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
RNA serves a number of functions in the cell: mRNAs are the carriers of information between gene and protein, tRNAs and rRNAs are involved in the synthesis of proteins, whereas a number of additional RNA species are responsible for other functions in the cell. The quality of the different RNAs as well as the controlled turnover of these in response to changing surrounding conditions is of vital importance to ensure optimal fitness of a cell. 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. We have solved the structures of two nucleases involved in 3'-5' degradation of RNA; the S. pombe Pop2p and the S. cerevisiae Rrp6p. Pop2p is part of the main cytoplasmatic deadenylation complex in yeast, which also contains the nuclease Ccr4p. Deadenylation, where the poly(A)-tail is removed form the 3'-end of mRNA, is normally the first and also rate-limiting step in cellular mRNA degradation and therefore a key process in the control of eukaryotic mRNA turnover. Since Ccr4p is believed to be the main deadenylase the precise role of Pop2p in the complex is less clear. Nevertheless, Pop2p has a DEDD-type exonuclease signature and has also been shown to possess deadenylase activity in vitro but it is possible that Pop2p is mainly required for more specialised roles in vivo. These could for instance be in the regulation or targeting of the deadenylation process or to degrade some specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures of very similar nucleases provide a visualisation of the catalytic cycle of the S. pombe Pop2p protein. In addition, structural comparison of S. pombe Pop2p to other similar proteins identifies Pop2p and deadenylase specific regions near the active site. Contrary to Pop2p Rrp6p is solely a nuclear protein. In the nucleus Rrp6p associates with the exosome and participates in the degradation of improperly processed precursor mRNAs and trimming of stable RNAs. The crystal structure of S. cerevisiae Rrp6p presented here displays a conserved DEDD nuclease core with a flanking HRDC domain believed to be involved in RNA binding. The HRDC domain is found in an unusual conformation in Rrp6p compared to the bacterial RNase D protein but functional studies shown that this orientation is important for the processing function of the enzyme. Complexes with AMP and UMP, the products of the RNA degradation process, reveal how the protein specifically recognizes ribonucleotides and their bases and the importance of specific divalent ions for the binding of these. Both Pop2p and Rrp6p belong to the family of DEDD nucleases with the active sites of the two proteins containing these four acidic residues as well as two divalent cations. However, they belong to two different subgroups within this nucleases family Pop2p being of the DEDDh subtype whereas Rrp6p is a DEDDy subtype nuclease i.e. the fifth active site residue is a histidine and a tyrosine, respectively. A structural comparison of the two structures reveals two fundamental different types of structure organization. Although both proteins contain a common core nuclease region surrounded by protein specific structural elements the placement of these divergent additional features in the protein sequences was quite different. In the Pop2p sequence the extra structural elements are mainly placed as insertions within the core exonuclease sequence whereas the Rrp6p instead has the N-terminal tail of the protein wrapped around the exonuclease domain thereby covering the surface of the domain.