2JVB

Solution Structure of Catalytic Domain of yDcp2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2.

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.

(2008) Mol Cell 29: 324-336

  • DOI: 10.1016/j.molcel.2007.11.027
  • Primary Citation of Related Structures:  
    2JVB

  • 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 ...

    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.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94107, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA-decapping enzyme subunit 2A146Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DCP2PSU1
EC: 3 (PDB Primary Data), 3.6.1.62 (UniProt)
Find proteins for P53550 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53550 
Go to UniProtKB:  P53550
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2JVB Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance