Figure 1.
Lysine, pyrrolysine and analogs used in this study.
Figure 2.
Cartoon representation of the overall structure of the catalytic domain of PylRS.
(A) Type-II tRNA-synthetase folding topology of the tRNA synthetase domain from PylRS, shown as cartoon representation, overlaid with its semi-transparent surface. The adenylated Kbu is highlighted as green stick model in the active site. (B-F) Zoom in the active site: PylRS in complex with Kalk (orange), Kbu (green), Kcr (blue) and Kpr (red), drawn as stick models. (r. m. s. d ∼0.35 Å). All four non-natural amino acids bind in the same position.
Figure 3.
Simulated annealing-omit Fo-DFc electron density contoured at 2 σ of PylRS in complex with (A) Kalk (orange), (B) Kbu (green), (C) Kcr (blue) and (D) Kpr (red).
The protein is shown as cartoon, overlaid with its semi-transparent surface representation. Amino acids providing key interactions are drawn as sticks, hydrogen-bonds as dashed lines.
Table 1.
Data collection, processing and structure refinement statistics.
Figure 4.
Comparison of the binding pockets of PylRS and LysRS.
Two-dimensional plot [52] of residues interacting with Lys (A), Pyl (B) and Kalk (C). Van-der-Waals contacts are shown as red half-spheres. Surface representation of the binding pockets of LysRS (D) and PylRS (E) with Lys, Pyl and Kalk, respectively. (F) Superposition of Pyl (grey), Kalk (orange), Kbu (green), Kcr (blue) and Kpr (red). The surface of the binding pocket is shown as mesh, with the charge distribution indicated by coloring (red = negative, blue = positive). The surrounding residues are drawn as sticks. (PDB codes PylRS: 2Q7H and LysRS: 3A74).