Ubiquitin and proteasomes

Themes and variations on ubiquitylation

Key Points

  • Ubiquitin is a highly conserved 76-amino-acid eukaryotic protein that is covalently attached to proteins as monomers or lysine-linked chains. This review provides an overview of the ubiquitin-conjugating system, highlighting recent insights into the enzymes involved in the addition and removal of ubiquitin from proteins and the consequences of this modification.

  • Ubiquitylation is the result of a highly specific multi-enzyme process, involving classes of enzymes known as E1s, E2s and E3s.There is a single known E1 (ubiquitin-activating enzyme) gene, several E2s (ubiquitin-conjugating enzymes) and a substantially greater number of potential E3s (ubiquitin protein ligases).

  • E2s are characterized by a conserved core domain. Differences among E2s both in the core domain and in amino- and carboxy-terminal extensions have the potential to determine the specificity of E3 interactions and their cellular locations.

  • Specificity in ubiquitylation is conferred primarily by E3s. There are two major classes of E3: HECT domain E3s and RING finger E3s. Crystal structures of members of both classes bound to E2 have now been solved.

  • HECT E3s include E6-AP, implicated in the HPV-E6-dependent degradation of p53, as well as a number of other proteins. Many HECT E3s have a amino-terminal C2 domain and several WW domains.

  • RING finger E3s include single subunit E3s, such as Mdm2 and c-Cbl as well as multisubunit E3s. The latter share the common feature of having a cullin family member as a component of the active complex.

  • Ubiquitylation is reversible. Removal of ubiquitin from proteins, disassembly of multi-ubiquitin chains, and processing of ubiquitin precursors to mature forms are among the jobs carried out by de-ubiquitylating enzymes.

  • Modification with ubiquitin is classically associated with protein degradation by targeting to proteasomes. However, ubiquitin has other cellular roles not obviously associated with proteasomal degradation and it is also evident that the types of ubiquitin linkages formed may influence protein fate.

Abstract

Ubiquitylation ? the conjugation of proteins with a small protein called ubiquitin ? touches upon all aspects of eukaryotic biology, and its defective regulation is manifest in diseases that range from developmental abnormalities and autoimmunity to neurodegenerative diseases and cancer. A few years ago, we could only have dreamt of the complex arsenal of enzymes dedicated to ubiquitylation. Why has nature come up with so many ways of doing what seems to be such a simple job?

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Figure 1: The ubiquitylation pathway.
Figure 2: The many functions of de-ubiquitylating enzymes.
Figure 3: E2?E3 interactions.
Figure 4: Representative E3?substrate interactions
Figure 5: Different functions for different ubiquitin linkages.

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Acknowledgements

I am grateful to the members of my laboratory for countless invaluable discussions. My apologies to colleagues whose important contributions to the field have been cited only indirectly because of space limitations.

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DATABASE LINKS

Ubiquitin

UCRP

RUB1

Nedd8

SUMO-1

Apg12

ubiquitin domain

HECT domain

RING finger

E1

Ubc9

Ubc12

BRUCE

Ubc7

UBCH7

E6-AP

c-Cbl

Ubc3

p53

HHR23A

Angelman syndrome

WW domains

C2 domain

Nedd4

Rsp5

SPT23

MGA2

NF-κB

Liddle syndrome

Rbx1

Skp1

Cul1

BRCA1

familial forms of breast and ovarian cancer

Mdm2

parkin

IBR

juvenile Parkinson's disease

BIR domain

von Hippel Lindau

Cul-2

elongin B

elongin C

Apc11

F Box

βTRCP

β-catenin

CD4

von Hippel?Lindau

HIF1α

SOCS

Ubc13

Mms2

Ubc2

Rad5

Rad18

L28

TRAF6

S5A

FURTHER INFORMATION

Weissman lab

Nottingham University ubiquitin site

Wilkinson lab

Ubiquitin and the biology of the cell

Ubiquitin and the biology of the cell

Cbl

CDCrel-1

VEGF

ENCYCLOPEDIA OF LIFE SCIENCES

Ubiquitin pathway

Proteins: postsynthetic modifications

Glossary

RUB1

(Nedd8 in metazoans). A ubiquitin-like (UBL) protein that is activated by its own E1- and E2-like molecules and modifies cullin family members.

HECT

Stands for homologous to E6-AP carboxyl terminus. The HECT domain is a 350-amino-acid domain, highly conserved among a family of E3 enzymes.

RING FINGER

Defined structurally by two interleaved metal-coordinating sites. The consensus sequence for the RING finger is: CX2CX(9?39)CX(1?3)HX(2?3)C/HX2CX(4?48)CX2C. The cysteines and histidines represent metal-binding sites with the first, second, fifth and sixth of these binding one zinc ion and the third, fourth, seventh and eighth binding the second.

BIR REPEAT

(Baculovirus inhibitor of apoptosis repeat). Cysteine-based motif of 65 amino acids. Inhibitors of apoptosis (IAPs) contain several BIR domains.

c-CBL

Multifunctional protein that modulates signalling through tyrosine-kinase-containing growth factor receptors and tyrosine-kinase-coupled receptors. Has RING-finger-dependent E3 activity.

WW DOMAIN

Protein interaction domain found in the amino-terminal halves of many HECT E3s, and also in other proteins. Characterized by a pair of tryptophans 20?22 amino acids apart, and an invariant proline within a region of 40 amino acids. WW domains interact with proline-rich regions, including those with phosphoserine or phosphothreonine.

F-BOX

A conserved 50-residue region found in proteins that associate with Skp1 and potentially form the SCF E3s. There are over a hundred distinct members of this family.

CULLIN FAMILY

Proteins with homology to Cul1, which was first shown to be involved in cell-cycle exit in Caenorhabditis elegans.

IκBα

Inhibitory subunit of the NF-κB transcription factor. It is phosphorylated, ubiquitylated and degraded in response to stimuli that activate NF-κB.

SOCS BOX

Suppressor of cytokine signalling box first identified in an inhibitor of Jak family kinases.

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Weissman, A. Themes and variations on ubiquitylation . Nat Rev Mol Cell Biol 2, 169–178 (2001). https://doi.org/10.1038/35056563

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