Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 158.10 kDa 
• Atom Count: 10979 
• Modelled Residue Count: 1321 
• Deposited Residue Count: 1348 
• Unique protein chains: 1

5K3J

Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP

• PDB DOI: 10.2210/pdb5K3J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-19 Released: 2016-08-24 
• Deposition Author(s): Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.
• Funding Organization(s): Research Corporation for Science Advancement, Ellison Medical Foundation, National Science Foundation (NSF, United States), Alfred P. Sloan Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.245 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans.

Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.

(2016) Proc Natl Acad Sci U S A 113: 10055-10060

• PubMed: 27551084 
• DOI: 10.1073/pnas.1608262113
• Primary Citation of Related Structures:  
  5K3G, 5K3H, 5K3I, 5K3J


• PubMed Abstract: 
  

Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal β-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.

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Organizational Affiliation: 

Department of Chemistry, University of Florida, Gainesville, FL 32611 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-coenzyme A oxidase	A, B	674	Caenorhabditis elegans	Mutation(s): 0  Gene Names: acox-2, CELE_F08A8.2, F08A8.2, acox-1.2
UniProt
Find proteins for O62137 (Caenorhabditis elegans) Explore O62137  Go to UniProtKB:  O62137

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QA	E [auth A], J [auth B]	~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 5-[(2~{R},3~{R},5~{R},6~{S})-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxypentanethioate C32 H54 N7 O21 P3 S OJJVYBQJWBBERR-XKGQWQQESA-N
FAD	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ATP	D [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	F [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.245 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.04	α = 90
b = 85.571	β = 91.43
c = 106.899	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-19 
• Released Date: 2016-08-24 
Deposition Author(s): Zhang, X., Li, K., Jones, R.A., Bruner, S.D., Butcher, R.A.

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Funding Organization	Location	Grant Number
Research Corporation for Science Advancement	United States	22844
Ellison Medical Foundation	United States	AG-NS-0963-12
National Science Foundation (NSF, United States)	United States	1555050
Alfred P. Sloan Foundation	United States	BR2014-071

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Database references
• Version 1.2: 2016-09-14
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence