Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation

Abstract

Isoprenyl diphosphate synthases (IDSs) catalyze condensation reactions of isoprene units to produce isoprenoids or terpenoids, the largest class of natural products on earth. IDSs are divided into trans-and cis-IDS superfamilies depending on the configuration of the resulting carbon−carbon double bonds. Compared with trans-IDSs, cis-IDS family members exhibit more variable active site structure and versatile function. The archetypal cis-IDSs are homodimers and produce linear isoprenoids via headto-tail condensation. Recently, heterodimeric cis-IDSs containing a noncatalytic subunit that also belongs to the cis-IDS superfamily have been identified. Moreover, several cis-IDS-fold members have been found to produce nonlinear isoprenoids via "head-to-middle" condensation. In this Review, we summarize the structural features and catalytic mechanism of the versatile cis-IDS superfamily. This information provides important guidance for research regarding biosynthesis of important natural products and medical intermediates, cellular metabolism, and disease control.

Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex

“…2a , Supplementary Fig. 1 ), in contrast to the seven α-helices and six β-strands found in the other cis -prenyltransferases 2 , 4 . Moreover, NgBR and its yeast homology, Nus1, do not share high structural similarity (RMSD = 1.33 Å), with the α3 of NgBR occupying the position of the antiparallel βC–βC’ in Nus1 (Supplementary Fig.…”

“…3b , Supplementary Figs. 4 and 6 , Supplementary Data 1 ) 2 , 4 . In accordance with the key role of D34 and the spatial restraints of Mg 2+ coordination, both the size and charge of aspartate at this position are crucial for catalysis, as substitution to A, E, or N resulted in ~5–20-fold reduction in catalytic activity (1.32 ± 0.09, 0.35 ± 0.07, 0.10 ± 0.01, and 0.08 ± 0.01 μmol/h/mg protein for WT, D34A, D34E, and D34N, respectively; n = 5–7, P < 0.001 for each mutant) (Fig.…”

“…Prenyltransferases are essential enzymes that synthesize isoprenoids, an enormous group of chemically diverse compounds participating in a myriad of cellular processes in all living cells 1 . With chain lengths varying from C 10 (geranyl diphosphate) to >C 10,000 (natural rubber), isoprenoids are synthesized by chain elongation of an allylic diphosphate primer via a variable number of condensation reactions with isopentenyl pyrophosphate (IPP, C 5 ) 2 – 4 . Prenyltransferases are classified as cis -prenyltransferase or trans -prenyltransferase according to the double bonds they form during the condensation reaction 3 .…”

“…Cis -prenyltransferases are further classified according to their product chain length into short-chain (C 15 ), medium-chain (C 50–55 ), long-chain (C 70–120 ), and rubber synthases 1 . Importantly, while short- and medium-chain cis -prenyltransferase complexes are homodimeric, long-chain cis -prenyltransferases and rubber synthases are formed by a heteromeric subunit assembly of unknown stoichiometry 1 , 4 , 5 . To date, only homodimeric enzymes were structurally characterized 6 – 9 .…”

“…Despite an immense body of work focusing on the biochemical and structural properties of cis -prenyltransferases, our mechanistic understanding of these enzymes arises mainly from investigations of homodimeric prokaryotic, plant, and fungal orthologs 2 , 4 . Thus, in contrast with the growing clinical relevance of h cis -PT, the basic mechanisms underlying its heteromeric assembly, intersubunit communication, and long-chain isoprenoid synthesis remain poorly understood.…”