FIG 4.

Structures of MycB3-CofC in complex with GPPG (crystal structure) and educts (model). (A) Ribbon diagram of the crystal structure of CofC with its product GPPG. (B) Final electron density of GPPG (2F_oF_c at 1.5 σ) and H-bonds for GPPG binding. Side chains are only shown for residues contacting the ligand. (C) Electrostatic surface representation of the protein shows a negatively charged deep pocket for GPPG. Two Mg²⁺-ions allow binding of the charged phosphates of GPPG. The electrostatic surface potential was calculated using APBS. Red: negative charge; blue: positive charge. (D) Possible educt conformations. GTP could position its α- and β-phosphates where GPPG binds to the Mg²⁺-ions (left side). With 3-PG binding in the same mode as the 3-PG moiety of GPPG the β- and γ-phosphates of GTP have to rotate out of the binding pocket, though (right side). The phosphate moiety of 3-PG is well poised for nucleophilic attack on the α-phosphate of GTP via a trigonal bipyramidal transition state. Figures were produced with PyMOL. A window around R28 is transparent to show the potential H-bond of GTP to the amide nitrogen. Electrostatic surface representations were made using the APBS electrostatics plugin in PyMOL. Carbon: yellow, oxygen: red, nitrogen: blue, magnesium: magenta.