7ffa - Revision history

OCA at 09:25, 9 October 2024

2024-10-09T09:25:15Z

← Older revision		Revision as of 09:25, 9 October 2024
Line 3:		Line 3:
	<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7ffa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquilaria_sinensis Aquilaria sinensis].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.98Å</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]] 1.98Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa 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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[https://www.uniprot.org/uniprot/A0A385MEG6_9ROSI A0A385MEG6_9ROSI]~~
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	2-(2-Phenylethyl)chromones (PECs) are the principal constituents contributing to the distinctive fragrance of agarwood. How PECs are biosynthesized is currently unknown. In this work, we describe a diarylpentanoid-producing polyketide synthase (PECPS) identified from Aquilaria sinensis. Through biotransformation experiments using fluorine-labeled substrate, transient expression of PECPS in Nicotiana benthamiana, and knockdown of PECPS expression in A. sinensis calli, we demonstrate that the C6-C5-C6 scaffold of diarylpentanoid is the common precursor of PECs, and PECPS plays a crucial role in PECs biosynthesis. Crystal structure (1.98 A) analyses and site-directed mutagenesis reveal that, due to its small active site cavity (247 A(3)), PECPS employs a one-pot formation mechanism including a "diketide-CoA intermediate-released" step for the formation of the C6-C5-C6 scaffold. The identification of PECPS, the pivotal enzyme of PECs biosynthesis, provides insight into not only the feasibility of overproduction of pharmaceutically important PECs using metabolic engineering approaches, but also further exploration of how agarwood is formed.

	Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood.,Wang XH, Gao BW, Nakashima Y, Mori T, Zhang ZX, Kodama T, Lee YE, Zhang ZK, Wong CP, Liu QQ, Qi BW, Wang J, Li J, Liu X, Abe I, Morita H, Tu PF, Shi SP Nat Commun. 2022 Jan 17;13(1):348. doi: 10.1038/s41467-022-27971-z. PMID:35039506<ref>PMID:35039506</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7ffa" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Aquilaria sinensis]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kodama T]]		[[Category: Kodama T]]

OCA at 17:15, 29 November 2023

2023-11-29T17:15:08Z

← Older revision		Revision as of 17:15, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ffa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ffa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquilaria_sinensis Aquilaria sinensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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]] 1.98Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa 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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A385MEG6_9ROSI A0A385MEG6_9ROSI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Aquilaria sinensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kodama, T]]		[[Category: Kodama T]]
	[[Category: Lee, Y]]		[[Category: Lee Y]]
	[[Category: Liu, Q]]		[[Category: Liu Q]]
	[[Category: Morita, H]]		[[Category: Morita H]]
	[[Category: Nakashima, Y]]		[[Category: Nakashima Y]]
	[[Category: Wong~~, C P]]~~		[[Category: Wong CP]]
	~~[[Category: Diarylpentanoid]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Type-iii polyketide synthase~~]]

OCA at 10:31, 6 April 2022

2022-04-06T10:31:32Z

← Older revision		Revision as of 10:31, 6 April 2022
Line 1:		Line 1:

	==Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis==		==Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis==
	<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]]' scene=''>		<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]], [[Resolution\|resolution]] 1.98Å' 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=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ffa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>
	</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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa ProSAT]</span></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			2-(2-Phenylethyl)chromones (PECs) are the principal constituents contributing to the distinctive fragrance of agarwood. How PECs are biosynthesized is currently unknown. In this work, we describe a diarylpentanoid-producing polyketide synthase (PECPS) identified from Aquilaria sinensis. Through biotransformation experiments using fluorine-labeled substrate, transient expression of PECPS in Nicotiana benthamiana, and knockdown of PECPS expression in A. sinensis calli, we demonstrate that the C6-C5-C6 scaffold of diarylpentanoid is the common precursor of PECs, and PECPS plays a crucial role in PECs biosynthesis. Crystal structure (1.98 A) analyses and site-directed mutagenesis reveal that, due to its small active site cavity (247 A(3)), PECPS employs a one-pot formation mechanism including a "diketide-CoA intermediate-released" step for the formation of the C6-C5-C6 scaffold. The identification of PECPS, the pivotal enzyme of PECs biosynthesis, provides insight into not only the feasibility of overproduction of pharmaceutically important PECs using metabolic engineering approaches, but also further exploration of how agarwood is formed.

			Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood.,Wang XH, Gao BW, Nakashima Y, Mori T, Zhang ZX, Kodama T, Lee YE, Zhang ZK, Wong CP, Liu QQ, Qi BW, Wang J, Li J, Liu X, Abe I, Morita H, Tu PF, Shi SP Nat Commun. 2022 Jan 17;13(1):348. doi: 10.1038/s41467-022-27971-z. PMID:35039506<ref>PMID:35039506</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7ffa" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kodama T]]		[[Category: Kodama, T]]
	[[Category: Lee Y]]		[[Category: Lee, Y]]
	[[Category: Liu Q]]		[[Category: Liu, Q]]
	[[Category: Morita H]]		[[Category: Morita, H]]
	[[Category: Nakashima Y]]		[[Category: Nakashima, Y]]
	[[Category: Wong CP]]		[[Category: Wong, C P]]
			[[Category: Diarylpentanoid]]
			[[Category: Transferase]]
			[[Category: Type-iii polyketide synthase]]

OCA at 07:27, 19 January 2022

2022-01-19T07:27:51Z

← Older revision		Revision as of 07:27, 19 January 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7ffa is ~~ON HOLD until Paper Publication~~		==Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis==
			<StructureSection load='7ffa' size='340' side='right'caption='[[7ffa]]' scene=''>
	~~Authors~~: ~~Morita~~, H., ~~Wong~~, C.P., ~~Liu, Q~~.~~, Kodama, T~~., ~~Lee, Y~~.~~, Nakashima, Y~~.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFA FirstGlance]. <br>
	~~Description: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis~~		</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=7ffa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffa OCA], [https://pdbe.org/7ffa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffa RCSB], [https://www.ebi.ac.uk/pdbsum/7ffa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffa ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Liu, Q~~]]		__TOC__
	[[Category: ~~Nakashima,~~ Y]]		</StructureSection>
	[[Category: ~~Morita, H~~]]		[[Category: Large Structures]]
	[[Category: ~~Lee, Y~~]]		[[Category: Kodama T]]
	[[Category: ~~Kodama, T~~]]		[[Category: Lee Y]]
	[[Category: Wong~~, C.P~~]]		[[Category: Liu Q]]
			[[Category: Morita H]]
			[[Category: Nakashima Y]]
			[[Category: Wong CP]]

OCA at 04:55, 18 August 2021

2021-08-18T04:55:18Z

← Older revision		Revision as of 04:55, 18 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7ffa is ON HOLD		The entry 7ffa is ON HOLD until Paper Publication

	Authors: Morita, H., Wong, C.P., Liu, Q., Kodama, T., Lee, Y., Nakashima, Y.		Authors: Morita, H., Wong, C.P., Liu, Q., Kodama, T., Lee, Y., Nakashima, Y.
Line 7:		Line 7:
	Description: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis		Description: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Liu, Q]]
	[[Category: Nakashima, Y]]		[[Category: Nakashima, Y]]
			[[Category: Morita, H]]
			[[Category: Lee, Y]]
	[[Category: Kodama, T]]		[[Category: Kodama, T]]
	~~[[Category: Liu, Q]]~~
	[[Category: Wong, C.P]]		[[Category: Wong, C.P]]
	~~[[Category: Morita, H]]~~
	~~[[Category: Lee, Y]]~~

OCA: Protected "7ffa" [edit=sysop:move=sysop]

2021-07-28T09:22:30Z

Protected "7ffa" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:22, 28 July 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7ffa is ON HOLD Authors: Morita, H., Wong, C.P., Liu, Q., Kodama, T., Lee, Y., Nakashima, Y. Description: Diarylpentanoid-producing polyketide synt...

2021-07-28T09:22:29Z

New page: '''Unreleased structure''' The entry 7ffa is ON HOLD Authors: Morita, H., Wong, C.P., Liu, Q., Kodama, T., Lee, Y., Nakashima, Y. Description: Diarylpentanoid-producing polyketide synt...

New page

'''Unreleased structure'''

The entry 7ffa is ON HOLD

Authors: Morita, H., Wong, C.P., Liu, Q., Kodama, T., Lee, Y., Nakashima, Y.

Description: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis
[[Category: Unreleased Structures]]
[[Category: Nakashima, Y]]
[[Category: Kodama, T]]
[[Category: Liu, Q]]
[[Category: Wong, C.P]]
[[Category: Morita, H]]
[[Category: Lee, Y]]