Crystallographic Structure of the Nuclease Domain of 3′hExo, a DEDDh Family Member, Bound to rAMP

A human 3′-5′-exoribonuclease (3′hExo) has recently been identified and shown to be responsible for histone mRNA degradation. Functionally, 3′hExo and a stem–loop binding protein (SLBP) target opposite faces of a unique highly conserved stem–loop RNA scaffold towards the 3′ end of histone mRNA, which is composed of a 6 bp stem and a 4 nt loop, followed by an ACCCA sequence. Its Caenorhabditis elegans homologue, ERI-1, has been shown to degrade small interfering RNA in vitro and to function as a negative regulator of RNA interference in neuronal cells. We have determined the structure of the nuclease domain (Nuc) of 3′hExo complexed with rAMP in the presence of Mg2+ at 1.6 Å resolution. The Nuc domain adopts an α/β globular fold, with four acidic residues coordinating a binuclear metal cluster within the active site, whose topology is related to DEDDh exonuclease family members, despite a very low level of primary sequence identity. The two magnesium cations in the Nuc active site are coordinated to D134, E136, D234 and D298, and together with H293, which can potentially act as a general base, provide a platform for hydrolytic cleavage of bound RNA in the 3′→5′ direction. The bound rAMP is positioned within a deep active-site pocket, with its purine ring close-packed with the hydrophobic F185 and L189 side-chains and its sugar 2′-OH and 3′-OH groups hydrogen bonded to backbone atoms of Nuc. There are striking similarities between the active sites of Nuc and ε186, an Escherichia coli DNA polymerase III proofreading domain, providing a common hydrolytic cleavage mechanism for RNA degradation and DNA editing, respectively.