Structural Basis for Recruitment of Ubc12 by an E2 Binding Domain in NEDD8's E1

Huang, Danny T.; Paydar, Amir; Zhuang, Min; Waddell, M. Brett; Holton, James M.; Schulman, Brenda A.

doi:10.1016/j.molcel.2004.12.020

Cited by 171 publications

(203 citation statements)

References 54 publications

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“…Therefore, the segment encompassing residues 486 -499 of SAE2 undergoes folding and unfolding equilibrium. In conjunction with previous studies of the NEDD8 E1-E2 interaction, the folded conformation was similar to that of the E2-bound state (27).…”

Section: Two Conformational States At the E2-binding Surface Of Thesupporting

confidence: 84%

Conformational Transition Associated with E1-E2 Interaction in Small Ubiquitin-like Modifications

Wang¹,

Lee²,

Cai³

et al. 2009

Journal of Biological Chemistry

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Ubiquitin-like modifications regulate nearly every aspect of cellular functions. A key step in these modifications is the recognition of the carrier enzyme (E2) by the activating enzyme (E1). In this study, we have found that a critical E2-binding surface on the E1 of the small ubiquitin-like modifier has unusually high populations in both ordered and disordered states. Upon binding the E2, the disordered state is converted to the ordered state, which resembles the structure of the bound conformation, providing a mechanism to resolve the "Levinthal Paradox" search problem in a folding-upon-binding process. The significance of the folding-unfolding equilibrium is shown by the loss of functions of the mutations that shift the equilibrium to the folded state. This study highlights the importance of conformational flexibility in the molecular recognition event.The conjugation of ubiquitin or ubiquitin-like proteins to other cellular proteins is one of the most important mechanisms in regulating cellular functions in eukaryotic systems and is broadly involved in controlling the life spans, trafficking, and functions of a wide range of proteins (1-4). Among the ubiquitin-like modifiers, the small ubiquitin-like modifier (SUMO) 5 is the most studied, and its modification regulates many essential functions, such as gene transcription, hormone response, DNA repair, and nuclear import (5-7). Multiple enzymes are required for post-translational modifications by ubiquitin or ubiquitin-like proteins (1,8). A ubiquitin-like protein (Ublp) is first activated by E1. The E1 required for SUMO modification is a tight heterodimer of two proteins, known as SUMO activation enzymes 1 and 2 (SAE1 and SAE2), which are homologous to the N-terminal and C-terminal portions of the ubiquitin E1, respectively (9). E1 catalyzes the adenylation of the C-terminal carboxyl group of the Ublp, and it then forms a thioester bond between the -SH group of the active site Cys residue and the C-terminal carboxyl group of the Ublp. The Ublp is then transferred to E2 (known as Ubc9 in the SUMO pathway), forming a thioester bond with the -SH group of the active site Cys residue. In the final step, the Ublp is attached to target proteins by forming an isopeptide bond between its C-terminal carboxyl group and the ⑀-amino group of a Lys residue on the target protein. This step generally requires another enzyme, isopeptide ligase.During the transfer of Ublp from E1 to E2, the E2 enzyme is recruited to the E1-SUMO thioester conjugate by binding to multiple sites on E1, including the Cys domain (the domain containing the active Cys residue) and the ubiquitin-like (Ubl) domain (10, 11). Among these multiple binding sites, the Ubl domain has the highest binding affinity, and thus it is the key E2-binding site. The multivalent interaction produces high affinity binding between E1 and E2, which accounts for the efficiency of E1 at low concentrations. At the same time, the low to medium affinity of each of the individual interactions allows fast turnover of the enzym...

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Section: Two Conformational States At the E2-binding Surface Of Thesupporting

confidence: 84%

Conformational Transition Associated with E1-E2 Interaction in Small Ubiquitin-like Modifications

Wang¹,

Lee²,

Cai³

et al. 2009

Journal of Biological Chemistry

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“…The RWD-binding surface on Ubc9 overlaps with the surface that binds the UFD of SAE2 (9,11,23) (Fig. 4A, left panel).…”

Section: The Crystal Structure Of Ubc9-rwd Complex and Validationmentioning

confidence: 98%

RWD Domain as an E2 (Ubc9)-Interaction Module

Alontaga¹,

Ambaye²,

Li³

et al. 2015

Journal of Biological Chemistry

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Background: RWD is a conserved domain in human proteome with unknown function. Results: We solved the crystal structure of an RWD domain in complex with a Ubc9 homodimer and conducted a biochemical investigation. Conclusion:The RWD domain binds to a Ubc9 surface that also must interact with E1, E3, and SUMO. Significance: This study establishes a function for the evolutionary conserved RWD domain.

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“…The binding of E3 ligases to E2s often occurs on the surface of the E2 that is recognized by its corresponding E1 enzyme 37 . The E1 interaction site of Ubc12 requires the H88 and D89 residues within the ab core domain and amino acids 1-26 within the N-terminal region 38 . Strikingly, Smurf1 could no longer bind to Ubc12 if the Ubc12 H88A-D89A or DN26 mutant was tested for interaction (Fig.…”

Section: Smurf1 Interacts Withmentioning

confidence: 99%

The covalent modifier Nedd8 is critical for the activation of Smurf1 ubiquitin ligase in tumorigenesis

et al. 2014

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Neddylation, the covalent attachment of ubiquitin-like protein Nedd8, of the Cullin-RING E3 ligase family regulates their ubiquitylation activity. However, regulation of HECT ligases by neddylation has not been reported to date. Here we show that the C2-WW-HECT ligase Smurf1 is activated by neddylation. Smurf1 physically interacts with Nedd8 and Ubc12, forms a Nedd8-thioester intermediate, and then catalyses its own neddylation on multiple lysine residues. Intriguingly, this autoneddylation needs an active site at C426 in the HECT N-lobe. Neddylation of Smurf1 potently enhances ubiquitin E2 recruitment and augments the ubiquitin ligase activity of Smurf1. The regulatory role of neddylation is conserved in human Smurf1 and yeast Rsp5. Furthermore, in human colorectal cancers, the elevated expression of Smurf1, Nedd8, NAE1 and Ubc12 correlates with cancer progression and poor prognosis. These findings provide evidence that neddylation is important in HECT ubiquitin ligase activation and shed new light on the tumour-promoting role of Smurf1.

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Structural Basis for Recruitment of Ubc12 by an E2 Binding Domain in NEDD8's E1

Cited by 171 publications

References 54 publications

Conformational Transition Associated with E1-E2 Interaction in Small Ubiquitin-like Modifications

Conformational Transition Associated with E1-E2 Interaction in Small Ubiquitin-like Modifications

RWD Domain as an E2 (Ubc9)-Interaction Module

The covalent modifier Nedd8 is critical for the activation of Smurf1 ubiquitin ligase in tumorigenesis

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