7w86 - Revision history

OCA at 19:44, 29 May 2024

OCA — Wed, 29 May 2024 19:44:05 GMT

←Older revision		Revision as of 19:44, 29 May 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/PPR74_ARATH PPR74_ARATH] Plays a major role in single RNA editing events in chloroplasts. Acts as a site-recognition transacting factor involved in the edition of the site 1 of ndhD (ndhD-1 site corresponding to cytidine-2), which is a plastid-encoded subunit of the NADH-plastoquinone oxidoreductase. The interaction with CRR4 is required for its function in editing the ndhD-1 site.<ref>PMID:23001034</ref>		[https://www.uniprot.org/uniprot/PPR74_ARATH PPR74_ARATH] Plays a major role in single RNA editing events in chloroplasts. Acts as a site-recognition transacting factor involved in the edition of the site 1 of ndhD (ndhD-1 site corresponding to cytidine-2), which is a plastid-encoded subunit of the NADH-plastoquinone oxidoreductase. The interaction with CRR4 is required for its function in editing the ndhD-1 site.<ref>PMID:23001034</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA-binding pentatricopeptide repeat (PPR) proteins catalyze hundreds of cytidine to uridine RNA editing events in plant organelles; these editing events are essential for proper gene expression. More than half of the PPR-type RNA editing factors, however, lack the DYW cytidine deaminase domain. Genetic analyses have suggested that their cytidine deaminase activity arises by association with a family of DYW1-like proteins that contain an N-terminally truncated DYW domain, but their molecular mechanism has been unclear. Here, we report the crystal structure of the Arabidopsis thaliana DYW1 deaminase domain at 1.8 A resolution. DYW1 has a cytidine deaminase fold lacking the PG box. The internal insertion within the deaminase fold shows an alpha-helical fold instead of the beta-finger reported for the gating domain of the A. thaliana ORGANELLE TRANSCRIPT PROCESSING 86. The substrate-binding pocket is incompletely formed and appears to be complemented in the complex by the E2 domain and the PG box of the interacting PPR protein. In vivo RNA editing assays corroborate the activation model for DYW1 deaminase. Our study demonstrates the common activation mechanism of the DYW1-like proteins by molecular complementation of the DYW domain and reconstitution of the substrate-binding pocket.
		+
		+	Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.,Toma-Fukai S, Sawada Y, Maeda A, Shimizu H, Shikanai T, Takenaka M, Shimizu T Plant Cell. 2023 May 29;35(6):1888-1900. doi: 10.1093/plcell/koac318. PMID:36342219<ref>PMID:36342219</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7w86" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:24, 28 June 2023

OCA — Wed, 28 Jun 2023 21:24:41 GMT

←Older revision		Revision as of 21:24, 28 June 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7w86]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W86 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7w86]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W86 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7w86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w86 OCA], [https://pdbe.org/7w86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w86 RCSB], [https://www.ebi.ac.uk/pdbsum/7w86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w86 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=7w86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w86 OCA], [https://pdbe.org/7w86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w86 RCSB], [https://www.ebi.ac.uk/pdbsum/7w86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w86 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:02, 14 December 2022

OCA — Wed, 14 Dec 2022 10:02:53 GMT

←Older revision		Revision as of 10:02, 14 December 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7w86 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the DYW domain of DYW1==
-		+	<StructureSection load='7w86' size='340' side='right'caption='[[7w86]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[7w86]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W86 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7w86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w86 OCA], [https://pdbe.org/7w86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w86 RCSB], [https://www.ebi.ac.uk/pdbsum/7w86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w86 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PPR74_ARATH PPR74_ARATH] Plays a major role in single RNA editing events in chloroplasts. Acts as a site-recognition transacting factor involved in the edition of the site 1 of ndhD (ndhD-1 site corresponding to cytidine-2), which is a plastid-encoded subunit of the NADH-plastoquinone oxidoreductase. The interaction with CRR4 is required for its function in editing the ndhD-1 site.<ref>PMID:23001034</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arabidopsis thaliana]]
		+	[[Category: Large Structures]]
		+	[[Category: Sawada Y]]
		+	[[Category: Shimizu H]]
		+	[[Category: Shimizu T]]
		+	[[Category: Toma-Fukai S]]

OCA at 11:37, 4 May 2022

OCA — Wed, 04 May 2022 11:37:05 GMT

←Older revision		Revision as of 11:37, 4 May 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w86 is ON HOLD	+	The entry 7w86 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 10:28, 27 April 2022

OCA — Wed, 27 Apr 2022 10:28:57 GMT

←Older revision		Revision as of 10:28, 27 April 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w86 is ON HOLD ~~until Paper Publication~~	+	The entry 7w86 is ON HOLD

	Authors:		Authors:

OCA at 05:39, 27 January 2022

OCA — Thu, 27 Jan 2022 05:39:14 GMT

←Older revision		Revision as of 05:39, 27 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w86 is ON HOLD	+	The entry 7w86 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7w86" [edit=sysop:move=sysop]

OCA — Wed, 15 Dec 2021 15:50:07 GMT

Protected "7w86" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:50, 15 December 2021

OCA: New page: '''Unreleased structure''' The entry 7w86 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Dec 2021 15:50:06 GMT

New page: '''Unreleased structure''' The entry 7w86 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7w86 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]