5v59 - Revision history

OCA at 13:41, 4 October 2023

OCA — Wed, 04 Oct 2023 13:41:49 GMT

←Older revision		Revision as of 13:41, 4 October 2023
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	<StructureSection load='5v59' size='340' side='right'caption='[[5v59]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='5v59' size='340' side='right'caption='[[5v59]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v59]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V59 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V59 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v59]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V59 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=8X1:5-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine'>8X1</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]] 2.03Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5v58\|5v58~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8X1:5-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine'>8X1</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AARS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN])</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=5v59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v59 OCA], [https://pdbe.org/5v59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v59 RCSB], [https://www.ebi.ac.uk/pdbsum/5v59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v59 ProSAT]</span></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Alanine~~--~~tRNA_ligase Alanine~~--~~tRNA ligase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7~~] </~~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=5v59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v59 OCA], [~~http~~://pdbe.org/5v59 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v59 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v59 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v59 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN]] Autosomal dominant Charcot-Marie-Tooth disease type 2N. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN] Autosomal dominant Charcot-Marie-Tooth disease type 2N. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged tRNA(Ala) via its editing domain.[HAMAP-Rule:MF_03133]	+	[https://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged tRNA(Ala) via its editing domain.[HAMAP-Rule:MF_03133]
	<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: ~~Alanine--tRNA ligase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Schimmel, P]]	+	[[Category: Schimmel P]]
-	[[Category: Song, Y]]	+	[[Category: Song Y]]
-	[[Category: Zhou, H]]	+	[[Category: Zhou H]]
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Non-proteinogenic amino acid~~]]	+

OCA at 09:28, 1 January 2020

OCA — Wed, 01 Jan 2020 09:28:15 GMT

←Older revision		Revision as of 09:28, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA==		==Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA==
-	<StructureSection load='5v59' size='340' side='right' caption='[[5v59]], [[Resolution\|resolution]] 2.03Å' scene=''>	+	<StructureSection load='5v59' size='340' side='right'caption='[[5v59]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v59]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V59 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v59]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V59 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X1:5-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine'>8X1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X1:5-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine'>8X1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v58\|5v58]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v58\|5v58]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AARS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=5v59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v59 OCA], [http://pdbe.org/5v59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v59 RCSB], [http://www.ebi.ac.uk/pdbsum/5v59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v59 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=5v59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v59 OCA], [http://pdbe.org/5v59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v59 RCSB], [http://www.ebi.ac.uk/pdbsum/5v59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v59 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5v59" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v59" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Schimmel, P]]		[[Category: Schimmel, P]]
	[[Category: Song, Y]]		[[Category: Song, Y]]

OCA at 08:28, 10 January 2018

OCA — Wed, 10 Jan 2018 08:28:08 GMT

←Older revision		Revision as of 08:28, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v59 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA==
		+	<StructureSection load='5v59' size='340' side='right' caption='[[5v59]], [[Resolution\|resolution]] 2.03Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v59]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V59 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8X1:5-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine'>8X1</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v58\|5v58]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=5v59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v59 OCA], [http://pdbe.org/5v59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v59 RCSB], [http://www.ebi.ac.uk/pdbsum/5v59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v59 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN]] Autosomal dominant Charcot-Marie-Tooth disease type 2N. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYAC_HUMAN SYAC_HUMAN]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged tRNA(Ala) via its editing domain.[HAMAP-Rule:MF_03133]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hundreds of non-proteinogenic (np) amino acids (AA) are found in plants and can in principle enter human protein synthesis through foods. While aminoacyl-tRNA synthetase (AARS) editing potentially provides a mechanism to reject np AAs, some have pathological associations. Co-crystal structures show that vegetable-sourced azetidine-2-carboxylic acid (Aze), a dual mimic of proline and alanine, is activated by both human prolyl- and alanyl-tRNA synthetases. However, it inserts into proteins as proline, with toxic consequences in vivo. Thus, dual mimicry increases odds for mistranslation through evasion of one but not both tRNA synthetase editing systems.

-	~~Authors: Zhou, H~~., Song, Y., ~~Schimmel~~, P.	+	Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.,Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, Vargas-Rodriguez O, Diedrich JK, Yates JR, Kishi S, Musier-Forsyth K, Schimmel P Nat Commun. 2017 Dec 22;8(1):2281. doi: 10.1038/s41467-017-02201-z. PMID:29273753<ref>PMID:29273753</ref>

-	~~Description: Crystal structure~~ of ~~catalytic fragment~~ of ~~human AlaRS in complex with Aze-SA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Zhou, H]]~~	+	<div class="pdbe-citations 5v59" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Song, Y~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alanine--tRNA ligase]]
	[[Category: Schimmel, P]]		[[Category: Schimmel, P]]
		+	[[Category: Song, Y]]
		+	[[Category: Zhou, H]]
		+	[[Category: Aminoacyl-trna synthetase]]
		+	[[Category: Ligase]]
		+	[[Category: Non-proteinogenic amino acid]]

OCA at 13:54, 27 September 2017

OCA — Wed, 27 Sep 2017 13:54:03 GMT

←Older revision		Revision as of 13:54, 27 September 2017
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Zhou, H]]		[[Category: Zhou, H]]
-	[[Category: Schimmel, P]]
	[[Category: Song, Y]]		[[Category: Song, Y]]
		+	[[Category: Schimmel, P]]

OCA: Protected "5v59" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:37:02 GMT

Protected "5v59" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:37, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v59 is ON HOLD until Paper Publication Authors: Zhou, H., Song, Y., Schimmel, P. Description: Crystal structure of catalytic fragment of human Ala...

OCA — Wed, 05 Apr 2017 11:37:00 GMT

New page: '''Unreleased structure''' The entry 5v59 is ON HOLD until Paper Publication Authors: Zhou, H., Song, Y., Schimmel, P. Description: Crystal structure of catalytic fragment of human Ala...

New page

'''Unreleased structure'''

The entry 5v59 is ON HOLD until Paper Publication

Authors: Zhou, H., Song, Y., Schimmel, P.

Description: Crystal structure of catalytic fragment of human AlaRS in complex with Aze-SA
[[Category: Unreleased Structures]]
[[Category: Zhou, H]]
[[Category: Schimmel, P]]
[[Category: Song, Y]]