2yxn: Difference between revisions

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{{Seed}}
[[Image:2yxn.png|left|200px]]


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==Structual basis of azido-tyrosine recognition by engineered bacterial Tyrosyl-tRNA synthetase==
The line below this paragraph, containing "STRUCTURE_2yxn", creates the "Structure Box" on the page.
<StructureSection load='2yxn' size='340' side='right'caption='[[2yxn]], [[Resolution|resolution]] 1.80&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'>[[2yxn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._W3110 Escherichia coli str. K-12 substr. W3110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXN 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]] 1.8&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZY:3-AZIDO-L-TYROSINE'>AZY</scene></td></tr>
{{STRUCTURE_2yxn|  PDB=2yxn  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxn OCA], [https://pdbe.org/2yxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxn RCSB], [https://www.ebi.ac.uk/pdbsum/2yxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxn ProSAT], [https://www.topsan.org/Proteins/RSGI/2yxn TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYY_ECOLI SYY_ECOLI] 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).[HAMAP-Rule:MF_02006]
== 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/yx/2yxn_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=2yxn ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Non-natural amino acids have been genetically encoded in living cells, using aminoacyl-tRNA synthetase-tRNA pairs orthogonal to the host translation system. In the present study, we engineered Escherichia coli cells with a translation system orthogonal to the E. coli tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pair, to use E. coli TyrRS variants for non-natural amino acids in the cells without interfering with tyrosine incorporation. We showed that the E. coli TyrRS-tRNA(Tyr) pair can be functionally replaced by the Methanocaldococcus jannaschii and Saccharomyces cerevisiae tyrosine pairs, which do not cross-react with E. coli TyrRS or tRNA(Tyr). The endogenous TyrRS and tRNA(Tyr) genes were then removed from the chromosome of the E. coli cells expressing the archaeal TyrRS-tRNA(Tyr) pair. In this engineered strain, 3-iodo-L-tyrosine and 3-azido-L-tyrosine were each successfully encoded with the amber codon, using the E. coli amber suppressor tRNATyr and a TyrRS variant, which was previously developed for 3-iodo-L-tyrosine and was also found to recognize 3-azido-L-tyrosine. The structural basis for the 3-azido-L-tyrosine recognition was revealed by X-ray crystallography. The present engineering allows E. coli TyrRS variants for non-natural amino acids to be developed in E. coli, for use in both eukaryotic and bacterial cells for genetic code expansion.


===Structual basis of azido-tyrosine recognition by engineered bacterial Tyrosyl-tRNA synthetase===
Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion.,Iraha F, Oki K, Kobayashi T, Ohno S, Yokogawa T, Nishikawa K, Yokoyama S, Sakamoto K Nucleic Acids Res. 2010 Jun;38(11):3682-91. Epub 2010 Feb 16. PMID:20159998<ref>PMID:20159998</ref>


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


==About this Structure==
==See Also==
2YXN is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXN OCA].
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
[[Category: Escherichia coli]]
== References ==
[[Category: Tyrosine--tRNA ligase]]
<references/>
[[Category: Kobayashi, T.]]
__TOC__
[[Category: Oki, K.]]
</StructureSection>
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Escherichia coli str. K-12 substr. W3110]]
[[Category: Sakamoto, K.]]
[[Category: Large Structures]]
[[Category: Yokoyama, S.]]
[[Category: Kobayashi T]]
[[Category: Ligase]]
[[Category: Oki K]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Sakamoto K]]
[[Category: Nppsfa]]
[[Category: Yokoyama S]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Trna synthetases class i]]
 
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Retrieved from "https://proteopedia.org/2yxn"