Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15

Pyridoxal phosphate-dependent enzymes able to use oxygenas a co-substratehave emerged in multiple protein families. Here, we use crystallographyto solve the 2.40 & ANGS; resolution crystal structure of Cap15, anucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylationof glycyl uridine. Our structural study captures the internal aldimine,pinpointing the active site lysine as K230 and showing the site ofphosphate binding. Our docking studies reveal how Cap15 is able tocatalyze a stereoselective deprotonation reaction, and bioinformaticanalysis reveals active site residues that distinguish Cap15 fromthe structurally related d-glucosaminate-6-phosphate ammonialyase and l-seryl-tRNA(Sec) selenium transferase (SelA).Our work provides the structural basis for further mechanistic investigationof a unique biosynthetic enzyme and provides a blueprint for understandinghow oxygen reactivity emerged in the SelA-like protein family.