Evidence for Bidentate Substrate Binding As the Basis for the K48 Linkage Specificity of Otubain 1

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2009 Feb 13

PMID 19211026

Citations 87

Authors

Tao Wang

Luming Yin

Eric M Cooper

Ming-Yih Lai

Seth Dickey

Cecile M Pickart

David Fushman

Keith D Wilkinson

Robert E Cohen

Cynthia Wolberger

Affiliations

Soon will be listed here.

Abstract

Otubain 1 belongs to the ovarian tumor (OTU) domain class of cysteine protease deubiquitinating enzymes. We show here that human otubain 1 (hOtu1) is highly linkage-specific, cleaving Lys48 (K48)-linked polyubiquitin but not K63-, K29-, K6-, or K11-linked polyubiquitin, or linear alpha-linked polyubiquitin. Cleavage is not limited to either end of a polyubiquitin chain, and both free and substrate-linked polyubiquitin are disassembled. Intriguingly, cleavage of K48-diubiquitin by hOtu1 can be inhibited by diubiquitins of various linkage types, as well as by monoubiquitin. NMR studies and activity assays suggest that both the proximal and distal units of K48-diubiquitin bind to hOtu1. Reaction of Cys23 with ubiquitin-vinylsulfone identified a ubiquitin binding site that is distinct from the active site, which includes Cys91. Occupancy of the active site is needed to enable tight binding to the second site. We propose that distinct binding sites for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among different isopeptide linkages in polyubiquitin substrates. Bidentate binding may be a general strategy used to achieve linkage-specific deubiquitination.

Citing Articles

Target deubiquitinase OTUB1 as a therapeatic strategy for BLCA via β-catenin/necroptosis signal pathway.

Liao Y, Liang J, Wang Y, Li A, Liu W, Zhong B Int J Biol Sci. 2024; 20(10):3784-3801.

PMID: 39113709 PMC: 11302878. DOI: 10.7150/ijbs.94013.

In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases.

Campos Alonso M, Knobeloch K Front Mol Biosci. 2024; 11:1349509.

PMID: 38455765 PMC: 10919355. DOI: 10.3389/fmolb.2024.1349509.

The Deubiquitylase Otub1 Regulates the Chemotactic Response of Splenic B Cells by Modulating the Stability of the γ-Subunit Gng2.

Luo V, Shen C, Worme S, Bhagrath A, Simo-Cheyou E, Findlay S Mol Cell Biol. 2024; 44(1):1-16.

PMID: 38270191 PMC: 10829841. DOI: 10.1080/10985549.2023.2290434.

Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation.

Lemma B, Zhang D, Vamisetti G, Wentz B, Suga H, Brik A Nat Commun. 2023; 14(1):7212.

PMID: 37938554 PMC: 10632358. DOI: 10.1038/s41467-023-43025-4.

Phosphorylation of OTUB1 at Tyr 26 stabilizes the mTORC1 component, Raptor.

Seo S, Woo S, Kim M, Lee E, Min K, Kwon T Cell Death Differ. 2022; 30(1):82-93.

PMID: 35927303 PMC: 9883261. DOI: 10.1038/s41418-022-01047-3.

References

Hofmann R, Pickart C . Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair. Cell. 1999; 96(5):645-53. DOI: 10.1016/s0092-8674(00)80575-9. View

Soares L, Seroogy C, Skrenta H, Anandasabapathy N, Lovelace P, Chung C . Two isoforms of otubain 1 regulate T cell anergy via GRAIL. Nat Immunol. 2003; 5(1):45-54. DOI: 10.1038/ni1017. View

Pickart C, Fushman D . Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol. 2004; 8(6):610-6. DOI: 10.1016/j.cbpa.2004.09.009. View

Yao T, Cohen R . A cryptic protease couples deubiquitination and degradation by the proteasome. Nature. 2002; 419(6905):403-7. DOI: 10.1038/nature01071. View

Wilkinson K, Gan-Erdene T, Kolli N . Derivitization of the C-terminus of ubiquitin and ubiquitin-like proteins using intein chemistry: methods and uses. Methods Enzymol. 2005; 399:37-51. DOI: 10.1016/S0076-6879(05)99003-4. View

Evans P, Smith T, Lai M, Williams M, Burke D, Heyninck K . A novel type of deubiquitinating enzyme. J Biol Chem. 2003; 278(25):23180-6. DOI: 10.1074/jbc.M301863200. View

Sato Y, Yoshikawa A, Yamagata A, Mimura H, Yamashita M, Ookata K . Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature. 2008; 455(7211):358-62. DOI: 10.1038/nature07254. View

Wing S . Deubiquitinating enzymes--the importance of driving in reverse along the ubiquitin-proteasome pathway. Int J Biochem Cell Biol. 2003; 35(5):590-605. DOI: 10.1016/s1357-2725(02)00392-8. View

Naviglio S, Mattecucci C, Matoskova B, Nagase T, Nomura N, Di Fiore P . UBPY: a growth-regulated human ubiquitin isopeptidase. EMBO J. 1998; 17(12):3241-50. PMC: 1170662. DOI: 10.1093/emboj/17.12.3241. View

10.

Pickart C, Eddins M . Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta. 2004; 1695(1-3):55-72. DOI: 10.1016/j.bbamcr.2004.09.019. View

11.

Li M, Chen D, Shiloh A, Luo J, Nikolaev A, Qin J . Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature. 2002; 416(6881):648-53. DOI: 10.1038/nature737. View

12.

Rumpf S, Jentsch S . Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone. Mol Cell. 2006; 21(2):261-9. DOI: 10.1016/j.molcel.2005.12.014. View

13.

Boone D, Turer E, Lee E, Ahmad R, Wheeler M, Tsui C . The ubiquitin-modifying enzyme A20 is required for termination of Toll-like receptor responses. Nat Immunol. 2004; 5(10):1052-60. DOI: 10.1038/ni1110. View

14.

Schlieker C, Weihofen W, Frijns E, Kattenhorn L, Gaudet R, Ploegh H . Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol Cell. 2007; 25(5):677-87. PMC: 7110467. DOI: 10.1016/j.molcel.2007.01.033. View

15.

Yao T, Cohen R . Cyclization of polyubiquitin by the E2-25K ubiquitin conjugating enzyme. J Biol Chem. 2000; 275(47):36862-8. DOI: 10.1074/jbc.M006050200. View

16.

Hochstrasser M . Lingering mysteries of ubiquitin-chain assembly. Cell. 2006; 124(1):27-34. DOI: 10.1016/j.cell.2005.12.025. View

17.

Makarova K, Aravind L, Koonin E . A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem Sci. 2000; 25(2):50-2. DOI: 10.1016/s0968-0004(99)01530-3. View

18.

Frias-Staheli N, Giannakopoulos N, Kikkert M, Taylor S, Bridgen A, Paragas J . Ovarian tumor domain-containing viral proteases evade ubiquitin- and ISG15-dependent innate immune responses. Cell Host Microbe. 2007; 2(6):404-16. PMC: 2184509. DOI: 10.1016/j.chom.2007.09.014. View

19.

Lam Y, Xu W, DeMartino G, Cohen R . Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature. 1997; 385(6618):737-40. DOI: 10.1038/385737a0. View

20.

Mizuno E, Kitamura N, Komada M . 14-3-3-dependent inhibition of the deubiquitinating activity of UBPY and its cancellation in the M phase. Exp Cell Res. 2007; 313(16):3624-34. DOI: 10.1016/j.yexcr.2007.07.028. View