Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.84 kDa 
• Atom Count: 3624 
• Modelled Residue Count: 385 
• Deposited Residue Count: 388 
• Unique protein chains: 1

3MS5

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

• DOI: 10.2210/pdb3MS5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2010-04-29 Released: 2010-05-12 
• Deposition Author(s): Krojer, T., Kochan, G., McDonough, M.A., von Delft, F., Leung, I.K.H., Henry, L., Claridge, T.D.W., Pilka, E., Ugochukwu, E., Muniz, J., Filippakopoulos, P., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

---

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 

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

• PubMed: 21168767 
• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-butyrobetaine dioxygenase	A	388	Homo sapiens	Mutation(s): 0  Gene Names: BBH, BBOX, BBOX1 EC: 1.14.11.1
Find proteins for O75936 (Homo sapiens) Explore O75936  Go to UniProtKB:  O75936
NIH Common Fund Data Resources
PHAROS:  O75936 GTEx:  ENSG00000129151

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REE	A	2-(2-carboxyethyl)-1,1,1-trimethyldiazanium C6 H15 N2 O2 PVBQYTCFVWZSJK-UHFFFAOYSA-O
OGA	A	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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 = 107.366	α = 90
b = 107.366	β = 90
c = 205.054	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-29 
• Released Date: 2010-05-12 
Deposition Author(s): Krojer, T., Kochan, G., McDonough, M.A., von Delft, F., Leung, I.K.H., Henry, L., Claridge, T.D.W., Pilka, E., Ugochukwu, E., Muniz, J., Filippakopoulos, P., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

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