1CKN

STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

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This is version 1.3 of the entry. See complete history. 


Literature

X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.

Hakansson, K., Doherty, A.J., Shuman, S., Wigley, D.B.

(1997) Cell 89: 545-553

  • DOI: https://doi.org/10.1016/s0092-8674(00)80236-6
  • Primary Citation of Related Structures:  
    1CKM, 1CKN

  • PubMed Abstract: 

    We have solved the crystal structure of an mRNA capping enzyme at 2.5 A resolution. The enzyme comprises two domains with a deep, but narrow, cleft between them. The two molecules in the crystallographic asymmetric unit adopt very different conformations; both contain a bound GTP, but one protein molecule is in an open conformation while the other is in a closed conformation. Only in the closed conformation is the enzyme able to bind manganese ions and undergo catalysis within the crystals to yield the covalent guanylated enzyme intermediate. These structures provide direct evidence for a mechanism that involves a significant conformational change in the enzyme during catalysis.

    • Organizational Affiliation: 

    Laboratory of Molecular Biophysics, University of Oxford, United Kingdom.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MRNA CAPPING ENZYME330Paramecium bursaria Chlorella virus 1Mutation(s): 0 
EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1)
Explore Q84424 
Go to UniProtKB:  Q84424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84424
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MRNA CAPPING ENZYME330Paramecium bursaria Chlorella virus 1Mutation(s): 0 
EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1)
Explore Q84424 
Go to UniProtKB:  Q84424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84424
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GPL
Query on GPL
B
L-PEPTIDE LINKINGC16 H26 N7 O9 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.906α = 90
b = 212.953β = 90
c = 105.016γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description