Critical evaluation of three cryo-EM structures of particulate methane monooxygenase by quantum refinement.

Gayathri Yuvaraj, Kristoffer J M Lundgren, Elija Veenman, Esko Oksanen, Ulf Ryde

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Article in Acta crystallographica. Section D, Structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

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5 authors.

Gayathri YuvarajDepartment of Computational Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden.ORCID 0009-0001-8716-8505

Kristoffer J M LundgrenDepartment of Computational Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden.ORCID 0009-0002-2611-7883

Elija VeenmanDepartment of Computational Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden.

Esko OksanenDepartment of Computational Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden.ORCID 0000-0002-1841-4813

Ulf RydeDepartment of Computational Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden.ORCID 0000-0001-7653-8489

Funding

HORIZON EUROPE Marie Sklodowska-Curie Actions 101081419Vetenskapsrådet 2020-06176Vetenskapsrådet 2022-04978

6 · The paper itself

Abstract

Particulate methane monooxygenase (pMMO) is an enzyme that converts methane into methanol at ambient temperature and pressure. Over the past three decades, the metal content and location of the active site have been highly controversial. Recent single-particle cryogenic electron-microscopy (cryo-EM) structures have furthered this debate. In this study, three cryo-EM structures (PDB entries 7s4h, 7s4j and 7ev9) are analysed by quantum refinement (QR). This approach augments traditional structural refinement with quantum-mechanical (QM) calculations for a small but interesting part of the protein (in this case, the copper sites). Our results indicate that the bis-His (Cu

Indexed as

Cryoelectron MicroscopyOxygenasesCatalytic DomainCopperModels, MolecularProtein ConformationQuantum TheoryCoppermethane monooxygenaseOxygenasescoppercryogenic electron-microscopyparticulate methane monooxygenasequantum refinement

Identifiers

PMID41059946

DOI10.1107/S2059798325008356

PMCPMC12576850

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