Structures of proteases for ubiqutin and ubiquitin-like modifiers

Ha, Byung Hak; Kim, Eunice EunKyeong

doi:10.5483/bmbrep.2008.41.6.435

Cited by 23 publications

(21 citation statements)

References 71 publications

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“…SUMO-conjugated Ubc9 directly recognizes the sumoylation motif (ΨKxE/D, Ψ is a bulky aliphatic residue) within target proteins and transfers the SUMO moiety to a Lys side chain in the target protein (15)(16)(17). Ubiquitination by a RING-E3 enzyme in vivo would be more complicate than during in vitro ubiquitination in the E2 fusion protein system.…”

Section: Discussionmentioning

confidence: 99%

Direct characterization of E2-dependent target specificity and processivity using an artificial p27-linker-E2 ubiquitination system

Ryu

Choi²,

Ko³

et al. 2008

BMB Reports

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Little attention has been paid to the specificity between E2 and the target protein during ubiquitination, although RING-E3 induces a potential intra-molecular reaction by mediating the direct transfer of ubiquitin from E2 to the target protein. We have constructed artificial E2 fusion proteins in which a target protein (p27) is tethered to one of six E2s via a flexible linker. Interestingly, only three E2s (UbcH5b, hHR6b, and Cdc34) are able to ubiquitinate p27 via an intra-molecular reaction in this system. Although the first ubiquitination of p27 (p27-Ub) by Cdc34 is less efficient than that of UbcH5b and hHR6b, the additional ubiquitin attachment to p27-Ub by Cdc34 is highly efficient. The E2 core of Cdc34 provides specificity to p27, and the residues 184-196 are required for possessive ubiquitination by Cdc34. We demonstrate direct E2 specificity for p27 and also show that differential ubiquitin linkages can be dependent on E2 alone. [BMB reports 2008; 41(12): 852-857]

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Section: Discussionmentioning

confidence: 99%

Direct characterization of E2-dependent target specificity and processivity using an artificial p27-linker-E2 ubiquitination system

Ryu

Choi²,

Ko³

et al. 2008

BMB Reports

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“…The most prominent K48-linked poly-ubiquitination is a signal for proteasomal degradation, whereas other forms of ubiquitination alter protein function or localization (Vucic et al, 2011). Ubiquitination is a strictly regulated but reversible process catalyzed by deubiquitinating enzymes (DUBs), which can be categorized in five classes and are either cysteine proteases or metalloproteases (Nijman et al, 2005; Ha and Kim, 2008). …”

Section: Introductionmentioning

confidence: 99%

Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense

Fischer

Harrison

Ramirez

et al. 2017

eLife

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Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound vacuole called inclusion, which serves as a signaling interface with the host cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes in the inclusion membrane and faces the cytosol with the active deubiquitinating enzyme domain. The structure of this domain revealed high similarity to mammalian deubiquitinases with a unique α-helix close to the substrate-binding pocket. We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1 and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1 and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally, inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNγ and impaired infection in mice. Thus, the chlamydial inclusion serves as an enriched site for a deubiquitinating activity exerting a function in selective stabilization of host proteins and protection from host defense.DOI: http://dx.doi.org/10.7554/eLife.21465.001

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“…Investigating whether other USP proteins use similar mechanisms to distinguish between Ub and NEDD8 is critical; however, most USPs remain poorly characterized 43, 44 . The crystal structure of the USP2 catalytic core, comprising residues 259–605, in complex with Ub reveals that the Ub core (residues 1–71) binds into the Fingers-Palm-Thumb structural elements, whereas its five C-terminal residues (72–76) bind into a narrow channel and reach for the active site cysteine 35 .…”

Section: Introductionmentioning

confidence: 99%

The molecular determinants for distinguishing between ubiquitin and NEDD8 by USP2

Shin

Chen

Chang

2017

Sci Rep

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Ubiquitin (Ub) shares the highest sequence identity with neuronal-precursor-cell-expressed developmentally downregulated protein-8 (NEDD8) in the Ub-like protein family. However, different enzyme systems are precisely employed for targeting Ub and NEDD8 to specific substrates. The molecular determinants for distinguishing between Ub and NEDD8 by Ub-specific peptidases (USPs) remain poorly characterized. By replacing the non-conserved residues of Ub with their NEDD8 equivalents by mutagenesis, and vice versa, we observed that the Ub4K, Ub12E, and Ub14E mutants partially and the Ub4K/12E/14E/72A mutant completely prevented their hydrolysis by USP2. The NEDD84F and NEDD814T mutants were slightly hydrolyzed by USP2; however, the NEDD812T/14T/72R and NEDD84F/12T/14T/72R mutants were accessible for hydrolysis by USP2, suggesting that Ub and NEDD8 residues 4, 12, 14, and 72 serve as the molecular determinants for specific recognition by USP2. We also demonstrated that the level of inhibition caused by Ub mutants with multiple mutation sites was not purely additive when compared with the single mutation results. Furthermore, USP2 was determined to bind to the N-terminus of Ub to form a stable interaction, after which it binds with the C-terminus of Ub to ensure substrate specificity. The same results were also discovered when Ub, Ub4K/12E/14E/72A, NEDD8, and NEDD84F/12T/14T/72R were incubated with USP21.

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Structures of proteases for ubiqutin and ubiquitin-like modifiers

Abstract: Ubiquitin and ubiquitination

Cited by 23 publications

References 71 publications

Direct characterization of E2-dependent target specificity and processivity using an artificial p27-linker-E2 ubiquitination system

Direct characterization of E2-dependent target specificity and processivity using an artificial p27-linker-E2 ubiquitination system

Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense

The molecular determinants for distinguishing between ubiquitin and NEDD8 by USP2

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