5y0q - Revision history

OCA at 08:18, 22 November 2023

2023-11-22T08:18:38Z

←Older revision		Revision as of 08:18, 22 November 2023
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	==Crystal structure of BsTmcAL bound with AMPCPP==		==Crystal structure of BsTmcAL bound with AMPCPP==
-	<StructureSection load='5y0q' size='340' side='right' caption='[[5y0q]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5y0q' size='340' side='right'caption='[[5y0q]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y0Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>B4417_3650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</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=5y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0q OCA], [~~http~~://pdbe.org/5y0q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y0q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y0q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0q 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=5y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0q OCA], [https://pdbe.org/5y0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y0q RCSB], [https://www.ebi.ac.uk/pdbsum/5y0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TMCAL_BACSU TMCAL_BACSU] 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]<ref>PMID:30150682</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
-	[[Category: ~~Tomita, K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Yamashita, S~~]]	+	[[Category: Tomita K]]
-	[[Category: ~~Acetate ligase]]~~	+	[[Category: Yamashita S]]
-	~~[[Category: Ligase~~]]	+

OCA at 08:31, 26 December 2018

2018-12-26T08:31:11Z

←Older revision		Revision as of 08:31, 26 December 2018
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	<StructureSection load='5y0q' size='340' side='right' caption='[[5y0q]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5y0q' size='340' side='right' caption='[[5y0q]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B4417_3650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=5y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0q OCA], [http://pdbe.org/5y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0q RCSB], [http://www.ebi.ac.uk/pdbsum/5y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0q 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=5y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0q OCA], [http://pdbe.org/5y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0q RCSB], [http://www.ebi.ac.uk/pdbsum/5y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0q 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 5y0q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Tomita, K]]		[[Category: Tomita, K]]
	[[Category: Yamashita, S]]		[[Category: Yamashita, S]]
	[[Category: Acetate ligase]]		[[Category: Acetate ligase]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Ligase]]

OCA at 07:29, 18 July 2018

2018-07-18T07:29:48Z

←Older revision		Revision as of 07:29, 18 July 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5y0q is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of BsTmcAL bound with AMPCPP==
-		+	<StructureSection load='5y0q' size='340' side='right' caption='[[5y0q]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y0q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0Q FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0q OCA], [http://pdbe.org/5y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0q RCSB], [http://www.ebi.ac.uk/pdbsum/5y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0q ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tomita, K]]
		+	[[Category: Yamashita, S]]
		+	[[Category: Acetate ligase]]
		+	[[Category: Transferase]]

OCA: Protected "5y0q" [edit=sysop:move=sysop]

2017-09-27T16:00:23Z

Protected "5y0q" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:00, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y0q is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T16:00:22Z

New page: '''Unreleased structure''' The entry 5y0q is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y0q is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]