4CWD | pdb_00004cwd

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

• PDB DOI: https://doi.org/10.2210/pdb4CWD/pdb

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


• Deposited: 2014-04-02 Released: 2014-09-17 
• Deposition Author(s): McDonough, M.A., Kochan, G., Rydzik, A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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

• PubMed: 25164544 
• DOI: https://doi.org/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.4 kDa 
• Atom Count: 3,553 
• Modelled Residue Count: 385 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-BUTYROBETAINE DIOXYGENASE	A	388	Homo sapiens	Mutation(s): 0  EC: 1.14.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75936 (Homo sapiens) Explore O75936  Go to UniProtKB:  O75936
PHAROS:  O75936 GTEx:  ENSG00000129151

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
449	D [auth A]	4-carboxy-1,1-dimethylpiperidin-1-ium C8 H16 N O2 ZUZDUOOCVXTRAU-UHFFFAOYSA-O
OGA	E [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.518	α = 90
b = 106.518	β = 90
c = 205.347	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): McDonough, M.A., Kochan, G., Rydzik, A., Schofield, C.J.

Revision History  

• 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
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description