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Molecular and Cellular Biology, October 1998, p. 5908-5920, Vol. 18, No. 10
0270-7306/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Productive and Nonproductive Complexes of Ku and DNA-Dependent Protein Kinase at DNA Termini

Robert B. West,1 Mariana Yaneva,2 and Michael R. Lieber1,*

Departments of Pathology and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California School of Medicine, Los Angeles, California 90033,1 and Lexicon Genetics, Inc., The Woodlands, Texas 773812

Received 20 April 1998/Returned for modification 9 June 1998/Accepted 26 June 1998

DNA-dependent protein kinase (DNA-PK) is the only eukaryotic protein kinase known to be specifically activated by double-stranded DNA (dsDNA) termini, accounting for its importance in repair of dsDNA breaks and its role in physiologic processes involving dsDNA breaks, such as V(D)J recombination. In this study we conducted kinase and binding analyses using DNA-PK on DNA termini of various lengths in the presence and absence of Ku. We confirmed our previous observations that DNA-PK can bind DNA termini in the absence of Ku, and we determined rate constants for binding. However, in the presence of Ku, DNA-PK can assume either a productive or a nonproductive configuration, depending on the length of the DNA terminus. For dsDNA greater than 26 bp, the productive mode is achieved and Ku increases the affinity of the DNA-PK for the Ku:DNA complex. The change in affinity is achieved by increases in both the kinetic association rate and reduction in the kinetic dissociation rate. For dsDNA smaller than 26 bp, the nonproductive mode, in which DNA-PK is bound to Ku:DNA but is inactive as a kinase, is assumed. Both the productive and nonproductive configurations are likely to be of physiologic importance, depending on the distance of the dsDNA break site to other protein complexes, such as nucleosomes.

* Corresponding author. Mailing address: Norris Comprehensive Cancer Center, Rm. 5425, University of Southern California School of Medicine, Departments of Pathology and of Biochemistry and Molecular Biology, 1441 Eastlake Ave., Mail Stop 73, Los Angeles, CA 90033. Phone: (323) 865-0568. Fax: (323) 865-3019. E-mail: lieber_m{at}froggy.hsc.usc.edu.

Molecular and Cellular Biology, October 1998, p. 5908-5920, Vol. 18, No. 10
0270-7306/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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