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Dynamics and mechanism of repair of ultraviolet-induced (6–4) photoproduct by photolyase

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Abstract

One of the detrimental effects of ultraviolet radiation on DNA is the formation of the (6–4) photoproduct, 6–4PP, between two adjacent pyrimidine rings1. This lesion interferes with replication and transcription, and may result in mutation and cell death2. In many organisms, a flavoenzyme called photolyase uses blue light energy to repair the 6–4PP (ref. 3). The molecular mechanism of the repair reaction is poorly understood. Here, we use ultrafast spectroscopy to show that the key step in the repair photocycle is a cyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, we followed the function evolution and observed direct electron transfer from the excited flavin cofactor to the 6–4PP in 225 picoseconds, but surprisingly fast back electron transfer in 50 picoseconds without repair. We found that the catalytic proton transfer between a histidine residue in the active site and the 6–4PP, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6–4PP, occurs in 425 picoseconds and leads to 6–4PP repair in tens of nanoseconds. These key dynamics define the repair photocycle and explain the underlying molecular mechanism of the enzyme’s modest efficiency.

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Figure 1: Enzyme–substrate complex structure and a possible repair scheme.
Figure 2: Femtosecond-resolved dynamics of flavin species involved in the repair of damaged DNA by (6–4) photolyase enzyme (E6–4PL).
Figure 3: Femtosecond-resolved transient absorption dynamics of various species involved in the damaged DNA repair.
Figure 4: Repair photocycle of (6–4) thymine photoproduct by (6–4) photolyase.

Change history

  • 11 August 2010

    A correction was made to the x-axis labels of the Fig. 2a inset.

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Acknowledgements

We thank T. Todo and T. Kitagawa for the generous gift of Arabidopsis thaliana (6–4) photolyase plasmid; C. Forsyth for discussions; and Y.-T. Kao and C.-W. Chang for help during the experiments. This work is supported in part by the National Institutes of Health (research grant GM074813) and the Packard fellowship.

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D.Z. designed the research. J.L., Z.L., C.T., X.G. and L.W. performed the research. J.L., Z.L., C.T. and D.Z. analysed the data. J.L., Z.L., A.S. and D.Z. wrote the paper. All authors discussed and edited the manuscript.

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Correspondence to Dongping Zhong.

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The authors declare no competing financial interests.

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This file contains Supplementary Kinetic Data Analysis, Supplementary Table 1 and Supplementary Figures 1S-3S with legends. (PDF 151 kb)

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Li, J., Liu, Z., Tan, C. et al. Dynamics and mechanism of repair of ultraviolet-induced (6–4) photoproduct by photolyase. Nature 466, 887–890 (2010). https://doi.org/10.1038/nature09192

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