Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2648 
• Modelled Residue Count: 291 
• Deposited Residue Count: 307 
• Unique protein chains: 1

3MAG

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE

• PDB DOI: 10.2210/pdb3MAG/pdb

• Classification: MRNA PROCESSING
• Organism(s): Vaccinia virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-07-12 Released: 1999-07-22 
• Deposition Author(s): Hu, G., Hodel, A.E., Gershon, P.D., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

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 U S A 96: 7149-7154

• PubMed: 10377383 
• DOI: 10.1073/pnas.96.13.7149
• Primary Citation of Related Structures:  
  1B42, 1BKY, 1EAM, 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP39	A	307	Vaccinia virus	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
3MA	C [auth A]	6-AMINO-3-METHYLPURINE C6 H8 N5 YLIQVEPMZVVUEK-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
3MA	Binding MOAD:  3MAG	Kd: 8.60e+4 (nM) from 1 assay(s)
	PDBBind:  3MAG	Kd: 8.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.5	α = 90
b = 67.21	β = 117.3
c = 79.56	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SMART	data reduction
SAINT	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-12 
• Released Date: 1999-07-22 
Deposition Author(s): Hu, G., Hodel, A.E., Gershon, P.D., Quiocho, F.A.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance