4K6E

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme dcp2.

Aglietti, R.A.Floor, S.N.McClendon, C.L.Jacobson, M.P.Gross, J.D.

(2013) Structure 21: 1571-1580

  • DOI: 10.1016/j.str.2013.06.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. He ...

    Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.


    Organizational Affiliation

    Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA-decapping enzyme subunit 2
A
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DCP2 (PSU1)
EC: 3.6.1.62
Find proteins for P53550 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: DCP2
Go to UniProtKB:  P53550
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.153 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 85.054α = 90.00
b = 85.054β = 90.00
c = 48.749γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description