Crystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and Sinefungin

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

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Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase.

Czarnota, S.Johannissen, L.O.Baxter, N.J.Rummel, F.Wilson, A.L.Cliff, M.J.Levy, C.W.Scrutton, N.S.Waltho, J.P.Hay, S.

(2019) ACS Catal 9: 4394-4401

  • DOI: https://doi.org/10.1021/acscatal.9b00174
  • Primary Citation of Related Structures:  
    6I3C, 6I3D

  • PubMed Abstract: 

    Catechol- O -methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg 2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.

  • Organizational Affiliation

    Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catechol O-methyltransferase
A, B
232Homo sapiensMutation(s): 0 
Gene Names: COMT
UniProt & NIH Common Fund Data Resources
Find proteins for P21964 (Homo sapiens)
Explore P21964 
Go to UniProtKB:  P21964
PHAROS:  P21964
GTEx:  ENSG00000093010 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21964
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.961α = 90
b = 75.797β = 94.62
c = 64.345γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2019-09-18 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
European CommissionUnited KingdomPITN-GA-2013-ITN 606831

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description