9NH9

Crystal Structure of N-oxygenase HrmI with the diferric cofactor and the N(6)-hydroxy-L-lysine product bound

This is a non-PDB format compatible entry.

Summary for 9NH9

• Entry DOI: 10.2210/pdb9nh9/pdb
• Related: 9N1A 9N1E 9N1X 9N2A
• Descriptor: HrmI, FE (III) ION, N~6~-hydroxy-L-lysine, ... (5 entities in total)
• Functional Keywords: metalloenzyme, oxygenase, diiron, oxidoreductase
• Biological source: Streptomyces griseoflavus
• Total number of polymer chains: 1
• Total formula weight: 41480.07

Authors

Skirboll, S.S.,Phan, H.N.,Swartz, P.D.,Makris, T.M. (deposition date: 2025-02-24, release date: 2025-08-20, Last modification date: 2025-08-27)

Primary citation

Skirboll, S.S.,Gangopadhyay, M.,Phan, H.N.,Hartsell, J.,Mudireddy, A.,Hilovsky, D.,Swartz, P.D.,Liu, X.,Guo, Y.,Makris, T.M.
The Heme Oxygenase-Like Diiron Enzyme HrmI Reveals Altered Regulatory Mechanisms for Dioxygen Activation and Substrate N-Oxygenation.
J.Am.Chem.Soc., 147:30210-30221, 2025

PubMed Abstract: Nonheme diiron enzymes activate dioxygen (O) to affect various biochemical outcomes. HrmI, a member of the recently discovered and functionally versatile heme oxygenase-like dimetal oxidase/oxygenase (HDO) superfamily, catalyzes the N-oxygenation of L-Lysine to yield 6-nitronorleucine for the biosynthesis of the antibiotic hormaomycin. Unlike other characterized HDO N-oxygenases that have an additional carboxylate ligand thought to be key for regulating dioxygen activation and ensuing N-oxygenation, the predicted primary coordination sphere of HrmI resembles those of HDOs that instead perform C-C fragmentation of substrates. We show that diferrous HrmI reacts with O in a substrate-independent manner to form a presumptive μ-1,2 (Fe) peroxo (or ) intermediate common to the catalytic scheme of many HDOs. is rapidly converted to a second species with both optical and Mössbauer properties that resemble an activated peroxodiferric adduct (). The substrate-dependent acceleration of decay suggests that it, rather than , initiates l-Lysine metabolism. X-ray crystallographic studies of HrmI in several redox and ligand-bound states provide a stepwise view of structural changes during catalysis and, together with analytical approaches, capture a hydroxylamino metabolic intermediate en route to 6-nitronorleucine formation. The activation of peroxo species provides a key strategy that enables functional adaptation within the widely distributed HDO structural scaffold.

PubMed: 40774922
DOI: 10.1021/jacs.5c08814

Experimental method

X-RAY DIFFRACTION (1.96 Å)