Researchers at Ehime University have uncovered the atomic-level structure of D-apionate oxidoisomerase (ApnO), a rare enzyme discovered in 2018 that defies conventional biochemical classification by catalyzing two distinct reactions within a single active site.
Traditionally, biochemists sort enzymes into strict categories using the Enzyme Commission number system, operating under the assumption that a single active site governs one type of chemical transformation. However, a small group of enzymes—including ApnO and ketol-acid reductoisomerase (KARI)—breaks this rule. Until now, the structural mechanisms allowing ApnO to manage dual chemistry remained unexamined.
Published in the Journal of Biological Chemistry, the new study utilized X-ray crystallography and the anomalous dispersion effect to resolve the three-dimensional atomic arrangement of ApnO. The analysis revealed that despite having no significant sequence homology with KARI, ApnO shares a closely resembling overall three-dimensional fold.
Inside its active site, ApnO features a hybrid metal arrangement. While one metal position maintains a canonical octahedral coordination geometry with a manganese ion—indicating a shared evolutionary origin with KARI—the second position binds zinc or manganese with a tetrahedral coordination geometry. This structural mosaic suggests that while one metal-binding site was inherited from a shared ancestor, the other evolved independently, demonstrating how evolutionary convergence enables novel dual-reaction capabilities.