Schizosaccharomyces pombe Dcp2-Dcp1-Edc1 mRNA-decapping Complex

Naomi Kennel '25 and Lauren Lehr '25

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I. Introduction

The Schizosaccharomyces pombe Dcp2-Dcp1-Edc1 mRNA-decapping complex is involved with the removal of the mRNA 5' cap which shuts down translation and commits the target mRNA to degradation. This is a critical step in the regulation of gene expression and many cellular RNA decay pathways such as bulk 5'-3' decay, nonsense-mediated decay, microRNA-mediated decay, decay of long-noncoding RNA, and decay of transcripts containing non-optimal codons. The Dcp2-Dcp1-Edc1 complex is highly dynamic and undergoes conformational changes that correlate with activity and substrate selectivity. Dcp2 is a pyrophosphatase that catalyzes decapping through hydrolysis which releases m7GDP and 5' monophosphate RNA, which can then be degraded by 5'-3' exonucleases. Dcp2 is bound by Dcp1 which then forms the core of the decapping complex. Catalysis occurs at a split active site formed between two Dcp2 domains and a conformational change must occur from a closed to open complex for catalysis to occur. This conformational change is regulated by enhancers of decapping (Edcs).

An important Edc for the Dcp2-Dcp1 activated complex is which promotes the conformational change necessary to activate decapping by rotating the catalytic domain of Dcp2 to form a cleft to accommodate the mRNA substrate. This rotation allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding and for a composite active site to form. 

II. General Structure

consists of a which is connected to an "N-terminal regulatory domain (NRD)" by a . The flexible hinge is essential in allowing the enzyme to adopt different conformations. The CD contains a positively charged patch for the RNA binding and a loop-helix-loop Nudix motif with conserved glutamine residues that bind through water-mediated contacts to perform cap hydrolysis chemistry. The NRD domain enhances decapping activity by recognizing the m7G nucleotide of the cap and binding the to further accelerate decapping. In the presence of the Dcp1 EVH1 domain, two conformations of the Dcp2-Dcp1 complex have been visualized by X-ray crystallography. First, an open conformation in which the CD and NRD are splayed apart and second, a closed conformation where the two Dpc2 domains face each other.

Edc1 promotes the catalytically active complex conformation through its 25 most C-terminal residues which are a conserved decapping-activator motif (DAM). The DAM contains a conserved YAGX2F motif followed by a which binds the Dcp1 The YAGX2F activation motif mediates a three-way interface between Dcp1 and the Dcp2 NRD and CD by threading through a channel between these domains. It contains N-terminal Dcp2-binding residues (DBR) which form a beta strand to reinforce the Beta-sheet of the Dcp2 CD and is followed by a loop that contacts the Dcp2 NRD domain.  

III. Dcp1 Binding

The formation of the Dcp2-Dcp1-Edc1 mRNA-decapping complex occurs in a stepwise manner as first, Dcp2 recruits Dcp1 which is achieved through the stabilization of the NRD domain. The Dcp2-Dcp1 complex has a closed formation which represents the stabilized state of the complex. Then, Edc1 mediates the activation of Dcp2-Dcp1 through its YAGX2F motif that stabilizes the active conformation. The first step of recruiting Dcp1 is done through binding Dcp1 to the NRD of Dcp2. Dcp1 contains a binding platform for proline-rich peptide ligands that can recruit other mRNA decay factors and so it uses a to recruit Edc1 through its PRS. Dcp1 must recruit Edc1 to activate the Dcp2-Dcp1 conformation because Dcp1 binding forms the closed state of the complex. The on the Nudix helix are positioned too far from the bound mRNA substrate to carry out hydrolysis chemistry. Thus, activation of Edc1 is necessary to induce a conformational change in the complex in the presence of its substrate RNA. 

IV. Activation by Edc1

Decapping activation of the Dcp2-Dcp1 complex requires the entire DAM peptide and occurs through a cascade of interactions. The DAM peptide binds to the Dcp1 EVH1 domain through hydrophobic contacts along the PRS. The PRS has highly conserved residues along with invariant residues that interact in a with aromatic Dcp1 residues. The YAGX2F motif of Edc1 has additionally hydrophobic stacking interactions with the Dcp2 NRD domain which are mediated by on Edc1 . These interactions cause a 120 degree rotation of the Nudix domain. During this rotation, the invariant Dcp2 residue W43 on the alpha3 of the NRD acts as a that is between I156 and Y158 of the Edc1 beta-strand. The resulting rotation brings the RNA-binding residues of the Box B helix and additional Nudix residues into a that forms between the Nudix domain and the the NRD-Dcp1 module with the Edc1 beta-strand at its base. The cleft formation and rotation of the Nudix domain represent the active complex conformation.

Reorganization of RNA-binding surfaces in the presence of Edc1

Figure 1. Reorganization of RNA-binding surfaces in the presence of Edc1. (a) Dcp2-Dcp1 closed complex (b) Dcp2-Dcp1-Edc1 activated complex. In the presence of Edc1, rotation of the Nudix domain forms an RNA binding channel lined by positively charged residues from Dcp1 (dotted green) and the Box-B helix (dotted purple). (Valkov et al, 2016)

V. RNA Binding

RNA binding is improved in the activated conformation with the addition of Edc1 to the Dcp2-Dcp1 complex. In the absence of Edc1, the RNA binding channel is buried in the closed structure of Dcp2-Dcp1. In the presence of Edc1, the Dcp1 EVH1 domain helps to stabilize Nudix-domain orientation and the RNA-binding channel. It does this through the Dcp1 NR-loop22 , where N72 is fixed by the Q40 in Dcp2 NRD. Additionally, Dcp1 makes main and side chain contacts with that connect to the edge of the Edc1 Beta-strand. The EVH1 domain contains RNA-binding residues (K230, K231, K234 and K235) on the Nudix Box B helix and additional residues (K44 and K47) to form the . The surface of this wall is hydrophilic and positively charged in order to accommodate RNA-binding.


VI. References

Chang CT, Bercovich N, Loh B, Jonas S, Izaurralde E. The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1. Nucleic Acids Res. 2014 Apr;42(8):5217-33. doi: 10.1093/nar/gku129. Epub 2014 Feb 8. PMID: 24510189; PMCID: PMC4005699.

Mugridge, J.S., Tibble, R.W., Ziemniak, M. et al. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun 9, 1152 (2018). https://doi.org/10.1038/s41467-018-03536-x

Robin A. Aglietti, Stephen N. Floor, Chris L. McClendon, Matthew P. Jacobson, John D. Gross, Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2 Structure, Cell Press, Volume 21, Issue 9, 2013, Pages 1571-1580, ISSN 0969-2126, https://doi.org/10.1016/j.str.2013.06.021.

She M, Decker CJ, Svergun DI, Round A, Chen N, Muhlrad D, Parker R, Song H. Structural basis of dcp2 recognition and activation by dcp1. Mol Cell. 2008 Feb 15;29(3):337-49. doi: 10.1016/j.molcel.2008.01.002. PMID: 18280239; PMCID: PMC2323275.

Valkov, E., Muthukumar, S., Chang, CT. et al. Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation. Nat Struct Mol Biol 23, 574–579 (2016). https://doi.org/10.1038/nsmb.3232

Wurm JP, Holdermann I, Overbeck JH, Mayer PHO, Sprangers R. Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6034-6039. doi: 10.1073/pnas.1704496114. Epub 2017 May 22. PMID: 28533364; PMCID: PMC5468633.

Wurm JP, Sprangers R. Dcp2: an mRNA decapping enzyme that adopts many different shapes and forms. Curr Opin Struct Biol. 2019 Dec;59:115-123. doi: 10.1016/j.sbi.2019.07.009. Epub 2019 Aug 29. PMID: 31473440; PMCID: PMC6900585.

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