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Nucleic Acids Research, 2003, Vol. 31, No. 6 1633-1639
© 2003 Oxford University Press

Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix

Karen A. Bunting, S. Mark Roe, Anthony Headley1, Tom Brown2, Renos Savva3 and Laurence H. Pearl

Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK, 1 Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK, 2 Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK and 3 Laboratory of Molecular Biology, Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK

*To whom correspondence should be addressed. Tel: +44 207 970 6045; Fax: +44 207 970 6051; Email: l.pearl{at}icr.ac.uk

Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-pMe5C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.


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