Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain

Biochem J. 2014 Aug 15;462(1):53-65. doi: 10.1042/BJ20140521.

Abstract

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs / physiology
  • Nuclear Magnetic Resonance, Biomolecular
  • Nuclear Proteins / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • Scattering, Small Angle
  • Small Ubiquitin-Related Modifier Proteins / metabolism*
  • Transcription Factors / metabolism*
  • Ubiquitin-Protein Ligases / metabolism
  • X-Ray Diffraction

Substances

  • Nuclear Proteins
  • RNF4 protein, human
  • Small Ubiquitin-Related Modifier Proteins
  • Transcription Factors
  • Ubiquitin-Protein Ligases