6DAX

X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate

Summary for 6DAX

• Entry DOI: 10.2210/pdb6dax/pdb
• Descriptor: Alpha-ketoglutarate-dependent L-arginine hydroxylase, 2-OXOGLUTARIC ACID, L-HOMOARGININE, ... (5 entities in total)
• Functional Keywords: desaturase, hydroxylase, oxygenase, metalloenzyme, desaturation, hydroxylation, viomycin, oxidoreductase
• Biological source: Streptomyces vinaceus
• Total number of polymer chains: 1
• Total formula weight: 37883.24

Authors

Dunham, N.P.,Mitchell, A.J.,Boal, A.K. (deposition date: 2018-05-02, release date: 2018-05-16, Last modification date: 2024-03-13)

Primary citation

Dunham, N.P.,Chang, W.C.,Mitchell, A.J.,Martinie, R.J.,Zhang, B.,Bergman, J.A.,Rajakovich, L.J.,Wang, B.,Silakov, A.,Krebs, C.,Boal, A.K.,Bollinger, J.M.
Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance.
J. Am. Chem. Soc., 140:7116-7126, 2018

PubMed Abstract: 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 (H) 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 H or H. 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 H. 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.

PubMed: 29708749
DOI: 10.1021/jacs.8b01933

Experimental method

X-RAY DIFFRACTION (1.7 Å)