5J3Y

Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex

Summary for 5J3Y

• Entry DOI: 10.2210/pdb5j3y/pdb
• Related: 5J3Q 5J3T
• Descriptor: mRNA-decapping enzyme subunit 1, mRNA decapping complex subunit 2 (2 entities in total)
• Functional Keywords: hydrolase, decapping, mrna decay, evh1, nudix
• Biological source: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast); More
• Cellular location: Cytoplasm : Q9P805; Cytoplasm, P-body : O13828
• Total number of polymer chains: 4
• Total formula weight: 87388.49

Authors

Valkov, E.,Muthukumar, S.,Chang, C.T.,Jonas, S.,Weichenrieder, O.,Izaurralde, E. (deposition date: 2016-03-31, release date: 2016-05-18, Last modification date: 2024-01-10)

Primary citation

Valkov, E.,Muthukumar, S.,Chang, C.T.,Jonas, S.,Weichenrieder, O.,Izaurralde, E.
Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.
Nat.Struct.Mol.Biol., 23:574-579, 2016

PubMed Abstract: The removal of the mRNA 5' cap (decapping) by Dcp2 shuts down translation and commits mRNA to full degradation. Dcp2 activity is enhanced by activator proteins such as Dcp1 and Edc1. However, owing to conformational flexibility, the active conformation of Dcp2 and the mechanism of decapping activation have remained unknown. Here, we report a 1.6-Å-resolution crystal structure of the Schizosaccharomyces pombe Dcp2-Dcp1 heterodimer in an unprecedented conformation that is tied together by an intrinsically disordered peptide from Edc1. In this ternary complex, an unforeseen rotation of the Dcp2 catalytic domain allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding, thus explaining decapping activation by increased substrate affinity. The architecture of the Dcp2-Dcp1-Edc1 complex provides a rationale for the conservation of a sequence motif in Edc1 that is also present in unrelated decapping activators, thus indicating that the presently described mechanism of decapping activation is evolutionarily conserved.

PubMed: 27183195
DOI: 10.1038/nsmb.3232

Experimental method

X-RAY DIFFRACTION (3.288 Å)