The Ubiquitin Code

  title={The Ubiquitin Code},
  author={David Komander and Michael Rap{\'e}},
  journal={The Ubiquitin Code},
The posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells. Ubiquitin can be attached to substrate proteins as a single moiety or in the form of polymeric chains in which successive ubiquitin molecules are connected through specific isopeptide bonds. Reminiscent of a code, the various ubiquitin modifications adopt distinct conformations and lead to different outcomes in cells. Here, we discuss the structure, assembly, and… 

The evolving world of ubiquitin: transformed polyubiquitin chains

These novel forms of ubiquitin signal are reviewed, with a focus on fibril formation of polyubiquitin chains and its underlying biological relevance.

The emerging complexity of ubiquitin architecture

This review describes mass spectrometry-based methods to characterize the ubiquitin signal and describes recent advances in the understanding of complex ubiquitIn architectures, including the own findings concerning ubiquit in acetylation and branching within polyubiquitin chains.

The Ubiquitin–Proteasome System of Saccharomyces cerevisiae

The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins.

Ubiquitomics: An Overview and Future

Different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as “ubiquitomics” are reviewed, aiming to understand this system’s biological diversity.

The increasing complexity of the ubiquitin code

How the increasing complexity of ubiquitylation is employed to ensure robust and faithful signal transduction in eukaryotic cells is discussed.

Studying Protein Ubiquitylation in Yeast.

Ubiquitylation is a reversible posttranslational modification that is critical for most, if not all, cellular processes and essential for viability. Ubiquitin conjugates to substrate proteins either

Ubiquitin modifications

An overview of the various ubiquitin modifications present in cells, and recent findings in the field of ubiquit in acetylation and phosphorylation are discussed, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation.

Building ubiquitin chains: E2 enzymes at work

The E2s are able to govern the switch from ubiquitin chain initiation to elongation, regulate the processivity of chain formation and establish the topology of assembled chains, thereby determining the consequences of ubiquitylation for the modified proteins.

Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation

Crystal structures of the Nedd4 HECT domain show a new binding mode involving two surfaces on ubiquitin and both subdomains of the HECT N‐lobe, which suggest a model for HECT‐to‐substrate ubiquitIn transfer, in which the growing chain on the substrate is kept close to the catalytic cysteine to promote processivity.

Recognition of the polyubiquitin proteolytic signal

The properties of the substrates studied here implicate substrate unfolding as a kinetically dominant step in the proteolysis of properly folded proteins, and suggest that extraproteasomal chaperones are required for efficient degradation of certain proteasome substrates.

Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2).

A model for the interaction of diubiquitin and a ubiquitin conjugating enzyme (E2) is proposed and suggests determinants for recognition of multiubiquITin chains.

Mechanisms underlying ubiquitination.

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Recent findings reveal that all known E3s utilize one of just two catalytic domains--a HECT domain or a RING finger--and crystal structures have provided the first detailed views of an active site of each type.

A ubiquitin-interacting motif protects polyubiquitinated Met4 from degradation by the 26S proteasome

Covalent attachment of ubiquitin to proteins regulates a host of cellular events by proteolysis dependent and independent mechanisms. A variety of protein domains that bind non-covalently to

Breaking the chains: structure and function of the deubiquitinases

DUBs are subject to multiple layers of regulation that modulate both their activity and their specificity, and due to their wide-ranging involvement in key regulatory processes, these enzymes might provide new therapeutic targets.

Proteasome-Independent Functions of Ubiquitin in Endocytosis and Signaling

The proteasome-independent roles of ubiquitination in signaling and endocytosis are discussed, which are implicated in pathogenesis of some diseases, certain malignancies, neurodegenerative disorders, and pathologies of the inflammatory immune response.