The discovery of RNA-mediated gene-silencing pathways, including RNA interference1,2,3, highlights a fundamental role of short RNAs in eukaryotic gene regulation4,5,6,7,8,9,10 and antiviral defence11,12. Members of the Dicer and Argonaute protein families are essential components of these RNA-silencing pathways13,14,15,16,17,18,19. Notably, these two families possess an evolutionarily conserved PAZ (Piwi/Argonaute/Zwille) domain whose biochemical function is unknown. Here we report the nuclear magnetic resonance solution structure of the PAZ domain from Drosophila melanogaster Argonaute 1 (Ago1). The structure consists of a left-handed, six-stranded β-barrel capped at one end by two α-helices and wrapped on one side by a distinctive appendage, which comprises a long β-hairpin and a short α-helix. Using structural and biochemical analyses, we demonstrate that the PAZ domain binds a 5-nucleotide RNA with 1:1 stoichiometry. We map the RNA-binding surface to the open face of the β-barrel, which contains amino acids conserved within the PAZ domain family, and we define the 5′-to-3′ orientation of single-stranded RNA bound within that site. Furthermore, we show that PAZ domains from different human Argonaute proteins also bind RNA, establishing a conserved function for this domain.
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We thank R. W. Williams for providing a D. melanogaster Ago1 expressed sequenced tag clone, T. Tuschl for complementary DNAs encoding human Argonaute proteins, and T. A. Edwards for discussions. K.S.Y. is a recipient of a National Institutes of Health (NIH) predoctoral training grant fellowship. M.-M.Z. is supported by NIH grants, and is a member of the New York Structural Biology Center.
The authors declare that they have no competing financial interests.
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Yan, K., Yan, S., Farooq, A. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 469–474 (2003). https://doi.org/10.1038/nature02129
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