Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.
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.
Camy C-H
CC
Kung
*Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.
Mandar T
MT
Naik
§Scientific Instrument Center, Academia Sinica, Taipei 11529, Taiwan.
Szu-Huan
SH
Wang
*Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.
Hsiu-Ming
HM
Shih
∥Graduate Institute of Translational Medicine, Taipei Medical University, Taipei 110, Taiwan.
Che-Chang
CC
Chang
¶Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
Li-Ying
LY
Lin
Chia-Lin
CL
Chen
¶Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
Che
C
Ma
¶Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
Chi-Fon
CF
Chang
Tai-Huang
TH
Huang
D020816:Amino Acid Motifs / Q000502:physiology; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D053838:Scattering, Small Angle; D025841:Small Ubiquitin-Related Modifier Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D044767:Ubiquitin-Protein Ligases / Q000378:metabolism; D014961:X-Ray Diffraction
D009687:Nuclear Proteins; C114070:RNF4 protein, human; D025841:Small Ubiquitin-Related Modifier Proteins; D014157:Transcription Factors; D044767:Ubiquitin-Protein Ligases