Cryo-EM Structures of Alcohol Oxidase Isozymes Reveal Structural Determinants of Cofactor Variation and Enzymatic Activity in Ogataea methanolica.

Ogataea methanolica is a methylotrophic yeast that can produce diverse recombinant proteins using methanol as the sole carbon and energy source. Unlike most yeast species, which possess a single alcohol oxidase, O. methanolica encodes two isoenzymes, Mod1p and Mod2p. This study examines the structural and functional differences between Mod1p and Mod2p homooctamers. Both enzymes were purified from MOD-disrupted strains and analysed using cryogenic electron microscopy, achieving resolutions of 1.9 and 2.7 Å for Mod1p and Mod2p, respectively. The two isozymes assemble as tetramers of dimers stabilized by extensive intersubunit interactions, largely mediated by protruding loop regions and C-terminal extensions. Despite overall structural similarities, Mod1p and Mod2p exhibit subtle differences in surface charge distribution and sequence composition within the FAD-binding domain. These variations correlate with distinct cofactor preferences, with Mod1p binding arabityl FAD and Mod2p binding canonical FAD. Thin-section electron microscopy further revealed that Mod1p and Mod2p form both homomeric and hybrid octamers that assemble into peroxisomal crystalloids essential for methanol metabolism. Collectively, our findings provide mechanistic insight into alcohol oxidase diversity in methylotrophic yeasts, advancing our understanding of methanol utilization and its applications in biotechnology.