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TitleSimultaneous occupancy of Cu and Cu in the ammonia monooxygenase active site.
Journal, issue, pagesChem Sci, Year 2025
Publish dateDec 18, 2025
AuthorsFrank J Tucci / Madeline B Ho / Aaron A B Turner / Lisa Y Stein / Brian M Hoffman / Amy C Rosenzweig /
PubMed AbstractAmmonia monooxygenase (AMO), a copper-dependent membrane enzyme, catalyzes the first and rate-limiting step of nitrification: the oxidation of ammonia to hydroxylamine. Despite its central role in ...Ammonia monooxygenase (AMO), a copper-dependent membrane enzyme, catalyzes the first and rate-limiting step of nitrification: the oxidation of ammonia to hydroxylamine. Despite its central role in the global nitrogen cycle and its biotechnological relevance, structural characterization of AMO has lagged behind that of its homolog, particulate methane monooxygenase (pMMO), due to the slow growth rates of ammonia-oxidizing bacteria and the instability of AMO upon purification. Recent cryoEM studies of AMO and (Bath) pMMO in native membranes revealed new structural features, including two adjacent copper-binding sites in the transmembrane region, Cu and Cu, believed to constitute the active site. Although multiple structures were determined under various conditions, simultaneous occupancy of Cu and Cu was never observed, leaving their potential functional interplay unresolved. Here we report the 2.6 Å resolution cryoEM structure of AMO from C-128 in isolated native membranes. This structure reveals the first instance of simultaneous copper occupancy of the Cu and Cu sites, along with occupancy of the periplasmic Cu site. Electron paramagnetic resonance (EPR) spectroscopic data indicate that the Cu site is primarily occupied by Cu(ii), while Cu and Cu are primarily occupied by diamagnetic ions, presumably Cu(i). Notably, a lipid molecule is bound between the Cu and Cu sites, separating them by ∼8.0 Å. The results underscore the importance of studying these enzymes in their native environments across species to resolve conserved and divergent molecular features.
External linksChem Sci / PubMed:41541579 / PubMed Central
MethodsEM (single particle)
Resolution2.58 Å
Structure data

71966

9pxf

EMDB-71966, PDB-9pxf:
Ammonia monooxygenase in native membranes from N. briensis
Method: EM (single particle) / Resolution: 2.58 Å

Chemicals

ChemComp-CU:
COPPER (II) ION

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

ChemComp-HOH:
WATER

Source
  • nitrosospira briensis (bacteria)
KeywordsOXIDOREDUCTASE / ammonia oxidation / copper enzyme / membrane protein / active site

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