Structural variability of the ubiquitin specific protease DUSP-UBL double domains

Abstract

Edited by Noboru Mizushima Keywords:Ubiquitin specific protease DUSP UBL X-ray a b s t r a c t USP4, 11 and 15 are three closely related paralogues of the ubiquitin specific protease (USP) family of deubiquitinating enzymes. The DUSP domain and the UBL domain in these proteins are juxtaposed which may provide a functional unit conferring specificity. We determined the structures of the USP15 DUSP-UBL double domain unit in monomeric and dimeric states. We then conducted comparative analysis of the structural and physical properties of all three DUSP-UBL units. We identified structural features that dictate different dispositions between constituent domains, which in turn may influence respective binding properties. Structured summary of protein interactions:USP15 and USP15 bind by molecular sieving (View Interaction: 1, 2) USP15 and USP15 physically interact by molecular sieving (View interaction) USP4 and USP4 bind by molecular sieving (View Interaction: 1, 2) USP15 and USP15 bind by X ray scattering (View interaction) USP11 and USP11 bind by molecular sieving (View interaction) USP4 and USP4 bind by nuclear magnetic resonance (View interaction) USP15 and USP15 bind by X-ray crystallography (View interaction)

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

“…Domain Swapping and Hinge Residues-Several previous studies (18,(27)(28)(29) have analyzed the structures and dimerization of the DUSP-UBL domain of USP4, USP11, and USP15 in detail and identified residues on the DU finger and the DUSP domain to be the main cause of different oligomerization mechanisms of the USPs. USP4 exists as a dimer in the solution and in the crystal lattice.…”

“…USP4 exists as a dimer in the solution and in the crystal lattice. In contrast, USP15 could crystallize as a monomer (PDB codes 4A3O and 3T9L), as a domain-swapped dimer (18,28), or a tetramer composed of a dimer of a domainswapped dimer (PDB code 3PPA). Surprisingly, USP11 could also exist as a monomer and a domain-swapped dimer (29) even though its DU finger lacks the three residues key for SART3 binding.…”

“…During purification, we observed two separate peaks during anion exchange, corresponding to different oligomeric states of USP15, which suggest the interconversion between monomer and oligomer is kinetically unfavorable. However, the kinetic barrier can be overcome by the binding of SART3, as shown by a K D of 28 M between the oligomeric forms of USP15 with SART3 (USP15(1-233) Q2 in Table 2) or by raising the temperature of the solution (28). The DU finger of USP15 also serves as the hinge loop for domain swapping (18,28).…”

“…However, the kinetic barrier can be overcome by the binding of SART3, as shown by a K D of 28 M between the oligomeric forms of USP15 with SART3 (USP15(1-233) Q2 in Table 2) or by raising the temperature of the solution (28). The DU finger of USP15 also serves as the hinge loop for domain swapping (18,28). We observed that the G121A mutation breaks down the kinetic barrier of the conversion between the monomeric and dimeric forms of USP15 (Fig.…”

“…Previous studies (18,(27)(28)(29) established that the USP4 DUSP-UBL domain forms a dimer in solution and in the crystal. Detailed structural analysis revealed the DU finger of one USP4 molecule interacts with a hydrophobic patch on the DUSP domain of the other molecule (Fig.…”