Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3

Artavanis‐Tsakonas, Katerina; Weihofen, W.A.; Antos, John M.; Coleman, Bradley I.; Comeaux, Christy; Duraisingh, Manoj T.; Gaudet, Rachelle; Ploegh, Hidde L.

doi:10.1074/jbc.m109.072405

Cited by 61 publications

(78 citation statements)

References 38 publications

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“…The UCH37 active site structure is highly conserved in the RPN13 CTD complex, and contacts to ubiquitin superimpose closely with those of the isolated Trichinella spiralis UCH37 UCH domain in complex with ubiquitin vinyl methyl ester (Morrow et al, 2013) and other UCH enzymes with ubiquitin aldehyde or ubiquitin vinyl methyl ester (Artavanis-Tsakonas et al, 2010; Boudreaux et al, 2010; Johnston et al, 1999; Misaghi et al, 2005) (Figure 1B). As expected, the catalytic cysteine side chain is turned away from the ubiquitin carboxylate in order to accommodate formation of the product complex.…”

Section: Resultsmentioning

confidence: 81%

Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase

et al. 2015

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SUMMARY The UCH37 deubiquitylase functions in two large and very different complexes, the 26S proteasome and the INO80 chromatin remodeler. We have performed biochemical characterization and determined crystal structures of UCH37 in complexes with RPN13 and NFRKB, which mediate its recruitment to proteasome and INO80, respectively. RPN13 and NFRKB make similar contacts to the UCH37 C-terminal domain, but quite different contacts to the catalytic UCH domain. RPN13 can activate UCH37 by disrupting dimerization, although physiologically-relevant activation likely results from stabilization of a surface competent for ubiquitin binding and modulation of the active-site crossover loop. In contrast, NFRKB inhibits UCH37 by blocking the ubiquitin-binding site and by disrupting the enzyme active site. These findings reveal remarkable commonality in mechanisms of recruitment, yet very different mechanisms of regulating enzyme activity, and provide a foundation for understanding the role of UCH37 in the unrelated proteasome and INO80 complexes.

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Section: Resultsmentioning

confidence: 81%

Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase

et al. 2015

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“…In the apo form of UCHL3, the closest homolog of UCH37, the loop is disordered but becomes ordered when ubiquitin is bound (48, 50) . The ubiquitin-bound structures of PfUCHL3 and the yeast ubiquitin hydrolase Yuh1 show an ordered crossover loop making contacts with side chains on the C-terminal tail of ubiquitin (73, 78) . In contrast, the structures of the TsUCH37-UbVME constructs present the only examples so far of a UCH DUB in which the crossover loop is still disordered even after ubiquitin is bound, indicating that the loop is flexible and does not contribute to ubiquitin binding.…”

Section: Resultsmentioning

confidence: 99%

Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity

et al. 2013

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Ubiquitination is countered by a group of enzymes collectively called deubiquitinases (DUBs) - about 100 of them can be found in the human genome. One of the most interesting aspects of these enzymes is the ability of some members to selectively recognize specific linkage types between ubiquitin in polyubiquitin chains and their endo and exo specificity. The structural basis of exo-specific deubiquitination catalyzed by a DUB is poorly understood. UCH37, a cysteine DUB conserved from fungi to humans, is a proteasome-associated factor that regulates the proteasome by sequentially cleaving polyubiquitin chains from their distal ends, i.e., by exo-specific deubiquitination. In addition to the catalytic domain, the DUB features a functionally uncharacterized UCH37-like domain (ULD), presumed to keep the enzyme in an inhibited state in its proteasome-free form. Herein we report the crystal structure of two constructs of UCH37 from Trichinella spiralis in complex with a ubiquitin-based suicide inhibitor, ubiquitin vinyl methyl ester (UbVME). These structures show that the ULD makes direct contact with ubiquitin stabilizing a highly unusual intra-molecular salt bridge between Lys48 and Glu51 of ubiquitin, an interaction that would be favored only with the distal ubiquitin but not with the internal ones in a Lys48-linked polyubiquitin chain. An inspection of 39 DUB-ubiquitin structures in the protein data bank reveals the uniqueness of the salt bridge in ubiquitin bound to UCH37, an interaction that disappears when the ULD is deleted, as revealed in the structure of the catalytic domain alone bound to UbVME. The structural data are consistent with previously reported mutational data on the mammalian enzyme, which, together with the fact that the ULD residues that bind to ubiquitin are conserved, points to a similar mechanism behind the exo specificity of the human enzyme. To the best of our knowledge, these data provide the only structural example so far of how the exo specificity of a DUB can be determined by its non-catalytic domain. Thus, our data show that, contrary to its proposed inhibitory role, the ULD actually contributes to substrate recognition and could be a major determinant of proteasome-associated function of UCH37. Moreover, our structures show that the unproductively oriented catalytic cysteine in the free enzyme is aligned correctly when ubiquitin binds, suggesting a mechanism for ubiquitin selectivity.

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“…PfUCHL3 is thought to be essential for parasite survival. Importantly, this DUB could be a possible target for selective drugs due to significant structural differences in ubiquitin binding between PfUCHL3 and its human homologue, as well as unique characteristic of PfUCHL3 to cleave Nedd8, which is absent from human UCHL3 [114]. PfUCH54 is another DUB in P. falciparum.…”

Section: Dubs In Infections With Pathogenic Fungi and Parasitesmentioning

confidence: 99%

Deubiquitinating Enzymes as Promising Drug Targets for Infectious Diseases

Nanduri

Suvarnapunya²,

Venkatesan³

et al. 2013

CPD

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Deubiquitinating enzymes (DUBs) remove ubiquitin and ubiquitin-like modifications from proteins and they have been known to contribute to processes relevant in microbial infection, such as immune responses pathways. Numerous viral and bacterial DUBs have been identified, and activities of several host DUBs are known to be modulated during the infection process, either by a pathogen or by a host. Recently there have been attempts to take advantage of this feature and design therapeutic inhibitors of DUBs that can be used to limit the spread of infection. This review is focused on exploring the potential of DUBs in the treatment of infectious diseases.

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Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3

Cited by 61 publications

References 38 publications

Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase

Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase

Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity

Deubiquitinating Enzymes as Promising Drug Targets for Infectious Diseases

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