Structure and function of TatD exonuclease in DNA repair
Yi-Chen Chen1,†, Chia-Lung Li1,†, Yu-Yuan Hsiao2, Yulander Duh1 and Hanna S. Yuan1,3,*1Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC, 2Department of Biological Science and
Technology, National Chiao Tung University, Hsinchu 30068, Taiwan, ROC and 3Graduate Institute of Biochemistry
and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan, ROC
Received April 23, 2014; Revised July 29, 2014; Accepted July 29, 2014
TatD
is an evolutionarily conserved proteinwith thousands of homologues in
all kingdoms of life. It has been suggested that TatD participates in
DNA fragmentation during apoptosis in eukaryotic cells. However,
the cellular functions and biochemical properties of TatD in bacterial and non-apoptotic eukaryotic cells remain elusive. Here we show that Escherichia coli TatD is a Mg2+-dependent 3–5 exonuclease that prefers to digest single-stranded DNA and RNA. TatD-knockout cells are less resistant to the DNA damaging agent hydrogen peroxide, and TatD can remove damaged deaminated nucleotides from a DNA chain, suggesting that it may play a role in the H2O2-induced DNA repair. The crystal structure of the apo-form TatD and TatD bound to a singlestranded three-nucleotide DNA was determined by X-ray diffraction methods at a resolution of 2.0 and 2.9 A° , respectively. TatD has a TIM-barrel fold and the single-stranded DNA is bound at the loop region on the top of the barrel. Mutational studies further identify important conserved metal ion-binding and catalytic residues in the TatD active site for DNA hydrolysis. We thus conclude that TatD is a new class of TIM-barrel 3–5 exonuclease that not only degrades chromosomal DNA during apoptosis but also processes single-stranded DNA during DNA repair.
the cellular functions and biochemical properties of TatD in bacterial and non-apoptotic eukaryotic cells remain elusive. Here we show that Escherichia coli TatD is a Mg2+-dependent 3–5 exonuclease that prefers to digest single-stranded DNA and RNA. TatD-knockout cells are less resistant to the DNA damaging agent hydrogen peroxide, and TatD can remove damaged deaminated nucleotides from a DNA chain, suggesting that it may play a role in the H2O2-induced DNA repair. The crystal structure of the apo-form TatD and TatD bound to a singlestranded three-nucleotide DNA was determined by X-ray diffraction methods at a resolution of 2.0 and 2.9 A° , respectively. TatD has a TIM-barrel fold and the single-stranded DNA is bound at the loop region on the top of the barrel. Mutational studies further identify important conserved metal ion-binding and catalytic residues in the TatD active site for DNA hydrolysis. We thus conclude that TatD is a new class of TIM-barrel 3–5 exonuclease that not only degrades chromosomal DNA during apoptosis but also processes single-stranded DNA during DNA repair.
Crystal structures of the apo-form and DNA-bound TatD
