Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment

Gong, W., O'Gara, M., Blumenthal, R. M., Cheng, X. (July 1997) Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Research, 25 (14). pp. 2702-15. ISSN 0305-1048

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DOI: 10.1093/nar/25.14.2702


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.

Item Type: Paper
Uncontrolled Keywords: Amino Acid Sequence Binding Sites Deoxyribonucleases, Type II Site-Specific/ chemistry/metabolism Evolution, Molecular Models, Molecular Molecular Sequence Data Protein Conformation Protein Folding Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. S-Adenosylmethionine/chemistry/metabolism Site-Specific DNA Methyltransferase (Cytosine-Specific)/ chemistry/metabolism
Subjects: bioinformatics > genomics and proteomics > design > amino acid design
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
CSHL Authors:
Communities: CSHL labs
Depositing User: Kathleen Darby
Date: 15 July 1997
Date Deposited: 07 May 2014 20:28
Last Modified: 07 May 2014 20:28
PMCID: PMC146797
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