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Nucleic Acids Symposium Series 2000 44(1):57-58; doi:10.1093/nass/44.1.57
© 2000 by Oxford University Press
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Structural bases for substrate recognition and repair system of base-excision DNA repair proteins

Satoshi Fujii1 and Yuriko Yamagata2

1 School of Pharmaceutical Sciences, University of Shizuoka, Yada, Shizuoka, Shizuoka 422-8526, Japan, 2 Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan

The model structure of Escherichia coli AlkA (3-methyladenine-DNA glycosylase II) protein complexed with the double helical DNA is elucidated from X-ray structures of related DNA glycosylase enzymes and mutagenic studies. The free enzyme structure has no difficulty in building the platform to afford the bended and wedge DNA with the flipped out nucleotide. The helix-hairpin-helix motif and the insertion residue L125 in free structure can be located without severe contacts. The alkylated base is surrounded with a variety of aromatic rings, such as W218, W272, Y273 and F18. The aromatic indole ring of tryptophan is a good candidate for forming the stacking with the positively charged base moiety {pi} cation interaction). Some hydrophobic residues, such as V128 and L240, also attend to substrate recognition.


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