OCA at 13:35, 24 January 2024

OCA — Wed, 24 Jan 2024 13:35:40 GMT

←Older revision		Revision as of 13:35, 24 January 2024
Line 1:		Line 1:

-	====	+	==Crystal structure of Uba4 from Chaetomium thermophilum==
-	<StructureSection load='6yub' size='340' side='right'caption='[[6yub]]' scene=''>	+	<StructureSection load='6yub' size='340' side='right'caption='[[6yub]], [[Resolution\|resolution]] 2.19Å' 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'>[[6yub]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum Chaetomium thermophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YUB 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=6yub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yub OCA], [~~http~~://pdbe.org/6yub PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yub RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yub PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yub 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]] 2.195Å</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=6yub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yub OCA], [https://pdbe.org/6yub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yub RCSB], [https://www.ebi.ac.uk/pdbsum/6yub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yub ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G0SC54_CHATD G0SC54_CHATD] Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Also essential during biosynthesis of the molybdenum cofactor. Acts by mediating the C-terminal thiocarboxylation of sulfur carriers urm1 and MOCS2A. Its N-terminus first activates urm1 and MOCS2A as acyl-adenylates (-COAMP), then the persulfide sulfur on the catalytic cysteine is transferred to urm1 and MOCS2A to form thiocarboxylation (-COSH) of their C-terminus. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards urm1 and MOCS2A. Subsequently, a transient disulfide bond is formed. Does not use thiosulfate as sulfur donor; nfs1 probably acting as a sulfur donor for thiocarboxylation reactions.[HAMAP-Rule:MF_03049]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The chemical modification of tRNA bases by sulfur is crucial to tune translation and to optimize protein synthesis. In eukaryotes, the ubiquitin-related modifier 1 (Urm1) pathway is responsible for the synthesis of 2-thiolated wobble uridine (U34 ). During the key step of the modification cascade, the E1-like activating enzyme ubiquitin-like protein activator 4 (Uba4) first adenylates and thiocarboxylates the C-terminus of its substrate Urm1. Subsequently, activated thiocarboxylated Urm1 (Urm1-COSH) can serve as a sulfur donor for specific tRNA thiolases or participate in ubiquitin-like conjugation reactions. Structural and mechanistic details of Uba4 and Urm1 have remained elusive but are key to understand the evolutionary branch point between ubiquitin-like proteins (UBL) and sulfur-relay systems. Here, we report the crystal structures of full-length Uba4 and its heterodimeric complex with its substrate Urm1. We show how the two domains of Uba4 orchestrate recognition, binding, and thiocarboxylation of the C-terminus of Urm1. Finally, we uncover how the catalytic domains of Uba4 communicate efficiently during the reaction cycle and identify a mechanism that enables Uba4 to protect itself against self-conjugation with its own product, namely activated Urm1-COSH.
		+
		+	Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.,Pabis M, Termathe M, Ravichandran KE, Kienast SD, Krutyholowa R, Sokolowski M, Jankowska U, Grudnik P, Leidel SA, Glatt S EMBO J. 2020 Sep 9:e105087. doi: 10.15252/embj.2020105087. PMID:32901956<ref>PMID:32901956</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yub" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of Ubiquitin activating enzyme\|3D structures of Ubiquitin activating enzyme]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chaetomium thermophilum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Ethiraju Ravichandran K]]
		+	[[Category: Glatt S]]
		+	[[Category: Grudnik P]]
		+	[[Category: Pabis M]]

OCA at 10:57, 22 July 2020

OCA — Wed, 22 Jul 2020 10:57:12 GMT

←Older revision		Revision as of 10:57, 22 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yub ~~is ON HOLD~~	+	====
-		+	<StructureSection load='6yub' size='340' side='right'caption='[[6yub]]' scene=''>
-	~~Authors~~:	+	== 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~~:	+	</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=6yub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yub OCA], [http://pdbe.org/6yub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yub RCSB], [http://www.ebi.ac.uk/pdbsum/6yub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yub ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "6yub" [edit=sysop:move=sysop]

OCA — Wed, 06 May 2020 04:40:50 GMT

Protected "6yub" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:40, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 6yub is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 May 2020 04:40:49 GMT

New page: '''Unreleased structure''' The entry 6yub is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6yub is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6yub - Revision history

OCA at 13:35, 24 January 2024

OCA at 10:57, 22 July 2020

OCA: Protected "6yub" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6yub is ON HOLD Authors: Description: Category: Unreleased Structures