Mechanistic Study of Uba5 Enzyme and the Ufm1 Conjugation Pathway

E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target proteins or lipids. Ubiquitin-fold modifier 1 (Ufm1) is activated by the E1 enzyme Uba5, and this pathway is proposed to play an important role...

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Published inThe Journal of biological chemistry Vol. 289; no. 33; pp. 22648 - 22658
Main Authors Gavin, James M., Hoar, Kara, Xu, Qing, Ma, Jingya, Lin, Yafang, Chen, Jiejin, Chen, Wei, Bruzzese, Frank J., Harrison, Sean, Mallender, William D., Bump, Nancy J., Sintchak, Michael D., Bence, Neil F., Li, Ping, Dick, Lawrence R., Gould, Alexandra E., Chen, Jesse J.
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 15.08.2014
American Society for Biochemistry and Molecular Biology
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Abstract E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target proteins or lipids. Ubiquitin-fold modifier 1 (Ufm1) is activated by the E1 enzyme Uba5, and this pathway is proposed to play an important role in the endoplasmic reticulum (ER) stress response. However, the mechanisms of Ufm1 activation by Uba5 and subsequent transfer to the conjugating enzyme (E2), Ufc1, have not been studied in detail. In this work, we found that Uba5 activated Ufm1 via a two-step mechanism and formed a binary covalent complex of Uba5∼Ufm1 thioester. This feature contrasts with the three-step mechanism and ternary complex formation in ubiquitin-activating enzyme Uba1. Uba5 displayed random ordered binding with Ufm1 and ATP, and its ATP-pyrophosphate (PPi) exchange activity was inhibited by both AMP and PPi. Ufm1 activation and Uba5∼Ufm1 thioester formation were stimulated in the presence of Ufc1. Furthermore, binding of ATP to Uba5∼Ufm1 thioester was required for efficient transfer of Ufm1 from Uba5 to Ufc1 via transthiolation. Consistent with the two-step activation mechanism, the mechanism-based pan-E1 inhibitor, adenosine 5′-sulfamate (ADS), reacted with the Uba5∼Ufm1 thioester and formed a covalent, tight-binding Ufm1-ADS adduct in the active site of Uba5, which prevented further substrate binding or catalysis. ADS was also shown to inhibit the Uba5 conjugation pathway in the HCT116 cells through formation of the Ufm1-ADS adduct. This suggests that further development of more selective Uba5 inhibitors could be useful in interrogating the roles of the Uba5 pathway in cells.
AbstractList E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target proteins or lipids. Ubiquitin-fold modifier 1 (Ufm1) is activated by the E1 enzyme Uba5, and this pathway is proposed to play an important role in the endoplasmic reticulum (ER) stress response. However, the mechanisms of Ufm1 activation by Uba5 and subsequent transfer to the conjugating enzyme (E2), Ufc1, have not been studied in detail. In this work, we found that Uba5 activated Ufm1 via a two-step mechanism and formed a binary covalent complex of Uba5∼Ufm1 thioester. This feature contrasts with the three-step mechanism and ternary complex formation in ubiquitin-activating enzyme Uba1. Uba5 displayed random ordered binding with Ufm1 and ATP, and its ATP-pyrophosphate (PPi) exchange activity was inhibited by both AMP and PPi. Ufm1 activation and Uba5∼Ufm1 thioester formation were stimulated in the presence of Ufc1. Furthermore, binding of ATP to Uba5∼Ufm1 thioester was required for efficient transfer of Ufm1 from Uba5 to Ufc1 via transthiolation. Consistent with the two-step activation mechanism, the mechanism-based pan-E1 inhibitor, adenosine 5'-sulfamate (ADS), reacted with the Uba5∼Ufm1 thioester and formed a covalent, tight-binding Ufm1-ADS adduct in the active site of Uba5, which prevented further substrate binding or catalysis. ADS was also shown to inhibit the Uba5 conjugation pathway in the HCT116 cells through formation of the Ufm1-ADS adduct. This suggests that further development of more selective Uba5 inhibitors could be useful in interrogating the roles of the Uba5 pathway in cells.
Background: Human ubiquitin-like protein Ufm1 and its activating enzyme, Uba5, are involved in endoplasmic reticulum (ER) stress response. Results: The Uba5-Ufm1 conjugation pathway is characterized in both reconstituted systems and cellular settings. Conclusion: Uba5 activates Ufm1 via a distinct two-step mechanism. Significance: This study represents the first mechanistic characterization of Uba5, a homodimeric member of the E1 enzyme family. E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target proteins or lipids. Ubiquitin-fold modifier 1 (Ufm1) is activated by the E1 enzyme Uba5, and this pathway is proposed to play an important role in the endoplasmic reticulum (ER) stress response. However, the mechanisms of Ufm1 activation by Uba5 and subsequent transfer to the conjugating enzyme (E2), Ufc1, have not been studied in detail. In this work, we found that Uba5 activated Ufm1 via a two-step mechanism and formed a binary covalent complex of Uba5∼Ufm1 thioester. This feature contrasts with the three-step mechanism and ternary complex formation in ubiquitin-activating enzyme Uba1. Uba5 displayed random ordered binding with Ufm1 and ATP, and its ATP-pyrophosphate (PP i ) exchange activity was inhibited by both AMP and PP i . Ufm1 activation and Uba5∼Ufm1 thioester formation were stimulated in the presence of Ufc1. Furthermore, binding of ATP to Uba5∼Ufm1 thioester was required for efficient transfer of Ufm1 from Uba5 to Ufc1 via transthiolation. Consistent with the two-step activation mechanism, the mechanism-based pan-E1 inhibitor, adenosine 5′-sulfamate (ADS), reacted with the Uba5∼Ufm1 thioester and formed a covalent, tight-binding Ufm1-ADS adduct in the active site of Uba5, which prevented further substrate binding or catalysis. ADS was also shown to inhibit the Uba5 conjugation pathway in the HCT116 cells through formation of the Ufm1-ADS adduct. This suggests that further development of more selective Uba5 inhibitors could be useful in interrogating the roles of the Uba5 pathway in cells.
Author Sintchak, Michael D.
Gould, Alexandra E.
Li, Ping
Chen, Jesse J.
Ma, Jingya
Chen, Jiejin
Bruzzese, Frank J.
Lin, Yafang
Bence, Neil F.
Chen, Wei
Mallender, William D.
Harrison, Sean
Dick, Lawrence R.
Hoar, Kara
Bump, Nancy J.
Gavin, James M.
Xu, Qing
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  surname: Mallender
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  givenname: Nancy J.
  surname: Bump
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  givenname: Michael D.
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  surname: Chen
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  email: jesse.chen@takeda.com
  organization: Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
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ContentType Journal Article
Copyright 2014 © 2014 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.
2014 by The American Society for Biochemistry and Molecular Biology, Inc.
2014 by The American Society for Biochemistry and Molecular Biology, Inc. 2014
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Issue 33
Keywords Enzyme Mechanisms
Ubiquitin-conjugating Enzyme (E2 enzyme)
Enzyme Inhibitors
Ufc1
Substrate-assisted Inhibitors
Uba5
Endoplasmic Reticulum Stress (ER Stress)
Enzyme Inactivation
Ufm1
Endoplasmic Reticulum (ER)
Enzyme Inhibitor
Language English
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2014 by The American Society for Biochemistry and Molecular Biology, Inc.
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Present address: Moderna Therapeutics, Inc. 200 Tech Square, Cambridge, MA 02139.
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Snippet E1 enzymes activate ubiquitin or ubiquitin-like proteins (Ubl) via an adenylate intermediate and initiate the enzymatic cascade of Ubl conjugation to target...
Background: Human ubiquitin-like protein Ufm1 and its activating enzyme, Uba5, are involved in endoplasmic reticulum (ER) stress response. Results: The...
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StartPage 22648
SubjectTerms Adenosine Triphosphate - chemistry
Adenosine Triphosphate - genetics
Adenosine Triphosphate - metabolism
Catalytic Domain
Cell Line
Enzyme Activation
Enzymology
Humans
Models, Chemical
Multiprotein Complexes - chemistry
Multiprotein Complexes - genetics
Multiprotein Complexes - metabolism
Protein Binding
Protein Structure, Quaternary
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Ubiquitin-Activating Enzymes - chemistry
Ubiquitin-Activating Enzymes - genetics
Ubiquitin-Activating Enzymes - metabolism
Ubiquitin-Conjugating Enzymes - chemistry
Ubiquitin-Conjugating Enzymes - genetics
Ubiquitin-Conjugating Enzymes - metabolism
Title Mechanistic Study of Uba5 Enzyme and the Ufm1 Conjugation Pathway
URI https://dx.doi.org/10.1074/jbc.M114.573972
https://www.ncbi.nlm.nih.gov/pubmed/24966333
https://search.proquest.com/docview/1555627886
https://pubmed.ncbi.nlm.nih.gov/PMC4132772
Volume 289
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