Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation

Mol Cell. 2008 Jan 18;29(1):23-35. doi: 10.1016/j.molcel.2007.12.012.

Abstract

Cullin-based E3 ubiquitin ligases are activated through modification of the cullin subunit with the ubiquitin-like protein Nedd8. Dcn1 regulates cullin neddylation and thus ubiquitin ligase activity. Here we describe the 1.9 A X-ray crystal structure of yeast Dcn1 encompassing an N-terminal ubiquitin-binding (UBA) domain and a C-terminal domain of unique architecture, which we termed PONY domain. A conserved surface on Dcn1 is required for direct binding to cullins and for neddylation. The reciprocal binding site for Dcn1 on Cdc53 is located approximately 18 A from the site of neddylation. Dcn1 does not require cysteine residues for catalytic function, and directly interacts with the Nedd8 E2 Ubc12 on a surface that overlaps with the E1-binding site. We show that Dcn1 is necessary and sufficient for cullin neddylation in a purified recombinant system. Taken together, these data demonstrate that Dcn1 is a scaffold-like E3 ligase for cullin neddylation.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalysis
  • Conserved Sequence
  • Crystallography, X-Ray
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Interaction Mapping
  • Protein Processing, Post-Translational / physiology*
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins / metabolism
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / physiology*
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Ubiquitin / metabolism
  • Ubiquitin-Protein Ligases / chemistry
  • Ubiquitin-Protein Ligases / metabolism
  • Ubiquitin-Protein Ligases / physiology*
  • Ubiquitination
  • Ubiquitins

Substances

  • Dcn1 protein, S cerevisiae
  • RUB1 protein, S cerevisiae
  • Recombinant Fusion Proteins
  • Saccharomyces cerevisiae Proteins
  • Ubiquitin
  • Ubiquitins
  • Ubiquitin-Protein Ligases

Associated data

  • PDB/3BQ3