Erratum: Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains

Sato, Yusuke; Yoshikawa, Azusa; Yamagata, Atsushi; Mimura, Hisatoshi; Yamashita, Masami; Ookata, Kayoko; Nureki, Osamu; Iwaï, Kazuhiro; Komada, Masayuki; Fukai, Shuya

doi:10.1038/nature07515

Cited by 2 publications

(1 citation statement)

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“…The crystal structure of STAMBPL1 JAMM catalytic domain in complex with K63-linked diUb revealed its linkage specificity towards K63-linked poly-Ub chains involves the catalytic groove and two insertions that are conserved in STAMBP subfamily JAMMs: ins-1 (aa 314-339) and ins-2 (aa 393-415) (32). The distal Ub interacts with ins-1 and the catalytic groove, and the proximal Ub interacts with ins-2 and the catalytic site.…”

Section: Introductionmentioning

confidence: 99%

Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1

Guo

Liu

Mallette

et al. 2021

Preprint

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Ubiquitination is one of the most crucial post-translational protein modifications involved in a myriad of biological pathways. This process is reversed by deubiquitinases (DUBs) that deconjugate the ubiquitin (Ub) moiety or poly-Ub chains from substrates. In the past decade, tremendous efforts have been focused on targeting DUBs for drug discovery. However, most chemical compounds with inhibitory activity for DUBs suffer from mild potency and low selectivity. To overcome these obstacles, we developed a phage display-based protein engineering strategy for generating Ub variant (UbV) inhibitors and have previously successfully applied it to the Ub-specific protease (USP) family of cysteine proteases. In this work, we leveraged the UbV platform to target STAMBP, a member of the JAB1/MPN/MOV34 (JAMM) metalloprotease family of DUB enzymes. We identified two UbVs (UbVSP.1 and UbVSP.3) that bind to STAMBP with high affinity but differ in their selectivity for the closely related paralog STAMBPL1. We determined the STAMBPL1-UbVSP.1 complex structure by X-ray crystallography, revealing hotspots of the tight JAMM-UbV interaction. Finally, we show that UbVSP.1 and UbVSP.3 are potent inhibitors of the STAMBP isopeptidase activity, far exceeding the reported small-molecule inhibitor BC-1471. This work demonstrates the UbV technology is suitable to develop tool molecules for metalloproteases. These tools can be used to understand the cellular function of JAMM family DUBs.

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Section: Introductionmentioning

confidence: 99%

Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1

Guo

Liu

Mallette

et al. 2021

Preprint

View full text Add to dashboard Cite

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Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

et al. 2016

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Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.

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Erratum: Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains

Cited by 2 publications

References 1 publication

Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1

Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1

Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

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