3GSI

Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde.

Tralau, T.Lafite, P.Levy, C.Combe, J.P.Scrutton, N.S.Leys, D.

(2009) J.Biol.Chem. 284: 17826-17834

  • DOI: 10.1074/jbc.M109.006262

  • PubMed Abstract: 
  • We report a synthetic biology approach to demonstrate substrate channeling in an unusual bifunctional flavoprotein dimethylglycine oxidase. The catabolism of dimethylglycine through methyl group oxidation can potentially liberate toxic formaldehyde, ...

    We report a synthetic biology approach to demonstrate substrate channeling in an unusual bifunctional flavoprotein dimethylglycine oxidase. The catabolism of dimethylglycine through methyl group oxidation can potentially liberate toxic formaldehyde, a problem common to many amine oxidases and dehydrogenases. Using a novel synthetic in vivo reporter system for cellular formaldehyde, we found that the oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channeling mechanism. We also showed that uncoupling of the active sites could be achieved by mutagenesis or deletion of the 5,10-methylenetetrahydrofolate synthase site and that this leads to accumulation of intracellular formaldehyde. Channeling occurs by nonbiased diffusion of the labile intermediate through a large solvent cavity connecting both active sites. This central "reaction chamber" is created by a modular protein architecture that appears primitive when compared with the sophisticated design of other paradigm substrate-channeling enzymes. The evolutionary origins of the latter were likely similar to dimethylglycine oxidase. This work demonstrates the utility of synthetic biology approaches to the study of enzyme mechanisms in vivo and points to novel channeling mechanisms that protect the cell milieu from potentially toxic reaction products.


    Organizational Affiliation

    Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N,N-dimethylglycine oxidase
A
827Arthrobacter globiformisMutation(s): 1 
Gene Names: dmg
EC: 1.5.3.10
Find proteins for Q9AGP8 (Arthrobacter globiformis)
Go to UniProtKB:  Q9AGP8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
THG
Query on THG

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Download CCD File 
A
(6S)-5,6,7,8-TETRAHYDROFOLATE
C19 H23 N7 O6
MSTNYGQPCMXVAQ-RYUDHWBXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.150 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.215α = 90.00
b = 224.548β = 90.00
c = 119.382γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
DNAdata collection
XDSdata reduction
PHENIXphasing
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance