6AM0

Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog

Summary for 6AM0

• Entry DOI: 10.2210/pdb6am0/pdb
• Descriptor: KLLA0F23980p, KLLA0E01827p, KLLA0A01474p, ... (6 entities in total)
• Functional Keywords: mrna decay, decapping, nudix, nucleotide analog, translation
• Biological source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast); More
• Total number of polymer chains: 8
• Total formula weight: 129816.62

Authors

Mugridge, J.S.,Gross, J.D. (deposition date: 2017-08-08, release date: 2018-03-21, Last modification date: 2023-10-04)

Primary citation

Mugridge, J.S.,Tibble, R.W.,Ziemniak, M.,Jemielity, J.,Gross, J.D.
Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis.
Nat Commun, 9:1152-1152, 2018

PubMed Abstract: The conserved decapping enzyme Dcp2 recognizes and removes the 5' eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1-Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1-Dcp1-Dcp2-Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis.

PubMed: 29559651
DOI: 10.1038/s41467-018-03536-x

Experimental method

X-RAY DIFFRACTION (2.84 Å)