4CWD

CRYSTAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE,2-OXOGLUTARATE IN COMPLEX WITH 449, A NOVEL SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Oxygenase-catalyzed desymmetrization of N,N-dialkyl-piperidine-4-carboxylic acids.

Rydzik, A.M.Leung, I.K.Kochan, G.T.McDonough, M.A.Claridge, T.D.Schofield, C.J.

(2014) Angew Chem Int Ed Engl 53: 10925-10927

  • DOI: 10.1002/anie.201406125
  • Primary Citation of Related Structures:  
    4CWD

  • PubMed Abstract: 
  • γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N-dialkyl piperidine-4-carboxylates to give products with two or three stereogenic centers ...

    γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N-dialkyl piperidine-4-carboxylates to give products with two or three stereogenic centers.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA (UK).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-BUTYROBETAINE DIOXYGENASE A388Homo sapiensMutation(s): 0 
Gene Names: BBOX1BBHBBOX
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
449
Query on 449

Download Ideal Coordinates CCD File 
A
4-carboxy-1,1-dimethylpiperidin-1-ium
C8 H16 N O2
ZUZDUOOCVXTRAU-UHFFFAOYSA-O
 Ligand Interaction
OGA
Query on OGA

Download Ideal Coordinates CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.518α = 90
b = 106.518β = 90
c = 205.347γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary