2JVB

Solution Structure of Catalytic Domain of yDcp2

Summary for 2JVB

• Entry DOI: 10.2210/pdb2jvb/pdb
• Descriptor: mRNA-decapping enzyme subunit 2 (1 entity in total)
• Functional Keywords: dcp2, mrna decay, decapping, cytoplasm, hydrolase, manganese, metal-binding, mrna processing, nonsense-mediated mrna decay, nucleus, phosphorylation, rna-binding
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Cytoplasm, P-body: P53550
• Total number of polymer chains: 1
• Total formula weight: 17378.91

Authors

Deshmukh, M.,Gross, J. (deposition date: 2007-09-16, release date: 2008-03-04, Last modification date: 2024-05-29)

Primary citation

Deshmukh, M.V.,Jones, B.N.,Quang-Dang, D.U.,Flinders, J.,Floor, S.N.,Kim, C.,Jemielity, J.,Kalek, M.,Darzynkiewicz, E.,Gross, J.D.
mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2.
Mol.Cell, 29:324-336, 2008

PubMed 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.

PubMed: 18280238
DOI: 10.1016/j.molcel.2007.11.027

Experimental method

SOLUTION NMR