6dx7 - Revision history

OCA at 14:37, 13 March 2024

OCA — Wed, 13 Mar 2024 14:37:35 GMT

←Older revision		Revision as of 14:37, 13 March 2024
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	<StructureSection load='6dx7' size='340' side='right'caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>		<StructureSection load='6dx7' size='340' side='right'caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Moss Moss~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Physcomitrium_patens Physcomitrium patens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PHYPA_029015 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=3218 Moss])</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]] 2.61Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naringenin~~-~~chalcone_synthase Naringenin-chalcone synthase]~~, ~~with EC number~~ [~~http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~3.1.74 2.3.1.74] </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=6dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dx7 OCA], [https://pdbe.org/6dx7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dx7 RCSB], [https://www.ebi.ac.uk/pdbsum/6dx7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dx7 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=6dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dx7 OCA], [~~http~~://pdbe.org/6dx7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dx7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dx7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dx7 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q2VAZ3_PHYPA Q2VAZ3_PHYPA]
-	Flavonoids are important polyphenolic natural products, ubiquitous in land plants, that play diverse functions in plants' survival in their ecological niches, including UV protection, pigmentation for attracting pollinators, symbiotic nitrogen fixation, and defense against herbivores. Chalcone synthase (CHS) catalyzes the first committed step in plant flavonoid biosynthesis and is highly conserved in all land plants. In several previously reported crystal structures of CHSs from flowering plants, the catalytic cysteine is oxidized to sulfinic acid, indicating enhanced nucleophilicity in this residue associated with its increased susceptibility to oxidation. In this study, we report a set of new crystal structures of CHSs representing all five major lineages of land plants (bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms), spanning 500 million years of evolution. We reveal that the structures of CHS from a lycophyte and a moss species preserve the catalytic cysteine in a reduced state, in contrast to the cysteine sulfinic acid seen in all euphyllophyte CHS structures. In vivo complementation, in vitro biochemical and mutagenesis analyses, and molecular dynamics simulations identified a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. We propose that the CHS active-site environment has evolved in euphyllophytes to further enhance the nucleophilicity of the catalytic cysteine since the divergence of euphyllophytes from other vascular plant lineages 400 million years ago. These changes in CHS could have contributed to the diversification of flavonoid biosynthesis in euphyllophytes, which in turn contributed to their dominance in terrestrial ecosystems.	+
-		+
-	~~Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.,Liou G, Chiang YC, Wang Y, Weng JK J Biol Chem. 2018 Oct 5. pii~~: ~~RA118.005695. doi: 10.1074~~/~~jbc.RA118.005695. PMID:30291143<ref>PMID:30291143<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6dx7" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Moss]]~~	+	[[Category: Physcomitrium patens]]
-	~~[[Category: Naringenin-chalcone synthase~~]]	+	[[Category: Chiang YC]]
-	[[Category: Chiang~~, Y C~~]]	+	[[Category: Liou G]]
-	[[Category: Liou, G]]	+	[[Category: Wang Y]]
-	[[Category: Wang, Y]]	+	[[Category: Weng JK]]
-	[[Category: Weng~~, J K]]~~	+
-	~~[[Category: Flavonoid]]~~	+
-	~~[[Category: Polyketide synthase]]~~	+
-	~~[[Category: Thiolase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:35, 27 November 2019

OCA — Wed, 27 Nov 2019 08:35:31 GMT

←Older revision		Revision as of 08:35, 27 November 2019
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	==Crystal structure of chalcone synthase from Physcomitrella patens==		==Crystal structure of chalcone synthase from Physcomitrella patens==
-	<StructureSection load='6dx7' size='340' side='right' caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>	+	<StructureSection load='6dx7' size='340' side='right'caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Moss Moss]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Moss Moss]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Moss]]		[[Category: Moss]]
	[[Category: Naringenin-chalcone synthase]]		[[Category: Naringenin-chalcone synthase]]

OCA at 08:51, 19 December 2018

OCA — Wed, 19 Dec 2018 08:51:46 GMT

←Older revision		Revision as of 08:51, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='6dx7' size='340' side='right' caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>		<StructureSection load='6dx7' size='340' side='right' caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Moss Moss]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naringenin-chalcone_synthase Naringenin-chalcone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.74 2.3.1.74] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PHYPA_029015 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3218 Moss])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naringenin-chalcone_synthase Naringenin-chalcone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.74 2.3.1.74] </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=6dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dx7 OCA], [http://pdbe.org/6dx7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dx7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dx7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dx7 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=6dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dx7 OCA], [http://pdbe.org/6dx7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dx7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dx7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dx7 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Moss]]
	[[Category: Naringenin-chalcone synthase]]		[[Category: Naringenin-chalcone synthase]]
	[[Category: Chiang, Y C]]		[[Category: Chiang, Y C]]

OCA at 07:59, 17 October 2018

OCA — Wed, 17 Oct 2018 07:59:08 GMT

←Older revision		Revision as of 07:59, 17 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dx7 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of chalcone synthase from Physcomitrella patens==
		+	<StructureSection load='6dx7' size='340' side='right' caption='[[6dx7]], [[Resolution\|resolution]] 2.61Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dx7]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DX7 FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naringenin-chalcone_synthase Naringenin-chalcone synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.74 2.3.1.74] </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=6dx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dx7 OCA], [http://pdbe.org/6dx7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dx7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dx7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dx7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Flavonoids are important polyphenolic natural products, ubiquitous in land plants, that play diverse functions in plants' survival in their ecological niches, including UV protection, pigmentation for attracting pollinators, symbiotic nitrogen fixation, and defense against herbivores. Chalcone synthase (CHS) catalyzes the first committed step in plant flavonoid biosynthesis and is highly conserved in all land plants. In several previously reported crystal structures of CHSs from flowering plants, the catalytic cysteine is oxidized to sulfinic acid, indicating enhanced nucleophilicity in this residue associated with its increased susceptibility to oxidation. In this study, we report a set of new crystal structures of CHSs representing all five major lineages of land plants (bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms), spanning 500 million years of evolution. We reveal that the structures of CHS from a lycophyte and a moss species preserve the catalytic cysteine in a reduced state, in contrast to the cysteine sulfinic acid seen in all euphyllophyte CHS structures. In vivo complementation, in vitro biochemical and mutagenesis analyses, and molecular dynamics simulations identified a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. We propose that the CHS active-site environment has evolved in euphyllophytes to further enhance the nucleophilicity of the catalytic cysteine since the divergence of euphyllophytes from other vascular plant lineages 400 million years ago. These changes in CHS could have contributed to the diversification of flavonoid biosynthesis in euphyllophytes, which in turn contributed to their dominance in terrestrial ecosystems.

-	~~Authors: Liou~~, G., Chiang~~, Y.C.~~, Wang, Y., Weng, J.K.	+	Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.,Liou G, Chiang YC, Wang Y, Weng JK J Biol Chem. 2018 Oct 5. pii: RA118.005695. doi: 10.1074/jbc.RA118.005695. PMID:30291143<ref>PMID:30291143</ref>

-	~~Description: Crystal structure~~ of chalcone synthase ~~from Physcomitrella patens~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6dx7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Naringenin-chalcone synthase]]
		+	[[Category: Chiang, Y C]]
	[[Category: Liou, G]]		[[Category: Liou, G]]
-	[[Category: Weng, J.K]]
-	[[Category: Chiang, Y.C]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
		+	[[Category: Weng, J K]]
		+	[[Category: Flavonoid]]
		+	[[Category: Polyketide synthase]]
		+	[[Category: Thiolase]]
		+	[[Category: Transferase]]

OCA at 05:50, 25 July 2018

OCA — Wed, 25 Jul 2018 05:50:29 GMT

←Older revision		Revision as of 05:50, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dx7 is ON HOLD	+	The entry 6dx7 is ON HOLD until Paper Publication

	Authors: Liou, G., Chiang, Y.C., Wang, Y., Weng, J.K.		Authors: Liou, G., Chiang, Y.C., Wang, Y., Weng, J.K.

OCA: Protected "6dx7" [edit=sysop:move=sysop]

OCA — Wed, 04 Jul 2018 05:49:48 GMT

Protected "6dx7" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:49, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dx7 is ON HOLD Authors: Liou, G., Chiang, Y.C., Wang, Y., Weng, J.K. Description: Crystal structure of chalcone synthase from Physcomitrella paten...

OCA — Wed, 04 Jul 2018 05:49:47 GMT

New page: '''Unreleased structure''' The entry 6dx7 is ON HOLD Authors: Liou, G., Chiang, Y.C., Wang, Y., Weng, J.K. Description: Crystal structure of chalcone synthase from Physcomitrella paten...

New page

'''Unreleased structure'''

The entry 6dx7 is ON HOLD

Authors: Liou, G., Chiang, Y.C., Wang, Y., Weng, J.K.

Description: Crystal structure of chalcone synthase from Physcomitrella patens
[[Category: Unreleased Structures]]
[[Category: Liou, G]]
[[Category: Weng, J.K]]
[[Category: Chiang, Y.C]]
[[Category: Wang, Y]]