4s03: Difference between revisions
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==Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutant== | ==Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutant== | ||
<StructureSection load='4s03' size='340' side='right' caption='[[4s03]], [[Resolution|resolution]] 2.05Å' scene=''> | <StructureSection load='4s03' size='340' side='right'caption='[[4s03]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4s03]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S03 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4s03]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S03 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BIF:(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC+ACID'>BIF</scene></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=4s03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s03 OCA], [https://pdbe.org/4s03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s03 RCSB], [https://www.ebi.ac.uk/pdbsum/4s03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s03 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/SYT_PYRAB SYT_PYRAB] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4s03" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Baker | [[Category: Pyrococcus abyssi GE5]] | ||
[[Category: Han | [[Category: Baker D]] | ||
[[Category: Mills | [[Category: Han GW]] | ||
[[Category: Nasertorabi | [[Category: Mills JH]] | ||
[[Category: Pearson | [[Category: Nasertorabi F]] | ||
[[Category: Schultz | [[Category: Pearson AD]] | ||
[[Category: Song | [[Category: Schultz PG]] | ||
[[Category: Stevens | [[Category: Song Y]] | ||
[[Category: Stevens RC]] | |||
Latest revision as of 21:00, 20 September 2023
Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutantBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutant
Structural highlights
FunctionPublication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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