5LTH

Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM) in complex with the dimethylamine substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme.

Ortmayer, M.Lafite, P.Menon, B.R.Tralau, T.Fisher, K.Denkhaus, L.Scrutton, N.S.Rigby, S.E.Munro, A.W.Hay, S.Leys, D.

(2016) Nature 539: 593-597

  • DOI: 10.1038/nature20159
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The universal Per-ARNT-Sim (PAS) domain functions as a signal transduction module involved in sensing diverse stimuli such as small molecules, light, redox state and gases. The highly evolvable PAS scaffold can bind a broad range of ligands, includin ...

    The universal Per-ARNT-Sim (PAS) domain functions as a signal transduction module involved in sensing diverse stimuli such as small molecules, light, redox state and gases. The highly evolvable PAS scaffold can bind a broad range of ligands, including haem, flavins and metal ions. However, although these ligands can support catalytic activity, to our knowledge no enzymatic PAS domain has been found. Here we report characterization of the first PAS enzyme: a haem-dependent oxidative N-demethylase. Unrelated to other amine oxidases, this enzyme contains haem, flavin mononucleotide, 2Fe-2S and tetrahydrofolic acid cofactors, and specifically catalyses the NADPH-dependent oxidation of dimethylamine. The structure of the α subunit reveals that it is a haem-binding PAS domain, similar in structure to PAS gas sensors. The dimethylamine substrate forms part of a highly polarized oxygen-binding site, and directly assists oxygen activation by acting as both an electron and proton donor. Our data reveal that the ubiquitous PAS domain can make the transition from sensor to enzyme, suggesting that the PAS scaffold can support the development of artificial enzymes.


    Organizational Affiliation

    Manchester Institute of Biotechnology, School of Chemistry, 131 Princess Street, University of Manchester, Manchester M1 7DN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
heme dependent oxidative N-demethylase
A
344Pseudomonas mendocina (strain ymp)Mutation(s): 0 
Find proteins for A4XXY9 (Pseudomonas mendocina (strain ymp))
Go to UniProtKB:  A4XXY9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DMN
Query on DMN

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Download CCD File 
A
DIMETHYLAMINE
C2 H7 N
ROSDSFDQCJNGOL-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.380α = 90.00
b = 80.380β = 90.00
c = 144.790γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-09-06 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Ortmayer, M., Leys, D.

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references
  • Version 1.2: 2016-12-07
    Type: Database references
  • Version 1.3: 2016-12-21
    Type: Database references