1VPT

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

• PDB DOI: https://doi.org/10.2210/pdb1VPT/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-03-20 Released: 1996-08-17 
• Deposition Author(s): Hodel, A.E., Gershon, P.D., Shi, X., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.215 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

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

• PubMed: 8612277 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.32 kDa 
• Atom Count: 2,633 
• Modelled Residue Count: 291 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP39	A	348	Vaccinia virus WR	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.215 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.3	α = 90
b = 67.8	β = 118.4
c = 80.4	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-08-17 
Deposition Author(s): Hodel, A.E., Gershon, P.D., Shi, X., Quiocho, F.A.

Revision History  

• 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
• Version 1.5: 2024-02-14
  Changes: Data collection