This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4nda

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:56, 5 August 2016

Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3-nitro-tyrosine

Structural highlights

4nda is a 1 chain structure with sequence from Metja. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	4nd6, 4nd7
Gene:	MJ0389, tyrS, tyrS MJ0389 (METJA)
Activity:	Tyrosine--tRNA ligase, with EC number 6.1.1.1
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]

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^[2]

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

References

↑ 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
↑ Cooley RB, Feldman JL, Driggers CM, Bundy TA, Stokes AL, Karplus PA, Mehl RA. Structural Basis of Improved Second-Generation 3-Nitro-tyrosine tRNA Synthetases. Biochemistry. 2014 Apr 1;53(12):1916-24. doi: 10.1021/bi5001239. Epub 2014 Mar, 20. PMID:24611875 doi:http://dx.doi.org/10.1021/bi5001239

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4nda"

@@ Line 1: / Line 1: @@
 ==Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3-nitro-tyrosine==
 <StructureSection load='4nda' size='340' side='right' caption='[[4nda]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <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='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=4nda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nda OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nda RCSB], [http://www.ebi.ac.uk/pdbsum/4nda PDBsum]</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=4nda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nda OCA], [http://pdbe.org/4nda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nda RCSB], [http://www.ebi.ac.uk/pdbsum/4nda PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nda ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4nda" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4nda

From Proteopedia

Revision as of 08:56, 5 August 2016

Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3-nitro-tyrosine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox