Fig. 3
a Protein homology modeling of COQ1 (YBR003W) was performed using ModBase [159] and was viewed using Swiss PDB Viewer [160]. The template for modeling was based on the medium/long-chain length prenyl pyrophosphate synthase of Arabidopsis thaliana (3aq0A) with 42% sequence identity. Helix D and Helix H bind to the elongating isoprene chain and IPP, respectively, at the conserved DDXXD regions. Helix F contains Met-244 and Helix E contains Ser-231, which are thought to be the residues that regulate chain length elongation. The right figure represents the 180° view of that on the left and is superimposed with the structure of CoQ10. b Multiple sequence alignment of Q9X1M1_THEMA (T. maritime TM_1535), ISPB_ECOLI (E. coli IspB), COQ1_SCEREVISIAE (S. cerevisiae COQ1), DPS1_SPOMBE (S. pombe Dps1) and DPS1_HSAPIENS (Human PDSS1) using CLUSTAL W [161]. Helices D (grey), E (green), F (blue), and H (white) indicated in (a), are boxed in (b). Orange underline marks the DDXXD motif. Red asterisks indicate the positions of S. cerevisiae COQ1 Met-244, Ser-247 and Ser-231 residues. Met-244 corresponds to Leu-188 and Leu-231, and Ser-247 to Val-191 and Val-234 of S. pombe Dps1 and H. sapiens PDSS1, respectively. Labels of helices are marked with the same colors as those used for the helices in a