Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folic acid

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.

Leys, D.Basran, J.Scrutton, N.S.

(2003) EMBO J 22: 4038-4048

  • DOI: https://doi.org/10.1093/emboj/cdg395
  • Primary Citation of Related Structures:  
    1PJ5, 1PJ6, 1PJ7

  • PubMed Abstract: 

    Here we report crystal structures of dimethylglycine oxidase (DMGO) from the bacterium Arthrobacter globiformis, a bifunctional enzyme that catalyzes the oxidation of N,N-dimethyl glycine and the formation of 5,10-methylene tetrahydrofolate. The N-terminal region binds FAD covalently and oxidizes dimethylglycine to a labile iminium intermediate. The C-terminal region binds tetrahydrofolate, comprises three domains arranged in a ring-like structure and is related to the T-protein of the glycine cleavage system. The complex with folinic acid indicates that this enzyme selectively activates the N10 amino group for initial attack on the substrate. Dead-end reactions with oxidized folate are avoided by the strict stereochemical constraints imposed by the folate-binding funnel. The active sites in DMGO are approximately 40 A apart, connected by a large irregular internal cavity. The tetrahydrofolate-binding funnel serves as a transient entry-exit port, and access to the internal cavity is controlled kinetically by tetrahydrofolate binding. The internal cavity enables sequestration of the reactive iminium intermediate prior to reaction with tetrahydrofolate and avoids formation of toxic formaldehyde. This mode of channelling in DMGO is distinct from other channelling mechanisms.

  • Organizational Affiliation

    University of Leicester, Department of Biochemistry, University Road, Leicester LE1 7RH, UK. dl37@le.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N,N-dimethylglycine oxidase830Arthrobacter globiformisMutation(s): 0 
Find proteins for Q9AGP8 (Arthrobacter globiformis)
Explore Q9AGP8 
Go to UniProtKB:  Q9AGP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AGP8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.877α = 90
b = 222.506β = 90
c = 119.304γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description