The 2.5-Å resolution crystal structure of recombinant aristolochene synthase from the blue cheese mold, Penicillium roqueforti, is the first of a fungal terpenoid cyclase. The structure of the enzyme reveals active site features that participate in the cyclization of the universal sesquiterpene cyclase substrate, farnesyl diphosphate, to form the bicyclic hydrocarbon aristolochene. Metal-triggered carbocation formation initiates the cyclization cascade, which proceeds through multiple complex intermediates to yield one exclusive structural and stereochemical isomer of aristolochene. Structural homology of this fungal cyclase with plant and bacterial terpenoid cyclases, despite minimal amino acid sequence identity, suggests divergence from a common, primordial ancestor in the evolution of terpene biosynthesis.Aristolochene synthase is a terpenoid cyclase from the blue cheese mold, Penicillium roqueforti, that catalyzes the metal-dependent cyclization of farnesyl diphosphate to form the bicyclic hydrocarbon aristolochene (Fig. 1) (1). Farnesyl diphosphate is the universal precursor of myriad cyclic sesquiterpenes, so each sesquiterpene cyclase plays a critical role in governing the structural and stereochemical outcome of its particular cyclization reaction. Accordingly, sesquiterpene cyclase reactions maximize product diversity starting from a minimal substrate pool, indeed, a single substrate, and the structural basis of this catalytic diversity comprises a growing question at the interface of chemistry and biology.Aristolochene synthase is a 38-kDa monomeric sesquiterpene cyclase that has been cloned (2) and overexpressed (3) in Escherichia coli. Numerous enzymological studies of P. roqueforti and Aspergillus terreus aristolochene synthases using stereospecifically labeled substrates (4 -6), a mechanism-based inhibitor (7), and the anomalous substrate (7R)-6,7-dihydrofarnesyldiphosphate (8) indicate a complex cyclization cascade proceeding through at least two discrete intermediates. Aristolochene formation is the first committed step in the biosynthesis of a large group of sesquiterpenoid fungal toxins, the most lethal of which is the novel bis-epoxide PR-toxin (4). Interestingly, the (ϩ)-enantiomer of aristolochene is generated by the fungi P. roqueforti and A. terreus, but the (Ϫ)-enantiomer is generated by the plants Aristolochia indica (9) and Bixa orella (10). Accordingly, each aristolochene synthase must provide a different template for binding the flexible polyisoprenoid substrate and subsequent intermediates in productive conformations leading to correct stereoisomer formation.The diastereomeric sesquiterpene epi-aristolochene (4-epieremophila-9,11-diene) has been identified in tobacco (Nicotiana tabacum) (11-13) and results from the cyclization of farnesyl diphosphate by epi-aristolochene synthase (Fig. 1) (14). This enzyme catalyzes the cyclization of farnesyl diphosphate by a mechanism similar in some respects to that of P. roqueforti aristolochene synthase despite only 16% amino acid sequence ident...