3O2G

Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dioxygenase 1 (BBOX1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and mechanistic studies on gamma-butyrobetaine hydroxylase.

Leung, I.K.Krojer, T.J.Kochan, G.T.Henry, L.von Delft, F.Claridge, T.D.Oppermann, U.McDonough, M.A.Schofield, C.J.

(2010) Chem. Biol. 17: 1316-1324

  • DOI: 10.1016/j.chembiol.2010.09.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The final step in carnitine biosynthesis is catalyzed by γ-butyrobetaine (γBB) hydroxylase (BBOX), an iron/2-oxoglutarate (2OG) dependent oxygenase. BBOX is inhibited by trimethylhydrazine-propionate (THP), a clinically used compound. We report struc ...

    The final step in carnitine biosynthesis is catalyzed by γ-butyrobetaine (γBB) hydroxylase (BBOX), an iron/2-oxoglutarate (2OG) dependent oxygenase. BBOX is inhibited by trimethylhydrazine-propionate (THP), a clinically used compound. We report structural and mechanistic studies on BBOX and its reaction with THP. Crystallographic and sequence analyses reveal that BBOX and trimethyllysine hydroxylase form a subfamily of 2OG oxygenases that dimerize using an N-terminal domain. The crystal structure reveals the active site is enclosed and how THP competes with γBB. THP is a substrate giving formaldehyde (supporting structural links with histone demethylases), dimethylamine, malonic acid semi-aldehyde, and an unexpected product with an additional carbon-carbon bond resulting from N-demethylation coupled to oxidative rearrangement, likely via an unusual radical mechanism. The results provide a basis for development of improved BBOX inhibitors and may inspire the discovery of additional rearrangement reactions.


    Organizational Affiliation

    The Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX13TA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-butyrobetaine dioxygenase
A
388Homo sapiensMutation(s): 0 
Gene Names: BBOX1 (BBH, BBOX)
EC: 1.14.11.1
Find proteins for O75936 (Homo sapiens)
Go to Gene View: BBOX1
Go to UniProtKB:  O75936
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NM2
Query on NM2

Download SDF File 
Download CCD File 
A
3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM
C7 H16 N O2
JHPNVNIEXXLNTR-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 107.386α = 90.00
b = 107.386β = 90.00
c = 204.919γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
GDAdata collection
REFMACrefinement
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-03-20
    Type: Data collection, Database references, Derived calculations