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Structure of an aprataxin–DNA complex with insights into AOA1 neurodegenerative disease

Nature Structural & Molecular Biology volume 18, pages 1189–1195 (2011)Cite this article

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Abstract

DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5′-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5′-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx–DNA–AMP–Zn2+ complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove–binding C2HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5′-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5′-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).

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Figure 1: The X-ray crystal structure of the Aptx–DNA–AMP–Zn2+ quaternary complex.
Figure 2: Aptx structure-specific DNA binding.
Figure 3: Aptx DNA binding and deadenylation activity.
Figure 4: Aptx adenylate access and catalytic mechanism.
Figure 5: AOA1 mutations.
Figure 6: Nicked and gapped DNA binding by Aptx.

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Change history

  • 16 October 2011

    In the HTML version of this article initially published online, the corresponding author was given as Jessica S. Williams, instead of R. Scott Willliams. The error has been corrected in the HTML version of this article.

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Acknowledgements

This research was supported by the intramural research program of the US National Institutes of Health (NIH), National Institute of Environmental Health Sciences (NIEHS) (1Z01ES102765-01 to R.S.W.). We thank L. Pedersen, T. Kunkel and S. Wilson for discussions and critical reading of the manuscript, the Advanced Photon Source (APS) Southeast Regional Collaborative Access Team (SER-CAT) staff for assistance with crystallographic data collection, and we thank J. Williams of the NIEHS Protein Microcharacterization Core Facility for mass spectrometry analysis.

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Authors and Affiliations

  1. Department of Health and Human Services, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, US National Institutes of Health, North Carolina, USA

    Percy Tumbale, C Denise Appel, Patrick D Robertson, Jessica S Williams, Joe Krahn & R Scott Williams

  2. Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK

    Rolf Kraehenbuehl & Ivan Ahel

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  1. Percy Tumbale
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Contributions

P.T. conducted and analyzed experiments and helped write the manuscript. C.D.A., R.K. and J.S.W. conducted experiments. P.D.R. and J.K. analyzed results. I.A. designed experiments and analyzed results. R.S.W. designed research, did experiments, analyzed results and wrote the manuscript.

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Correspondence to R Scott Williams.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 3010 kb)

Supplementary Movie 1

Aptx engagement of a nicked or gapped DNA-adenylate. Aptx employs the helical wedge with Phe34 (Blue) to displace a stacked 5′-adenylate (orange). The DNA (green) morphs between a model B-DNA conformation and the backbone conformation observed in the Aptx–DNA–AMP–Zn complex structure. A slight under-winding of the duplex is observed upon binding. Grey DNA is a modeled conformation of the predicted positioning of the upstream region of nick or gapped duplex bearing a 5′-AMP. Intercalation of the wedge helix into the base stack necessitates displacement of the upstream DNA. HIT domain is shown in purple and Znf in gold/brown. (MOV 21034 kb)

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Tumbale, P., Appel, C., Kraehenbuehl, R. et al. Structure of an aprataxin–DNA complex with insights into AOA1 neurodegenerative disease. Nat Struct Mol Biol 18, 1189–1195 (2011). https://doi.org/10.1038/nsmb.2146

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