Characterization of a second class Ie ribonucleotide reductase
Abstract Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site....
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-07565-3 |
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| author | Juliane John Daniel Lundin Rui M. Branca Rohit Kumar Vivek Srinivas Hugo Lebrette Martin Högbom |
| author_facet | Juliane John Daniel Lundin Rui M. Branca Rohit Kumar Vivek Srinivas Hugo Lebrette Martin Högbom |
| author_sort | Juliane John |
| collection | DOAJ |
| description | Abstract Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site. The discovery of a metal-free R2 defined the new RNR subclass Ie. In R2e, three of the otherwise strictly conserved metal-binding glutamates in the active site are substituted. Two variants have been found, VPK and QSK. To date, the VPK version has been the focus of biochemical characterization. Here we characterize a QSK variant of R2e. We analyse the organismal distribution of the two R2e versions and find dozens of organisms relying solely on the QSK RNR for deoxyribonucleotide production. We demonstrate that the R2eQSK of the human pathogen Gardnerella vaginalis (Bifidobacterium vaginale) modifies the active site-adjacent tyrosine to DOPA. The amount of modified protein is shown to be dependent on coexpression with the other proteins encoded in the RNR operon. The DOPA containing R2eQSK can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2eQSK in the unmodified and DOPA states. |
| format | Article |
| id | doaj-art-e52d7b7f02a54d5b963dfe962413ef37 |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
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| series | Communications Biology |
| spelling | doaj-art-e52d7b7f02a54d5b963dfe962413ef372025-08-20T01:54:25ZengNature PortfolioCommunications Biology2399-36422025-02-018111010.1038/s42003-025-07565-3Characterization of a second class Ie ribonucleotide reductaseJuliane John0Daniel Lundin1Rui M. Branca2Rohit Kumar3Vivek Srinivas4Hugo Lebrette5Martin Högbom6Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural SciencesDepartment of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural SciencesCancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska InstitutetDepartment of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural SciencesDepartment of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural SciencesLaboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, CNRS – University of ToulouseDepartment of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural SciencesAbstract Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site. The discovery of a metal-free R2 defined the new RNR subclass Ie. In R2e, three of the otherwise strictly conserved metal-binding glutamates in the active site are substituted. Two variants have been found, VPK and QSK. To date, the VPK version has been the focus of biochemical characterization. Here we characterize a QSK variant of R2e. We analyse the organismal distribution of the two R2e versions and find dozens of organisms relying solely on the QSK RNR for deoxyribonucleotide production. We demonstrate that the R2eQSK of the human pathogen Gardnerella vaginalis (Bifidobacterium vaginale) modifies the active site-adjacent tyrosine to DOPA. The amount of modified protein is shown to be dependent on coexpression with the other proteins encoded in the RNR operon. The DOPA containing R2eQSK can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2eQSK in the unmodified and DOPA states.https://doi.org/10.1038/s42003-025-07565-3 |
| spellingShingle | Juliane John Daniel Lundin Rui M. Branca Rohit Kumar Vivek Srinivas Hugo Lebrette Martin Högbom Characterization of a second class Ie ribonucleotide reductase Communications Biology |
| title | Characterization of a second class Ie ribonucleotide reductase |
| title_full | Characterization of a second class Ie ribonucleotide reductase |
| title_fullStr | Characterization of a second class Ie ribonucleotide reductase |
| title_full_unstemmed | Characterization of a second class Ie ribonucleotide reductase |
| title_short | Characterization of a second class Ie ribonucleotide reductase |
| title_sort | characterization of a second class ie ribonucleotide reductase |
| url | https://doi.org/10.1038/s42003-025-07565-3 |
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