Nature Structural Biology
5, 872 - 877 (1998)
doi:10.1038/2312
Structures of HhaI methyltransferase complexed with substrates
containing mismatches at the target baseMargaret O'Gara1, John R. Horton2, Richard J. Roberts3
& Xiaodong Cheng21
Present address: Pfizer Central Research, Discovery Biology, Ramsgate Road, Sandwich, Kent CT13 3NJ England.
2
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.
3
New England Biolabs, 32 Tozer Road, Beverly, Massachusetts 01915, USA.
Correspondence should be addressed to Xiaodong Cheng xcheng@emory.edu
Three structures have been determined for complexes between HhaI
methyltransferase (M.HhaI) and oligonucleotides containing a G:A, G:U
or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base
pair. The mismatched adenine, uracil and abasic site are all flipped out of
the DNA helix and located in the enzyme's active-site pocket, adopting the
same conformation as in the flipped-out normal substrate. These results, particularly
the flipped-out abasic deoxyribose sugar, provide insight into the mechanism
of base flipping. If the process involves the protein pushing the base out
of the helix, then the push must take place not on the base, but rather on
the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably
the key to base flipping.
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