Abstract
Summary Lys48-linked ubiquitin chains act as the main targeting signals for protein degradation by the proteasome. Here we report selective binding of AIRAPL, a protein that associates with the proteasome upon exposure to arsenite, to Lys48-linked tri-ubiquitin chains. AIRAPL comprises two ubiquitin-interacting motifs in tandem (tUIMs) that are linked through a flexible inter-UIM region. In the complex crystal structure UIM1 binds the proximal ubiquitin, whereas UIM2 (the double-sided UIM) binds non-symmetrically to the middle and distal ubiquitin moieties on either side of the helix. Specificity of AIRAPL for Lys48-linked ubiquitin chains is determined by UIM2, and the flexible inter-UIM linker increases avidity by placing the two UIMs in an orientation that facilitates binding of the third ubiquitin to UIM1. Unlike middle and proximal ubiquitins, distal ubiquitin binds UIM2 through a novel surface, which leaves the Ile44 hydrophobic patch accessible for binding to the proteasomal ubiquitin receptors.
| Original language | English |
|---|---|
| Pages (from-to) | 412-422 |
| Number of pages | 11 |
| Journal | Structure |
| Volume | 24 |
| Issue number | 3 |
| DOIs | |
| State | Published - 1 Mar 2016 |
| Externally published | Yes |
Bibliographical note
Funding Information:We would like to thank staff of the Photon Factory BL-17A for their support with X-ray data collection, R. Sertchook for initial analysis of AIRAPL tUIM configuration, M. Edri and V. Bronner from Bio-Rad Haifa Protein Technologies for initial SPR experiments, F. Jabbarpour and V. Bhadkamkar for their help in the preparation of proteins for binding assays, and K. Husnjak, J. Hermann, and J. Tan for critical reading of the manuscript. The research was supported by the Israeli Science Foundation (ISF) grant 438/14 to A.S., and S.R. was a recipient of the JSPS Fellowship for Research in Japan (Long-Term) and Katherine McCormick Advanced Postdoctoral Fellowship at Stanford. S.W. is a Stanford Bio-X Affiliated Faculty and part of this work was conducted at the James H. Clark Center, the hub for Stanford Bio-X. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health National Institute of General Medical Sciences (including P41GM103393).
Funding Information:
We would like to thank staff of the Photon Factory BL-17A for their support with X-ray data collection, R. Sertchook for initial analysis of AIRAPL tUIM configuration, M. Edri and V. Bronner from Bio-Rad Haifa Protein Technologies for initial SPR experiments, F. Jabbarpour and V. Bhadkamkar for their help in the preparation of proteins for binding assays, and K. Husnjak, J. Hermann, and J. Tan for critical reading of the manuscript. The research was supported by the Israeli Science Foundation (ISF) grant 438/14 to A.S., and S.R. was a recipient of the JSPS Fellowship for Research in Japan (Long-Term) and Katherine McCormick Advanced Postdoctoral Fellowship at Stanford. S.W. is a Stanford Bio-X Affiliated Faculty and part of this work was conducted at the James H. Clark Center, the hub for Stanford Bio-X. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research , and by the National Institutes of Health National Institute of General Medical Sciences (including P41GM103393 ).
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