Cyclization of GPP as catalyzed by BPPS; note that the same diphosphate oxygen (red) is contained in the prenyl phosphoester linkages of GPP and BPP. Aza analogues of substrate and carbocation intermediates are shown in boxes.

Simulated annealing omit electron density maps of BPPS complexes contoured at 4σ; all inhibitor atoms and Mg²⁺ ions were omitted from structure factor calculations. Carbon, black (ligand) or gray (protein); oxygen, red; nitrogen, blue; phosphorus, magenta; Mg²⁺ ions, green; water molecules, orange. Metal coordination interactions are indicated by solid black lines and hydrogen bond interactions are indicated by dashed black lines. (A) Inorganic pyrophosphate (PP_i). In addition to interactions described in the text, E429 from helix F accepts hydrogen bonds from magnesium-bound water molecules. An ordered buffer molecule (bis-Tris) occupies the active site. (B) 3-Aza-2,3-dihydrogeranyl diphosphate (1). Two water molecules, #110 and #111, bind in the active site cavity along with the inhibitor. (C) BPP. Note that water #110 remains trapped in the active site along with the cyclization product.

GPP cyclization pathway in the active site of BPPS, represented by its solvent-accessible surface area. Note that water #110 comprises an integral part of the active site template. The modeling of GPP (A) is based on the binding conformation of inhibitor 1, which may not be a faithful representation of the native substrate. GPP can also bind in a more compact conformer that requires less rearrangement to form the (3R)-LPP (B and C).

(A) Stereoplot of the native BPPS monomer; the viewer is looking into the active site in the C-terminal domain (blue); helical segments are designated by the convention used for farnesyl diphosphate synthase (11). The aspartate-rich motif is red, and the second metal-binding motif starting at D496 is orange. The N-terminal domain is green. Disordered segments (E50–A63, E228–I233, T500–D509, and G579–S583) are indicated by dotted lines. (B) Stereoplot of the BPPS monomer complexed with PP_i (black); orientation is the same as in A. The diphosphate group of GPP similarly triggers conformational changes that order three polypeptide segments to cap the active site: most of the N terminus (I54–A63), the C-terminal portion of helix H and the H-α1 loop (T500–D509), and a portion of the J–K loop (G579–S583). (C) Structure of the BPPS dimer; the left-hand monomer is oriented ≈90° down from the orientation shown in A. The dimer interface is formed by the C terminus of helix A, and helices D1, D2, and E (1,167 Ų surface area per monomer is excluded from solvent).

BPPS–diphosphate recognition is mediated by metal coordination and hydrogen bond interactions. The binding positions and conformations of the diphosphate group, as PP_i (yellow), the prenyl diphosphate ester of 1, or the PP_i counterion to the carbocation intermediate analogues 2 and 3, are identical (for clarity, only the 3 PP_i complex is indicated in magenta). The binding position of the product diphosphate group is slightly different (blue), but all intermolecular interactions of the diphosphate group are conserved.