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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]] 2.20&Aring;' scene=''>
<StructureSection load='2pid' size='340' side='right'caption='[[2pid]], [[Resolution|resolution]] 2.20&Aring;' 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/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"><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]] 2.2&#8491;</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='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 ([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=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='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], [http://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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</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&reg;/PubMed&reg;, 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==
*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Large Structures]]
[[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]]

Latest revision as of 16:53, 13 March 2024

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analogCrystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog

Structural highlights

2pid is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SYYM_HUMAN Defects in YARS2 are the cause of myopathy with lactic acidosis and sideroblastic anemia type 2 (MLASA2) [MIM: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.[1] [2]

Function

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).[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Riley LG, Cooper S, Hickey P, Rudinger-Thirion J, McKenzie M, Compton A, Lim SC, Thorburn D, Ryan MT, Giege R, Bahlo M, Christodoulou J. Mutation of the mitochondrial tyrosyl-tRNA synthetase gene, YARS2, causes myopathy, lactic acidosis, and sideroblastic anemia--MLASA syndrome. Am J Hum Genet. 2010 Jul 9;87(1):52-9. doi: 10.1016/j.ajhg.2010.06.001. PMID:20598274 doi:10.1016/j.ajhg.2010.06.001
  2. ↑ Sasarman F, Nishimura T, Thiffault I, Shoubridge EA. A novel mutation in YARS2 causes myopathy with lactic acidosis and sideroblastic anemia. Hum Mutat. 2012 Aug;33(8):1201-6. doi: 10.1002/humu.22098. Epub 2012 May 7. PMID:22504945 doi:10.1002/humu.22098
  3. ↑ Bonnefond L, Fender A, Rudinger-Thirion J, Giege R, Florentz C, Sissler M. Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS. Biochemistry. 2005 Mar 29;44(12):4805-16. PMID:15779907 doi:10.1021/bi047527z

2pid, resolution 2.20Å

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