5d9v - Revision history

OCA at 10:27, 21 June 2023

2023-06-21T10:27:28Z

←Older revision		Revision as of 10:27, 21 June 2023
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	<StructureSection load='5d9v' size='340' side='right'caption='[[5d9v]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='5d9v' size='340' side='right'caption='[[5d9v]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d9v]] is a 1 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=5D9V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5D9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d9v]] is a 1 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=5D9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D9V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, ~~<scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=5d9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9v OCA], [https://pdbe.org/5d9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d9v RCSB], [https://www.ebi.ac.uk/pdbsum/5d9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d9v ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5d9t\|5d9t]], [[5d9w\|5d9w]], [[5d9x\|5d9x]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">P0496H07.8, Os05g0116100, OJ1654_B10.18 ([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~~://proteopedia.org/fgij/fg.htm?mol=5d9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9v OCA], [~~http~~://pdbe.org/5d9v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d9v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d9v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d9v ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DHAR1_ORYSJ DHAR1_ORYSJ] Involved in ascorbate homeostasis. Maintains redox pools of ascorbate by recycling dihydroascorbate (DHA) to ascorbate (Probable). Involved in scavenging reactive oxygen species (ROS) under oxidative stresses. Possesses dehydroascorbate reductase (DHAR) activity in vitro (PubMed:19011360). May function via a ping-pong reaction mechanism with an electron transfer at the active site (PubMed:26775680). Possesses chaperone-like activity in vitro (PubMed:26775680).<ref>PMID:19011360</ref> <ref>PMID:26775680</ref> <ref>PMID:23519921</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: Large Structures]]
-	~~[[Category: Do, H]]~~	+	[[Category: Oryza sativa Japonica Group]]
-	~~[[Category: Lee, J H]]~~	+	[[Category: Do H]]
-	~~[[Category: Ascorbate]]~~	+	[[Category: Lee JH]]
-	[[Category: Oryza sativa ~~l. japonica~~]]	+
-	[[Category: ~~Osdhar~~]]	+
-	[[Category: ~~Plant protein~~]]	+

OCA at 07:56, 8 April 2020

2020-04-08T07:56:31Z

←Older revision		Revision as of 07:56, 8 April 2020
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		+
	==Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica==		==Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica==
-	<StructureSection load='5d9v' size='340' side='right' caption='[[5d9v]], [[Resolution\|resolution]] 1.69Å' scene=''>	+	<StructureSection load='5d9v' size='340' side='right'caption='[[5d9v]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d9v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D9V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d9v]] is a 1 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=5D9V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5D9V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d9t\|5d9t]], [[5d9w\|5d9w]], [[5d9x\|5d9x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d9t\|5d9t]], [[5d9w\|5d9w]], [[5d9x\|5d9x]]</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=5d9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9v OCA], [http://pdbe.org/5d9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d9v RCSB], [http://www.ebi.ac.uk/pdbsum/5d9v PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P0496H07.8, Os05g0116100, OJ1654_B10.18 ([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://proteopedia.org/fgij/fg.htm?mol=5d9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9v OCA], [http://pdbe.org/5d9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d9v RCSB], [http://www.ebi.ac.uk/pdbsum/5d9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d9v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Japanese rice]]
		+	[[Category: Large Structures]]
	[[Category: Do, H]]		[[Category: Do, H]]
	[[Category: Lee, J H]]		[[Category: Lee, J H]]

OCA at 15:40, 3 February 2016

2016-02-03T15:40:39Z

←Older revision		Revision as of 15:40, 3 February 2016
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-	'''~~Unreleased~~ structure'''	+	==Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica==
		+	<StructureSection load='5d9v' size='340' side='right' caption='[[5d9v]], [[Resolution\|resolution]] 1.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5d9v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D9V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d9t\|5d9t]], [[5d9w\|5d9w]], [[5d9x\|5d9x]]</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=5d9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9v OCA], [http://pdbe.org/5d9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d9v RCSB], [http://www.ebi.ac.uk/pdbsum/5d9v PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound, and GSH-bound forms and refined their resolutions to 1.9, 1.7, and 1.7 A, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice.

-	~~The entry 5d9v is ON HOLD until Paper Publication~~	+	Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica.,Do H, Kim IS, Jeon BW, Lee CW, Park AK, Wi AR, Shin SC, Park H, Kim YS, Yoon HS, Kim HW, Lee JH Sci Rep. 2016 Jan 18;6:19498. doi: 10.1038/srep19498. PMID:26775680<ref>PMID:26775680</ref>

-	~~Authors: Do~~, H.~~, Lee, J~~.H.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica~~	+	<div class="pdbe-citations 5d9v" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Do, H]]		[[Category: Do, H]]
-	[[Category: Lee, J.H]]	+	[[Category: Lee, J H]]
		+	[[Category: Ascorbate]]
		+	[[Category: Oryza sativa l. japonica]]
		+	[[Category: Osdhar]]
		+	[[Category: Plant protein]]

OCA at 09:57, 9 September 2015

2015-09-09T09:57:52Z

←Older revision		Revision as of 09:57, 9 September 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d9v is ON HOLD	+	The entry 5d9v is ON HOLD until Paper Publication

	Authors: Do, H., Lee, J.H.		Authors: Do, H., Lee, J.H.

OCA at 11:21, 2 September 2015

2015-09-02T11:21:30Z

←Older revision		Revision as of 11:21, 2 September 2015
Line 3:		Line 3:
	The entry 5d9v is ON HOLD		The entry 5d9v is ON HOLD

-	Authors: Do, H., Lee, J. H.	+	Authors: Do, H., Lee, J.H.

	Description: Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica		Description: Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Do, H]]		[[Category: Do, H]]
-	[[Category: Lee, J. H]]	+	[[Category: Lee, J.H]]

OCA: Protected "5d9v" [edit=sysop:move=sysop]

2015-08-26T12:37:15Z

Protected "5d9v" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:37, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d9v is ON HOLD Authors: Do, H., Lee, J. H. Description: Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. jap...

2015-08-26T12:37:14Z

New page: '''Unreleased structure''' The entry 5d9v is ON HOLD Authors: Do, H., Lee, J. H. Description: Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. jap...

New page

'''Unreleased structure'''

The entry 5d9v is ON HOLD

Authors: Do, H., Lee, J. H.

Description: Crystal structure of oxidized dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica
[[Category: Unreleased Structures]]
[[Category: Do, H]]
[[Category: Lee, J. H]]