Capture of long-missing heme oxygenases that degrade both heme b and heme c

Heme serves as a crucial cofactor for hemoproteins and as an iron reservoir; yet, its accumulation is toxic, necessitating efficient degradation pathways. While the catabolism of free heme b is well characterized, the enzymes that disrupt its counterpart covalently tethered to a peptide (heme c) have remained elusive. Here, through a pipeline of multiple in silico analyses, we predict a distinct Core-only type of heme oxygenases (HOs) within the HugZ superfamily to have the potential to degrade both heme b and peptide-tethered heme c. Biochemical and physiological characterization confirms that representative Core-only-type HOs confer balanced dual-substrate specificity. In contrast, the C-extension and N-fusion-type HOs degrade heme b, but not heme c, because the entry of heme c into the active pocket is blocked by their extra domains. Moreover, we show that the degradation of heme c by the Core-only-type HOs requires proteolytic digestion of heme c-carrying proteins by a protease such as DegQ, which occurs in the periplasm. Overall, this work provides an integrated evolutionary, structural, biochemical, and physiological framework that defines a novel strategy for heme recycling and adaptive metabolic flexibility in bacteria.