5KQ1

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of mRNA-cap recognition by Dcp1-Dcp2.

Mugridge, J.S.Ziemniak, M.Jemielity, J.Gross, J.D.

(2016) Nat Struct Mol Biol 23: 987-994

  • DOI: 10.1038/nsmb.3301
  • Primary Citation of Related Structures:  
    5KQ4, 5KQ1

  • PubMed Abstract: 
  • Removal of the 5' cap on mRNA by the decapping enzyme Dcp2 is a critical step in 5'-to-3' mRNA decay. Understanding the structural basis of Dcp2 activity has been a challenge because Dcp2 is dynamic and has weak affinity for the cap substrate. Here we present a 2 ...

    Removal of the 5' cap on mRNA by the decapping enzyme Dcp2 is a critical step in 5'-to-3' mRNA decay. Understanding the structural basis of Dcp2 activity has been a challenge because Dcp2 is dynamic and has weak affinity for the cap substrate. Here we present a 2.6-Å-resolution crystal structure of a heterotrimer of fission yeast Dcp2, its essential activator Dcp1, and the human NMD cofactor PNRC2, in complex with a tight-binding cap analog. Cap binding is accompanied by a conformational change in Dcp2, thereby forming a composite nucleotide-binding site comprising conserved residues in the catalytic and regulatory domains. Kinetic analysis of PNRC2 revealed that a conserved short linear motif enhances both substrate affinity and the catalytic step of decapping. These findings explain why Dcp2 requires a conformational change for efficient catalysis and reveals that coactivators promote RNA binding and the catalytic step of decapping, possibly through different conformational states.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA-decapping enzyme subunit 1 AD130Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dcp1SPBC3B9.21
Find proteins for Q9P805 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P805 
Go to UniProtKB:  Q9P805
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proline-rich nuclear receptor coactivator 2 CF31Homo sapiensMutation(s): 0 
Gene Names: PNRC2HSPC208
Find proteins for Q9NPJ4 (Homo sapiens)
Explore Q9NPJ4 
Go to UniProtKB:  Q9NPJ4
NIH Common Fund Data Resources
PHAROS:  Q9NPJ4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA decapping complex subunit 2 BE249Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dcp2SPAC19A8.12
EC: 3
Find proteins for O13828 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13828 
Go to UniProtKB:  O13828
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.622α = 90
b = 118.727β = 102.77
c = 93.174γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM078360
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM105313

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence