Building ubiquitin chains: E2 enzymes at work

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA.
Nature Reviews Molecular Cell Biology (Impact Factor: 36.46). 11/2009; 10(11):755-64. DOI: 10.1038/nrm2780
Source: PubMed

ABSTRACT The modification of proteins with ubiquitin chains can change their localization, activity and/or stability. Although ubiquitylation requires the concerted action of ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s), it is the E2s that have recently emerged as key mediators of chain assembly. These enzymes 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.

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Available from: Yihong Ye, Jul 19, 2015
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    • "All the E2 enzymes across all the species, including ~35 coded by the human genome, share a structurally conserved ubiquitin conjugating (UBC) domain of ~150 residues harboring the catalytic cysteine. Despite this structural conservation, UBC cores from different E2s show significant sequence diversity justifying differences in their E3 selectivity and catalytic activity [23]. Besides the UBC domain, some of the E2s also contain extended regions in their C-(Class II E2s), or N-(Class III E2s) terminal ends, or both (Class IV E2s). "
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    ABSTRACT: Ubiquitination of a target protein is accomplished through sequential actions of the E1, E2s, and the E3s. E2s dictate the modification topology while E3 ligases confer substrate specificity and recruit the cognate E2. Human genome codes for ~35 different E2 proteins; all of which contain the characteristic UBC core domain sufficient for catalysis. Many of these E2 enzymes also have N- or C-terminal extensions; roles of which are not very well understood. We show that the N-terminal extension of Ube2E1 undergoes intramolecular autoubiquitination. This self-ubiquitination activity is enhanced in the presence of interacting RING E3 ligases and results in a progressive attenuation of the E2 activity towards substrate/E3 modification. We also find that the N-terminal ubiquitination sites are conserved in all the three Ube2Es and replacing them with arginine renders all three full-length Ube2Es equally active as their core UBC domains. Based on these results we propose that E3-catalyzed self-ubiquitination acts as a key regulatory mechanism that controls the activity of Ube2E class of Ubiquitin E2s. Copyright © 2015. Published by Elsevier Ltd.
    Journal of Molecular Biology 05/2015; 81(13). DOI:10.1016/j.jmb.2015.04.011 · 3.96 Impact Factor
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    • "This is the case for UBE2W and UBE2E2, this dimer initiating Ub chain initiation when combined with the E3 ligase BRCA1 and UBE2N-UBE2V1 dimer elongating Ub chains (Christensen et al., 2007). Similarly, UBE2D was proposed to only initiate ubiquitination and other E2 enzymes might be responsible for the development of Ub chains, which is the case for UBE2D-UBE2K ubiquitination activity within the APC complex (Rodrigo-Brenni and Morgan, 2007; Ye and Rape, 2009). E2 combinations represent thus a possibility of control of Ub chain formation by cells, together with posttranslational modifications and binding with other partners. "
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    ABSTRACT: The Ubiquitin Proteasome System (UPS) is a major actor of muscle wasting during various physio-pathological situations. In the past 15 years, increasing amounts of data have depicted a picture, although incomplete, of the mechanisms implicated in myofibrillar protein degradation, from the discovery of muscle-specific E3 ligases to the identification of the signaling pathways involved. The targeting specificity of the UPS relies on the capacity of the system to first recognize and then label the proteins to be degraded with a poly-ubiquitin (Ub) chain. It is fairly assumed that the recognition of the substrate is accomplished by the numerous E3 ligases present in mammalian cells. However, most E3s do not possess any catalytic activity and E2 enzymes may be more than simple Ub-providers for E3s since they are probably important actors in the ubiquitination machinery. Surprisingly, most authors have tried to characterize E3 substrates, but the exact role of E2s in muscle protein degradation is largely unknown. A very limited number of the 35 E2s described in humans have been studied in muscle protein breakdown experiments and the vast majority of studies were only descriptive. We review here the role of E2 enzymes in skeletal muscle and the difficulties linked to their study and provide future directions for the identification of muscle E2s responsible for the ubiquitination of contractile proteins.
    Frontiers in Physiology 03/2015; 6:59. DOI:10.3389/fphys.2015.00059 · 3.50 Impact Factor
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    • "Assembly of K29-Linked PolyUb PolyUb of several linkage types, including K11, K48, and K63, can be assembled in vitro by E2 enzymes (Bremm et al., 2010; Pickart and Raasi, 2005; Ye and Rape, 2009). In addition, HECT-family ligases have been used to catalyze assembly of K6-linked polyUb (Hospenthal et al., 2013). "
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    ABSTRACT: Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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