6ia8 - Revision history

OCA at 11:50, 24 January 2024

OCA — Wed, 24 Jan 2024 11:50:19 GMT

←Older revision		Revision as of 11:50, 24 January 2024
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	==Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19)==		==Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19)==
-	<StructureSection load='6ia8' size='340' side='right' caption='[[6ia8]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6ia8' size='340' side='right'caption='[[6ia8]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ia8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ia8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_infernus Methanocaldococcus infernus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IA8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia8 OCA], [~~http~~://pdbe.org/6ia8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ia8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ia8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia8 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=6ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia8 OCA], [https://pdbe.org/6ia8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ia8 RCSB], [https://www.ebi.ac.uk/pdbsum/6ia8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ELP3_METIM ELP3_METIM] tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:25151136, PubMed:30733442). 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 (PubMed:25151136). Does not show protein lysine acetyltransferase activity (PubMed:30733442).<ref>PMID:25151136</ref> <ref>PMID:30733442</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6ia8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ia8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone acetyltransferase 3D structures\|Histone acetyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone acetyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Glatt, S~~]]	+	[[Category: Methanocaldococcus infernus]]
-	[[Category: ~~Lin, T Y~~]]	+	[[Category: Glatt S]]
-	[[Category: ~~Acetyl-coa hydrolysis]]~~	+	[[Category: Lin TY]]
-	~~[[Category: Elongator complex]]~~	+
-	~~[[Category: Non-canonical acetyltransferase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trna binding~~]]	+

OCA at 06:46, 21 February 2019

OCA — Thu, 21 Feb 2019 06:46:57 GMT

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

-	~~The entry~~ 6ia8 is ~~ON HOLD until Paper~~ Publication	+	==Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19)==
		+	<StructureSection load='6ia8' size='340' side='right' caption='[[6ia8]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ia8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IA8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></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=6ia8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia8 OCA], [http://pdbe.org/6ia8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ia8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ia8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia8 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:~~ Lin, ~~T.Y.~~, ~~Glatt~~, S.	+	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: Apo crystal structure~~ of ~~archaeal Methanocaldococcus infernus Elp3 (del1~~-~~19)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6ia8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone acetyltransferase]]
	[[Category: Glatt, S]]		[[Category: Glatt, S]]
-	[[Category: Lin, T.Y]]	+	[[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 05:04:39 GMT

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

-	The entry 6ia8 is ON HOLD	+	The entry 6ia8 is ON HOLD until Paper Publication

	Authors: Lin, T.Y., Glatt, S.		Authors: Lin, T.Y., Glatt, S.

OCA: Protected "6ia8" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:01:36 GMT

Protected "6ia8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ia8 is ON HOLD Authors: Lin, T.Y., Glatt, S. Description: Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19) [[Category:...

OCA — Wed, 05 Dec 2018 05:01:35 GMT

New page: '''Unreleased structure''' The entry 6ia8 is ON HOLD Authors: Lin, T.Y., Glatt, S. Description: Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19) [[Category:...

New page

'''Unreleased structure'''

The entry 6ia8 is ON HOLD

Authors: Lin, T.Y., Glatt, S.

Description: Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19)
[[Category: Unreleased Structures]]
[[Category: Glatt, S]]
[[Category: Lin, T.Y]]