Nucleic Acids Research, Vol 25, Issue 14 2702-2715, Copyright © 1997 by Oxford University Press
W Gong, M O'Gara, RM Blumenthal and X Cheng
We have determined the structure of Pvu II methyltransferase (M. Pvu II)
complexed with S -adenosyl-L-methionine (AdoMet) by multiwavelength
anomalous diffraction, using a crystal of the selenomethionine- substituted
protein. M. Pvu II catalyzes transfer of the methyl group from AdoMet to
the exocyclic amino (N4) nitrogen of the central cytosine in its
recognition sequence 5'-CAGCTG-3'. The protein is dominated by an open
alpha/beta-sheet structure with a prominent V- shaped cleft: AdoMet and
catalytic amino acids are located at the bottom of this cleft. The size and
the basic nature of the cleft are consistent with duplex DNA binding. The
target (methylatable) cytosine, if flipped out of the double helical DNA as
seen for DNA methyltransferases that generate 5-methylcytosine, would fit
into the concave active site next to the AdoMet. This M. Pvu
IIalpha/beta-sheet structure is very similar to those of M. Hha I (a
cytosine C5 methyltransferase) and M. Taq I (an adenine N6
methyltransferase), consistent with a model predicting that DNA
methyltransferases share a common structural fold while having the major
functional regions permuted into three distinct linear orders. The main
feature of the common fold is a seven-stranded beta-sheet (6 7 5 4 1 2 3)
formed by five parallel beta-strands and an antiparallel beta-hairpin. The
beta- sheet is flanked by six parallel alpha-helices, three on each side.
The AdoMet binding site is located at the C-terminal ends of strands beta1
and beta2 and the active site is at the C-terminal ends of strands beta4
and beta5 and the N-terminal end of strand beta7. The AdoMet- protein
interactions are almost identical among M. Pvu II, M. Hha I and M. Taq I,
as well as in an RNA methyltransferase and at least one small molecule
methyltransferase. The structural similarity among the active sites of M.
Pvu II, M. Taq I and M. Hha I reveals that catalytic amino acids essential
for cytosine N4 and adenine N6 methylation coincide spatially with those
for cytosine C5 methylation, suggesting a mechanism for amino methylation.
ARTICLES
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment
W.M.Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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