Figure 3
From: Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI
A model of AspBHI in complex with DNA.
(a) Superimposition of the AspBHI N-terminal domain (in green) with the SRA domain of mouse UHRF1 (in yellow; PDB 3FDE). (b) The flipped 5mC nucleotide can be docked into the binding pocket of AspBHI. (c) Superimposition of the AspBHI C-terminal endonuclease domain (in green) and the HindIII–DNA complex (conserved secondary elements in yellow and additional in grey) (PDB 2E52). (d) The scissile phosphate group (shown as an orange ball) is near the proposed catalytic residues (Glu303 and Lys305 in AspBHI). The side chain of conserved Asp282 in AspBHI, pointing away from the active site, might undergo conformational change upon DNA binding. (e) A model of the AspBHI N-terminal domain docked with a DNA (taken from PDB 3FDE) containing a flipped 5mC (which is faded in the background). The opposite guanine is labeled. The Loop-B3 occupies the DNA minor groove 5′ to the 5mC, while the Loop-2B occupies the minor groove 3′ to the 5mC.
