_TOBAC 5EAS_TOBAC] Catalyzes the cyclization of trans,trans-farnesyl diphosphate (FPP) to the bicyclic intermediate 5-epi-aristolochene, initial step in the conversion of FPP to the sesquiterpenoid antifungal phytoalexin capsidiol. Produces germacrene A as an enzyme-bound intermediate that is not released by the enzyme, but is further cyclized to produce the bicyclic 5-epi-aristolochene.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 5-epiaristolochene synthase]]
-	[[Category: American tobacco]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bowman, M]]	+	[[Category: Nicotiana tabacum]]
-	[[Category: Koo~~, H J~~]]	+	[[Category: Bowman M]]
-	[[Category: Louie~~, G V~~]]	+	[[Category: Koo HJ]]
-	[[Category: Noel~~, J P~~]]	+	[[Category: Louie GV]]
-	[[Category: Xu, Y]]	+	[[Category: Noel JP]]
-	~~[[Category: Diphosphate]]~~	+	[[Category: Xu Y]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tea]]~~	+
-	~~[[Category: Terpene synthase~~]]	+

OCA at 07:21, 3 June 2020

2020-06-03T07:21:59Z

←Older revision		Revision as of 07:21, 3 June 2020
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	==Tobacco 5-epi-aristolochene synthase with PPi==		==Tobacco 5-epi-aristolochene synthase with PPi==
-	<StructureSection load='5ika' size='340' side='right' caption='[[5ika]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5ika' size='340' side='right'caption='[[5ika]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ika]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ika]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/American_tobacco American tobacco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ik0\|5ik0]], [[5ik6\|5ik6]], [[5ik9\|5ik9]], [[5ikh\|5ikh]], [[5il3\|5il3]], [[5il8\|5il8]], [[5ild\|5ild]], [[5ilh\|5ilh]], [[5ili\|5ili]], [[5ilj\|5ilj]], [[5ilk\|5ilk]], [[5ily\|5ily]], [[5ilz\|5ilz]], [[5im1\|5im1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ik0\|5ik0]], [[5ik6\|5ik6]], [[5ik9\|5ik9]], [[5ikh\|5ikh]], [[5il3\|5il3]], [[5il8\|5il8]], [[5ild\|5ild]], [[5ilh\|5ilh]], [[5ili\|5ili]], [[5ilj\|5ilj]], [[5ilk\|5ilk]], [[5ily\|5ily]], [[5ilz\|5ilz]], [[5im1\|5im1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EAS3, EAS4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4097 American tobacco])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-epiaristolochene_synthase 5-epiaristolochene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.61 4.2.3.61] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-epiaristolochene_synthase 5-epiaristolochene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.61 4.2.3.61] </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=5ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ika OCA], [http://pdbe.org/5ika PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ika RCSB], [http://www.ebi.ac.uk/pdbsum/5ika PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ika 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=5ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ika OCA], [http://pdbe.org/5ika PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ika RCSB], [http://www.ebi.ac.uk/pdbsum/5ika PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ika ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: 5-epiaristolochene synthase]]		[[Category: 5-epiaristolochene synthase]]
		+	[[Category: American tobacco]]
		+	[[Category: Large Structures]]
	[[Category: Bowman, M]]		[[Category: Bowman, M]]
	[[Category: Koo, H J]]		[[Category: Koo, H J]]

OCA at 21:28, 5 October 2016

2016-10-05T21:28:15Z

←Older revision		Revision as of 21:28, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ika is ~~ON HOLD until Paper~~ Publication	+	==Tobacco 5-epi-aristolochene synthase with PPi==
		+	<StructureSection load='5ika' size='340' side='right' caption='[[5ika]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ika]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IKA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ik0\|5ik0]], [[5ik6\|5ik6]], [[5ik9\|5ik9]], [[5ikh\|5ikh]], [[5il3\|5il3]], [[5il8\|5il8]], [[5ild\|5ild]], [[5ilh\|5ilh]], [[5ili\|5ili]], [[5ilj\|5ilj]], [[5ilk\|5ilk]], [[5ily\|5ily]], [[5ilz\|5ilz]], [[5im1\|5im1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-epiaristolochene_synthase 5-epiaristolochene synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.61 4.2.3.61] </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=5ika FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ika OCA], [http://pdbe.org/5ika PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ika RCSB], [http://www.ebi.ac.uk/pdbsum/5ika PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ika ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/5EAS_TOBAC 5EAS_TOBAC]] Catalyzes the cyclization of trans,trans-farnesyl diphosphate (FPP) to the bicyclic intermediate 5-epi-aristolochene, initial step in the conversion of FPP to the sesquiterpenoid antifungal phytoalexin capsidiol. Produces germacrene A as an enzyme-bound intermediate that is not released by the enzyme, but is further cyclized to produce the bicyclic 5-epi-aristolochene.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The plant terpene synthase (TPS) family is responsible for the biosynthesis of a variety of terpenoid natural products possessing diverse biological functions. TPSs catalyze the ionization and, most commonly, rearrangement and cyclization of prenyl diphosphate substrates, forming linear and cyclic hydrocarbons. Moreover, a single TPS often produces several minor products in addition to a dominant product. We characterized the catalytic profiles of Hyoscyamus muticus premnaspirodiene synthase (HPS) and compared it with the profile of a closely related TPS, Nicotiana tabacum 5-epi-aristolochene synthase (TEAS). The profiles of two previously studied HPS and TEAS mutants, each containing nine interconverting mutations, dubbed HPS-M9 and TEAS-M9, were also characterized. All four TPSs were compared under varying temperature and pH conditions. In addition, we solved the X-ray crystal structures of TEAS and a TEAS quadruple mutant complexed with substrate and products to gain insight into the enzymatic features modulating product formation. These informative structures, along with product profiles, provide new insight into plant TPS catalytic promiscuity.

-	~~Authors~~: Koo, ~~H.J.~~, Xu, Y., Louie, ~~G.V.~~, Bowman, M., ~~Noel~~, J.P.	+	Biosynthetic potential of sesquiterpene synthases: product profiles of Egyptian Henbane premnaspirodiene synthase and related mutants.,Koo HJ, Vickery CR, Xu Y, Louie GV, O'Maille PE, Bowman M, Nartey CM, Burkart MD, Noel JP J Antibiot (Tokyo). 2016 Jul;69(7):524-33. doi: 10.1038/ja.2016.68. Epub 2016 Jun, 22. PMID:27328867<ref>PMID:27328867</ref>

-	~~Description: Tobacco 5~~-~~epi~~-~~aristolochene synthase with PPi~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Louie, G.V]]~~	+	<div class="pdbe-citations 5ika" style="background-color:#fffaf0;"></div>
-	~~[[Category: Koo, H.J]]~~	+	== References ==
-	[[Category: ~~Xu, Y~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 5-epiaristolochene synthase]]
	[[Category: Bowman, M]]		[[Category: Bowman, M]]
-	[[Category: Noel, J.P]]	+	[[Category: Koo, H J]]
		+	[[Category: Louie, G V]]
		+	[[Category: Noel, J P]]
		+	[[Category: Xu, Y]]
		+	[[Category: Diphosphate]]
		+	[[Category: Lyase]]
		+	[[Category: Tea]]
		+	[[Category: Terpene synthase]]

OCA at 00:34, 11 May 2016

2016-05-11T00:34:31Z

←Older revision		Revision as of 00:34, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Koo, H.J., Xu, Y., Louie, G.V., Bowman, M., Noel, J.P.		Authors: Koo, H.J., Xu, Y., Louie, G.V., Bowman, M., Noel, J.P.

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

2016-03-10T02:29:07Z

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

←Older revision

Revision as of 02:29, 10 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ika is ON HOLD Authors: Koo, H.J., Xu, Y., Louie, G.V., Bowman, M., Noel, J.P. Description: Tobacco 5-epi-aristolochene synthase with PPi [[Catego...

2016-03-10T02:29:05Z

New page: '''Unreleased structure''' The entry 5ika is ON HOLD Authors: Koo, H.J., Xu, Y., Louie, G.V., Bowman, M., Noel, J.P. Description: Tobacco 5-epi-aristolochene synthase with PPi [[Catego...

New page

'''Unreleased structure'''

The entry 5ika is ON HOLD

Authors: Koo, H.J., Xu, Y., Louie, G.V., Bowman, M., Noel, J.P.

Description: Tobacco 5-epi-aristolochene synthase with PPi
[[Category: Unreleased Structures]]
[[Category: Louie, G.V]]
[[Category: Koo, H.J]]
[[Category: Xu, Y]]
[[Category: Bowman, M]]
[[Category: Noel, J.P]]