5yy6 - Revision history

OCA at 05:58, 10 October 2019

OCA — Thu, 10 Oct 2019 05:58:29 GMT

←Older revision		Revision as of 05:58, 10 October 2019
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	<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=5yy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy6 OCA], [http://pdbe.org/5yy6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy6 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=5yy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy6 OCA], [http://pdbe.org/5yy6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery. The unknown binding mode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novel HPPD inhibitor design. Herein, we determined the first crystal structure of Arabidopsis thaliana HPPD (AtHPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 A. Then, combination of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations confirmed that HPPA takes keto rather than enol form inside the HPPD active pocket. Subsequent site-directed mutagenesis and kinetic analysis further showed that residues (Phe424, Asn423, Glu394, Gln307, Asn282, and Ser267) played important roles in substrate binding and catalytic cycle. Structural comparison between HPPA-AtHPPD and holo-AtHPPD revealed that Gln293 underwent a remarkable rotation upon the HPPA binding and formed H-bond network of Ser267-Asn282-Gln307-Gln293, resulting in the transformation of HPPD from an inactive state to active state. Finally, taking the conformation change of Gln293 as a target, we proposed a new strategy of blocking the transformation of HPPD from inactive state to active state to design a novel inhibitor with K i value of 24.10 nM towards AtHPPD. The inhibitor has entered into industry development as the first selective herbicide used for the weed control in sorghum field. The crystal structure of AtHPPD in complex with the inhibitor (2.40 A) confirmed the rationality of the design strategy. We believe that the present work provides a new starting point for the understanding of enzymatic reaction mechanism and the design of next generation HPPD inhibitors.
		+
		+	Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery.,Lin HY, Chen X, Chen JN, Wang DW, Wu FX, Lin SY, Zhan CG, Wu JW, Yang WC, Yang GF Research (Wash D C). 2019 Jul 8;2019:2602414. doi: 10.34133/2019/2602414., eCollection 2019. PMID:31549053<ref>PMID:31549053</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yy6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:59, 2 October 2019

OCA — Wed, 02 Oct 2019 10:59:01 GMT

←Older revision		Revision as of 10:59, 2 October 2019
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	==Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with Benquitrione==		==Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with Benquitrione==
-	<StructureSection load='5yy6' size='340' side='right' caption='[[5yy6]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5yy6' size='340' side='right'caption='[[5yy6]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yy6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yy6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94L:3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione'>94L</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94L:3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione'>94L</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cto\|5cto]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cto\|5cto]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, PDS1, At1g06570, F12K11.9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </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=5yy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy6 OCA], [http://pdbe.org/5yy6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy6 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=5yy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy6 OCA], [http://pdbe.org/5yy6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy6 ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
		+	[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Chen, J N]]		[[Category: Chen, J N]]
	[[Category: Yang, G F]]		[[Category: Yang, G F]]

OCA at 11:57, 16 January 2019

OCA — Wed, 16 Jan 2019 11:57:39 GMT

←Older revision		Revision as of 11:57, 16 January 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5yy6 is ~~ON HOLD until Jan 30 2020~~	+	==Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with Benquitrione==
-		+	<StructureSection load='5yy6' size='340' side='right' caption='[[5yy6]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Yang~~, W.C., ~~Chen~~, J.N., ~~Yang~~, G.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yy6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY6 FirstGlance]. <br>
-	~~Description: Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with Quinotrione~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94L:3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione'>94L</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cto\|5cto]]</td></tr>
-	[[Category: Chen, J.N]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>
-	[[Category: Yang, ~~W.C~~]]	+	<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=5yy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy6 OCA], [http://pdbe.org/5yy6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy6 ProSAT]</span></td></tr>
-	[[Category: Yang, ~~G.F~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
		+	[[Category: Chen, J N]]
		+	[[Category: Yang, G F]]
		+	[[Category: Yang, W C]]
		+	[[Category: Drug discovery]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Type i tyrosinemia]]

OCA at 05:01, 12 December 2018

OCA — Wed, 12 Dec 2018 05:01:41 GMT

←Older revision		Revision as of 05:01, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yy6 is ON HOLD until ~~Paper Publication~~	+	The entry 5yy6 is ON HOLD until Jan 30 2020

	Authors: Yang, W.C., Chen, J.N., Yang, G.F.		Authors: Yang, W.C., Chen, J.N., Yang, G.F.

OCA at 03:48, 20 June 2018

OCA — Wed, 20 Jun 2018 03:48:28 GMT

←Older revision		Revision as of 03:48, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yy6 is ON HOLD	+	The entry 5yy6 is ON HOLD until Paper Publication

	Authors: Yang, W.C., Chen, J.N., Yang, G.F.		Authors: Yang, W.C., Chen, J.N., Yang, G.F.

OCA: Protected "5yy6" [edit=sysop:move=sysop]

OCA — Wed, 13 Dec 2017 05:49:38 GMT

Protected "5yy6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:49, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yy6 is ON HOLD Authors: Yang, W.C., Chen, J.N., Yang, G.F. Description: Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed ...

OCA — Wed, 13 Dec 2017 05:49:37 GMT

New page: '''Unreleased structure''' The entry 5yy6 is ON HOLD Authors: Yang, W.C., Chen, J.N., Yang, G.F. Description: Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed ...

New page

'''Unreleased structure'''

The entry 5yy6 is ON HOLD

Authors: Yang, W.C., Chen, J.N., Yang, G.F.

Description: Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with Quinotrione
[[Category: Unreleased Structures]]
[[Category: Chen, J.N]]
[[Category: Yang, W.C]]
[[Category: Yang, G.F]]