Summary
CLYBL encodes a ubiquitously expressed mitochondrial enzyme, conserved
across all vertebrates, whose cellular activity and pathway assignment are
unknown. Its homozygous loss is tolerated in seemingly healthy individuals, with
reduced circulating B12 levels being the only and consistent
phenotype reported to date. Here, by combining enzymology, structural biology
and activity-based metabolomics we report that CLYBL operates as a
citramalyl-CoA lyase in mammalian cells. Cells lacking CLYBL accumulate
citramalyl-CoA, an intermediate in the C5-dicarboxylate metabolic pathway that
includes itaconate, a recently identified human antimicrobial metabolite and
immunomodulator. We report that CLYBL loss leads to a cell autonomous defect in
the mitochondrial B12 metabolism and that itaconyl-CoA is a
cofactor-inactivating, substrate-analogue inhibitor of the mitochondrial
B12-dependent methylmalonyl-CoA mutase (MUT). Our work de-orphans
the function of human CLYBL and reveals that a consequence of exposure to the
immunomodulatory metabolite itaconate is B12 inactivation.