1RI1

Structure and mechanism of mRNA cap (guanine N-7) methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanism of mRNA cap (Guanine-n7) methyltransferase

Fabrega, C.Hausmann, S.Shen, V.Shuman, S.Lima, C.D.

(2004) Mol.Cell 13: 77-89

  • Primary Citation of Related Structures:  1RI2, 1RI3, 1RI4, 1RI5

  • PubMed Abstract: 
  • A suite of crystal structures is reported for a cellular mRNA cap (guanine-N7) methyltransferase in complex with AdoMet, AdoHcy, and the cap guanylate. Superposition of ligand complexes suggests an in-line mechanism of methyl transfer, albeit without ...

    A suite of crystal structures is reported for a cellular mRNA cap (guanine-N7) methyltransferase in complex with AdoMet, AdoHcy, and the cap guanylate. Superposition of ligand complexes suggests an in-line mechanism of methyl transfer, albeit without direct contacts between the enzyme and either the N7 atom of guanine (the attacking nucleophile), the methyl carbon of AdoMet, or the sulfur of AdoMet/AdoHcy (the leaving group). The structures indicate that catalysis of cap N7 methylation is accomplished by optimizing proximity and orientation of the substrates, assisted by a favorable electrostatic environment. The enzyme-ligand structures, together with new mutational data, fully account for the biochemical specificity of the cap guanine-N7 methylation reaction, an essential and defining step of eukaryotic mRNA synthesis.


    Organizational Affiliation

    Biochemistry Department, Structural Biology Program, Weill Medical College, Cornell University, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA CAPPING ENZYME
A
298Encephalitozoon cuniculi (strain GB-M1)Gene Names: ABD1
EC: 2.1.1.56
Find proteins for Q8SR66 (Encephalitozoon cuniculi (strain GB-M1))
Go to UniProtKB:  Q8SR66
Small Molecules
Ligands 2 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
GTG
Query on GTG

Download SDF File 
Download CCD File 
A
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
MRNA CAP ANALOG N7-METHYL GPPPG
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.644α = 90.00
b = 63.644β = 90.00
c = 112.443γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance