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Nucleic Acids Research, 2003, Vol. 31, No. 6 1585-1596
© 2003 Oxford University Press

The enzymatic basis of processivity in {lambda} exonuclease

Krithika Subramanian, Wiriya Rutvisuttinunt, Walter Scott and Richard S. Myers

Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33136-6129, USA

*To whom correspondence should be addressed. Tel: +1 305 243 2056; Fax: +1 305 243 3955; Email: rmyers{at}molbio.med.miami.edu

{lambda} Exonuclease is a highly processive 5'->3' exonuclease that degrades double-stranded (ds)DNA. The single-stranded DNA produced by {lambda} exonuclease is utilized by homologous pairing proteins to carry out homologous recombination. The extensive studies of {lambda} biology, {lambda} exonuclease enzymology and the availability of the X-ray crystallographic structure of {lambda} exonuclease make it a suitable model to dissect the mechanisms of processivity. {lambda} Exonuclease is a toroidal homotrimeric molecule and this quaternary structure is a recurring theme in proteins engaged in processive reactions in nucleic acid metabolism. We have identified residues in {lambda} exonuclease involved in recognizing the 5'-phosphate at the ends of broken dsDNA. The preference of {lambda} exonuclease for a phosphate moiety at 5' dsDNA ends has been established in previous studies; our results indicate that the low activity in the absence of the 5'-phosphate is due to the formation of inert enzyme–substrate complexes. By examining a {lambda} exonuclease mutant impaired in 5'-phosphate recognition, the significance of catalytic efficiency in modulating the processivity of {lambda} exonuclease has been elucidated. We propose a model in which processivity of {lambda} exonuclease is expressed as the net result of competition between pathways that either induce forward translocation or promote reverse translocation and dissociation.


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