Tom Ellenberger, D.V.M., Ph.D.


Biochemistry and Molecular Biophysics





Research in the Ellenberger laboratory focuses on the molecular structures and cellular functions of proteins that replicate DNA, repair chemical damage, and regulate chromatin structure. These enzymes and regulatory proteins ensure the faithful transmission of our genetic blueprint to future generations.

tom ellenberger research image

Most Recent Publications

    • Kukshal, V., Kim, I.K., Hura, G.L., Tomkinson, A.E., Tainer, J.A. and Ellenberger, T.
      Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining.
      Nucleic Acids Res. 43:7021-7031 (2015). [Abstract]

    • Pascal, J.M. and Ellenberger, T.
      RNA ligase does the AMP shuffle.
      Nat Struct Mol Biol 13:950-951 (2006). [Abstract]

    • Pascal, J.M., Tsodikov, O.V., Hura, G.L., Song, W., Cotner, E.A., Classen, S., Tomkinson, A.E., Tainer, J.A. and Ellenberger, T.
      A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.
      Mol Cell 24:279-291 (2006). [Abstract]

    • King, D.A., Hall, B.E., Iwamoto, M.A., Win, K.Z., Chang, J.F. and Ellenberger, T.
      Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.
      J Biol Chem 281:20107-20119 (2006). [Abstract]

    • Chen, X., Pascal, J., Vijayakumar, S., Wilson, G.M., Ellenberger, T. and Tomkinson, A.E.
      Human DNA ligases I, III, and IV-purification and new specific assays for these enzymes.
      Methods in Enzymology 409:39-52 (2006). [Abstract]

    • Radman-Livaja, M., Biswas, T., Ellenberger, T., Landy, A. and Aihara, H.
      DNA arms do the legwork to ensure the directionality of lambda site-specific recombination.
      Curr Opin Struct Biol 16:42-50 (2006). [Abstract]

    • Tomkinson, A.E., Vijayakumar, S., Pascal, J.M. and Ellenberger, T.
      DNA ligases: structure, reaction mechanism, and function.
      Chem Rev 106:687-699 (2006). [Abstract]

    • Kim, T.W., Brieba, L.G., Ellenberger, T. and Kool, E.T.
      Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs.
      J Biol Chem 281:2289-2295 (2006). [Abstract]


  • Pascal, J.M. and Ellenberger, T. The rise and fall of poly(ADP-ribose): An enzymatic perspective. DNA Repair 43:7021-7031 (2015). [Abstract]

  • Chen, X., Kim, IK., Honaker, Y., Paudval, S.C., Koh, W.K., Sparks, M., Lis, S., Piwnica-Worms, H., Ellenberger, T. and You, Z. 14-3-3 proteins restrain the Exo1 nuclease to prevent over-resection. J Biol Chem 290″12300-12312 (2015). [Abstract]

  • Ghisays, F., Brace, C.S., Yackly, S.M., Kwon, H.J., Mills, K.F., Kashentseva, E., Dmitriev, I.P., Curiel, D.T., Imai, S.I. and Ellenberger, T. The N-terminal domain of SIRT1 is a positive regulator of endogenous SIRT1-dependent deacetylation and transcriptional outputs. Cell Rep. S2211-1247:00182-00185 (2015). [Abstract]

  • Kim, IK., Stegeman, R.A., Brosey, C.A. and Ellenberger, T. A quantitative assay reveals ligand specificity of the DNA scaffold repair protein XRCC1 and efficent disassembly of complexes of XRCC1 and the poly (ADP-ribose) polymerase 1 by PAR glycohydrolase. J Biol Chem 290:3775-3783 (2015.) [Abstract]

  • Wallen, J.R., Majka, J. and Ellenberger, T. Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase. Biochemistry 52:4026-4036 (2013). [Abstract]

  • Della-Maria, J., Hegde, M.L., McNeill, D.R., Matsumoto, Y., Tsai, M.S., Ellenberger, T., Wilson, D.M., Mitra, S. and Tomkinson, A.E. The interaction between polynucleotide kinase phosphatase and the DNA repair protein XRCC1 is critical for repair of DNA alkylation damage and stable association at DNA damage sites. J Biol Chem 287:39233-39244 (2012). [Abstract]

  • Kim, I.K., Kiefer, J.R., Ho, C.M., Stegeman, R.A., Classen, S., Tainer, J.A. and Ellenberger, T. Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat Struct Mol Biol 19:653-656 (2012). [Abstract]

  • Ellenberger, T. An arresting development in transcription. Mol Cell. 46:3-4 (2012). [Abstract]

  • Sperry, J.B., Smith, C.L., Caparon, M.G., Ellenberger, T. and Gross, M.L. Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes. Biochem 50:4038-4045 (2011). [Abstract]

  • Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD(+) glycohydrolase toxin. Structure 19:192-202 (2011). [Abstract]

  • Cotner-Gohara, E., Kim, I.K., Tainer, J.A., Tomkinson, A.E. and Ellenberger, T. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA bound states. Biochemistry 49:6165-6176 (2010). [Abstract]

  • Han, Z., Pinkner, J.S., Ford, B., Obermann, R., Nolan, W., Wildman, S.A., Hobbs, D., Ellenberger, T., Cusumano, C.K., Hultgren, S.J. and Janetka, J.W. Structure-based drug design and optimization of mannoside bacterial FimH antagonists. J Med Chem 53:4779-4792 (2010). [Abstract]

  • Perry, J.J. and Cotner-Gohara, E., Ellenberger, T. and Tainer, J.A. Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol 20:283-294 (2010). [Abstract]

  • Orelli, B., McClendon, T.B., Tsodikov, O.V., Ellenberger, T., Niedernhofer, L.J. and Scharer, O.D. The XPA-binding domain of ERCC1 is required for nucleotide excision repair but not other DNA repair pathways. J Biol Chem 285:3705-3712 (2010). [Abstract]