Activity modulation in anaerobicribonucleotide reductases: nucleotidebinding: HDX-MS data

ABSTRACT: A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of mostribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates theenzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs hasrevealed a plethora of ways in which dATP inhibits activity by inducing oligomerization andpreventing 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 thebasis for their dATP-dependent inhibition is completely unknown. We present biochemical,biophysical and structural information on the effects of ATP and dATP binding to theanaerobic RNR from Prevotella copri . The enzyme exists in a dimer-tetramer equilibriumbiased towards dimers when two ATP molecules are bound and tetramers when two dATPmolecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully orderedglycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-coneresults in loss of activity and disordering of the GRD. The glycyl radical is formed even in thedATP-bound form, but the substrate does not bind, suggesting that dATP inhibition inanaerobic RNRs acts by disordering of the GRD more than 30 Å away from the dATP molecule,thereby preventing both substrate binding and radical mobilisation. The structures implicatea complex network of activity regulation involving the GRD, the allosteric substratespecificity site and a conserved but previously unseen flap over the active site.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Prevotella Corporis Dsm 18810 = Jcm 8529

SUBMITTER: Simon Ekström  

LAB HEAD: Derek Logan

PROVIDER: PXD047943 | Pride | 2024-08-10

REPOSITORIES: Pride