5yz7 - Revision history

OCA at 08:41, 22 November 2023

2023-11-22T08:41:25Z

←Older revision		Revision as of 08:41, 22 November 2023
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	==Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD==		==Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD==
-	<StructureSection load='5yz7' size='340' side='right' caption='[[5yz7]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5yz7' size='340' side='right'caption='[[5yz7]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Japanese_rice Japanese rice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZ7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=94X:(2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic+acid'>94X</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]] 1.898Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxk\|3vxk]]~~, [[~~3wio~~\|~~3wio~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=94X:(2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic+acid'>94X</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=39947 Japanese rice]~~)</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=5yz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz7 OCA], [https://pdbe.org/5yz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yz7 RCSB], [https://www.ebi.ac.uk/pdbsum/5yz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz7 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=5yz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz7 OCA], [~~http~~://pdbe.org/5yz7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yz7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yz7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/D14_ORYSJ D14_ORYSJ]] Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.<ref>PMID:19542179</ref> <ref>PMID:23301669</ref>	+	[https://www.uniprot.org/uniprot/D14_ORYSJ D14_ORYSJ] Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.<ref>PMID:19542179</ref> <ref>PMID:23301669</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Japanese rice~~]]	+	[[Category: Large Structures]]
-	[[Category: Asami, T]]	+	[[Category: Oryza sativa Japonica Group]]
-	[[Category: Hirabayashi, K]]	+	[[Category: Asami T]]
-	[[Category: Jiang, K]]	+	[[Category: Hirabayashi K]]
-	[[Category: Miyakawa, T]]	+	[[Category: Jiang K]]
-	[[Category: Tanokura, M]]	+	[[Category: Miyakawa T]]
-	[[Category: Xu, Y]]	+	[[Category: Tanokura M]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Xu Y]]
-	~~[[Category: Plant hormone]]~~	+
-	~~[[Category: Plant signalling]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Strigolactone~~]]	+

OCA at 07:53, 29 August 2018

2018-08-29T07:53:08Z

←Older revision		Revision as of 07:53, 29 August 2018
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	<StructureSection load='5yz7' size='340' side='right' caption='[[5yz7]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5yz7' size='340' side='right' caption='[[5yz7]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94X:(2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic+acid'>94X</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94X:(2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic+acid'>94X</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxk\|3vxk]], [[3wio\|3wio]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxk\|3vxk]], [[3wio\|3wio]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=5yz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz7 OCA], [http://pdbe.org/5yz7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz7 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz7 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=5yz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz7 OCA], [http://pdbe.org/5yz7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz7 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz7 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Japanese rice]]
	[[Category: Asami, T]]		[[Category: Asami, T]]
	[[Category: Hirabayashi, K]]		[[Category: Hirabayashi, K]]

OCA at 05:29, 30 May 2018

2018-05-30T05:29:26Z

←Older revision		Revision as of 05:29, 30 May 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yz7 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD==
		+	<StructureSection load='5yz7' size='340' side='right' caption='[[5yz7]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yz7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=94X:(2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic+acid'>94X</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vxk\|3vxk]], [[3wio\|3wio]]</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=5yz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz7 OCA], [http://pdbe.org/5yz7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz7 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz7 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/D14_ORYSJ D14_ORYSJ]] Involved in strigolactone signaling pathway. May function downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form. Strigolactones are hormones that inhibit tillering and shoot branching through the MAX-dependent pathway, contribute to the regulation of shoot architectural response to phosphate-limiting conditions and function as rhizosphere signal that stimulates hyphal branching of arbuscular mycorrhizal fungi and trigger seed germination of root parasitic weeds.<ref>PMID:19542179</ref> <ref>PMID:23301669</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Strigolactones (SLs) are plant hormones that inhibit shoot branching and act as signals in communications with symbiotic fungi and parasitic weeds in the rhizosphere. SL signaling is mediated by DWARF14 (D14), which is an alpha/beta-hydrolase that cleaves SLs into an ABC tricyclic lactone and a butenolide group (i.e., D-ring). This cleavage reaction (hydrolysis and dissociation) is important for inducing the interaction between D14 and its target proteins, including D3 and D53. In this study, a hydrolysis-resistant SL analog was predicted to inhibit the activation of the D14 receptor, thereby disrupting the SL signaling pathway. To test this prediction, carba-SL compounds, in which the ether oxygen of the D-ring or the phenol ether oxygen of the SL agonist (GR24 or 4-bromo debranone) was replaced with a methylene group, were synthesized as novel D14 antagonists. Subsequent biochemical and physiological studies indicated that carba-SLs blocked the interaction between D14 and D53 by inhibiting D14 hydrolytic activity. They also suppressed the SL-induced inhibition of rice tiller outgrowths. Additionally, carba-SLs antagonized the SL response in a Striga parasitic weed species. Structural analyses revealed that the D-ring of 7'-carba-4BD was hydrolyzed by D14 but did not dissociate from the 4BD skeleton. Thus, 7'-carba-4BD functioned as an antagonist rather than an agonist. Thus, the hydrolysis of the D-ring of SLs may be insufficient for activating the receptor. This study provides data relevant to designing SL receptor antagonists.

-	~~Authors~~:	+	Rationally Designed Strigolactone Analogs as Antagonists of the D14 Receptor.,Takeuchi J, Jiang K, Hirabayashi K, Imamura Y, Wu Y, Xu Y, Miyakawa T, Nakamura H, Tanokura M, Asami T Plant Cell Physiol. 2018 May 2. pii: 4990988. doi: 10.1093/pcp/pcy087. PMID:29727000<ref>PMID:29727000</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yz7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Asami, T]]
		+	[[Category: Hirabayashi, K]]
		+	[[Category: Jiang, K]]
		+	[[Category: Miyakawa, T]]
		+	[[Category: Tanokura, M]]
		+	[[Category: Xu, Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Plant hormone]]
		+	[[Category: Plant signalling]]
		+	[[Category: Receptor]]
		+	[[Category: Strigolactone]]

OCA at 03:48, 25 April 2018

2018-04-25T03:48:36Z

←Older revision		Revision as of 03:48, 25 April 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yz7 is ON HOLD	+	The entry 5yz7 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:28, 4 April 2018

2018-04-04T04:28:17Z

←Older revision		Revision as of 04:28, 4 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yz7 is ON HOLD ~~until Paper Publication~~	+	The entry 5yz7 is ON HOLD

-	Authors: ~~Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M.~~	+	Authors:

-	Description: ~~Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Miyakawa, T]]
-	[[Category: Hirabayashi, K]]
-	[[Category: Jiang, K]]
-	[[Category: Xu, Y]]
-	[[Category: Tanokura, M]]
-	[[Category: Asami, T]]

OCA at 04:50, 3 January 2018

2018-01-03T04:50:40Z

←Older revision		Revision as of 04:50, 3 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yz7 is ON HOLD	+	The entry 5yz7 is ON HOLD until Paper Publication

	Authors: Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M.		Authors: Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M.
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	Description: Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD		Description: Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xu, Y]]
-	[[Category: Asami, T]]
-	[[Category: Tanokura, M]]
	[[Category: Miyakawa, T]]		[[Category: Miyakawa, T]]
	[[Category: Hirabayashi, K]]		[[Category: Hirabayashi, K]]
	[[Category: Jiang, K]]		[[Category: Jiang, K]]
		+	[[Category: Xu, Y]]
		+	[[Category: Tanokura, M]]
		+	[[Category: Asami, T]]

OCA: Protected "5yz7" [edit=sysop:move=sysop]

2017-12-20T04:52:48Z

Protected "5yz7" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yz7 is ON HOLD Authors: Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M. Description: Crystal structure of OsD14 in compl...

2017-12-20T04:52:47Z

New page: '''Unreleased structure''' The entry 5yz7 is ON HOLD Authors: Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M. Description: Crystal structure of OsD14 in compl...

New page

'''Unreleased structure'''

The entry 5yz7 is ON HOLD

Authors: Hirabayashi, K., Jiang, K., Xu, Y., Miyakawa, T., Asami, T., Tanokura, M.

Description: Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD
[[Category: Unreleased Structures]]
[[Category: Xu, Y]]
[[Category: Asami, T]]
[[Category: Tanokura, M]]
[[Category: Miyakawa, T]]
[[Category: Hirabayashi, K]]
[[Category: Jiang, K]]