7Q86 | pdb_00007q86

Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, FAD-bound-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of apo- and FAD-bound human peroxisomal acyl-CoA oxidase provide mechanistic basis explaining clinical observations.

Sonani, R.R.Blat, A.Dubin, G.

(2022) Int J Biol Macromol 205: 203-210

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.02.008
  • Primary Citation Related Structures: 
    7Q84, 7Q86

  • PubMed Abstract: 

    Peroxisomal acyl-CoA oxidase 1a (ACOX1a) catalyzes the first and rate-limiting step of fatty acid oxidation, the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The dysfunction of human ACOX1a (hACOX1a) leads to deterioration of the nervous system manifesting in myeloneuropathy, hypotonia and convulsions. Crystal structures of hACOX1a in apo- and cofactor (FAD)-bound forms were solved at 2.00 and 2.09 Å resolution, respectively. hACOX1a exists as a homo-dimer with solvation free energy gain (ΔG o ) of -44.7 kcal mol -1 . Two FAD molecules bind at the interface of protein monomers completing the active sites. The substrate binding cleft of hACOX1a is wider compared to human mitochondrial very-long chain specific acyl-CoA dehydrogenase. Mutations (p.G178C, p.M278V and p.N237S) reported to cause dysfunctionality of hACOX1a are analyzed on its 3D-structure to understand structure-function related perturbations and explain the associated phenotypes.


  • Organizational Affiliation
    • Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.

Macromolecule Content 

  • Total Structure Weight: 153.08 kDa 
  • Atom Count: 10,219 
  • Modeled Residue Count: 1,219 
  • Deposited Residue Count: 1,334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1
A, B
667Homo sapiensMutation(s): 0 
Gene Names: ACOX1ACOX
EC: 1.3.3.6

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.961α = 90
b = 124.063β = 90
c = 142.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2017/26/M/NZ1/00797
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary