6ia6 - Revision history

OCA at 11:50, 24 January 2024

OCA — Wed, 24 Jan 2024 11:50:17 GMT

←Older revision		Revision as of 11:50, 24 January 2024
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	==Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA==		==Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA==
-	<StructureSection load='6ia6' size='340' side='right' caption='[[6ia6]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='6ia6' size='340' side='right'caption='[[6ia6]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ia6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ia6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dehalococcoides_mccartyi_BTF08 Dehalococcoides mccartyi BTF08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IA6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.7Å</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=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [~~http~~://pdbe.org/6ia6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [https://pdbe.org/6ia6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ELP3_DEHMC ELP3_DEHMC] tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:27455459). The proposed mechanism is the following: (i) recruits S-adenosyl-L-methionine and cleaves it to generate a 5'-deoxyadenosine radical (5'-dA) in the radical S-adenosyl-L-methionine (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-acetyltransferase domain and (iii) an acetyl radical is formed by the products of the two domains and (iv) is transferred onto the C5 position of uridine(34) in the bound tRNA molecule. Does not show protein lysine acetyltransferase activity (By similarity).[UniProtKB:D5VRB9]<ref>PMID:27455459</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Glatt, S~~]]	+	[[Category: Dehalococcoides mccartyi BTF08]]
-	[[Category: ~~Lin, T Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Acetyl-coa hydrolysis~~]]	+	[[Category: Glatt S]]
-	[[Category: ~~Elongator complex]]~~	+	[[Category: Lin TY]]
-	~~[[Category: Non-canonical acetyltransferase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trna binding~~]]	+

OCA at 06:46, 21 February 2019

OCA — Thu, 21 Feb 2019 06:46:46 GMT

←Older revision		Revision as of 06:46, 21 February 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6ia6 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA==
		+	<StructureSection load='6ia6' size='340' side='right' caption='[[6ia6]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ia6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IA6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [http://pdbe.org/6ia6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm(5)) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme.

-	~~Authors~~:	+	The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.,Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442<ref>PMID:30733442</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6ia6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glatt, S]]
		+	[[Category: Lin, T Y]]
		+	[[Category: Acetyl-coa hydrolysis]]
		+	[[Category: Elongator complex]]
		+	[[Category: Non-canonical acetyltransferase]]
		+	[[Category: Transferase]]
		+	[[Category: Trna binding]]

OCA at 05:04, 12 December 2018

OCA — Wed, 12 Dec 2018 05:04:36 GMT

←Older revision		Revision as of 05:04, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ia6 is ON HOLD	+	The entry 6ia6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ia6" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:01:25 GMT

Protected "6ia6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ia6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Dec 2018 05:01:24 GMT

New page: '''Unreleased structure''' The entry 6ia6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ia6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]