6XCV

Crystal structure of apo SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697

Summary for 6XCV

• Entry DOI: 10.2210/pdb6xcv/pdb
• Descriptor: Cupin domain-containing diiron protein (2 entities in total)
• Functional Keywords: diiron, n-oxygenase, n-methyl-l-arginine, heme oxygenase, oxidoreductase
• Biological source: Streptomyces achromogenes subsp. streptozoticus
• Total number of polymer chains: 2
• Total formula weight: 112085.09

Authors

McBride, M.J.,Boal, A.K. (deposition date: 2020-06-09, release date: 2021-01-13, Last modification date: 2023-10-18)

Primary citation

McBride, M.J.,Pope, S.R.,Hu, K.,Okafor, C.D.,Balskus, E.P.,Bollinger Jr., J.M.,Boal, A.K.
Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N -nitrosourea-producing enzyme SznF.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: In biosynthesis of the pancreatic cancer drug streptozotocin, the tridomain nonheme-iron oxygenase SznF hydroxylates and ' of -methyl-l-arginine before oxidatively rearranging the triply modified guanidine to the -methyl--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 hydroxylating heme-oxygenase-like (HO-like) central domain. We leveraged our recent observation that the -oxygenating µ-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-reactive Fe(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 -oxygenating HDO but not in two HDOs that cleave carbon-hydrogen and carbon-carbon bonds to install olefins. Among ∼9,600 sequences identified bioinformatically as members of the emerging HDO superfamily, ∼25% conserve this additional carboxylate residue and are thus tentatively assigned as -oxygenases.

PubMed: 33468680
DOI: 10.1073/pnas.2015931118

Experimental method

X-RAY DIFFRACTION (1.77 Å)