Dcp2: an mRNA decapping enzyme that adopts many different shapes and forms

Abstract

Eukaryotic mRNAs contain a 5' cap structure that protects the transcript against rapid exonucleolytic degradation. The regulation of cellular mRNA levels therefore depends on a precise control of the mRNA decapping pathways. The major mRNA decapping enzyme in eukaryotic cells is Dcp2. It is regulated by interactions with several activators, including Dcp1, Edc1, and Edc3, as well as by an autoinhibition mechanism. The structural and mechanistical characterization of Dcp2 complexes has long been impeded by the high flexibility and dynamic nature of the enzyme. Here we review recent insights into the catalytically active conformation of the mRNA decapping complex, the mode of action of decapping activators and the large interactions network that Dcp2 is embedded in.

Graphical abstract

Figure 1

Overview of Dcp2 mediated mRNA decapping. (a) Structure of m⁷G capped mRNA. The Dcp2 mediated decapping reaction produces m⁷GDP and 5’-monophosphate mRNA (b) 5’-3’ mRNA decay pathway: Shortening of the polyA tail by the CCr4–Not complex and Pan2/3 leads to dissociation of the PABP and recruitment of the LSm1-7:Pat1 complex. The interaction between Pat1 and the IDR of Dcp2 facilitates binding of the Dcp1:Dcp2 complex. After decapping of the mRNA by Dcp2, the exonuclease Xrn1 is recruited and rapidly degrades the mRNA in the 5’-3’ direction. (c) Domain organization of the S. pombe Dcp1:Dcp2 complex.

Figure 2

Structures of the Dcp2 enzyme. (a) Crystal structures of Dcp2 in isolation and in different complexes. The orientation of the Dcp2 RD (dark blue) is identical in all structures and the structures are grouped according to the orientation between RD and CD (yellow) of Dcp2. The catalytic NUDIX helix is shown in red, bound ligands in green, Edc1 and Edc3 in pink and Dcp1 in light blue. References and PDB codes are shown below the structures. (b) The split active site in the catalytically competent orientation 6a. The cap structure is recognized by W43 and D47 in the RD and by R190 and K191 in the CD. The catalytically important Mg²⁺ ions (green spheres) are bound by the NUDIX helix and come close to the triphosphate linkage. (c) The active conformation in the Dcp1:Dcp2:Edc1:m⁷GDP complex (orientation 6a). m⁷GDP and the YAG activation motif of Edc1 are sandwiched between the CD and RD of Dcp2. The proline rich region in Edc1 interacts with Dcp1. (d) The RNA body binds to a positively charged surface in the active conformation (conformation 6c). Dcp2 is colored according to the electrostatic surface potential (blue positive, red negative, other proteins are colored as in (a)). The RNA binding path is indicated in green. The structure of the two-headed cap analog used for crystallization is shown at the bottom.

Figure 3

Conformations that Dcp2 adopts in solution. Free Dcp2 (top left) equally populates a dynamic, open state (grey) and the closed state (conformation 4, orange). Binding of Dcp1 stabilizes the closed state (top middle), whereas binding of Edc1 has no influence on the conformations of Dcp2 (top right). Binding of capped RNA to the Dcp1:Dcp2:Edc1 complex locks Dcp2 in the active state (bottom right, conformation 6, red). Addition of capped mRNA to Dcp1:Dcp2 in the absence of Edc1 is not sufficient to lock Dcp2 in the active state but competes with the closed state and leads to a mixture of open and active state (bottom middle).

Figure 4

The Dcp1:Dcp2 complex is part of a dense interaction network of mRNA decay factors. Known interaction partners of Dcp1:Dcp2 are shown and the interactions between them are indicated. Interactions are colored according to the interaction partners (black: interactions between folded domains, red: interactions involving a SLiM, grey: interaction sites are unknown). Many of the interactions are mediated by SLiMs and known structures of SLiMs bound to folded domains are shown (SLiMs are colored red, folded domains orange, PDB codes are shown below the structures). Note that the Pdc1 protein is not present in all yeast species.