9DWS

X-ray crystal structure of Francisella hispaniensis apo ribonucleotide reductase beta subunit

Summary for 9DWS

• Entry DOI: 10.2210/pdb9dws/pdb
• Descriptor: ribonucleoside-diphosphate reductase, CHLORIDE ION (3 entities in total)
• Functional Keywords: diiron, tyrosyl radical, ferritin, four-helix bundle, oxidoreductase
• Biological source: Francisella hispaniensis
• Total number of polymer chains: 2
• Total formula weight: 76057.77

Authors

Peduzzi, O.M.,Lin, C.-Y.,Boal, A.K. (deposition date: 2024-10-10, release date: 2025-09-17, Last modification date: 2025-09-24)

Primary citation

Peduzzi, O.M.,Palowitch, G.M.,Gajewski, J.P.,Hu, K.,Wheeler, A.,Laremore, T.N.,Silletti, S.,Komives, E.A.,Allen, B.D.,Silakov, A.,Krebs, C.,Bollinger Jr., J.M.,Lin, C.Y.,Boal, A.K.
A Structurally Divergent Class Ia Ribonucleotide Reductase from a Tick-Borne Pathogen.
Biochemistry, 64:3935-3955, 2025

PubMed Abstract: Ribonucleotide reductases (RNRs) generate 2'-deoxynucleotides for DNA biosynthesis, a reaction essential to all life. Class I RNRs have two subunits, α and β. α binds and reduces the substrate, whereas β oxidizes one of the cysteines in α to a C3'-H-bond-cleaving thiyl radical to begin the reaction. The α-Cys oxidant in β is variously a tyrosyl radical (Y) generated by a diiron or dimanganese cluster, a high-valent dimetal cluster [Mn(IV)/Fe(III) or Mn(IV/III)], or a dihydroxylphenylalanine (DOPA) radical that operates without need of a transition metal. The metal (in)dependence of the Cys oxidant in β correlates loosely with sequence-similarity groupings. We show here that () β, which lies within an uncharacterized sequence cluster that contains orthologs from multiple human pathogens, harbors a Fe(III/III)/Y cofactor, as in class Ia RNRs from eukaryotes and . β has several unusual structural features that may reflect adaptation to the bacterium's environment(s). In its apo form, an unwound helix everts a metal ligand toward solvent, and the radical-harboring Y points away from the diiron cluster. An additional aromatic residue (W194), conserved within the sequence cluster, is found close to the universally conserved W37, which is thought to mediate α-Cys oxidation in all class I enzymes. The Y in resting β is remarkably resistant to reduction by hydroxyurea but becomes 8000 times more sensitive when β is engaged in turnover with α. These structural and functional distinctions could be counter measures against host redox defenses that would target the pathogen's RNR and its cofactor.

PubMed: 40877217
DOI: 10.1021/acs.biochem.5c00316

Experimental method

X-RAY DIFFRACTION (2.3 Å)