Tom Ellenberger

Department of Biological Chemistry and Molecular Pharmacology
Harvard Medical School
Building C2, Room 226a
240 Longwood Avenue
Boston, MA 02115
Tel: (617) 432-0458
Fax: (617) 432-3380
Email: tome@hms.harvard.edu
Web Page: The Ellenberger Lab Page
16 postdoctoral fellows, 2 graduate students

We are studying complexes of proteins that replicate, repair, or recombine DNA strands in a variety of biological contexts. These proteins include DNA polymerases, helicases, base excision glycosylases, and a site-specific DNA recombinase. In each case, the enzyme recognizes the structure or sequence of a DNA substrate and carries out a complex series of reactions that are fundamental to the maintenance of life. We are using biochemical and spectroscopic methods in combination with x-ray crystallography to probe the structures and mechanisms of these enzymes.

DNA polymerases replicate genomic DNA in concert with accessory factors that unwind the double helix and prime the synthesis of Okazaki fragments on the lagging strand of the replication fork. We have been examining the phage T7 replisome to understand how these proteins work together to efficiently copy double-stranded DNA. We have recently begun collaborative single molecule studies of these enzymes with Professor Sunney Xie (Dept. of Chemistry and Chemical Biology, Harvard).

DNA base excision glycosylases recognize modified bases in duplex DNA and cleave the N-glycosylic bond to release the damaged base from the DNA backbone during the first step of base excision repair. These enzymes flip modified nucleotides out of the DNA double helix and into the active site of the repair enzyme. We have determined crystal structures of bacterial and human enzymes that excise alkylation-damaged bases from DNA. Current projects are focused on understanding how abnormal bases are recognized and how the DNA glycosylases interact with other DNA repair proteins.

The bacteriophage lambda integrase protein (Int) is archetypic of site-specific DNA recombinases that cleave and recombine two DNAs having limited sequence homology. We have recently determined structures of Int complexed to DNA intermediates that address the mechanism of cooperativity between two different DNA binding surfaces of the Int protein. Lambda Int is a model system for understanding the allosteric effects of DNA bending on cleavage activity and the physical basis for controlling an ordered series of DNA strand cleavage and exchange reactions.

References:

• O'Brien, P.J., and Ellenberger, T. 2003. Dissecting the broad substrate specificity of human 3-methyladenine DNA glycosylase. J. Biol. Chem. 279, 9750-9757.
• Toth, E.A., Li, Y., Sawaya, M.R., Cheng, Y., and Ellenberger, T. 2003. Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7. Mol. Cell 12, 1113-1123.
• Aihara, H., Kwon, H.J., Nunes-Düby, S.E., Landy, A., and Ellenberger, T. 2003. A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase. Mol. Cell 12, 187-198.
• Kato, M., Ito, T., Wagner, G., Richardson, C.C., and Ellenberger, T. 2003. Modular Architecture of the Bacteriophage T7 Primase Couples RNA Primer Synthesis to DNA Synthesis. Mol. Cell 11, 1349-1360.