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J. Biol. Chem., Vol. 279, Issue 6, 4760-4767, February 6, 2004

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Structure of the Ubiquitin-interacting Motif of S5a Bound to the Ubiquitin-like Domain of HR23B^*

Kenichiro Fujiwara, Takeshi Tenno, Kaoru Sugasawa¶, Jun-Goo Jee||, Izuru Ohki**, Chojiro Kojima, Hidehito Tochio, Hidekazu Hiroaki, Fumio Hanaoka¶, and Masahiro Shirakawa||¶¶

From the Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, the Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, the ^¶Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, the ^||Genomic Sciences Center, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, the ^**Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, the Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, and the Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan

Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves signaling functions that control several cellular processes. The ubiquitination signal is recognized by downstream effectors, many of which carry a ubiquitin-interacting motif (UIM). Such interactions can be modulated by regulators carrying a ubiquitin-like (UbL) domain, which binds UIM by mimicking ubiquitination. Of them, HR23B regulates the proteasomal targeting of ubiquitinated substrates, DNA repair factors, and other proteins. Here we report the structure of the UIM of the proteasome subunit S5a bound to the UbL domain of HR23B. The UbL domain presents one hydrophobic and two polar contact sites for interaction with UIM. The residues in these contact sites are well conserved in ubiquitin, but ubiquitin also presents a histidine at the interface. The pH-dependent protonation of this residue interferes with the access of ubiquitin to the UIM and the ubiquitin-associated domain (UBA), and its mutation to a smaller residue increases the affinity of ubiquitin for UIM.

Received for publication, August 26, 2003 , and in revised form, October 6, 2003.

The atomic coordinates and structure factors (code 1UEL) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

Addendum—After submission of this manuscript, the solution structures of the UbL of HR23A in complexed with S5a UIM (53) and the Vps27 UIM-ubiquitin complex (54) were published. The structure of HR23A UbL-UIM is similar to that of HR23B-UIM shown in this paper. The possibility of the interference of ubiquitin His⁶⁸ for UIM binding was also discussed based on the structure. In contrast, Swanson et al. (54) showed that alanine substitution of His⁶⁸ of ubiquitin impairs the binding of ubiquitin to the N-terminal UIM of Vps27.

^* This work was supported by grants from the Japanese Ministry of Education, Science, Sports and Culture (to M. S. and H. T.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^¶¶ To whom correspondence should be addressed. Tel.: 81-45-508-7213; Fax: 81-45-508-7361; E-mail: shirakawa{at}tsurumi.yokohama-cu.ac.jp.

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