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RRP6 is a 3′–5′ exoribonuclease associated to the eukaryotic exosome, a multiprotein complex essential for various RNA processing and degradation pathways. In  Trypanosoma brucei , RRP6 associates with the exosome in stoichiometric amounts and was localized in both cytoplasm and nucleus, in contrast to yeast Rrp6 which is exclusively nuclear. Here we report the biochemical and structural characterization of  T. brucei  RRP6 ( Tb RRP6) and its interaction with the so-called  T. brucei  Exosome Associated Protein 3 ( Tb EAP3), a potential orthologue of the yeast Rrp6 interacting protein, Rrp47. Recombinant  Tb EAP3 is a thermo stable homodimer in solution, however it forms a heterodimeric complex with  Tb RRP6 with 1∶1 stoichiometry. The crystallographic structure of the  Tb RRP6 catalytic core exposes for the first time the native catalytic site of this RNase and also reveals a disulfide bond linking two helices of the HRDC domain. RNA degradation assays show the distributive exoribonuclease activity of  Tb RRP6 and novel findings regarding the structural range of its RNA substrates.  Tb RRP6 was able to degrade single and double-stranded RNAs and also RNA substrates containing stem-loops including those with 3′ stem-loop lacking single-stranded extensions. Finally, association with  Tb EAP3 did not significantly interfere with the  Tb RRP6 catalytic activity  in vitro .

plos one

RRP6 from Trypanosoma brucei: Crystal Structure of the Catalytic Domain, Association with EAP3 and Activity towards Structured and Non-Structured RNA Substrates