1j1u: Difference between revisions

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{{Seed}}
[[Image:1j1u.png|left|200px]]


<!--
==Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine==
The line below this paragraph, containing "STRUCTURE_1j1u", creates the "Structure Box" on the page.
<StructureSection load='1j1u' size='340' side='right'caption='[[1j1u]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1j1u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J1U FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
{{STRUCTURE_1j1u|  PDB=1j1u  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1u OCA], [https://pdbe.org/1j1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j1u RCSB], [https://www.ebi.ac.uk/pdbsum/1j1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1u ProSAT], [https://www.topsan.org/Proteins/RSGI/1j1u TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYY_METJA SYY_METJA] 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).<ref>PMID:10585437</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/j1/1j1u_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/main_output.php?pdb_ID=1j1u ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The archaeal/eukaryotic tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pairs do not cross-react with their bacterial counterparts. This 'orthogonal' condition is essential for using the archaeal pair to expand the bacterial genetic code. In this study, the structure of the Methanococcus jannaschii TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A, reveals that this archaeal TyrRS strictly recognizes the C1-G72 base pair, whereas the bacterial TyrRS recognizes the G1-C72 in a different manner using different residues. These diverse tRNA recognition modes form the basis for the orthogonality. The common tRNA(Tyr) identity determinants (the discriminator, A73 and the anticodon residues) are also recognized in manners different from those of the bacterial TyrRS. Based on this finding, we created a mutant TyrRS that aminoacylates the amber suppressor tRNA with C34 65 times more efficiently than does the wild-type enzyme.


===Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine===
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.,Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S Nat Struct Biol. 2003 Jun;10(6):425-32. PMID:12754495<ref>PMID:12754495</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1j1u" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_12754495}}, adds the Publication Abstract to the page
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 12754495 is the PubMed ID number.
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-->
== References ==
{{ABSTRACT_PUBMED_12754495}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1J1U is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1U OCA].
[[Category: Large Structures]]
 
==Reference==
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion., Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S, Nat Struct Biol. 2003 Jun;10(6):425-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12754495 12754495]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Cusack S]]
[[Category: Cusack, S.]]
[[Category: Ishitani R]]
[[Category: Ishitani, R.]]
[[Category: Kobayashi T]]
[[Category: Kobayashi, T.]]
[[Category: Nureki O]]
[[Category: Nureki, O.]]
[[Category: Sakamoto K]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Tukalo M]]
[[Category: Sakamoto, K.]]
[[Category: Yokoyama S]]
[[Category: Tukalo, M.]]
[[Category: Yokoyama, S.]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Ligase]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Trna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 10:49:56 2008''

Latest revision as of 02:40, 28 December 2023

Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosineCrystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine

Structural highlights

1j1u is a 2 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SYY_METJA 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).[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

The archaeal/eukaryotic tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pairs do not cross-react with their bacterial counterparts. This 'orthogonal' condition is essential for using the archaeal pair to expand the bacterial genetic code. In this study, the structure of the Methanococcus jannaschii TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A, reveals that this archaeal TyrRS strictly recognizes the C1-G72 base pair, whereas the bacterial TyrRS recognizes the G1-C72 in a different manner using different residues. These diverse tRNA recognition modes form the basis for the orthogonality. The common tRNA(Tyr) identity determinants (the discriminator, A73 and the anticodon residues) are also recognized in manners different from those of the bacterial TyrRS. Based on this finding, we created a mutant TyrRS that aminoacylates the amber suppressor tRNA with C34 65 times more efficiently than does the wild-type enzyme.

Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.,Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S Nat Struct Biol. 2003 Jun;10(6):425-32. PMID:12754495[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Steer BA, Schimmel P. Major anticodon-binding region missing from an archaebacterial tRNA synthetase. J Biol Chem. 1999 Dec 10;274(50):35601-6. PMID:10585437
  2. ↑ Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol. 2003 Jun;10(6):425-32. PMID:12754495 doi:10.1038/nsb934

1j1u, resolution 1.95Å

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