7bv5 - Revision history

OCA at 15:36, 29 November 2023

OCA — Wed, 29 Nov 2023 15:36:34 GMT

←Older revision		Revision as of 15:36, 29 November 2023
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-	====	+	==Crystal structure of the yeast heterodimeric ADAT2/3==
-	<StructureSection load='7bv5' size='340' side='right'caption='[[7bv5]]' scene=''>	+	<StructureSection load='7bv5' size='340' side='right'caption='[[7bv5]], [[Resolution\|resolution]] 2.80Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bv5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BV5 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=7bv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bv5 OCA], [~~http~~://pdbe.org/7bv5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7bv5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7bv5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7bv5 ProSAT]</span></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]] 2.8Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7bv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bv5 OCA], [https://pdbe.org/7bv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bv5 RCSB], [https://www.ebi.ac.uk/pdbsum/7bv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bv5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TAD2_YEAST TAD2_YEAST] Deaminates adenosine-34 to inosine in many tRNAs.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear. RESULTS: Here, we report a 2.8-A crystal structure of Saccharomyces cerevisiae ADAT2/3 (ScADAT2/3), revealing its heterodimeric assembly and substrate recognition mechanism. While each subunit clearly contains a domain resembling their prokaryotic homolog TadA, suggesting an evolutionary gene duplication event, they also display accessory domains for additional structural or functional purposes. The N-lobe of ScADAT3 exhibits a positively charged region with a potential role in the recognition and binding of tRNA, supported by our biochemical analysis. Interestingly, ScADAT3 employs its C-terminus to block tRNA's entry into its pseudo-active site and thus inactivates itself for deamination despite the preservation of a zinc-binding site, a mechanism possibly shared only among yeasts. CONCLUSIONS: Combining the structural with biochemical, bioinformatic, and in vivo functional studies, we propose a stepwise model for the pathway of deamination by ADAT2/3. Our work provides insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis.
		+
		+	Crystal structure of the yeast heterodimeric ADAT2/3 deaminase.,Liu X, Chen R, Sun Y, Chen R, Zhou J, Tian Q, Tao X, Zhang Z, Luo GZ, Xie W BMC Biol. 2020 Dec 3;18(1):189. doi: 10.1186/s12915-020-00920-2. PMID:33272269<ref>PMID:33272269</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bv5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenosine deaminase 3D structures\|Adenosine deaminase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Chen R]]
		+	[[Category: Liu X]]
		+	[[Category: Sun Y]]
		+	[[Category: Tian Q]]
		+	[[Category: Xie W]]
		+	[[Category: Zhou J]]

OCA at 09:40, 18 November 2020

OCA — Wed, 18 Nov 2020 09:40:43 GMT

←Older revision		Revision as of 09:40, 18 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7bv5 ~~is ON HOLD until Apr 09 2022~~	+	====
-		+	<StructureSection load='7bv5' size='340' side='right'caption='[[7bv5]]' scene=''>
-	~~Authors~~: ~~Xie, W~~.~~, Liu, X~~.~~, Chen, R~~.~~, Sun, Y~~.~~, Chen, R~~.~~, Zhou, J~~.~~, Tian, Q~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the yeast heterodimeric ADAT2~~/3	+	</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=7bv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bv5 OCA], [http://pdbe.org/7bv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bv5 RCSB], [http://www.ebi.ac.uk/pdbsum/7bv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bv5 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Liu, X~~]]	+	__TOC__
-	[~~[Category~~: ~~Xie, W~~]]	+	</StructureSection>
-	[~~[Category~~: ~~Zhou, J~~]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Chen~~, R]]	+	[[Category: Z-disk]]
-	[[Category: ~~Tian, Q~~]]	+
-	[[Category: ~~Sun, Y~~]]	+

OCA at 04:35, 22 April 2020

OCA — Wed, 22 Apr 2020 04:35:38 GMT

←Older revision		Revision as of 04:35, 22 April 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7bv5 is ON HOLD	+	The entry 7bv5 is ON HOLD until Apr 09 2022

	Authors: Xie, W., Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q.		Authors: Xie, W., Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q.
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	Description: Crystal structure of the yeast heterodimeric ADAT2/3		Description: Crystal structure of the yeast heterodimeric ADAT2/3
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xie, W]]
-	[[Category: Tian, Q]]
	[[Category: Liu, X]]		[[Category: Liu, X]]
-	[[Category: ~~Chen~~, R]]	+	[[Category: Xie, W]]
	[[Category: Zhou, J]]		[[Category: Zhou, J]]
		+	[[Category: Chen, R]]
		+	[[Category: Tian, Q]]
	[[Category: Sun, Y]]		[[Category: Sun, Y]]

OCA: Protected "7bv5" [edit=sysop:move=sysop]

OCA — Wed, 15 Apr 2020 05:45:01 GMT

Protected "7bv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:45, 15 April 2020

OCA: New page: '''Unreleased structure''' The entry 7bv5 is ON HOLD Authors: Xie, W., Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q. Description: Crystal structure of the yeast heterodimeri...

OCA — Wed, 15 Apr 2020 05:45:00 GMT

New page: '''Unreleased structure''' The entry 7bv5 is ON HOLD Authors: Xie, W., Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q. Description: Crystal structure of the yeast heterodimeri...

New page

'''Unreleased structure'''

The entry 7bv5 is ON HOLD

Authors: Xie, W., Liu, X., Chen, R., Sun, Y., Chen, R., Zhou, J., Tian, Q.

Description: Crystal structure of the yeast heterodimeric ADAT2/3
[[Category: Unreleased Structures]]
[[Category: Xie, W]]
[[Category: Tian, Q]]
[[Category: Liu, X]]
[[Category: Chen, R]]
[[Category: Zhou, J]]
[[Category: Sun, Y]]