Structural conservation of distinctive N-terminal acetylation-dependent interactions across a family of mammalian NEDD8 ligation enzymes

Structure. 2013 Jan 8;21(1):42-53. doi: 10.1016/j.str.2012.10.013. Epub 2012 Nov 29.

Abstract

Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetylation
  • Amino Acid Sequence
  • Animals
  • Cell Cycle Proteins / chemistry
  • Crystallography, X-Ray
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • NEDD8 Protein
  • NIH 3T3 Cells
  • Peptide Fragments / chemistry
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Processing, Post-Translational
  • Protein Structure, Secondary
  • Proteins
  • Proto-Oncogene Proteins / chemistry*
  • Structural Homology, Protein
  • Substrate Specificity
  • Ubiquitin-Conjugating Enzymes / chemistry*
  • Ubiquitin-Conjugating Enzymes / metabolism
  • Ubiquitins / chemistry*

Substances

  • Cell Cycle Proteins
  • DCUN1D1 protein, human
  • DCUN1D3 protein, human
  • NEDD8 Protein
  • NEDD8 protein, human
  • Peptide Fragments
  • Proteins
  • Proto-Oncogene Proteins
  • Ubiquitins
  • Ubiquitin-Conjugating Enzymes
  • UBE2F protein, human

Associated data

  • PDB/4GAO
  • PDB/4GBA