1VPT

AS11 VARIANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.

Hodel, A.E.Gershon, P.D.Shi, X.Quiocho, F.A.

(1996) Cell 85: 247-256

  • DOI: 10.1016/s0092-8674(00)81101-0
  • Primary Citation of Related Structures:  
    1VPT

  • PubMed Abstract: 
  • VP39 is a bifunctional vaccinia virus protein that acts as both an mRNA cap-specific RNA 2'-O-methyltransferase and a poly(A) polymerase processivity factor. Here, we report the 1.85 A crystal structure of a VP39 variant complexed with its AdoMet cofactor ...

    VP39 is a bifunctional vaccinia virus protein that acts as both an mRNA cap-specific RNA 2'-O-methyltransferase and a poly(A) polymerase processivity factor. Here, we report the 1.85 A crystal structure of a VP39 variant complexed with its AdoMet cofactor. VP39 comprises a single core domain with structural similarity to the catalytic domains of other methyltransferases. Surface features and mutagenesis data suggest two possible RNA-binding sites with novel underlying architecture, one of which forms a cleft spanning the region adjacent to the methyltransferase active site. This report provides a prototypic structure for an RNA methyltransferase, a protein that interacts with the mRNA 5' cap, and an intact poxvirus protein.


    Related Citations: 
    • Methyltransferase-Specific Domains within Vp39, a Bifunctional Enzyme which Participates in the Modification of Both Mrna Ends
      Shi, X., Yao, P., Jose, T., Gershon, P.D.
      () To be published --: --
    • Mutational Analysis of a Multifunctional Protein, with Mrna 5' CAP-Specific (Nucleoside-2'-O-)-Methyltransferase and 3'-Adenylyltransferase Stimulatory Activities, Encoded by Vaccinia Virus
      Schnierle, B.S., Gershon, P.D., Moss, B.
      (1994) J Biol Chem 269: 20700

    Organizational Affiliation

    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP39A348Vaccinia virus WRMutation(s): 1 
Gene Names: PAPSVACWR095J3R
EC: 2.7.7.19 (PDB Primary Data), 2.1.1.57 (UniProt)
UniProt
Find proteins for P07617 (Vaccinia virus (strain Western Reserve))
Explore P07617 
Go to UniProtKB:  P07617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07617
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.3α = 90
b = 67.8β = 118.4
c = 80.4γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations