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==Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form==
==Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form==
<StructureSection load='4nd6' size='340' side='right' caption='[[4nd6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='4nd6' size='340' side='right'caption='[[4nd6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4nd6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ND6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ND6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4nd6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ND6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ND6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nd7|4nd7]], [[4nda|4nda]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0389, tyrS, tyrS MJ0389 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=4nd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nd6 OCA], [https://pdbe.org/4nd6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nd6 RCSB], [https://www.ebi.ac.uk/pdbsum/4nd6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nd6 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=4nd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nd6 OCA], [http://pdbe.org/4nd6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nd6 RCSB], [http://www.ebi.ac.uk/pdbsum/4nd6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nd6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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>
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Genetic code expansion has provided the ability to site-specifically incorporate a multitude of noncanonical amino acids (ncAAs) into proteins for a wide variety of applications, but low ncAA incorporation efficiency can hamper the utility of this powerful technology. When investigating proteins containing the post-translational modification 3-nitro-tyrosine (nitroTyr), we developed second-generation amino-acyl tRNA synthetases (RS) that incorporate nitroTyr at efficiencies roughly an order of magnitude greater than those previously reported and that advanced our ability to elucidate the role of elevated cellular nitroTyr levels in human disease (e.g., Franco, M. et al. Proc. Natl. Acad. Sci. U.S.A 2013 , 110 , E1102 ). Here, we explore the origins of the improvement achieved in these second-generation RSs. Crystal structures of the most efficient of these synthetases reveal the molecular basis for the enhanced efficiencies observed in the second-generation nitroTyr-RSs. Although Tyr is not detectably incorporated into proteins when expression media is supplemented with 1 mM nitroTyr, a major difference between the first- and second-generation RSs is that the second-generation RSs have an active site more compatible with Tyr binding. This feature of the second-generation nitroTyr-RSs appears to be the result of using less stringent criteria when selecting from a library of mutants. The observation that a different selection strategy performed on the same library of mutants produced nitroTyr-RSs with dramatically improved efficiencies suggests the optimization of established selection protocols could lead to notable improvements in ncAA-RS efficiencies and thus the overall utility of this technology.


Structural Basis of Improved Second-Generation 3-Nitro-tyrosine tRNA Synthetases.,Cooley RB, Feldman JL, Driggers CM, Bundy TA, Stokes AL, Karplus PA, Mehl RA Biochemistry. 2014 Apr 1;53(12):1916-24. doi: 10.1021/bi5001239. Epub 2014 Mar, 20. PMID:24611875<ref>PMID:24611875</ref>
==See Also==
 
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4nd6" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Metja]]
[[Category: Large Structures]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Methanocaldococcus jannaschii DSM 2661]]
[[Category: Cooley, R B]]
[[Category: Cooley RB]]
[[Category: Driggers, C M]]
[[Category: Driggers CM]]
[[Category: Karplus, P A]]
[[Category: Karplus PA]]
[[Category: Mehl, R A]]
[[Category: Mehl RA]]
[[Category: 3-nitro-tyrosine amino-acyl trna synthetase]]
[[Category: Ligase]]
[[Category: Rossmann fold]]
[[Category: Trna]]

Latest revision as of 15:32, 1 March 2024

Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open formCrystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form

Structural highlights

4nd6 is a 1 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

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

4nd6, resolution 2.00Å

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