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Breaking the chains: structure and function of the deubiquitinases

Key Points

  • Ubiquitylation is a reversible post-translational modification involved in a myriad of cellular functions.

  • A superfamily of approximately 100 ubiquitin-specific proteases, called deubiquitylating enzymes, deubiquitinases or DUBs, remove ubiquitin from target proteins, disassemble polymeric ubiquitin chains and process ubiquitin precursor polypeptides to maintain ubiquitin homeostasis in cells.

  • Most DUBs are Cys proteases; a small group are metalloproteases.

  • DUBs are classified into five families (ubiquitin C-terminal hydrolases (UCHs), ubiquitin-specific proteases (USPs), Ovarian tumour proteases (OTUs), Josephins and JAB1/MPN/Mov34 metalloenzymes (JAMMs, also known as MPN+) that are structurally unrelated, but all interact with a common hydrophobic patch on ubiquitin.

  • Multiple layers of regulation modulate the activity and specificity of these enzymes. Specificity also entails recognition of and selective activity towards particular ubiquitin chain types, at least eight of which are now known to coexist in yeast and mammalian cells.

  • DUBs might function to regulate both the stability and the activity of target proteins, which include oncogenes and tumour suppressors. Their wide-ranging involvement in key regulatory processes makes DUBs attractive targets for drug therapy.

Abstract

Ubiquitylation is a reversible protein modification that is implicated in many cellular functions. Recently, much progress has been made in the characterization of a superfamily of isopeptidases that remove ubiquitin: the deubiquitinases (DUBs; also known as deubiquitylating or deubiquitinating enzymes). Far from being uniform in structure and function, these enzymes display a myriad of distinct mechanistic features. The small number (<100) of DUBs might at first suggest a low degree of selectivity; however, DUBs are subject to multiple layers of regulation that modulate both their activity and their specificity. Due to their wide-ranging involvement in key regulatory processes, these enzymes might provide new therapeutic targets.

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Figure 1: Domain structure of ubiquitin-specific proteases.
Figure 2: Domain structure of UCH, Josephin, OTU and JAMM/MPN+ DUBs.
Figure 3: General roles of DUBs.
Figure 4: Structures of Cys DUBs.
Figure 5: Structures of a JAMM/MPN+ metalloprotease.
Figure 6: Diverse roles for DUB–E3 ligase interactions.

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Acknowledgements

We thank K. Hofmann and D. Rigden for bioinformatic discussions and advice. S.U. is a Cancer Research UK Senior Research Fellow.

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Supplementary information

Supplementary information S1 (figure) | Mechanism and catalytic centre of Cys-DUBs. (PDF 286 kb)

Supplementary information S2 (figure) | Structures of USP domains. (PDF 267 kb)

Supplementary information S3 (figure) | Structures of OTU domains. (PDF 283 kb)

Supplementary information S4 (figure) | Structures of the Josephin domain of Ataxin-3. (PDF 245 kb)

Supplementary information S5 (figure) | Mechanism of JAMM family deubiquitinases (PDF 446 kb)

Supplementary information S6 (figure) | Ubiquitin interactions with DUBs. (PDF 237 kb)

Supplementary information S7 (table) | Carboxyl termini of human ubiquitin-like modifiers (PDF 161 kb)

Supplementary information S8 (figure) | The seven Lys residues of ubiquitin. (PDF 723 kb)

41580_2009_BFnrm2731_MOESM10_ESM.pdf

Supplementary information S9 (table) | Analysis of the linkage context for all types of polyubiquitin chains. (PDF 170 kb)

Supplementary information S10 (box) | Assays for DUB activity (PDF 191 kb)

Supplementary information S11 (box) | Inhibitors for DUBs (PDF 196 kb)

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FURTHER INFORMATION

David Komander's homepage

Michael J. Clague's homepage

Sylvie Urbé's homepage

HHPRED

Interpro

Pfam

PROSITE

PSORTII

SMART

RefSeq

Glossary

Metalloenzyme

An enzyme that requires a metal ion, such as zinc, for its activity and catalytic mechanism. The positive charge of the metal is used to position components of the reaction cycles.

Zinc finger ubiquitin-specific protease domain

(ZnF-UBP domain). A zinc finger that is present in histone deacetylase 6 and several ubiquitin-specific proteases, and which in some but not all cases has been shown to bind ubiquitin.

Ubiquitin-associated domain

(UBA domain). A short (40 amino acid) sequence motif, first found in proteins associated with the ubiquitylation pathway, that mediates (poly)ubiquitin binding.

Ubiquitin-like fold

(UBL fold). Ubiquitin contains a distinct three-dimensional fold, which has been used in many proteins related to the ubiquitin system and also in unrelated proteins.

MIT

A domain found in microtubule-interacting and trafficking proteins that forms a three-helix bundle. Some MIT domains, including those of AMSH and USP8, bind to charged multi-vesicular body proteins.

pKa

The log10 acid dissociation constant. The pKa of a given molecule corresponds to the pH value at which its acid and conjugate base forms are balanced.

Acyl intermediate

An intermediate in the Cys DUB reaction mechanism, in which the DUB is covalently bound to the C terminus of the distal ubiquitin. A sulphur acyl bond is formed between the C-terminal Gly of ubiquitin and the catalytic Cys of the DUB.

Oxy-anion hole

Found next to the catalytic Cys of a DUB, this environment stabilizes the negative charge that is created during the transition state before the formation of the acyl intermediate, by supplying hydrogen-donating amide groups, for example on Asn or Gln.

Distal

Used here in the context of DUB cleavage to refer to the relative position of ubiquitin moieties in a ubiquitin chain; in a ubiquitin dimer, distal corresponds to the ubiquitin molecule that is conjugated through its C-terminal Gly.

B-box

A small zinc-binding fold resembling a RING domain, but lacking E3 ligase activity. It is frequently found in the tripartite motif (TRIM) ubiquitin E3 ligases in a conserved array consisting of RING, B-box and coiled coil domains. The function is unknown.

Machado–Joseph disease

(MJD). A rare hereditary ataxia — that is, a disease characterized by lack of muscle control — also called spinocerebrellar ataxia type 3. The name derives from two families of Portuguese and Azorean descent, who were among the first patients described.

26S proteasome

A large multisubunit protease complex that selectively degrades multi-ubiquitylated proteins. It contains a 20S particle, which incorporates three distinct proteolytic activities, and one or two regulatory 19S particles.

COP9 signalosome

An eight-subunit protein complex that regulates protein ubiquitylation and turnover in various developmental and physiological contexts. Extensively characterized in plants but fundamental to all eukaryotes, this complex post-translationally modifies the cullin subunit of E3 ubiquitin ligases by cleaving off the covalently coupled peptide NEDD8.

ESCRT machinery

(Endosomal sorting complex required for transport). A multimeric protein complex that was first identified biochemically in yeast. The ESCRT machinery controls the sorting of endosomal cargo proteins into internal vesicles of multivesicular bodies.

14-3-3 proteins

A family of regulatory proteins that bind to phosphorylated forms of various proteins, which are involved in signal transduction and cell cycle control.

Catalytic rate

The number of substrate molecules that are converted into a product by an enzyme molecule in a unit of time, when the enzyme is fully saturated with substrate.

WD40 domain

A domain consisting of 4–10 WD40 repeats of 44–60 amino acids, which assemble into a propeller-shaped scaffold. Many distinct protein- and peptide-binding sites have been described in these adaptor domains.

Nucleolus

A subnuclear electron-dense structure composed of protein and nucleic acids that has a key role in the biogenesis of ribosomal RNA.

Early endosome

(Also known as sorting endosome). A tubular, vesicular structure that receives material directly from the plasma membrane and is a precursor of the mature (late) endosome. Early endosomes have a key role in sorting material for recycling or degradation in lysosomes.

Lysosome

A membrane-bound organelle in higher eukaryotic cells that has an acidic interior and is the major storage site of the degradative enzymes (acidic hydrolases) that are responsible for the breakdown of internalized proteins and many membrane proteins. It is functionally equivalent to the yeast vacuole.

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Komander, D., Clague, M. & Urbé, S. Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 10, 550–563 (2009). https://doi.org/10.1038/nrm2731

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