PDBsum entry 5k3h

Oxidoreductase

PDB id: 5k3h

Contents

Protein chains

(+ 2 more) 634 a.a.

Waters ×1476

PDB id:

5k3h

Name:

Oxidoreductase

Title:

Crystals structure of acyl-coa oxidase-1 in caenorhabditis elegans, apo form-ii

Structure:

Acyl-coenzyme a oxidase. Chain: a, b, c, d, e, f, g, h. Engineered: yes

Source:

Caenorhabditis elegans. Organism_taxid: 6239. Gene: acox-1, cele_f08a8.1, f08a8.1. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.48Å R-factor: 0.193 R-free: 0.232

Authors:

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

Key ref:

X.Zhang et al. (2016). Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 113, 10055-10060. PubMed id: 27551084 DOI: 10.1073/pnas.1608262113

Date:

19-May-16 Release date: 24-Aug-16

Protein chains

O62140  (O62140_CAEEL) -  Acyl-coenzyme A oxidase acox-1.1 from Caenorhabditis elegans

Seq: 674 a.a.

Struc: 634 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.3.3.- - ?????
• Enzyme class 3: E.C.1.3.3.6 - acyl-CoA oxidase.
• Reaction: a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2
• Cofactor: FAD

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1608262113

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

PubMed id: 27551084

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

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

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.