2ix0

OverviewOverview

RNA degradation is a determining factor in the control of gene expression., The maturation, turnover and quality control of RNA is performed by many, different classes of ribonucleases. Ribonuclease II (RNase II) is a major, exoribonuclease that intervenes in all of these fundamental processes; it, can act independently or as a component of the exosome, an essential, RNA-degrading multiprotein complex. RNase II-like enzymes are found in all, three kingdoms of life, but there are no structural data for any of the, proteins of this family. Here we report the X-ray crystallographic, structures of both the ligand-free (at 2.44 A resolution) and RNA-bound, (at 2.74 A resolution) forms of Escherichia coli RNase II. In contrast to, sequence predictions, the structures show that RNase II is organized into, four domains: two cold-shock domains, one RNB catalytic domain, which has, an unprecedented alphabeta-fold, and one S1 domain. The enzyme establishes, contacts with RNA in two distinct regions, the 'anchor' and the, 'catalytic' regions, which act synergistically to provide catalysis. The, active site is buried within the RNB catalytic domain, in a pocket formed, by four conserved sequence motifs. The structure shows that the catalytic, pocket is only accessible to single-stranded RNA, and explains the, specificity for RNA versus DNA cleavage. It also explains the dynamic, mechanism of RNA degradation by providing the structural basis for RNA, translocation and enzyme processivity. We propose a reaction mechanism for, exonucleolytic RNA degradation involving key conserved residues. Our, three-dimensional model corroborates all existing biochemical data for, RNase II, and elucidates the general basis for RNA degradation. Moreover, it reveals important structural features that can be extrapolated to other, members of this family.

About this StructureAbout this Structure

2IX0 is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as Exoribonuclease II, with EC number 3.1.13.1 Known structural/functional Site: . Full crystallographic information is available from OCA.

ReferenceReference

Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex., Frazao C, McVey CE, Amblar M, Barbas A, Vonrhein C, Arraiano CM, Carrondo MA, Nature. 2006 Sep 7;443(7107):110-4. PMID:16957732

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