5YS9

Crystal structure of acyl-coA oxidase3 from Yarrowia lipolytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Acyl-CoA Oxidase 3 fromYarrowia lipolyticawith Specificity for Short-Chain Acyl-CoA.

Kim, S.Kim, K.J.

(2018) J Microbiol Biotechnol 28: 597-605

  • DOI: 10.4014/jmb.1711.11032
  • Primary Citation of Related Structures:  
    5YS9

  • PubMed Abstract: 
  • Acyl-CoA oxidases (ACOXs) play important roles in lipid metabolism, including peroxisomal fatty acid β-oxidation by the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The yeast Yarrowia lipolytica can utilize fatty acids as a carbon source and t ...

    Acyl-CoA oxidases (ACOXs) play important roles in lipid metabolism, including peroxisomal fatty acid β-oxidation by the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The yeast Yarrowia lipolytica can utilize fatty acids as a carbon source and thus has extensive biotechnological applications. The crystal structure of ACOX3 from Y. lipolytica ( Yl ACOX3) was determined at a resolution of 2.5 Å. It contained two molecules per asymmetric unit, and the monomeric structure was folded into four domains; Nα, Nβ, Cα1, and Cα2 domains. The cofactor flavin adenine dinucleotide was bound in the dimer interface. The substrate-binding pocket was located near the cofactor, and formed at the interface between the Nα, Nβ, and Cα1 domains. Comparisons with other ACOX structures provided structural insights into how Yl ACOX has a substrate preference for short-chain acyl-CoA. In addition, the structure of Yl ACOX3 was compared with those of medium- and long-chain ACOXs, and the structural basis for their differences in substrate specificity was discussed.


    Organizational Affiliation

    KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-coenzyme A oxidase 3 AB708Yarrowia lipolytica CLIB122Mutation(s): 0 
Gene Names: POX3ACO3YALI0D24750g
EC: 1.3.3.6
Find proteins for O74936 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore O74936 
Go to UniProtKB:  O74936
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.824α = 90
b = 160.824β = 90
c = 139.467γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-11-13 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Kim, S., Kim, K.-J.

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references