1EAM

VACCINIA METHYLTRANSFERASE VP39 MUTANT (EC: 2.7.7.19)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.

Hu, G.Gershon, P.D.Hodel, A.E.Quiocho, F.A.

(1999) Proc.Natl.Acad.Sci.USA 96: 7149-7154

  • Primary Citation of Related Structures:  1B42, 1BKY, 1EQA, 3MAG, 3MCT, 4DCG

  • PubMed Abstract: 
  • We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcy ...

    We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii) substantial areas of overlap in the two-stacked rings, (iii) a 3.4-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.


    Organizational Affiliation

    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (VP39)
A
307Vaccinia virus (strain Western Reserve)Gene Names: PAPS
EC: 2.1.1.57
Find proteins for P07617 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P07617
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.998α = 90.00
b = 67.506β = 117.42
c = 79.919γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance