Fig. 4
Crystallographic insight into allosteric activation and re-reduction of the catalytic site. a–c Shown in blue mesh are the mFO – DFC Polder omit maps for the ligands in the 2.50 Å dataset, contoured at 4.0σ. a TTP binds to the S-site and interacts with both chains of the S-dimer interface. b ADP binds to the I-site, displacing dAMP that was previously observed to bind this site in holo-NrdE31. c ATP is bound to a newly identified M-site. d The M-site and I-site are both found in the N-terminus (orange) in close proximity to each other. Binding of ATP at the M-site induces F47 to flip inward (orange) relative to its position in the I-dimer (gray, PDB: 6CGL)31. e In our 2.50 Å structure, we observe R117 making H-bonds to the 2′-OH of the ADP ribose and E119. f With dAMP bound to the I-site, R117 instead H-bonds with N42 and T45 (PDB: 6CGL)31. In this position, R117 forms part of the I-dimer interface (Supplementary Fig. 9a). R117 is thus important for discrimination of ribonucleotides and deoxyribonucleotides at this site. g The NrdE C-terminus (purple sticks) was captured in the catalytic site of the 2.55 Å reduced dataset, revealing specific interactions between highly conserved residues. C698 on the C-terminal tail is captured in a conformation well poised to initiate re-reduction of a C170–C409 disulfide that forms in the catalytic site after each turnover (Supplementary Fig. 10c, d)
