Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex

Xie, Shutao

doi:10.1107/s2053230x14014502

Cited by 18 publications

(22 citation statements)

References 23 publications

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“…1A). Although the C-terminal part of UBA5 was implicated in binding to UFM1 and UFC1 (32,33), we noticed that the 14-aa-long sequence IHEDNEWGIELVSE (aa 335-348 in human UBA5) contains a stretch of amino acids remotely resembling the LIR consensus sequence (Fig. 1B).…”

Section: Uba5 Interacts With Ufm1 and Lc3/gabarap Proteins Via An Evomentioning

confidence: 99%

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Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation

Habisov

Huber

Ichimura

et al. 2016

Journal of Biological Chemistry

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The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), which activates and transfers UFM1 to ubiquitin-fold modifierconjugating enzyme 1 (UFC1). The details of the interaction between UFM1 and UBA5 required for UFM1 activation and its downstream transfer are however unclear. In this study, we described and characterized a combined linear LC3-interacting region/UFM1-interacting motif (LIR/UFIM) within the C terminus of UBA5. This single motif ensures that UBA5 binds both UFM1 and light chain 3/␥-aminobutyric acid receptor-associated proteins (LC3/GABARAP), two ubiquitin (Ub)-like proteins. We demonstrated that LIR/UFIM is required for the full biological activity of UBA5 and for the effective transfer of UFM1 onto UFC1 and a downstream protein substrate both in vitro and in cells. Taken together, our study provides important structural and functional insights into the interaction between UBA5 and Ub-like modifiers, improving the understanding of the biology of the ufmylation pathway.

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Section: Uba5 Interacts With Ufm1 and Lc3/gabarap Proteins Via An Evomentioning

confidence: 99%

“…The strongest effect on the UFC1-UFM1 intermediate formation by the UBA5(1-330 aa) mutant, in which the whole C terminus was deleted, could in part be explained by the presence of the UFC1-binding domain (UFC1-BD) within the very C terminus of UBA5 (Ref. 33 and this study (Fig. 1, A and D)).…”

Section: Uba5 Interacts With Ufm1 and Lc3/gabarap Proteins Via An Evomentioning

confidence: 99%

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation

Habisov

Huber

Ichimura

et al. 2016

Journal of Biological Chemistry

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“… 139 A region of 23 residues with helical propensity in the E1 UBA5 C-terminus however appears to be sufficient for E2 UFC1 interaction, suggesting that the E1 UBA5 C-terminus does not adopt a ubiquitin fold. 143 The C-terminus of E1 UBA5 also contains an LIR/UFIM motif that interacts with UFM1. In the context of the homodimeric E1 UBA5 , this motif binds UFM1 in trans ( 140 ) to facilitate its activation.…”

Section: E1 Activating Enzymesmentioning

confidence: 99%

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism

2017

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Ubiquitin-like proteins (Ubl’s) are conjugated to target proteins or lipids to regulate their activity, stability, subcellular localization, or macromolecular interactions. Similar to ubiquitin, conjugation is achieved through a cascade of activities that are catalyzed by E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. In this review, we will summarize structural and mechanistic details of enzymes and protein cofactors that participate in Ubl conjugation cascades. Precisely, we will focus on conjugation machinery in the SUMO, NEDD8, ATG8, ATG12, URM1, UFM1, FAT10, and ISG15 pathways while referring to the ubiquitin pathway to highlight common or contrasting themes. We will also review various strategies used to trap intermediates during Ubl activation and conjugation.

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“…However, binding of UFM1 to UBA5 possessing the adenylation domain and the UIS, stabilizes the dimeric state which is needed for ATP binding and thereby for UFM1 activation [31]. Ultimately, in order to transfer UFM1 to UFC1, UBA5 contains a short sequence at the C-terminus that is required for UFC1 binding [32].…”

Section: Introductionmentioning

confidence: 99%

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation

Soudah¹,

Padala²,

Hassouna³

et al. 2019

Journal of Molecular Biology

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Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension.Currently the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding, but also affects how the adenylation domain interacts with ATP.Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.

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Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex

Cited by 18 publications

References 23 publications

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation

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