mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2

Abstract

Cap hydrolysis by Dcp2 is a critical step in several eukaryotic mRNA decay pathways. Processing requires access to cap-proximal nucleotides and the coordinated assembly of a decapping mRNP, but the mechanism of substrate recognition and regulation by protein interactions have remained elusive. Using NMR spectroscopy and kinetic analyses, we show that yeast Dcp2 resolves interactions with the cap and RNA body using a bipartite surface that forms a channel intersecting the catalytic and regulatory Dcp1-binding domains. The interaction with cap is weak but specific and requires binding of the RNA body to a dynamic interface. The catalytic step is stimulated by Dcp1 and its interaction domain, likely through a substrate-induced conformational change. Thus, activation of the decapping mRNP is restricted by access to 5'-proximal nucleotides, a feature that could act as a checkpoint in mRNA metabolism.

The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface

“…1A; She et al 2006). The catalytic domain contains the active site and an interaction groove for the RNA body (Deshmukh et al 2008). The N-terminal domain serves two purposes: First, it enhances the activity of the catalytic domain by recognizing part of the mRNA cap structure (Floor et al 2010), and secondly, it directly interacts with the decapping activator Dcp1 (She et al 2008).…”

mRNA Decapping Enzyme 1a (Dcp1a)-induced Translational Arrest through Protein Kinase R (PKR) Activation Requires the N-terminal Enabled Vasodilator-stimulated Protein Homology 1 (EVH1) Domain

“…Previous studies have demonstrated the involvement of Dcp1a in cellular signaling pathways through protein-protein interactions (36,37). All eukaryotic orthologues of Dcp1a contain an N-terminal EVH1 (enabled vasodilator-stimulated protein homology 1) domain (30,31,37,38). EVH1 domains are known to interact with a variety of proline-rich protein ligands (39 -41).…”

DCP1 forms asymmetric trimers to assemble into active mRNA decapping complexes in metazoa

“…Yeast DCP2 interacts directly with DCP1 and this interaction is required for decapping in vivo and in vitro (3)(4)(5)(6)(7). In humans, the DCP2-DCP1 interaction requires additional proteins, which together assemble into multimeric decapping complexes that also include the enhancers of decapping 3 and 4 (EDC3 and ECD4), and the DEAD-box protein DDX6/RCK (8,9).…”

“…In humans, the DCP2-DCP1 interaction requires additional proteins, which together assemble into multimeric decapping complexes that also include the enhancers of decapping 3 and 4 (EDC3 and ECD4), and the DEAD-box protein DDX6/RCK (8,9). DCP2 is highly conserved and most information on DCP2 activation stems mainly from studies in S. cerevisiae and S. pombe (3)(4)(5)(6)(7). Fungi, however, lack EDC4 as well as many extensions and additional domains present in decapping activators of metazoan orthologs (8)(9)(10).…”

“…Fungi, however, lack EDC4 as well as many extensions and additional domains present in decapping activators of metazoan orthologs (8)(9)(10). For example, all eukaryotic DCP1 proteins contain an N-terminal EVH1 domain (3,5,6); however, DCP1 orthologs from metazoa and plants also have a proline-rich C-terminal extension (9, 10). The sequence of this extension is not conserved except for a 14-residue short motif (motif I, MI) conserved in metazoa with the exception of C. elegans ( Fig.…”