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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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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.


    Related Citations: 
    • Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1 Change During Guanyl Transfer by Mrna Capping Enzymes
      Doherty, A.J., Hakansson, K., Ho, C.K., Shuman, S., Wigley, D.B.
      () To be published --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MRNA CAPPING ENZYMEA330Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A103R
EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1)
Explore Q84424 
Go to UniProtKB:  Q84424
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MRNA CAPPING ENZYMEB330Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A103R
EC: 2.7.7.50
UniProt
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1)
Explore Q84424 
Go to UniProtKB:  Q84424
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GPL
Query on GPL
BL-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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Ligand Structure Quality Assessment  



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