2VDW

Guanosine N7 methyl-transferase sub-complex (D1-D12) of the vaccinia virus mRNA capping enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insights Into the Mechanism and Evolution of the Vaccinia Virus Mrna CAP N7 Methyl- Transferase.

De La Pena, M.Kyrieleis, O.J.P.Cusack, S.

(2007) EMBO J 26: 4913

  • DOI: https://doi.org/10.1038/sj.emboj.7601912
  • Primary Citation of Related Structures:  
    2VDW

  • PubMed Abstract: 

    The vaccinia virus mRNA capping enzyme is a multifunctional heterodimeric protein associated with the viral polymerase that both catalyses the three steps of mRNA capping and regulates gene transcription. The structure of a subcomplex comprising the C-terminal N7-methyl-transferase (MT) domain of the large D1 subunit, the stimulatory D12 subunit and bound S-adenosyl-homocysteine (AdoHcy) has been determined at 2.7 A resolution and reveals several novel features of the poxvirus capping enzyme. The structure shows for the first time the critical role played by the proteolytically sensitive N-terminus of the MT domain in binding the methyl donor and in catalysis. In addition, the poxvirus enzyme has a completely unique mode of binding of the adenosine moiety of AdoHcy, a feature that could be exploited for design of specific anti-poxviral compounds. The structure of the poxvirus-specific D12 subunit suggests that it was originally an RNA cap 2'O-MT that has evolved to a catalytically inactive form that has been retained for D1 stabilisation and MT activity enhancement through an allosteric mechanism.


  • Organizational Affiliation

    Grenoble Outstation, European Molecular Biology Laboratory, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
A, C, E, G
302Vaccinia virusMutation(s): 0 
EC: 2.7.7.50
UniProt
Find proteins for P04298 (Vaccinia virus (strain Western Reserve))
Explore P04298 
Go to UniProtKB:  P04298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04298
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 ENZYME SMALL SUBUNIT
B, D, F, H
287Vaccinia virusMutation(s): 0 
EC: 2.1.1.56
UniProt
Find proteins for P04318 (Vaccinia virus (strain Western Reserve))
Explore P04318 
Go to UniProtKB:  P04318
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04318
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
J [auth A],
L [auth C],
O [auth E],
S [auth G]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]
K [auth C]
M [auth C]
N [auth E]
P [auth F]
I [auth A],
K [auth C],
M [auth C],
N [auth E],
P [auth F],
Q [auth F],
R [auth G],
T [auth H],
U [auth H],
V [auth H],
W [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.89α = 94.22
b = 61.02β = 92.95
c = 225.78γ = 108.26
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance