Structural characterization of pyruvic oxime dioxygenase, a key enzyme in heterotrophic nitrification.

Shuhei Tsujino, Yusuke Yamada, Miki Senda, Akihiko Nakamura, Toshiya Senda, Taketomo Fujiwara

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Article in Journal of bacteriology, 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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Authors and funding

6 authors.

Shuhei TsujinoDepartment of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan.ORCID 0009-0004-7542-3785

Yusuke YamadaInternational Center for Synchrotron Radiation Innovation Smart (SRIS), Tohoku University, Sendai, Japan.ORCID 0000-0003-0088-0549

Miki SendaStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Japan.ORCID 0000-0003-3863-4503

Akihiko NakamuraDepartment of Applied Life Sciences, Faculty of Agriculture, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.ORCID 0000-0003-0409-5759

Toshiya SendaStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Japan.ORCID 0000-0002-5153-928X

Taketomo FujiwaraDepartment of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.ORCID 0000-0002-0352-3849

Funding

Amano Institute of TechnologyJapan Agency for Medical Research and Development (AMED) JP23ama121001Ministry of Education, Culture, Sports, Science and Technology (MEXT) 17K00517, 21K12220, 24K15258

6 · The paper itself

Abstract

Nitrification by heterotrophic microorganisms is an important part of the nitrogen cycle in the environment. The enzyme responsible for the core function of heterotrophic nitrification is pyruvic oxime dioxygenase (POD). POD is a non-heme, Fe(II)-dependent enzyme that catalyzes the dioxygenation of pyruvic oxime to produce pyruvate and nitrite. To analyze the catalytic mechanism of POD, the crystal structure of POD from

Indexed as

Alcaligenes faecalisBacterial ProteinsDioxygenasesNitrificationCatalytic DomainCrystallography, X-RayHeterotrophic ProcessesModels, MolecularProtein ConformationBacterial ProteinsDioxygenasesAlcaligenes faecalisclass II aldolaseheterotrophic nitrificationpyruvic oxime dioxygenase

Identifiers

PMID39772954

DOI10.1128/jb.00342-24

PMCPMC11841055

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.