7dk8 - Revision history

OCA at 16:34, 29 November 2023

2023-11-29T16:34:48Z

←Older revision		Revision as of 16:34, 29 November 2023
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	<StructureSection load='7dk8' size='340' side='right'caption='[[7dk8]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='7dk8' size='340' side='right'caption='[[7dk8]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dk8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Indian_rice Indian rice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DK8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7DK8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Indica_Group Oryza sativa Indica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DK8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.99Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GH3.8, OsI_025789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=39946 Indian rice])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></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=7dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dk8 OCA], [~~http~~://pdbe.org/7dk8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7dk8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7dk8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7dk8 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=7dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dk8 OCA], [https://pdbe.org/7dk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dk8 RCSB], [https://www.ebi.ac.uk/pdbsum/7dk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dk8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GH38_ORYSI GH38_ORYSI]] May catalyze the synthesis of indole-3-acetic acid (IAA)-amino acid conjugates, providing a mechanism for the plant to cope with the presence of excess auxin.	+	[https://www.uniprot.org/uniprot/GH38_ORYSI GH38_ORYSI] May catalyze the synthesis of indole-3-acetic acid (IAA)-amino acid conjugates, providing a mechanism for the plant to cope with the presence of excess auxin.
	<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: Indian rice]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ming, Z H~~]]	+	[[Category: Oryza sativa Indica Group]]
-	[[Category: ~~Xu, G L~~]]	+	[[Category: Ming ZH]]
-	[[Category: ~~Zhang, Y K~~]]	+	[[Category: Xu GL]]
-	[[Category: ~~Active site]]~~	+	[[Category: Zhang YK]]
-	~~[[Category: Acyl acid amido synthetase]]~~	+
-	~~[[Category: Auxin]]~~	+
-	~~[[Category: Plant protein~~]]	+

OCA at 08:29, 20 January 2021

2021-01-20T08:29:29Z

←Older revision		Revision as of 08:29, 20 January 2021
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	==Crystal structure of OsGH3-8 with AMP==		==Crystal structure of OsGH3-8 with AMP==
-	<StructureSection load='7dk8' size='340' side='right'caption='[[7dk8]]' scene=''>	+	<StructureSection load='7dk8' size='340' side='right'caption='[[7dk8]], [[Resolution\|resolution]] 1.99Å' 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=7DK8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DK8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dk8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Indian_rice Indian rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DK8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DK8 FirstGlance]. <br>
-	</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=7dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dk8 OCA], [http://pdbe.org/7dk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dk8 RCSB], [http://www.ebi.ac.uk/pdbsum/7dk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dk8 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GH3.8, OsI_025789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39946 Indian rice])</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=7dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dk8 OCA], [http://pdbe.org/7dk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dk8 RCSB], [http://www.ebi.ac.uk/pdbsum/7dk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dk8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GH38_ORYSI GH38_ORYSI]] May catalyze the synthesis of indole-3-acetic acid (IAA)-amino acid conjugates, providing a mechanism for the plant to cope with the presence of excess auxin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Gretchen Hagen 3 (GH3) family of acyl acid amido synthetases regulate the levels and activities of plant hormones containing carboxyl groups, thereby modulating diverse physiological responses. While structure-function relationships have been elucidated for dicotyledonous GH3s, the catalytic mechanism of monocotyledonous GH3 remains elusive. Rice (Oryza sativa) is a representative monocot, and its yield is controlled by the natural growth hormone IAA (indole-3-acetic acid). OsGH3-8 is a model GH3 enzyme that conjugates excess IAA to amino acids in an ATP-dependent manner, ensuring auxin homeostasis and regulating disease resistance, growth and development. Here, we report the crystal structure of OsGH3-8 protein in complex with AMP to uncover the molecular and structural basis for the activity of monocotyledonous GH3-8. Structural and sequence comparisons with other GH3 proteins reveal that the AMP/ATP binding sites are highly conserved. Molecular docking studies with IAA, the GH3-inhibitor Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP), and Aspartate provide important information for substrate binding and selectivity of OsGH3-8. Moreover, the observation that AIEP nearly occupies the entire binding site for AMP, IAA and amino acid, offers a ready explanation for the inhibitory effect of AIEP. Taken together, the present study provides vital insights into the molecular mechanisms of monocot GH3 function, and will help to shape the future designs of effective inhibitors.
		+
		+	Crystal structure of the acyl acid amido synthetase GH3-8 from Oryza sativa.,Xu G, Zhang Y, Li M, Jiao X, Zhou L, Ming Z Biochem Biophys Res Commun. 2020 Nov 30. pii: S0006-291X(20)32142-2. doi:, 10.1016/j.bbrc.2020.11.098. PMID:33272567<ref>PMID:33272567</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dk8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Indian rice]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ming ZH]]	+	[[Category: Ming, Z H]]
-	[[Category: Xu GL]]	+	[[Category: Xu, G L]]
-	[[Category: Zhang YK]]	+	[[Category: Zhang, Y K]]
		+	[[Category: Active site]]
		+	[[Category: Acyl acid amido synthetase]]
		+	[[Category: Auxin]]
		+	[[Category: Plant protein]]

OCA at 10:39, 24 December 2020

2020-12-24T10:39:47Z

←Older revision		Revision as of 10:39, 24 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7dk8 ~~is ON HOLD~~	+	==Crystal structure of OsGH3-8 with AMP==
-		+	<StructureSection load='7dk8' size='340' side='right'caption='[[7dk8]]' scene=''>
-	~~Authors~~: ~~Zhang~~, Y.K., Xu, G.L., ~~Ming~~, Z.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DK8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DK8 FirstGlance]. <br>
-	~~Description: Crystal structure of OsGH3-8 with AMP~~	+	</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=7dk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dk8 OCA], [http://pdbe.org/7dk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dk8 RCSB], [http://www.ebi.ac.uk/pdbsum/7dk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dk8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Zhang, Y.K~~]]	+	__TOC__
-	[[Category: Xu~~, G.L~~]]	+	</StructureSection>
-	[[Category: ~~Ming, Z.H~~]]	+	[[Category: Large Structures]]
		+	[[Category: Ming ZH]]
		+	[[Category: Xu GL]]
		+	[[Category: Zhang YK]]

OCA: Protected "7dk8" [edit=sysop:move=sysop]

2020-12-02T05:42:32Z

Protected "7dk8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:42, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dk8 is ON HOLD Authors: Zhang, Y.K., Xu, G.L., Ming, Z.H. Description: Crystal structure of OsGH3-8 with AMP Category: Unreleased Structures [...

2020-12-02T05:42:30Z

New page: '''Unreleased structure''' The entry 7dk8 is ON HOLD Authors: Zhang, Y.K., Xu, G.L., Ming, Z.H. Description: Crystal structure of OsGH3-8 with AMP Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 7dk8 is ON HOLD

Authors: Zhang, Y.K., Xu, G.L., Ming, Z.H.

Description: Crystal structure of OsGH3-8 with AMP
[[Category: Unreleased Structures]]
[[Category: Zhang, Y.K]]
[[Category: Xu, G.L]]
[[Category: Ming, Z.H]]