2pid - Revision history

OCA at 13:53, 13 March 2024

2024-03-13T13:53:40Z

← Older revision		Revision as of 13:53, 13 March 2024
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pid ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pid ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain and resembles eubacterial TyrRSs with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class I synthetases. Two bulges at the enzyme surface, not seen in eubacterial TyrRSs, correspond to conserved sequences in mt-TyrRSs. The synthetase electrostatic surface potential differs from that of other TyrRSs, including the human cytoplasmic homolog and the mitochondrial one from Neurospora crassa. The homodimeric human mt-TyrRS shows an asymmetry propagating from the dimer interface toward the two catalytic sites and extremities of each subunit. Mutagenesis of the catalytic domain reveals functional importance of Ser200 in line with an involvement of A73 rather than N1-N72 in tyrosine identity.

	Crystal structure of human mitochondrial tyrosyl-tRNA synthetase reveals common and idiosyncratic features.,Bonnefond L, Frugier M, Touze E, Lorber B, Florentz C, Giege R, Sauter C, Rudinger-Thirion J Structure. 2007 Nov;15(11):1505-16. PMID:17997975<ref>PMID:17997975</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2pid" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==

OCA at 11:02, 30 August 2023

2023-08-30T11:02:28Z

← Older revision		Revision as of 11:02, 30 August 2023
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	<StructureSection load='2pid' size='340' side='right'caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2pid' size='340' side='right'caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PID FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pid]] is a 2 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=2PID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PID FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=YSA:5~~-~~O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</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]] 2.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[1vbm\|1vbm]], [[3ts1\|3ts1]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YARS2 ([https://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'>[https~~:~~//en.wikipedia.org/wiki/Tyrosine~~--~~tRNA_ligase Tyrosine~~--~~tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1~~] </~~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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [https://pdbe.org/2pid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [https://www.ebi.ac.uk/pdbsum/2pid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pid 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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [https://pdbe.org/2pid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [https://www.ebi.ac.uk/pdbsum/2pid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pid ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[https://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>		[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[https://omim.org/entry/613561 613561]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>		[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Tyrosine--tRNA ligase]]~~		[[Category: Bonnefond L]]
	[[Category: Bonnefond, L]]		[[Category: Florentz C]]
	[[Category: Florentz, C]]		[[Category: Frugier M]]
	[[Category: Frugier, M]]		[[Category: Giege R]]
	[[Category: Giege, R]]		[[Category: Lorber B]]
	[[Category: Lorber, B]]		[[Category: Rudinger-Thirion J]]
	[[Category: Rudinger-Thirion, J]]		[[Category: Sauter C]]
	[[Category: Sauter, C]]		[[Category: Touze E]]
	[[Category: Touze, E]]
	~~[[Category: Aminoacyl-trna synthetase]]~~
	~~[[Category: Atp-binding]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Mitochondrion]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Protein biosynthesis]]~~
	~~[[Category: Protein-substrate complex~~]]

OCA at 15:24, 17 June 2021

2021-06-17T15:24:46Z

← Older revision		Revision as of 15:24, 17 June 2021
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	==Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog==		==Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog==
	<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2pid' size='340' side='right'caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pid]] is a 2 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=2PID OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PID FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PID FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vbm\|1vbm]], [[3ts1\|3ts1]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([https://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/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [~~http~~://pdbe.org/2pid PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pid PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pid 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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [https://pdbe.org/2pid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [https://www.ebi.ac.uk/pdbsum/2pid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pid ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[~~http~~://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[~~http~~://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>		[[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[https://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>		[[https://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Bonnefond, L]]		[[Category: Bonnefond, L]]

OCA at 08:31, 29 August 2018

2018-08-29T08:31:59Z

← Older revision		Revision as of 08:31, 29 August 2018
Line 1:		Line 1:

	==Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog==		==Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog==
	<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([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/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://pdbe.org/2pid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://pdbe.org/2pid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pid ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pid_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pid_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 07:56, 10 February 2016

2016-02-10T07:56:44Z

← Older revision		Revision as of 07:56, 10 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pid ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:53, 11 September 2015

2015-09-11T06:53:56Z

← Older revision		Revision as of 06:53, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PID FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pid]] is a 2 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=2PID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PID FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([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/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://pdbe.org/2pid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 31:		Line 31:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2pid" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Bonnefond, L]]		[[Category: Bonnefond, L]]

OCA at 17:38, 19 January 2015

2015-01-19T17:38:21Z

← Older revision		Revision as of 17:38, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PID FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PID FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</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=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</span></td></tr>
	<table>		</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[http://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>		[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[http://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>
Line 40:		Line 40:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]
	[[Category: Bonnefond, L.]]		[[Category: Bonnefond, L]]
	[[Category: Florentz, C.]]		[[Category: Florentz, C]]
	[[Category: Frugier, M.]]		[[Category: Frugier, M]]
	[[Category: Giege, R.]]		[[Category: Giege, R]]
	[[Category: Lorber, B.]]		[[Category: Lorber, B]]
	[[Category: Rudinger-Thirion, J.]]		[[Category: Rudinger-Thirion, J]]
	[[Category: Sauter, C.]]		[[Category: Sauter, C]]
	[[Category: Touze, E.]]		[[Category: Touze, E]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 20:02, 30 September 2014

2014-09-30T20:02:35Z

← Older revision		Revision as of 20:02, 30 September 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2pid~~\| ~~PDB~~=2pid \| ~~SCENE~~= }}		==Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog==
	===~~Crystal~~ structure of human ~~mitochondrial~~ tyrosyl-tRNA synthetase in complex with an adenylate analog~~===~~		<StructureSection load='2pid' size='340' side='right' caption='[[2pid]], [[Resolution\|resolution]] 2.20Å' scene=''>
	~~{{ABSTRACT_PUBMED_17997975}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PID FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vbm\|1vbm]], [[3ts1\|3ts1]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YARS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pid RCSB], [http://www.ebi.ac.uk/pdbsum/2pid PDBsum]</span></td></tr>
			<table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[http://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref> <ref>PMID:22504945</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pid_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain and resembles eubacterial TyrRSs with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class I synthetases. Two bulges at the enzyme surface, not seen in eubacterial TyrRSs, correspond to conserved sequences in mt-TyrRSs. The synthetase electrostatic surface potential differs from that of other TyrRSs, including the human cytoplasmic homolog and the mitochondrial one from Neurospora crassa. The homodimeric human mt-TyrRS shows an asymmetry propagating from the dimer interface toward the two catalytic sites and extremities of each subunit. Mutagenesis of the catalytic domain reveals functional importance of Ser200 in line with an involvement of A73 rather than N1-N72 in tyrosine identity.

	~~==Disease==~~		Crystal structure of human mitochondrial tyrosyl-tRNA synthetase reveals common and idiosyncratic features.,Bonnefond L, Frugier M, Touze E, Lorber B, Florentz C, Giege R, Sauter C, Rudinger-Thirion J Structure. 2007 Nov;15(11):1505-16. PMID:17997975<ref>PMID:17997975</ref>
	~~[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause~~ of ~~myopathy with lactic acidosis~~ and ~~sideroblastic anemia type 2 (MLASA2) [MIM:[http://omim~~.~~org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia~~, ~~progressive lethargy~~, ~~muscle weakness~~, ~~and exercise intolerance associated with persistent lactic acidemia~~.~~<ref>~~PMID:~~20598274</ref>~~<ref>PMID:~~22504945~~</ref>

	~~==Function==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[http:~~/~~/www~~.~~uniprot~~.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of ~~tRNA(Tyr) (By similarity)~~.<~~ref~~>~~PMID:15779907~~</~~ref~~>		</div>

	~~==About this Structure==~~
	[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA].

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:017997975</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]

OCA at 02:24, 25 March 2013

2013-03-25T02:24:20Z

← Older revision		Revision as of 02:24, 25 March 2013
Line 1:		Line 1:
	~~[[Image:2pid.png\|left\|200px]]~~

	{{STRUCTURE_2pid\| PDB=2pid \| SCENE= }}		{{STRUCTURE_2pid\| PDB=2pid \| SCENE= }}
			===Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog===
			{{ABSTRACT_PUBMED_17997975}}

	===~~Crystal structure~~ of ~~human mitochondrial tyrosyl-tRNA synthetase in complex~~ with ~~an adenylate analog===~~		==Disease==
			[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM:[http://omim.org/entry/613561 613561]]. MLASA2 is a rare oxidative phosphorylation disorder specific to skeletal muscle and bone marrow. Affected individuals manifest sideroblastic anemia, progressive lethargy, muscle weakness, and exercise intolerance associated with persistent lactic acidemia.<ref>PMID:20598274</ref><ref>PMID:22504945</ref>

	~~{{ABSTRACT_PUBMED_17997975}}~~		==Function==
			[[http://www.uniprot.org/uniprot/SYYM_HUMAN SYYM_HUMAN]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity).<ref>PMID:15779907</ref>

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
	<ref group="xtra">PMID:017997975</ref><references group="xtra"/>		<ref group="xtra">PMID:017997975</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Tyrosine--tRNA ligase]]		[[Category: Tyrosine--tRNA ligase]]

OCA at 16:53, 20 October 2012

2012-10-20T16:53:16Z

← Older revision		Revision as of 16:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2pid]] is a 2 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA].		[[2pid]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PID OCA].

	==See Also==		==See Also==