Fig. 4: Comparison of active sites between Rv2067c and DOT1L.

a The complex between ubiquitinated nucleosome (UbNuc) and DOT1L^cat (middle panel). The substrate lysine (nucleosomal H3K79) binds in a narrow tunnel (cross sections across SAM, left and right panels). The length of the tunnel is about the length of the lysine side chain in its extended rotamer. b Cross sections (left and right panels) of substrate-binding trough of Rv2067c as depicted by planes passing through Rv2067c dimer (middle panel). The active site (broken circle) lies deep inside (right panel) and at one end (left panel) of the trough, and encompassed by catalytic domain and LSD. The active site, region opposite to methyl group of SAM is occluded and leaves no room for substrate lysine binding. a, b The radius 6.3 Å of the circle is equal to the length of lysine side chain in its extended rotamer. The substrate lysine must reach the encircled region to undergo methylation. c Non-accessibility of Rv2067c active site by nucleosomal H3K79 is shown by a hypothetical reaction complex model of nucleosome-Rv2067c and rotation scan. The total number of clashing atoms (TCA) for each pose is shown as a function of elemental rotation angles (α, β and γ) (left panel). Each subplot corresponds to the value of either α or β or γ at minimum TCA value (i.e., 211). The pose between Rv2067c and nucleosome reaction complex with minimum TCA (right panel). In this pose, nucleosomal H3K79 accesses the reaction center of Rv2067c via the SAM entry site. SAM: S-adenosyl-L-methionine, LSD: Large subdomain of dimerization domain, SSD: Small subdomain of dimerization domain, CTD: C-terminal domain. Scale bars 10 Å. The Source Data and plotting script for TCA plot are available at https://doi.org/10.5281/zenodo.8352903 and https://github.com/Venkat-Dadi/Rotation_Scan.