Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator

Mol Cell. 2013 Jan 24;49(2):273-82. doi: 10.1016/j.molcel.2012.10.022. Epub 2012 Nov 29.


Inhibitors of Apoptosis Protein (IAPs) are guardian ubiquitin ligases that keep classic proapoptotic proteins in check. Systematic identification of additional IAP substrates is challenged by the heterogeneity and sheer number of ubiquitinated proteins (>5,000). Here we report a powerful catalytic tagging tool, the NEDDylator, which fuses a NEDD8 E2-conjugating enzyme, Ubc12, to the ubiquitin ligase, XIAP or cIAP1. This permits transfer of the rare ubiquitin homolog NEDD8 to the ubiquitin E3 substrates, allowing them to be efficiently purified for LC-MS/MS identification. We have identified >50 potential IAP substrates of both cytosolic and mitochondrial origin that bear hallmark N-terminal IAP binding motifs. These substrates include the recently discovered protein phosphatase PGAM5, which we show is proteolytically processed, accumulates in cytosol during apoptosis, and sensitizes cells to death. These studies reveal mechanisms and antagonistic partners for specific IAPs, and provide a powerful technology for labeling binding partners in transient protein-protein complexes.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Apoptosis
  • Carrier Proteins / chemistry
  • Carrier Proteins / metabolism*
  • Caspase 7 / metabolism
  • Consensus Sequence
  • Humans
  • Inhibitor of Apoptosis Proteins / metabolism
  • Jurkat Cells
  • Mitochondrial Proteins / chemistry
  • Mitochondrial Proteins / metabolism*
  • Molecular Sequence Data
  • NEDD8 Protein
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Phosphoprotein Phosphatases
  • Protein Engineering
  • Protein Interaction Domains and Motifs
  • Protein Processing, Post-Translational*
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / metabolism
  • Ubiquitin-Protein Ligases / chemistry
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitination
  • Ubiquitins / chemistry
  • Ubiquitins / metabolism*
  • X-Linked Inhibitor of Apoptosis Protein / chemistry


  • Carrier Proteins
  • Inhibitor of Apoptosis Proteins
  • Mitochondrial Proteins
  • NEDD8 Protein
  • NEDD8 protein, human
  • Peptide Fragments
  • Recombinant Fusion Proteins
  • Ubiquitins
  • X-Linked Inhibitor of Apoptosis Protein
  • XIAP protein, human
  • Ubiquitin-Protein Ligases
  • PGAM5 protein, human
  • Phosphoprotein Phosphatases
  • CASP7 protein, human
  • Caspase 7