8RAH
Crystal structure of class Ie ribonucleotide reductase R2 subunit with post-translational modification of Y150 into a DOPA from Gardnerella vaginalis
Summary for 8RAH
| Entry DOI | 10.2210/pdb8rah/pdb |
| Descriptor | ribonucleoside-diphosphate reductase (2 entities in total) |
| Functional Keywords | ribonucleotide reductase r2e, class ie rnr, oxidoreductase, ferritin-like superfamily, nrdf, rnr beta-subunit |
| Biological source | Gardnerella vaginalis ATCC 14019 |
| Total number of polymer chains | 4 |
| Total formula weight | 171378.83 |
| Authors | John, J.,Hogbom, M. (deposition date: 2023-12-01, release date: 2024-12-11, Last modification date: 2025-03-05) |
| Primary citation | John, J.,Lundin, D.,Branca, R.M.,Kumar, R.,Srinivas, V.,Lebrette, H.,Hogbom, M. Characterization of a second class Ie ribonucleotide reductase. Commun Biol, 8:281-281, 2025 Cited by PubMed 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 R2e 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 R2e can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2e in the unmodified and DOPA states. PubMed: 39987380DOI: 10.1038/s42003-025-07565-3 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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