4S02

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant

4S02 の概要

• エントリーDOI: 10.2210/pdb4s02/pdb
• 関連するPDBエントリー: 1y2q
• 分子名称: Threonine--tRNA ligase, DI(HYDROXYETHYL)ETHER (3 entities in total)
• 機能のキーワード: beta-alpha-beta fold, editing domain, trna-synthetase, ligase, biphenylalanine and unnatural amino acid, threonine-trna ligase
• 由来する生物種: Pyrococcus abyssi GE5
• 細胞内の位置: Cytoplasm : Q9UZ14
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 17751.37

構造登録者

Pearson, A.D.,Mills, J.H.,Song, Y.,Nasertorabi, F.,Han, G.W.,Baker, D.,Stevens, R.C.,Schultz, P.G. (登録日: 2014-12-30, 公開日: 2015-03-18, 最終更新日: 2023-09-20)

主引用文献

Pearson, A.D.,Mills, J.H.,Song, Y.,Nasertorabi, F.,Han, G.W.,Baker, D.,Stevens, R.C.,Schultz, P.G.
Transition states. Trapping a transition state in a computationally designed protein bottle.
Science, 347:863-867, 2015

PubMed Abstract: 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.

PubMed: 25700516
DOI: 10.1126/science.aaa2424

実験手法

X-RAY DIFFRACTION (1.95 Å)