Fig. 1
Allosteric sites of the Bacillus subtilis class Ib ribonucleotide reductase. a A 2.50 Å crystal structure of B. subtilis NrdE (α subunit) obtained under activating conditions depicts an S-shaped dimer (“S-dimer”) interfacing at the “specificity” or S-site (lavender). A specificity effector TTP (green) is bound to the S-site, and activating nucleotides, ADP (pink) and ATP (salmon), are bound to two allosteric sites that evolved near the N-terminus of B. subtilis NrdE. A catalytically essential radical is generated at a central cysteine in the catalytic site, C382 (yellow sphere). b B. subtilis NrdF (β subunit) is dimeric and utilizes a dimanganic tyrosyl cofactor (purple spheres) to initiate radical chemistry (PDB: 4DR0)21. A disordered region of the NrdF C-terminus (black dotted lines) is critical for radical transfer. c A recent structure of B. subtilis NrdE co-crystallized with dAMP (purple) depicts a partially inhibited, non-canonical “I-dimer” with the interface formed by the truncated ATP-cone (orange) (PDB: 6CGL)31. d In class Ia RNRs, ATP or dATP binds to the “activity” or A-site in the ATP-cone domain (orange) to mediate changes in quaternary structure and tune overall activity (PDB: 3R1R)20. e Class Ib RNRs only contain partial ATP-cones (orange). B. subtilis NrdE is unusual in that it displays activity regulation and binds dAMP (purple) in the N-terminally located I-site (PDB: 6CGL). f The partial N-terminal cone of class Ib RNRs (top) is structurally homologous to the last two helices of the canonical ATP-cone found in many class Ia RNRs (bottom) but lacks A-site residues
