1CKO

STRUCTURE OF MRNA CAPPING ENZYME IN COMPLEX WITH THE CAP ANALOG GPPPG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping.

Hakansson, K.Wigley, D.B.

(1998) Proc Natl Acad Sci U S A 95: 1505-1510

  • DOI: 10.1073/pnas.95.4.1505
  • Primary Citation of Related Structures:  
    1CKO

  • PubMed Abstract: 
  • Paramecium bursaria Chlorella virus PBCV-1 mRNA guanylyl transferase (capping enzyme) has been complexed with an mRNA cap analogue G[5']ppp[5']G and crystallized. The crystals belong to space group C2221 with unit cell dimensions a = 78.4 A, b = 164. ...

    Paramecium bursaria Chlorella virus PBCV-1 mRNA guanylyl transferase (capping enzyme) has been complexed with an mRNA cap analogue G[5']ppp[5']G and crystallized. The crystals belong to space group C2221 with unit cell dimensions a = 78.4 A, b = 164.1 A, c = 103.3 A, and diffraction data to 3.1 A has been collected by using synchrotron radiation. The structure has been solved by molecular replacement by using each of the two domains in the previously determined structure of the enzyme in complex with GTP. The conformation is open with respect to the active site cleft, and all contacts between enzyme and ligand are mediated by domain 1. One of the guanine bases is bound in the same pocket that is utilized by GTP. The conformation of the ligand positions the beta phosphate and the active site lysine on opposite sides of the alpha phosphate. This geometry is optimal for nucleophilic substitution reactions and has previously been found for GTP in the closed conformational form of the capping enzyme, where the lysine can be guanylylated upon treatment with excess manganese(II) ions. The remainder of the cap analogue runs along the conserved active site Lys82 Thr83 Asp84 Gly85 Ile86 Arg87 motif, and the second guanine, corresponding to the 5' RNA base, is stacked against the hydrophobic Ile86. The ligand displays approximate 2-fold symmetry with intramolecular hydrogen bonding between the 2' and 3' hydroxyls of the two ribose rings.


    Related Citations: 
    • Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1
      Doherty, A.J., Hakansson, K., Ho, C.K., Shuman, S., Wigley, D.B.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 482
    • 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

    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, 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
Find proteins for Q84424 (Paramecium bursaria Chlorella virus 1)
Explore Q84424 
Go to UniProtKB:  Q84424
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GP3
Query on GP3

Download CCD File 
A
DIGUANOSINE-5'-TRIPHOSPHATE
C20 H27 N10 O18 P3
AAXYAFFKOSNMEB-MHARETSRSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.476α = 90
b = 164.013β = 90
c = 103.502γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance