{
  "abstract": "Complete ammonia oxidizers (comammox) are widespread nitrifiers that can dominate ammonia oxidation in diverse environments by efficiently converting ammonia to nitrate within a single cell, yet the molecular basis distinguishing their ammonia monooxygenase (AMO) from those of canonical bacterial AMO remains unresolved. Here we report cryo-electron microscopy (cryo-EM) structures of AMO from the comammox Nitrospira inopinata (NiAMO) in inhibitor-free and allylthiourea (ATU)-bound states at 2.47 and 2.68 angstrom, respectively. NiAMO displays distinctive auxiliary-subunit organization, copper-site configuration and hydrophobic-channel architecture. Integrative molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations support a methyl-plastoquinol (methyl-PQH2)-coupled, CuD-centric catalytic model, with CuC potentially facilitating quinone redox cycling. N. inopinata exhibited broad susceptibility to several known nitrification inhibitors, and ATU-bound NiAMO structure localized the inhibitor to the CuC-CuD region, accompanied by constriction of the hydrophobic channel, which is consistent with the competitive role of ATU demonstrated in recovery assays. Multi-omics analyses further revealed an energy-limited stress response to ATU, including induction of urea transport and utilization systems. Collectively, these findings define a methyl-PQ-linked catalytic and inhibitor-responsive architecture of comammox AMO and establish a mechanistic framework for lineage-aware management of nitrification in natural and engineered ecosystems.",
  "abstract_shown": true,
  "affiliations": [
    "Southern university of science and technology"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "name": "T.-Q. Mao"
    },
    {
      "name": "X. Yang"
    },
    {
      "name": "Z.-C. He"
    },
    {
      "name": "J. Yang"
    },
    {
      "name": "R. Wu"
    },
    {
      "name": "K. M. Y. Leung"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Li"
    },
    {
      "name": "P. Han"
    },
    {
      "name": "W. Peng"
    },
    {
      "affs": [
        0
      ],
      "name": "Z. Li"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6nf8tfy45exh3.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.02.748776",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.02.748776v1.full",
  "id": "6nf8tfy45exh3",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.02.748776v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "2310|Wastewater Treatment and Nitrogen Removal"
    ]
  ],
  "openalex": "W7210287307",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.02.748776v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6nf8tfy45exh3.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:40Z",
      "native_id": "10.64898/2026.09.02.748776",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.02.748776v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "Catalytic and inhibitory architecture of comammox ammonia monooxygenase",
  "title_text": "Catalytic and inhibitory architecture of comammox ammonia monooxygenase",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:40Z",
  "url": "https://research.draconitic.com/paper/6nf8tfy45exh3",
  "venue": "bioRxiv",
  "versions": []
}