3MS5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
    3O2G, 3MS5

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-butyrobetaine dioxygenaseA388Homo sapiensMutation(s): 0 
Gene Names: BBHBBOXBBOX1
EC: 1.14.11.1
Find proteins for O75936 (Homo sapiens)
Explore O75936 
Go to UniProtKB:  O75936
NIH Common Fund Data Resources
PHAROS  O75936
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REE
Query on REE

Download CCD File 
A
2-(2-carboxyethyl)-1,1,1-trimethyldiazanium
C6 H15 N2 O2
PVBQYTCFVWZSJK-UHFFFAOYSA-O
 Ligand Interaction
OGA
Query on OGA

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A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.366α = 90
b = 107.366β = 90
c = 205.054γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2019-03-20
    Changes: Data collection, Database references