Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown

Nat Struct Mol Biol. 2013 Jul;20(7):827-35. doi: 10.1038/nsmb.2593. Epub 2013 May 26.

Abstract

The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Anaphase-Promoting Complex-Cyclosome
  • Antigens, CD
  • Cadherins / chemistry*
  • Cell Cycle Proteins / chemistry*
  • Cell Cycle Proteins / metabolism
  • Cell Cycle Proteins / pharmacology
  • Cell Cycle Proteins / ultrastructure
  • F-Box Proteins / chemistry*
  • F-Box Proteins / metabolism
  • F-Box Proteins / pharmacology
  • F-Box Proteins / ultrastructure
  • Humans
  • Microscopy, Electron
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • Protein Folding
  • Protein Processing, Post-Translational
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship
  • Substrate Specificity
  • Ubiquitin-Protein Ligase Complexes / antagonists & inhibitors
  • Ubiquitin-Protein Ligase Complexes / chemistry*
  • Ubiquitin-Protein Ligase Complexes / metabolism
  • Ubiquitin-Protein Ligase Complexes / ultrastructure
  • Ubiquitin-Protein Ligases / antagonists & inhibitors
  • Ubiquitinated Proteins / metabolism
  • Ubiquitination
  • Ultracentrifugation

Substances

  • Antigens, CD
  • CDH1 protein, human
  • Cadherins
  • Cell Cycle Proteins
  • F-Box Proteins
  • FBXO5 protein, human
  • Ubiquitinated Proteins
  • Ubiquitin-Protein Ligase Complexes
  • Anaphase-Promoting Complex-Cyclosome
  • Ubiquitin-Protein Ligases