6MYX

EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical filament of NrdE alpha subunit with dATP

Summary for 6MYX

• Entry DOI: 10.2210/pdb6myx/pdb
• Related: 6MT9 6MV9 6MVE
• EMDB information: 9272 9293
• Descriptor: Ribonucleoside-diphosphate reductase, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (2 entities in total)
• Functional Keywords: ribonucleotide reductase, allostery, nucleotide metabolism, filament, datp, atp, oxidoreductase, protein fibril
• Biological source: Bacillus subtilis
• Total number of polymer chains: 4
• Total formula weight: 327095.33

Authors

Thomas, W.C.,Bacik, J.P.,Chen, J.Z.,Ando, N. (deposition date: 2018-11-02, release date: 2019-06-19, Last modification date: 2024-03-13)

Primary citation

Thomas, W.C.,Brooks 3rd, F.P.,Burnim, A.A.,Bacik, J.P.,Stubbe, J.,Kaelber, J.T.,Chen, J.Z.,Ando, N.
Convergent allostery in ribonucleotide reductase.
Nat Commun, 10:2653-2653, 2019

PubMed Abstract: Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

PubMed: 31201319
DOI: 10.1038/s41467-019-10568-4

Experimental method

ELECTRON MICROSCOPY (6 Å)