8P2C

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric state produced in the presence of dATP and CTP

Summary for 8P2C

• Entry DOI: 10.2210/pdb8p2c/pdb
• Related: 8P23 8P27 8P28 8P2D 8P2S 8P39
• EMDB information: 17357 17358 17359 17360 17361 17373 17385
• Descriptor: Anaerobic ribonucleoside-triphosphate reductase, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: ribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis, oxidoreductase, biosynthetic protein
• Biological source: Segatella copri
• Total number of polymer chains: 4
• Total formula weight: 344535.62

Authors

Banerjee, I.,Bimai, O.,Sjoberg, B.M.,Logan, D.T. (deposition date: 2023-05-15, release date: 2023-09-13, Last modification date: 2024-09-25)

Primary citation

Bimai, O.,Banerjee, I.,Rozman Grinberg, I.,Huang, P.,Hultgren, L.,Ekstrom, S.,Lundin, D.,Sjoberg, B.M.,Logan, D.T.
Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding.
Elife, 12:-, 2024

PubMed Abstract: A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from . The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.

PubMed: 38968292
DOI: 10.7554/eLife.89292

Experimental method

ELECTRON MICROSCOPY (2.59 Å)