5y0t - Revision history

OCA at 08:18, 22 November 2023

OCA — Wed, 22 Nov 2023 08:18:43 GMT

←Older revision		Revision as of 08:18, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5y0t' size='340' side='right'caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5y0t' size='340' side='right'caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [~~http~~://pdbe.org/5y0t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t 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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [https://pdbe.org/5y0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [https://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TMCAL_THEMA TMCAL_THEMA] Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34.[HAMAP-Rule:MF_01539]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Tomita, K~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: ~~Yamashita, S~~]]	+	[[Category: Tomita K]]
-	[[Category: ~~Acetate ligase]]~~	+	[[Category: Yamashita S]]
-	~~[[Category: Ligase~~]]	+

OCA at 07:02, 14 October 2020

OCA — Wed, 14 Oct 2020 07:02:46 GMT

←Older revision		Revision as of 07:02, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)==		==Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)==
-	<StructureSection load='5y0t' size='340' side='right' caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5y0t' size='340' side='right'caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [http://pdbe.org/5y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [http://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</span></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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [http://pdbe.org/5y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [http://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Tomita, K]]		[[Category: Tomita, K]]
	[[Category: Yamashita, S]]		[[Category: Yamashita, S]]
	[[Category: Acetate ligase]]		[[Category: Acetate ligase]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 08:31, 26 December 2018

OCA — Wed, 26 Dec 2018 08:31:24 GMT

←Older revision		Revision as of 08:31, 26 December 2018
Line 3:		Line 3:
	<StructureSection load='5y0t' size='340' side='right' caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5y0t' size='340' side='right' caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [http://pdbe.org/5y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [http://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [http://pdbe.org/5y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [http://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N(4)-acetylcytidine (ac(4)C) is present at the anticodon first position (position 34) of bacterial elongator tRNA(Met). Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac(4)C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac(4)C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac(4)C34 formation. The DeltatmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNA(Ile) to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the DeltatmcAL strain upon tilS repression suggests that ac(4)C34 modification of tRNA(Met) and L34 modification of tRNA(Ile) act cooperatively to prevent misdecoding of the AUA codon.
		+
		+	Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.,Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, Suzuki T Nat Chem Biol. 2018 Nov;14(11):1010-1020. doi: 10.1038/s41589-018-0119-z. Epub, 2018 Aug 27. PMID:30150682<ref>PMID:30150682</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y0t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Tomita, K]]		[[Category: Tomita, K]]
	[[Category: Yamashita, S]]		[[Category: Yamashita, S]]
	[[Category: Acetate ligase]]		[[Category: Acetate ligase]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Ligase]]

OCA at 07:30, 18 July 2018

OCA — Wed, 18 Jul 2018 07:30:19 GMT

←Older revision		Revision as of 07:30, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y0t is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)==
-		+	<StructureSection load='5y0t' size='340' side='right' caption='[[5y0t]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y0t]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0T FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TAT:ADENOSINE-5-RP-ALPHA-THIO-TRIPHOSPHATE'>TAT</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=5y0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0t OCA], [http://pdbe.org/5y0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0t RCSB], [http://www.ebi.ac.uk/pdbsum/5y0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0t ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tomita, K]]
		+	[[Category: Yamashita, S]]
		+	[[Category: Acetate ligase]]
		+	[[Category: Transferase]]

OCA: Protected "5y0t" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:00:31 GMT

Protected "5y0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:00, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y0t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:00:30 GMT

New page: '''Unreleased structure''' The entry 5y0t is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y0t is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]