5FHQ | pdb_00005fhq

Crystal structure of (WT) Rat Catechol-O-Methyltransferase in complex with AdoMet and 3,5-dinitrocatechol (DNC)

• PDB DOI: https://doi.org/10.2210/pdb5FHQ/pdb

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


• Deposited: 2015-12-22 Released: 2016-02-03 
• Deposition Author(s): Levy, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase.

Law, B.J., Bennett, M.R., Thompson, M.L., Levy, C., Shepherd, S.A., Leys, D., Micklefield, J.

(2016) Angew Chem Int Ed Engl 55: 2683-2687

• PubMed: 26797714 
• DOI: https://doi.org/10.1002/anie.201508287
• Primary Citation Related Structures: 
  5FHQ, 5FHR


• PubMed Abstract: 
  

  Catechol-O-methyltransferase (COMT), an important therapeutic target in the treatment of Parkinson's disease, is also being developed for biocatalytic processes, including vanillin production, although lack of regioselectivity has precluded its more widespread application. By using structural and mechanistic information, regiocomplementary COMT variants were engineered that deliver either meta- or para-methylated catechols. X-ray crystallography further revealed how the active-site residues and quaternary structure govern regioselectivity. Finally, analogues of AdoMet are accepted by the regiocomplementary COMT mutants and can be used to prepare alkylated catechols, including ethyl vanillin.

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Organizational Affiliation: 
• School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
School of Chemistry & Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.6 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 213 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	213	Rattus norvegicus	Mutation(s): 0  Gene Names: Comt 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	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
DNC	C [auth A]	3,5-DINITROCATECHOL C6 H4 N2 O6 VDCDWNDTNSWDFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DNC	BindingDB:  5FHQ	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.72	α = 90
b = 50.72	β = 90
c = 167.55	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Levy, C.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-02-24
  Changes: Database references
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Refinement description