4S02

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

Summary for 4S02

• Entry DOI: 10.2210/pdb4s02/pdb
• Related: 1y2q
• Descriptor: Threonine--tRNA ligase, DI(HYDROXYETHYL)ETHER (3 entities in total)
• Functional Keywords: beta-alpha-beta fold, editing domain, trna-synthetase, ligase, biphenylalanine and unnatural amino acid, threonine-trna ligase
• Biological source: Pyrococcus abyssi GE5
• Cellular location: Cytoplasm : Q9UZ14
• Total number of polymer chains: 1
• Total formula weight: 17751.37

Authors

Pearson, A.D.,Mills, J.H.,Song, Y.,Nasertorabi, F.,Han, G.W.,Baker, D.,Stevens, R.C.,Schultz, P.G. (deposition date: 2014-12-30, release date: 2015-03-18, Last modification date: 2023-09-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.95 Å)