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Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways

Nature Reviews Molecular Cell Biology volume 10, pages 319–331 (2009)Cite this article

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Key Points

  • At the start of each ubiquitin-like protein (UBL) cascade is an E1 enzyme, which activates the UBL and then directs the UBL to downstream pathways. UBL proteins and E1 (or activating) enzymes have their origins in prokaryotic biosynthetic pathways.

  • In humans, eight E1 enzymes are known to initiate UBL conjugation. We refer to E1s for ubiquitin (UBA1 and UBA6 (also known as UBE1L2)), SUMO (SAE1–UBA2), NEDD8 (NAE1–UBA3) and ISG15 (UBA7) as canonical, owing to their related domain structures and enzymatic mechanisms, and to the more divergent E1s for URM1 (UBA4), UFM1 (UBA5) and ATG12 and ATG8 isoforms (ATG7) as non-canonical. (ATG is autophagy-related protein; ISG15 is interferon-stimulated gene 15; NAE1 is NEDD8-activating enzyme 1; SAE1 is SUMO-activating enzyme 1; UBA is ubiquitin-activating enzyme; UFM1 is ubiquitin-fold modifier 1; URM1 is ubiquitin-related modifier 1).

  • Canonical E1 structures all have an adenylation domain that resembles prokaryotic ancestors, and two domains that are specific to canonical E1s: a catalytic Cys domain that contains the Cys that is involved in the E1∼UBL thioester linkage and a carboxyl-terminal ubiquitin-fold domain that resembles ubiquitin and that binds E2.

  • In addition to their chemical roles in initiating UBL conjugation cascades, E1s also establish specificity, by matching a particular UBL with only cognate E2s. Rules for how this specificity is achieved are only beginning to emerge, but it is clear that specificity is achieved at multiple levels.

  • A particularly intriguing non-canonical E1 is UBA4 (MOCS3 in humans). Recent data indicate that UBA4 initiates a sulphur transfer pathway, in a manner related to bacterial E1-like enzymes.

  • E1s are unique in the UBL conjugating pathway in that they are the only components that use ATP, and this property is being exploited to develop selective inhibitors. The potential for the use of such inhibitors in therapy is high, given the links seen between components of UBL cascades and human disease.

Abstract

Attachment of ubiquitin or ubiquitin-like proteins (known as UBLs) to their targets through multienzyme cascades is a central mechanism to modulate protein functions. This process is initiated by a family of mechanistically and structurally related E1 (or activating) enzymes. These activate UBLs through carboxy-terminal adenylation and thiol transfer, and coordinate the use of UBLs in specific downstream pathways by charging cognate E2 (or conjugating) enzymes, which then interact with the downstream ubiquitylation machinery to coordinate the modification of the target. A broad understanding of how E1 enzymes activate UBLs and how they selectively coordinate UBLs with downstream function has come from enzymatic, structural and genetic studies.

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Figure 1: Diverse functions of ubiquitin-like proteins.
Figure 2: Activation of a prokaryotic ubiquitin-like protein, MoaD, by MoeB.
Figure 3: E1 domain structures.
Figure 4: Canonical E1 domain rotation in ubiquitin-like protein transfer to E2s.
Figure 5: Model for a thioester switch modulating E1–E2 interactions.
Figure 6: The UBA4 pathway.

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Change history

  • 09 April 2009

    In the main text, 'inorganic phosphate' in the following two sentences should read 'inorganic pyrophosphate': "The basic side chains of MoaD or ThiS would stabilize the developing negative charge from the ensuing pentacovalent phosphate intermediate, allowing the generation of MoaD∼adenylate or ThiS∼adenylate and inorganic phosphate." And: "Progression of the cascade is driven by the release of the small molecule products inorganic phosphate and AMP in the first and second steps, respectively56,57,58,62,63."

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Acknowledgements

We thank the National Institutes of Health (J.W.H. and B.A.S.) and Millennium Pharmaceuticals, Inc. (J.W.H.) for funding our work on E1 enzymes and C. Regni for assistance with figure 2. B.A.S. is an Investigator of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Departments of Structural Biology, Howard Hughes Medical Institute, and Genetics and Tumour Cell Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA. brenda.schulman@stjude.org,

    Brenda A. Schulman

  2. Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA. wade_harper@hms.harvard.edu,

    J. Wade Harper

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Brenda A. Schulman is a consultant for Millennium Pharmaceuticals.

J. Wade Harper is also a consultant for and receives grant support from Millennium Pharmaceuticals.

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DATABASES

Protein Data Bank

1JWA

1R4M

1U9B

1Y8R

1Y8X

2AYZ

2NVU

3CMM

FURTHER INFORMATION

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Glossary

Adenylation

The synthesis of a phosphodiester bond between a hydroxyl group and the phosphate group of AMP. In the case of ubiquitin-like protein (UBL) conjugation cascades, the hydroxyl is from the carboxyl terminus of the UBL.

Thioester bond

Covalent linkage of a sulphur with an acyl group. In the case of ubiquitin-like protein (UBL) cascades, the Cys sulphur of an enzyme is linked to the terminal carbon of a UBL.

26S proteasome

A large multisubunit protease complex that selectively degrades polyubiquitylated proteins. It contains a 20S particle that carries the catalytic activity and two regulatory 19S particles.

UBL fold

A structural motif, also known as βGRASP fold, that has a domain with a structure of two β-sheets, followed by an α-helix and two additional β-sheets.

Rhodanese homology domain

A domain that shares sequence and structural homology to rhodanese, a mitochondrial enzyme that catalyses Cys-mediated sulphur transfer reactions.

PP loop ATPase domain

A structural motif found in a family of conserved ATP-binding proteins that serve as tRNA-modifying enzymes and activate the tRNA through adenylation.

Elongator complex

An enzyme complex that replaces the hydrogen atom on position 5 of uridine at nucleotide 34 of tRNAs by a methoxycarbonylmethyl group.

Thiouridinylation

An enzymatic process in which the 2' oxygen of uridine in the anticodon of a tRNA is replaced by sulphur.

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Schulman, B., Wade Harper, J. Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways. Nat Rev Mol Cell Biol 10, 319–331 (2009). https://doi.org/10.1038/nrm2673

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