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==Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol==
==Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol==
<StructureSection load='2j5b' size='340' side='right' caption='[[2j5b]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2j5b' size='340' side='right'caption='[[2j5b]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2j5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J5B FirstGlance]. <br>
<table><tr><td colspan='2'>[[2j5b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J5B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYE:4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL'>TYE</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='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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYE:4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL'>TYE</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=2j5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j5b OCA], [http://pdbe.org/2j5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j5b RCSB], [http://www.ebi.ac.uk/pdbsum/2j5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j5b 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=2j5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j5b OCA], [https://pdbe.org/2j5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j5b RCSB], [https://www.ebi.ac.uk/pdbsum/2j5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j5b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SYY_MIMIV SYY_MIMIV]] 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:15486256</ref> <ref>PMID:16510997</ref>
[https://www.uniprot.org/uniprot/SYY_MIMIV SYY_MIMIV] 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:15486256</ref> <ref>PMID:16510997</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=2j5b 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=2j5b ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes.
Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS.,Abergel C, Rudinger-Thirion J, Giege R, Claverie JM J Virol. 2007 Nov;81(22):12406-17. Epub 2007 Sep 12. PMID:17855524<ref>PMID:17855524</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2j5b" 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: Apmv]]
[[Category: Acanthamoeba polyphaga mimivirus]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Large Structures]]
[[Category: Abergel, C]]
[[Category: Abergel C]]
[[Category: Claverie, J M]]
[[Category: Claverie JM]]
[[Category: Giege, R]]
[[Category: Giege R]]
[[Category: Rudinger-thirion, J]]
[[Category: Rudinger-thirion J]]
[[Category: Atp-binding]]
[[Category: Ligase]]
[[Category: Protein biosynthesis]]

Latest revision as of 09:41, 1 May 2024

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynolStructure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol

Structural highlights

2j5b is a 2 chain structure with sequence from Acanthamoeba polyphaga mimivirus. 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

Function

SYY_MIMIV 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).[1] [2]

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. ↑ Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of Mimivirus. Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14. PMID:15486256 doi:http://dx.doi.org/1101485
  2. ↑ Abergel C, Chenivesse S, Byrne D, Suhre K, Arondel V, Claverie JM. Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Feb 1;61(Pt, 2):212-5. Epub 2005 Jan 20. PMID:16510997 doi:10.1107/S174430910500062X

2j5b, resolution 2.20Å

Drag the structure with the mouse to rotate

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