title: Linear free energy relationships demonstrate a catalytic role for the flavin mononucleotide coenzyme of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
abstract: The type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the reversible isomerization of the two ubiquitous isoprene units, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are required to initiate the biosynthesis of all isoprenoid compounds found in nature. The overall chemical transformation catalyzed by IDI-2 involves a net 1,3-proton addition/elimination reaction. Surprisingly, IDI-2 requires a reduced flavin mononucleotide (FMN) coenzyme to carry out this redox neutral isomerization. The exact function of FMN in catalysis has not yet been clearly defined. To provide mechanistic insight into the role of the reduced flavin in IDI-2 catalysis, several FMN analogues with altered electronic properties were chemoenzymatically prepared, and their effects on the kinetic properties of the IDI-2 catalyzed reaction were investigated. Linear free energy relationships (LFERs) between the electronic properties of the flavin and the steady state kinetic parameters of the IDI-2 catalyzed reaction were observed. The LFER studies are complemented with kinetic isotope effect studies and kinetic characterization of an active site mutant enzyme (Q154N). Cumulatively, the data presented in this work (and in other studies) suggest that the reduced FMN coenzyme of IDI-2 functions as an acid/base catalyst, with the N5 atom of the flavin likely playing a critical role in the deprotonation of IPP en route to DMAPP formation. Several potential chemical mechanisms involving the reduced flavin as an acid/base catalyst are presented and discussed.
authors.affiliation: Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry and Biochemistry, and Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Thibodeaux
authors.forename: Wei-chen
authors.initials: WC
authors.lastname: Chang
authors.forename: Hung-wen
authors.initials: HW
authors.lastname: Liu
mesh_terms: D055162:Biocatalysis; D019748:Carbon-Carbon Double Bond Isomerases / Q000737:chemistry / Q000378:metabolism*; D004583:Electrons; D005486:Flavin Mononucleotide / Q000737:chemistry / Q000378:metabolism*; D045782:Hemiterpenes; D007700:Kinetics; D016014:Linear Models; D010084:Oxidation-Reduction; D013211:Staphylococcus aureus / Q000201:enzymology; D013816:Thermodynamics
chemical_list: D045782:Hemiterpenes; D005486:Flavin Mononucleotide; D019748:Carbon-Carbon Double Bond Isomerases; C021453:isopentenyldiphosphate delta-isomerase