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Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus

2024-04Artigo científico Acesso aberto
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dc.contributor.authorPomowski, Anja
dc.contributor.authorDell’Acqua, Simone
dc.contributor.authorWüst, Anja
dc.contributor.authorPauleta, Sofia R.
dc.contributor.authorMoura, Isabel
dc.contributor.authorEinsle, Oliver
dc.contributor.institutionDQ - Departamento de Química
dc.contributor.institutionUCIBIO - Applied Molecular Biosciences Unit
dc.contributor.institutionLAQV@REQUIMTE
dc.contributor.pblSpringer
dc.date.accessioned2024-06-27T22:24:04Z
dc.date.available2024-06-27T22:24:04Z
dc.date.issued2024-04
dc.descriptionFunding Information: This work was supported by the Deutsche Forschungsgemeinschaft (RTG 1976, Project No. 235777276, and PP 1927, Project No. 311061829 to O.E.) and the European Research Council (Grant No. 310656 to O.E.). The authors thank Lin Zhang for the helpful discussions. Funding Information: Open Access funding enabled and organized by Projekt DEAL. This work was funded by European Molecular Biology Organization, ASTF 282.00-2010, Deutsche Forschungsgemeinschaft, PP 1927, Project No. 311061829, RTG 1976, Project No. 235777276, FP7 Publisher Copyright: © The Author(s) 2024.
dc.description.abstractCopper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N2O to yield N2. It contains two metal centers, the binuclear electron transfer site CuA, and the unique, tetranuclear CuZ center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N2OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The CuA site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the CuZ cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca2+, K+, and Cl–. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] CuZ site, a mechanistic model is presented, with a structurally flexible CuZ center that does not require the complete dissociation of a sulfide prior to N2O binding. Graphical Abstract: The [4Cu:2S] CuZ site in M. nauticus N 2O reductase. The electron density map shown is contoured at the 5 σ level, highlighting the presence of two sulfide ligands. 705x677mm (72 x 72 DPI) (Figure presented.)en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent12
dc.format.extent4278805
dc.identifier.doi10.1007/s00775-024-02056-y
dc.identifier.issn0949-8257
dc.identifier.otherPURE: 91795484
dc.identifier.otherPURE UUID: f270159a-cee7-4119-a03b-5fcb41917d70
dc.identifier.otherScopus: 85192532192
dc.identifier.otherWOS: 001216086300001
dc.identifier.otherPubMed: 38720157
dc.identifier.otherORCID: /0000-0002-2149-9416/work/185101158
dc.identifier.urihttp://hdl.handle.net/10362/169152
dc.identifier.urlhttps://www.scopus.com/pages/publications/85192532192
dc.language.isoeng
dc.peerreviewedyes
dc.relationinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04378%2F2020/PT
dc.relationApplied Molecular Biosciences Unit
dc.relationApplied Molecular Biosciences Unit
dc.relationinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/LA%2FP%2F0140%2F2020/PT
dc.relationAssociated Laboratory for Green Chemistry - Clean Technologies and Processes
dc.relationinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F50006%2F2020/PT
dc.relationInstitute for Health and Bioeconomy
dc.relationAssociated Laboratory for Green Chemistry - Clean Technologies and Processes
dc.relationinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/LA%2FP%2F0140%2F2020/PT
dc.relationNitrogenase and Nitrous Oxide Reductase: Biomolecular Engineering of Complex Redox Enzymes
dc.relationinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F50006%2F2020/PT
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/310656/EU
dc.subjectCopper-containing enzyme
dc.subjectDenitrification
dc.subjectNO reductase
dc.subjectNitrogen cycle
dc.subjectNitrous oxide
dc.subjectX-ray crystallography
dc.subjectBiochemistry
dc.subjectInorganic Chemistry
dc.titleRevisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticusen
dc.typejournal article
degois.publication.firstPage279
degois.publication.issue3
degois.publication.lastPage290
degois.publication.titleJournal of Biological Inorganic Chemistry
degois.publication.volume29
dspace.entity.typePublication
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oaire.awardTitleApplied Molecular Biosciences Unit
oaire.awardTitleApplied Molecular Biosciences Unit
oaire.awardTitleAssociated Laboratory for Green Chemistry - Clean Technologies and Processes
oaire.awardTitleInstitute for Health and Bioeconomy
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oaire.awardTitleNitrogenase and Nitrous Oxide Reductase: Biomolecular Engineering of Complex Redox Enzymes
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04378%2F2020/PT
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oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/2022.01152.PTDC/PT
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oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F50006%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/EC/FP7/310656/EU
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