7o4e - Revision history

OCA at 06:13, 19 June 2024

2024-06-19T06:13:32Z

← Older revision		Revision as of 06:13, 19 June 2024
Line 3:		Line 3:
	<StructureSection load='7o4e' size='340' side='right'caption='[[7o4e]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7o4e' size='340' side='right'caption='[[7o4e]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7o4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4E FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4E FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.5Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[7o4f\|7o4f]]~~<~~/div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~PCMP-H83, OTP86, At3g63370, F16M2_220 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~</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=7o4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4e OCA], [https://pdbe.org/7o4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4e RCSB], [https://www.ebi.ac.uk/pdbsum/7o4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4e 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=7o4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4e OCA], [https://pdbe.org/7o4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4e RCSB], [https://www.ebi.ac.uk/pdbsum/7o4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4e ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[[https://www.uniprot.org/uniprot/PP296_ARATH PP296_ARATH]] Involved in RNA editing event in chloroplasts. Required for the editing of a single site in rps14 transcript.<ref>PMID:19934379</ref>~~
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	RNA editosomes selectively deaminate cytidines to uridines in plant organellar transcripts-mostly to restore protein functionality and consequently facilitate mitochondrial and chloroplast function. The RNA editosomal pentatricopeptide repeat proteins serve target RNA recognition, whereas the intensively studied DYW domain elicits catalysis. Here we present structures and functional data of a DYW domain in an inactive ground state and activated. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural zinc atoms, respectively. A conserved gating domain within the deaminase fold regulates the active site sterically and mechanistically in a process that we termed gated zinc shutter. Based on the structures, an autoinhibited ground state and its activation are cross-validated by RNA editing assays and differential scanning fluorimetry. We anticipate that, in vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated cytidine deamination playing a key role in mitochondrial and chloroplast homeostasis.

	DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.,Takenaka M, Takenaka S, Barthel T, Frink B, Haag S, Verbitskiy D, Oldenkott B, Schallenberg-Rudinger M, Feiler CG, Weiss MS, Palm GJ, Weber G Nat Catal. 2021 Jun;4(6):510-522. doi: 10.1038/s41929-021-00633-x. Epub 2021 Jun , 21. PMID:34712911<ref>PMID:34712911</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7o4e" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Arath]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Barthel, T]]		[[Category: Barthel T]]
	[[Category: Feiler, C]]		[[Category: Feiler C]]
	[[Category: Palm~~, G J~~]]		[[Category: Palm GJ]]
	[[Category: Takenaka, M]]		[[Category: Takenaka M]]
	[[Category: Weber, G]]		[[Category: Weber G]]
	[[Category: Weiss~~, M S]]~~		[[Category: Weiss MS]]
	~~[[Category: Cytidine deaminase]]~~
	~~[[Category: Hydrolase~~]]

OCA at 08:00, 10 November 2021

2021-11-10T08:00:32Z

← Older revision		Revision as of 08:00, 10 November 2021
Line 1:		Line 1:

	==The DYW domain of A. thaliana OTP86 in its inactive state==		==The DYW domain of A. thaliana OTP86 in its inactive state==
	<StructureSection load='7o4e' size='340' side='right'caption='[[7o4e]]' scene=''>		<StructureSection load='7o4e' size='340' side='right'caption='[[7o4e]], [[Resolution\|resolution]] 2.50Å' 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=7O4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[7o4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4E FirstGlance]. <br>
	</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=7o4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4e OCA], [https://pdbe.org/7o4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4e RCSB], [https://www.ebi.ac.uk/pdbsum/7o4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4e 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=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7o4f\|7o4f]]</div></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PCMP-H83, OTP86, At3g63370, F16M2_220 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=7o4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4e OCA], [https://pdbe.org/7o4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4e RCSB], [https://www.ebi.ac.uk/pdbsum/7o4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4e ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/PP296_ARATH PP296_ARATH]] Involved in RNA editing event in chloroplasts. Required for the editing of a single site in rps14 transcript.<ref>PMID:19934379</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			RNA editosomes selectively deaminate cytidines to uridines in plant organellar transcripts-mostly to restore protein functionality and consequently facilitate mitochondrial and chloroplast function. The RNA editosomal pentatricopeptide repeat proteins serve target RNA recognition, whereas the intensively studied DYW domain elicits catalysis. Here we present structures and functional data of a DYW domain in an inactive ground state and activated. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural zinc atoms, respectively. A conserved gating domain within the deaminase fold regulates the active site sterically and mechanistically in a process that we termed gated zinc shutter. Based on the structures, an autoinhibited ground state and its activation are cross-validated by RNA editing assays and differential scanning fluorimetry. We anticipate that, in vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated cytidine deamination playing a key role in mitochondrial and chloroplast homeostasis.

			DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.,Takenaka M, Takenaka S, Barthel T, Frink B, Haag S, Verbitskiy D, Oldenkott B, Schallenberg-Rudinger M, Feiler CG, Weiss MS, Palm GJ, Weber G Nat Catal. 2021 Jun;4(6):510-522. doi: 10.1038/s41929-021-00633-x. Epub 2021 Jun , 21. PMID:34712911<ref>PMID:34712911</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7o4e" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Barthel T]]		[[Category: Barthel, T]]
	[[Category: Feiler C]]		[[Category: Feiler, C]]
	[[Category: Palm GJ]]		[[Category: Palm, G J]]
	[[Category: Takenaka M]]		[[Category: Takenaka, M]]
	[[Category: Weber G]]		[[Category: Weber, G]]
	[[Category: Weiss MS]]		[[Category: Weiss, M S]]
			[[Category: Cytidine deaminase]]
			[[Category: Hydrolase]]

OCA at 03:36, 2 July 2021

2021-07-02T03:36:12Z

← Older revision		Revision as of 03:36, 2 July 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	The ~~entry~~ 7o4e is ~~ON HOLD until Paper Publication~~		==The DYW domain of A. thaliana OTP86 in its inactive state==
			<StructureSection load='7o4e' size='340' side='right'caption='[[7o4e]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O4E FirstGlance]. <br>
	~~Description~~:		</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=7o4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o4e OCA], [https://pdbe.org/7o4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o4e RCSB], [https://www.ebi.ac.uk/pdbsum/7o4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o4e ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Barthel T]]
			[[Category: Feiler C]]
			[[Category: Palm GJ]]
			[[Category: Takenaka M]]
			[[Category: Weber G]]
			[[Category: Weiss MS]]

OCA at 11:11, 9 June 2021

2021-06-09T11:11:24Z

← Older revision		Revision as of 11:11, 9 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7o4e is ON HOLD		The entry 7o4e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7o4e" [edit=sysop:move=sysop]

2021-04-14T05:49:53Z

Protected "7o4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:49, 14 April 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7o4e is ON HOLD Authors: Description: Category: Unreleased Structures

2021-04-14T05:49:52Z

New page: '''Unreleased structure''' The entry 7o4e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7o4e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]