Structural factors governing alkane substrate specificity in the alkane monooxygenase (AlkB) family

Alkane monooxygenase (AlkB) is a family of integral membrane non-heme diiron enzymes that catalyzes the initial step in the oxidation of alkanes by numerous microorganisms. It plays a key role in the global carbon cycle, but the scope of this role is unknown. The AlkB family is thought to catalyze the oxidize alkanes from pentane to C₄₄H₉₀; implicit in this assertion is the idea that an individual AlkB only catalyzes the oxidization of a relatively narrow range of substrates. The structural basis of this discrimination is unclear. In this paper, eight AlkBs for which we possess reliable biochemical information about their substrate ranges were selected and AlphaFold3 was used to predict their three-dimensional structure. Several different cavity-determining programs were used to identify and measure the substrate channel in these predicted structures. Correlations between substrate selectivity and structure were made. Combining information available from different sources enables new hypotheses about the factors that control substrate selectivity in this important family of metalloenzymes to be made.