The structural relationship between protein prenyltransferase β subunits and squalene-hopene cyclases. (a) The complete structure of squalene-hopene cyclase from the bacterium Alicyclobacillus acidocaldarius (Protein Data Bank (PDB) identifier 3SQC ). (b) Structural superposition of the conserved (α-α)6 barrels of squalene-hopene cyclase (blue) and the rat FT β subunit (cyan; see Figure 3 for the full structure of the FT). Blue spheres, functionally important residues in the half of the squalene-hopene cyclase that is shown (the sphere indicates the van der Waals radius); pink spheres, farnesyl-pyrophosphate and Zn2+ bound to the β subunit of FT; pink residues in stick representation, the Ca1a2X peptide of the substrate protein. (c) Alignment of the two proteins on the basis of the structural superposition. Secondary structural elements are colored as in (b); black residues with colored background represent α helix and white residues with colored background represent β sheet. Conserved residues and similar residues are shown below the alignment; 1, polar; 2, small; 3, aromatic; 4, hydrophobic. The lower-case letters represent residues within 3SQC that were not easily superimposed on the 1D8D structure (that is, gaps in 1D8D). The molecular representations were created using VMD .