1RI1

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

• PDB DOI: https://doi.org/10.2210/pdb1RI1/pdb

• Classification: TRANSFERASE
• Organism(s): Encephalitozoon cuniculi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-11-16 Released: 2004-02-03 
• Deposition Author(s): Fabrega, C., Hausmann, S., Shen, V., Shuman, S., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.284 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

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

• PubMed: 14731396 
• DOI: https://doi.org/10.1016/s1097-2765(03)00522-7
• Primary Citation of Related Structures:  
  1RI1, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.01 kDa 
• Atom Count: 2,177 
• Modelled Residue Count: 252 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA CAPPING ENZYME	A	298	Encephalitozoon cuniculi	Mutation(s): 0  Gene Names: ECU10_0380 EC: 2.1.1.56
UniProt
Find proteins for Q8SR66 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR66  Go to UniProtKB:  Q8SR66

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTG	C [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE C21 H30 N10 O18 P3 FHHZHGZBHYYWTG-INFSMZHSSA-O
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.284 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.644	α = 90
b = 63.644	β = 90
c = 112.443	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-03 
Deposition Author(s): Fabrega, C., Hausmann, S., Shen, V., Shuman, S., Lima, C.D.

Revision History  

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations