4s0j | pdb_00004s0j

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79S, and 123V mutant

spinqualitylabelsall models 4s0j, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4s0j is a 1 chain structure with sequence from Pyrococcus abyssi GE5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.1Å Ligands: BIF Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function SYT_PYRAB 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Aminoacyl tRNA synthetase 3D structures

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