No Bridge Between Us: Two Distant Iron Ions Comprise the Active Site of Alkane Monooxygenase (AlkB)

Abstract

Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes the oxidation of liquid alkanes in the environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) data make visible numerous attributes of the enzyme that had previously been the source of speculation. The structure of the diiron active site is unusual: a histidine-rich center that binds two iron ions without a bridging ligand. This finding makes it difficult to understand how the iron ions coordinate oxidation state changes to achieve the high-valent conditions presumed necessary to activate strong C-H bonds. To ensure that potential photoreduction and radiation damage are not responsible for the absence of a bridging ligand in the resting state cryo-EM structures, spectroscopic methods are needed. We present the results of extended x-ray absorption fine structure (EXAFS) experiments collected under conditions where photodamage was avoided. Careful data analysis reveals an active site structure consistent with the cryo-EM structures in which the two iron ions are ligated by nine histidines and are separated by at least 5 Å. The EXAFS data were used to inform structural models for molecular dynamics (MD) simulations. The MD simulations corroborate EXAFS observations that neither of the two key carboxylate-containing residues (E281 and D190) are likely candidates for metal ion bridging. To further explore the role of these carboxylate residues, we used mutagenesis experiments, spectroscopy, and additional MD simulations to understand the role of these residues. A variant in which a carboxylate containing residue (E281) was changed to a methyl residue (E281A) showed little change in pre-edge features, consistent with the observation that it is not essential for activity and hence unlikely to serve as a bridging ligand at any point in the catalytic cycle. D190 variants had substantially diminished activity, suggesting an important role in catalysis not yet fully understood.