Letter | Published:

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease


Most eukaryotic messenger RNA precursors (pre-mRNAs) undergo extensive maturational processing, including cleavage and polyadenylation at the 3′-end1,2,3,4,5,6,7,8. Despite the characterization of many proteins that are required for the cleavage reaction, the identity of the endonuclease is not known4,9,10. Recent analyses indicated that the 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF-73) might be the endonuclease for this and related reactions10,11,12,13,14,15, although no direct data confirmed this. Here we report the crystal structures of human CPSF-73 at 2.1 Å resolution, complexed with zinc ions and a sulphate that might mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1) at 2.5 Å resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-β-lactamase domain and a novel β-CASP (named for metallo-β-lactamase, CPSF, Artemis, Snm1, Pso2) domain12. The active site of CPSF-73, with two zinc ions, is located at the interface of the two domains. Purified recombinant CPSF-73 possesses RNA endonuclease activity, and mutations that disrupt zinc binding in the active site abolish this activity. Our studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3′-end-processing endonuclease.

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We thank K. Ryan for discussions; B. Tweel for characterizing the fungus; R. Abramowitz, J. Schwanof and X. Yang for setting up the X4A beamline at the NSLS; and J. Khan and Y. Shen for help with data collection at the synchrotron. This research is supported in part by grants from the National Institutes of Health.

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Competing interests

The atomic coordinates have been deposited at the Protein Data Bank (accession numbers 2I7T, 2I7V and 2I7X). Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Correspondence to Liang Tong.

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Supplementary Notes

This file contains Supplementary Results, Supplementary Methods, Supplementary Tables 1 and 1 and Supplementary Figures 1–9. (PDF 3416 kb)

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Figure 1: Structures of human CPSF-73 and yeast CPSF-100 (Ydh1).
Figure 2: The β-CASP domain of CPSF-73 and CPSF-100.
Figure 3: The active site of CPSF-73.
Figure 4: CPSF-73 possesses endoribonuclease activity.


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