Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

HHAI methyltransferase (blue ribbon) bound to oligonucleotide (strands with bonds colored yellow and green) containing a pseudorotationally constrained sugar analogue at the target position (orange bonds with cyan atoms). The south-constrained pseudosugar is rotated about its flanking phosphodiester bonds, 90° from its initial position in B-form DNA, but short of a completely flipped position with 180° rotation. Thus, it is trapped in the middle of the flipping pathway via the major groove side. This structure provides clues to DNA-protein interactions in a potential transition state.