Structure of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine Covalent Complex with Abasic Site-containing DNA

Gali Golan, Dmitry O. Zharkov, Arthur P. Grollman, M. L. Dodson, Amanda K. McCullough, R. Stephen Lloyd*, Gil Shoham

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


The base excision repair (BER) pathway for ultraviolet light (UV)-induced cyclobutane pyrimidine dimers is initiated by DNA glycosylases that also possess abasic (AP) site lyase activity. The prototypical enzyme known to catalyze these reactions is the T4 pyrimidine dimer glycosylase (T4-Pdg). The fundamental chemical reactions and the critical amino acids that lead to both glycosyl and phosphodiester bond scission are known. Catalysis proceeds via a protonated imine covalent intermediate between the α-amino group of the N-terminal threonine residue and the C1′ of the deoxyribose sugar of the 5′ pyrimidine at the dimer site. This covalent complex can be trapped as an irreversible, reduced cross-linked DNA-protein complex by incubation with a strong reducing agent. This active site trapping reaction is equally efficient on DNA substrates containing pyrimidine dimers or AP sites. Herein, we report the co-crystal structure of T4-Pdg as a reduced covalent complex with an AP site-containing duplex oligodeoxynucleotide. This high-resolution structure reveals essential precatalytic and catalytic features, including flipping of the nucleotide opposite the AP site, a sharp kink (∼ 66°) in the DNA at the dimer site and the covalent bond linking the enzyme to the DNA. Superposition of this structure with a previously published co-crystal structure of a catalytically incompetent mutant of T4-Pdg with cyclobutane dimer-containing DNA reveals new insights into the structural requirements and the mechanisms involved in DNA bending, nucleotide flipping and catalytic reaction.

Original languageAmerican English
Pages (from-to)241-258
Number of pages18
JournalJournal of Molecular Biology
Issue number2
StatePublished - 15 Sep 2006

Bibliographical note

Funding Information:
We thank the staff at the National Synchrotron Light Source facility (X26C beamline) of the Brookhaven National Laboratory for their help in the X-ray synchrotron data collection and analysis. This research was supported in part by grants (ES04091 to R.S.L.; CA17395 to A.P.G.) from the National Institutes of Health. D.O.Z. acknowledges support from the Russian Foundation for Basic Research (05-04-48619) CRDF and the Wellcome Trust UK (070244/Z/03/Z). G.G. was supported by fellowships from the Wolf Foundation (Israel), the Chorafas Foundation (Switzerland) and the Clore Foundation (Israel).


  • DNA repair
  • T4-Pdg
  • base excision
  • endonuclease V
  • radiation damage


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