4C8R

Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of gamma-butyrobetaine hydroxylase.

Rydzik, A.M.Chowdhury, R.Kochan, G.T.Williams, S.T.McDonough, M.A.Kawamura, A.Schofield, C.J.

(2014) Chem Sci 5: 1765-1771

  • DOI: 10.1039/C4SC00020J

  • PubMed Abstract: 
  • Carnitine is essential for fatty acid metabolism, but is associated with both health benefits and risks, especially heart diseases. We report the identification of potent, selective and cell active inhibitors of γ-butyrobetaine hydroxylase (BBOX), wh ...

    Carnitine is essential for fatty acid metabolism, but is associated with both health benefits and risks, especially heart diseases. We report the identification of potent, selective and cell active inhibitors of γ-butyrobetaine hydroxylase (BBOX), which catalyses the final step of carnitine biosynthesis in animals. A crystal structure of BBOX in complex with a lead inhibitor reveals that it binds in two modes, one of which adopts an unusual 'U-shape' conformation stabilised by inter- and intra-molecular π-stacking interactions. Conformational changes observed on binding of the inhibitor to BBOX likely reflect those occurring in catalysis; they also rationalise the inhibition of BBOX by high levels of its substrate γ-butyrobetaine (GBB), as observed both with isolated BBOX protein and in cellular studies.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA-BUTYROBETAINE DIOXYGENASE
A, B, C, D, E, F
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, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, E, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
6YT
Query on 6YT

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine
C15 H15 N3 O4 S
KMBXCWNZAPWGKZ-NSHDSACASA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D, E, F
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 195.744α = 90.00
b = 91.659β = 90.00
c = 167.132γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Database references
  • Version 1.2: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.3: 2019-02-06
    Type: Data collection, Experimental preparation