Jonstrup, Anette Thyssen1; Midtgaard, Søren Fuglsang2; Van, Lan Bich4; Brodersen, Ditlev Egeskov4
1 Department of Molecular Biology, Faculty of Science, Aarhus University, Aarhus University2 Department of Molecular Biology and Genetics - Department of Molecular Biology, Department of Molecular Biology and Genetics, Science and Technology, Aarhus University3 Department of Molecular Biology and Genetics - Structural Biology, Department of Molecular Biology and Genetics, Science and Technology, Aarhus University4 Department of Molecular Biology and Genetics - Structural Biology, Department of Molecular Biology and Genetics, Science and Technology, Aarhus University
The precise regulation of the cellular levels of different RNA species is important for cell function as well as securing the integrity of each individual RNA. Central to both these processes is the degradation of RNA, either as a means of decreasing the level of particular RNAs or as a way to get rid of aberrant RNAs. Here we describe the structures of two 3'-5' exonucleases involved in controlled RNA decay in yeast, Pop2p and Rrp6p. Rrp6p is associated with the nuclear exosome where it participates in the degradation of improperly processed precursor mRNAs and trimming of stable RNAs . Pop2p is a catalytic subunit of the cytoplasmic deadenylase complex , which removes the poly(A) tail in the 3'-end of mRNA, the first and rate-limiting step of controlled mRNA turnover in the general eukaryotic mRNA degradation pathway . The crystal structure of the central part of S. cerevisiae Rrp6p including the exonuclease and HRDC domains was solved by MAD and MIR and determined to a resolution of 2.1 Å, whereas Pop2p from S. pombe was solved by SIRAS to 1.4 Å. In both was solved by SIRAS to 1.4 Å. In both cases, heavy atom derivatives were quick-soaked into the crystals by adding 500 mM of the respective derivative to the cryo buffer and soaking for a few seconds. The native Pop2p crystal showed a remarkably low solvent content of 28%. Both Pop2p and Rrp6p belong to the RNase D family of DEDD nucleases with the active sites of the two proteins containing these four acidic residues as well as two divalent cations. The Pop2p structure reveals that the ability of this enzyme to degrade poly(A)/(U)/(C), but not poly(G) may be determined by structural hindrance of interaction with this specific nucleotide. In Rrp6p, mutations known to confer specific RNA degradation phenotypes in yeast nuclei can now be understood from a structural point of view.  Phillips & Butler (2003). RNA, 9, 1098-1107.  Daugeron et al.(2001). Nucleic Acids Res., 29, 2448-2455.  Parker & Song (2004). Nat. Struct. Mol. Biol., 11(2), 121-127.