4s02: Difference between revisions

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'''Unreleased structure'''
==Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant==
<StructureSection load='4s02' size='340' side='right' caption='[[4s02]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4s02]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S02 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BIF:(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC+ACID'>BIF</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y2q|1y2q]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4s02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s02 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4s02 RCSB], [http://www.ebi.ac.uk/pdbsum/4s02 PDBsum]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.


The entry 4s02 is ON HOLD  until Paper Publication
Transition states. Trapping a transition state in a computationally designed protein bottle.,Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG Science. 2015 Feb 20;347(6224):863-7. doi: 10.1126/science.aaa2424. PMID:25700516<ref>PMID:25700516</ref>


Authors: Pearson, A.D., Mills, J.H., Song, Y., Nasertorabi, F., Han, G.W., Baker, D., Stevens, R.C., Schultz, P.G.
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
Description: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant
== References ==
[[Category: Unreleased Structures]]
<references/>
[[Category: Schultz, P.G]]
__TOC__
</StructureSection>
[[Category: Threonine--tRNA ligase]]
[[Category: Baker, D]]
[[Category: Han, G W]]
[[Category: Mills, J H]]
[[Category: Nasertorabi, F]]
[[Category: Nasertorabi, F]]
[[Category: Pearson, A D]]
[[Category: Schultz, P G]]
[[Category: Song, Y]]
[[Category: Song, Y]]
[[Category: Stevens, R.C]]
[[Category: Stevens, R C]]
[[Category: Han, G.W]]
[[Category: Beta-alpha-beta fold]]
[[Category: Baker, D]]
[[Category: Biphenylalanine and unnatural amino acid]]
[[Category: Mills, J.H]]
[[Category: Editing domain]]
[[Category: Pearson, A.D]]
[[Category: Ligase]]
[[Category: Threonine-trna ligase]]
[[Category: Trna-synthetase]]
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