Structural Basis of the Recruitment of Ubiquitin-specific Protease USP15 by Spliceosome Recycling Factor SART3

J Biol Chem. 2016 Aug 12;291(33):17283-92. doi: 10.1074/jbc.M116.740787. Epub 2016 Jun 2.


Ubiquitin-specific proteases (USPs) USP15 and USP4 belong to a subset of USPs featuring an N-terminal tandem domain in USP (DUSP) and ubiquitin-like (UBL) domain. Squamous cell carcinoma antigen recognized by T-cell 3 (SART3), a spliceosome recycling factor, binds to the DUSP-UBL domain of USP15 and USP4, recruiting them to the nucleus from the cytosol to control deubiquitination of histone H2B and spliceosomal proteins, respectively. To provide structural insight, we solved crystal structures of SART3 in the apo-form and in complex with the DUSP-UBL domain of USP15 at 2.0 and 3.0 Å, respectively. Structural analysis reveals SART3 contains 12 half-a-tetratricopeptide (HAT) repeats, organized into two subdomains, HAT-N and HAT-C. SART3 dimerizes through the concave surface of HAT-C, whereas the HAT-C convex surface binds USP15 in a novel bipartite mode. Isothermal titration calorimetry measurements and mutagenesis analysis confirmed key residues of USP15 involved in the interaction and indicated USP15 binds 20-fold stronger than USP4.

Keywords: crystal structure; deubiquitinase; dimerization; half-a-tetratricopeptide repeats; protein-protein interaction; site-directed mutagenesis; ubiquitin-dependent protease.

MeSH terms

  • Antigens, Neoplasm / chemistry*
  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / metabolism
  • Crystallography, X-Ray
  • Humans
  • Protein Binding
  • Protein Structure, Quaternary
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Repetitive Sequences, Amino Acid
  • Structure-Activity Relationship
  • Ubiquitin Thiolesterase / chemistry
  • Ubiquitin Thiolesterase / genetics
  • Ubiquitin Thiolesterase / metabolism
  • Ubiquitin-Specific Proteases / chemistry*
  • Ubiquitin-Specific Proteases / genetics
  • Ubiquitin-Specific Proteases / metabolism


  • Antigens, Neoplasm
  • RNA-Binding Proteins
  • SART3 protein, human
  • USP4 protein, human
  • USP15 protein, human
  • Ubiquitin Thiolesterase
  • Ubiquitin-Specific Proteases

Associated data

  • PDB/2OND
  • PDB/2OOE
  • PDB/2UYL
  • PDB/3EBA
  • PDB/3JYU
  • PDB/3PPA
  • PDB/3PV1
  • PDB/3T9L
  • PDB/4A3O
  • PDB/4A3P
  • PDB/4E85
  • PDB/4EBH
  • PDB/5JJW
  • PDB/5JJX