Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N-nitrosourea-producing enzyme SznF

In biosynthesis of the pancreatic cancer drug streptozotocin, the tridomain nonheme-iron oxygenase SznF hydroxylates N-delta and N-omega of N-omega-methyl-L-arginine before oxidatively rearranging the triply modified guanidine to the N-methyl-N-nitrosourea pharmacophore. A previously published structure visualized the monoiron cofactor in the enzyme's C-terminal cupin domain, which promotes the final rearrangement, but exhibited disorder and minimal metal occupancy in the site of the proposed diiron cofactor in the N-hydroxylating hemeoxygenase-like (HO-like) central domain. We leveraged our recent observation that the N-oxygenating mu-peroxodiiron (III/III) intermediate can form in the HO-like domain after the apo protein self-assembles its diiron (II/II) cofactor to solve structures of SznF with both of its iron cofactors bound. These structures of a biochemically validated member of the emerging heme-oxygenase-like diiron oxidase and oxygenase (HDO) superfamily with intact diiron cofactor reveal both the large-scale conformational change required to assemble the O-2-reactive Fe-2 (II/II) complex and the structural basis for cofactor instability-a trait shared by the other validated HDOs. During cofactor (dis)assembly, a ligand-harboring core helix dynamically (un)folds. The diiron cofactor also coordinates an unanticipated Glu ligand contributed by an auxiliary helix implicated in substrate binding by docking and molecular dynamics simulations. The additional carboxylate ligand is conserved in another N-oxygenating HDO but not in two HDOs that cleave carbon-hydrogen and carbon-carbon bonds to install olefins. Among similar to 9,600 sequences identified bioinformatically as members of the emerging HDO superfamily, similar to 25% conserve this additional carboxylate residue and are thus tentatively assigned as N-oxygenases.

Automated summary

The study identified the crucial role of SznF in the biosynthesis of streptozotocin, revealing the binding of two iron cofactors and addressing previous uncertainties about the cofactors. During the cofactor (dis)assembly process, dynamic changes in the core helix were observed, and an unexpected glutamate ligand was found to be involved.