1VID

CATECHOL O-METHYLTRANSFERASE

• PDB DOI: https://doi.org/10.2210/pdb1VID/pdb

• Classification: TRANSFERASE (METHYLTRANSFERASE)
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-01-05 Released: 1996-07-11 
• Deposition Author(s): Vidgren, J., Svensson, L.A., Liljas, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Crystal structure of catechol O-methyltransferase.

Vidgren, J., Svensson, L.A., Liljas, A.

(1994) Nature 368: 354-358

• PubMed: 8127373 
• DOI: https://doi.org/10.1038/368354a0
• Primary Citation of Related Structures:  
  1VID


• PubMed Abstract: 
  

  Catechol O-methyltransferase (COMT, EC 2.1.1.6) is important in the central nervous system because it metabolizes catecholamine neurotransmitters such as dopamine. The enzyme catalyses the transfer of the methyl group from S-adenosyl-L-methionine (AdoMet) to one hydroxyl group of catechols. COMT also inactivates catechol-type compounds such as L-DOPA. With selective inhibitors of COMT in combination with L-DOPA, a new principle has been realized in the therapy of Parkinson's disease. Here we solve the atomic structure of COMT to 2.0 A resolution, which provides new insights into the mechanism of the methyl transfer reaction. The co-enzyme-binding domain is strikingly similar to that of an AdoMet-dependent DNA methylase, indicating that all AdoMet methylases may have a common structure.

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Organizational Affiliation: 

Orion Corporation, Espoo, Finland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.4 kDa 
• Atom Count: 1,858 
• Modelled Residue Count: 213 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATECHOL O-METHYLTRANSFERASE	A	221	Rattus norvegicus	Mutation(s): 0  EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734  Go to UniProtKB:  P22734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
DNC	D [auth A]	3,5-DINITROCATECHOL C6 H4 N2 O6 VDCDWNDTNSWDFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DNC	BindingDB:  1VID	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.3	α = 90
b = 51.3	β = 90
c = 168.5	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Vidgren, J., Svensson, L.A., Liljas, A.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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, Other