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Published online 9 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 926-935
© 2004 Oxford University Press

Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase

Vladimir V. Koval1,2, Nikita A. Kuznetsov2, Dmitry O. Zharkov1,2, Alexander A. Ishchenko1, Kenneth T. Douglas3, Georgy A. Nevinsky1,2 and Olga S. Fedorova*,1,2

1 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia, 2 Novosibirsk State University, Novosibirsk 630090, Russia and 3 School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester M13 9PL, UK

*To whom correspondence should be addressed. Tel: +7 3832 34 42 74; Fax: +7 3832 33 36 77; Email: fedorova{at}niboch.nsc.ru

Formamidopyrimidine-DNA-glycosylase (Fpg pro tein, MutM) catalyses excision of 8-oxoguanine (8-oxoG) and other oxidatively damaged purines from DNA in a glycosylase/apurinic/apyrimidinic-lyase reaction. We report pre-steady-state kinetic analysis of Fpg action on oligonucleotide duplexes containing 8-oxo-2'-deoxyguanosine, natural abasic site or tetrahydrofuran (an uncleavable abasic site analogue). Monitoring Fpg intrinsic tryptophan fluorescence in stopped-flow experiments reveals multiple conformational transitions in the protein molecule during the catalytic cycle. At least four and five conformational transitions occur in Fpg during the interaction with abasic and 8-oxoG-containing substrates, respectively, within 2 ms to 10 s time range. These transitions reflect the stages of enzyme binding to DNA and lesion recognition with the mutual adjustment of DNA and enzyme structures to achieve catalytically competent conformation. Unlike these well-defined binding steps, catalytic stages are not associated with discernible fluorescence events. Only a single conformational change is detected for the cleavable substrates at times exceeding 10 s. The data obtained provide evidence that several fast sequential conformational changes occur in Fpg after binding to its substrate, converting the protein into a catalytically active conformation.


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