9OR1

N-hydroxylamine dehydratase (NohD) H2F/F4P/P5S/R6Y/A59N/R144Y/V96A/D172E/L172Q/D173P/R176V (P1/P2/A1/A2/A3) mutant crystal structure with heme and N-hydroxylated ornithine

Summary for 9OR1

• Entry DOI: 10.2210/pdb9or1/pdb
• Descriptor: N-hydroxylamine dehydratase (NohD), PROTOPORPHYRIN IX CONTAINING FE, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (5 entities in total)
• Functional Keywords: dehydratase, piperazate synthase, heme, n-n bond, hydroxylamine, biosynthetic protein
• Biological source: Actinomadura luzonensis
• Total number of polymer chains: 1
• Total formula weight: 23453.06

Authors

Higgins, M.A.,Shi, X.,Hoffarth, E.R.,Du, Y.L.,Ryan, K.S. (deposition date: 2025-05-21, release date: 2025-12-03)

Primary citation

Higgins, M.A.,Mirotadze, N.,Shi, X.,Hoffarth, E.R.,Du, Y.L.,Ryan, K.S.
Conversion of a Heme-Dependent Dehydratase to a Piperazate Synthase Reveals the Role of the Heme Propionate Group in N-N Bond-Formation.
J.Am.Chem.Soc., 147:39160-39168, 2025

PubMed Abstract: Enzymes that form nitrogen-nitrogen bonds are employed in natural product biosynthesis and the nitrogen cycle. Piperazate synthase forms the cyclic hydrazine l-piperazic acid from l--OH-ornithine, using heme as a cofactor. In this work, we discover sequence-related enzyme NohD that instead reacts with l--OH-ornithine to release ammonia, and we solve its structure to 1.4 Å resolution. We then employ structure-guided site-directed mutagenesis to endow variants of NohD with piperazate synthase activity. Crystal structures of the NohD variants reveal how the heme propionate changes conformation, positioning it upward toward the amino nitrogen, where it is likely to activate the amine for N-N bond-formation. This study highlights a key structural requirement for N-N bond-formation and sets the stage for the development of new N-N-bond-forming catalysts.

PubMed: 41101755
DOI: 10.1021/jacs.5c08886

Experimental method

X-RAY DIFFRACTION (1.5 Å)