5jcl - Revision history

OCA at 10:58, 6 September 2023

2023-09-06T10:58:57Z

←Older revision		Revision as of 10:58, 6 September 2023
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	<StructureSection load='5jcl' size='340' side='right'caption='[[5jcl]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5jcl' size='340' side='right'caption='[[5jcl]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jcl]] 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=5JCL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jcl]] 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=5JCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JCL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5jcn\|5jcn]], [[5jcm\|5jcm]], [[5jck\|5jck]], [[5jci\|5jci]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Os09g0567300, Os09g0567300, OJ1155_H10.27, OSNPB_090567300 ([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=5jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcl OCA], [https://pdbe.org/5jcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jcl RCSB], [https://www.ebi.ac.uk/pdbsum/5jcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcl ProSAT]</span></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=5jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcl OCA], [~~http~~://pdbe.org/5jcl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jcl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jcl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MDAR3_ORYSJ MDAR3_ORYSJ] Catalyzes the conversion of monodehydroascorbate to ascorbate, oxidizing NADH in the process. Ascorbate is a major antioxidant against reactive oxygen species (ROS) and nitric oxide (NO) (PubMed:24376554, PubMed:27652777). Can use NADPH as electron donor, but possesses lower activity compared to NADH as electron donor (PubMed:27652777).<ref>PMID:24376554</ref> <ref>PMID:27652777</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: ~~Kim, H W~~]]	+	[[Category: Oryza sativa Japonica Group]]
-	[[Category: ~~Park, A K~~]]	+	[[Category: Kim HW]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Park AK]]

OCA at 07:42, 10 June 2020

2020-06-10T07:42:30Z

←Older revision		Revision as of 07:42, 10 June 2020
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	==Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica==		==Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica==
-	<StructureSection load='5jcl' size='340' side='right' caption='[[5jcl]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5jcl' size='340' side='right'caption='[[5jcl]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jcl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JCL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jcl]] 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=5JCL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JCL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jcn\|5jcn]], [[5jcm\|5jcm]], [[5jck\|5jck]], [[5jci\|5jci]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jcn\|5jcn]], [[5jcm\|5jcm]], [[5jck\|5jck]], [[5jci\|5jci]]</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=5jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcl OCA], [http://pdbe.org/5jcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jcl RCSB], [http://www.ebi.ac.uk/pdbsum/5jcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcl ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Os09g0567300, Os09g0567300, OJ1155_H10.27, OSNPB_090567300 ([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=5jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcl OCA], [http://pdbe.org/5jcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jcl RCSB], [http://www.ebi.ac.uk/pdbsum/5jcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcl 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: Kim, H W]]		[[Category: Kim, H W]]
	[[Category: Park, A K]]		[[Category: Park, A K]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 17:42, 19 October 2016

2016-10-19T17:42:04Z

←Older revision		Revision as of 17:42, 19 October 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5jcl is ~~ON HOLD until Paper~~ Publication	+	==Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica==
		+	<StructureSection load='5jcl' size='340' side='right' caption='[[5jcl]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jcl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JCL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jcn\|5jcn]], [[5jcm\|5jcm]], [[5jck\|5jck]], [[5jci\|5jci]]</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=5jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jcl OCA], [http://pdbe.org/5jcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jcl RCSB], [http://www.ebi.ac.uk/pdbsum/5jcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jcl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ascorbic acid (AsA) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. The enzyme monodehydroascorbate reductase (MDHAR) regenerates AsA by catalysing the reduction of monodehydroascorbate, using NADH or NADPH as an electron donor. The detailed recycling mechanism of MDHAR remains unclear due to lack of structural information. Here, we present the crystal structures of MDHAR in the presence of cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), and complexed with AsA as well as its analogue, isoascorbic acid (ISD). The overall structure of MDHAR is similar to other iron-sulphur protein reductases, except for a unique long loop of 63-80 residues, which seems to be essential in forming the active site pocket. From the structural analysis and structure-guided point mutations, we found that the Arg320 residue plays a major substrate binding role, and the Tyr349 residue mediates electron transfer from NAD(P)H to bound substrate via FAD. The enzymatic activity of MDHAR favours NADH as an electron donor over NADPH. Our results show, for the first time, structural insights into this preference. The MDHAR-ISD complex structure revealed an alternative binding conformation of ISD, compared with the MDHAR-AsA complex. This implies a broad substrate (antioxidant) specificity and resulting greater protective ability of MDHAR.

-	~~Authors: Park~~, A.K., Kim, H.W.	+	Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica.,Park AK, Kim IS, Do H, Jeon BW, Lee CW, Roh SJ, Shin SC, Park H, Kim YS, Kim YH, Yoon HS, Lee JH, Kim HW Sci Rep. 2016 Sep 22;6:33903. doi: 10.1038/srep33903. PMID:27652777<ref>PMID:27652777</ref>

-	~~Description: Structure and catalytic mechanism~~ of ~~monodehydroascorbate reductase, MDHAR, from Oryza sativa L~~. ~~japonica~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Park, A.K]]	+	<div class="pdbe-citations 5jcl" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kim, H.W~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, H W]]
		+	[[Category: Park, A K]]
		+	[[Category: Oxidoreductase]]

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

2016-05-11T01:51:38Z

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

←Older revision

Revision as of 01:51, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jcl is ON HOLD until Paper Publication Authors: Park, A.K., Kim, H.W. Description: Structure and catalytic mechanism of monodehydroascorbate reduc...

2016-05-11T01:51:37Z

New page: '''Unreleased structure''' The entry 5jcl is ON HOLD until Paper Publication Authors: Park, A.K., Kim, H.W. Description: Structure and catalytic mechanism of monodehydroascorbate reduc...

New page

'''Unreleased structure'''

The entry 5jcl is ON HOLD until Paper Publication

Authors: Park, A.K., Kim, H.W.

Description: Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
[[Category: Unreleased Structures]]
[[Category: Park, A.K]]
[[Category: Kim, H.W]]