PMC

Ligands modeled in the disordered active site of Y71F TPL. A stereo view with the “relaxed” (yellow) and “tense” (gray) quinonoid molecules superimposed with the corresponding σ_A-weighted |F_o| – |F_c| omit electron density maps contoured at 3.0σ.

Stereo view of the closed active site of the wild-type TPL with bound PNO. The σ_A-weighted |F_o| – |F_c| omit electron density maps are contoured at 3.0σ. Residues are colored as in Figure . Hydrogen bonds are denoted by dashed lines. The alanine quinonoid, the phosphate anion, and the Wat2 solvent molecule were modeled with 0.5 occupancy.

Protein–substrate interactions during the three intermediate steps of the Cβ–Cγ bond cleavage observed in crystal structures. Hydrogen bonds are shown as dashed lines. A short van der Waals contact between the side chain of Phe448 and the substrate phenolic group is denoted by a hashed line. Label colors correspond to residue colors in Figure .

(a) Geometry of a 3-F-Tyr quinonoid molecule in the “tense” conformation observed in the closed active sites of F448H and Y71F TPL. (b) A stereo view of a 3-F-l-Tyr quinonoid in a closed active site of F448H refined using the standard (yellow) and relaxed (gray) geometrical restraints. The undistorted quinonoid geometry (thin black lines) is shown for comparison. The σ_A-weighted |F_o| – |F_c| omit electron density map is shown at 3.0σ.

Quinonoid intermediates of the Cβ–Cγ bond cleavage trapped in crystal structures (stereo views). The σ_A-weighted |F_o| – |F_c| omit electron density maps contoured at 3.0σ are in blue. Residues from the large domain are colored in orange, those from the small domain are in pink, and residues from the adjacent subunit are depicted in blue and labeled with an asterisk. Hydrogen bonds are denoted by dashed lines. (a) Open active site (B) of Y71F TPL with the “relaxed” 3-F-Tyr quinonoid. (b) One of the four closed active sites of F448H TPL with the “tense” 3-F-Tyr quinonoid. (c) The disordered active site (A) of Y71F TPL occupied mostly by the “tense” (gray; 0.67 occupancy) and partially by the “relaxed” 3-F-Tyr quinonoid (yellow; 0.33 occupancy). Only the closed active-site conformation could be modeled; a green hashed cylinder indicates a close contact between Phe448 and the “tense” quinonoid.