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Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe

Nature Structural & Molecular Biology volume 13, pages 63–70 (2006)Cite this article

Abstract

Decapping is a key step in both general and nonsense-mediated 5′ → 3′ mRNA-decay pathways. Removal of the cap structure is catalyzed by the Dcp1–Dcp2 complex. The crystal structure of a C-terminally truncated Schizosaccharomyces pombe Dcp2p reveals two distinct domains: an all-helical N-terminal domain and a C-terminal domain that is a classic Nudix fold. The C-terminal domain of both Saccharomyces cerevisiae and S. pombe Dcp2p proteins is sufficient for decapping activity, although the N-terminal domain can affect the efficiency of Dcp2p function. The binding of Dcp2p to Dcp1p is mediated by a conserved surface on its N-terminal domain, and the N-terminal domain is required for Dcp1p to stimulate Dcp2p activity. The flexible nature of the N-terminal domain relative to the C-terminal domain suggests that Dcp1p binding to Dcp2p may regulate Dcp2p activity through conformational changes of the two domains.

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Figure 1: Crystal structure of spDcp2n and comparison with other Nudix enzymes.
Figure 2: The Nudix motif of spDcp2n is a catalytic center.
Figure 3: Surface views of spDcp2n.
Figure 4: The N-terminal domain affects the efficiency of Dcp2p in vitro.
Figure 5: The N-terminal domain of Dcp2p is required for Dcp1p to stimulate decapping.
Figure 6: The N terminus of Dcp2p is absolutely required in vivo for decapping.
Figure 7: Dcp1p interacts with the N-terminal domain of Dcp2p.

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Acknowledgements

We would like to thank the beamline scientists at ID29 (European Synchrotron Radiation Facility) for assistance and access to their facilities. Plasmids and yeast strains used for the two-hybrid analysis were provided by S. Fields, Howard Hughes Medical Institute, University of Washington. pRP2075 was provided by J. Coller, Howard Hughes Medical Institute, University of Arizona. This work was financially supported by the Agency for Science, Technology and Research (A* Star) in Singapore (H.S.) and by the Howard Hughes Medical Institute (R.P.).

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Author notes

  1. Meipei She and Carolyn J Decker: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore

    Meipei She, Nan Chen & Haiwei Song

  2. Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, 85721, Arizona, USA

    Carolyn J Decker, Suneeta Tumati & Roy Parker

  3. Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543, Singapore

    Haiwei Song

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Correspondence to Roy Parker or Haiwei Song.

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Supplementary information

Supplementary Fig. 1

Sequence alignment of Dcp2 proteins. (PDF 267 kb)

Supplementary Fig. 2

CD spectra of the wild-type spDcp2n and its variants. (PDF 150 kb)

Supplementary Fig. 3

Mutations in scDcp2p do not significantly decrease the level of Dcp2 protein in vivo. (PDF 140 kb)

Supplementary Table 1

Phenotypes of S. pombe (Sp) and S. cerevisiae (Sc) Dcp2p point mutants (PDF 84 kb)

Supplementary Methods

Western analysis of Dcp2-GFP proteins (PDF 73 kb)

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She, M., Decker, C., Chen, N. et al. Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe. Nat Struct Mol Biol 13, 63–70 (2006). https://doi.org/10.1038/nsmb1033

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