Two Distinct Mechanisms for C–C Desaturation by Iron(II)- and 2‑(Oxo)glutarate-Dependent Oxygenases: Importance of α‑Heteroatom Assistance

• Published in: Journal of the American Chemical Society Vol. 140; no. 23; pp. 7116 - 7126
• Main Authors: Dunham, Noah P, Chang, Wei-chen, Mitchell, Andrew J, Martinie, Ryan J, Zhang, Bo, Bergman, Jonathan A, Rajakovich, Lauren J, Wang, Bo, Silakov, Alexey, Krebs, Carsten, Boal, Amie K, Bollinger, J. Martin
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 13.06.2018; American Chemical Society (ACS)
• Subjects: Binding Sites; Deuterium - chemistry; Homoarginine - chemistry; Hydroxylation; Iron - chemistry; Ketoglutaric Acids - chemistry; Kinetics; Mixed Function Oxygenases - chemistry; Models, Chemical; Oxidation-Reduction; Stereoisomerism
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.8b01933

Hydroxylation of aliphatic carbons by nonheme Fe­(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H•) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe­(III)-coordinated oxygen (termed rebound). Enzymes that use H•-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C–C desaturations, it has been proposed that a second HAT to the Fe­(III)–OH complex from the carbon α to the radical preempts rebound. Deuterium (2H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related l-arginine-modifying iron­(II)- and 2-(oxo)­glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the l-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H• first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors 1H or 2H. By contrast, an unexpected 3,4-desaturation of l-homoarginine (l-hArg) by VioC, the l-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors 2H. Anchimeric assistance by N6 permits removal of the C4–H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (≤3.5 Å) of both l-hArg carbons to the oxygen ligand in an X-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may make competing hydroxylation unavoidable, thus explaining the presence of α-heteroatoms in nearly all native substrates for Fe/2OG desaturases.