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Choi YS, Lee YJ, Lee SY, Shi L, Ha JH, Cheong HK, Cheong C, Cohen RE, Ryu KS. Differential ubiquitin binding by the acidic loops of Ube2g1 and Ube2r1 enzymes distinguishes their Lys-48-ubiquitylation activities. J Biol Chem 2014; 290:2251-63. [PMID: 25471371 DOI: 10.1074/jbc.m114.624809] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin E2 enzymes, Ube2g1 and Ube2r1, are able to synthesize Lys-48-linked polyubiquitins without an E3 ligase but how that is accomplished has been unclear. Although both E2s contain essential acidic loops, only Ube2r1 requires an additional C-terminal extension (184-196) for efficient Lys-48-ubiquitylation activity. The presence of Tyr-102 and Tyr-104 in the Ube2g1 acidic loop enhanced both ubiquitin binding and Lys-48-ubiquitylation and distinguished Ube2g1 from the otherwise similar truncated Ube2r1(1-183) (Ube2r1C). Replacement of Gln-105-Ser-106-Gly-107 in the acidic loop of Ube2r1C (Ube2r1C(YGY)) by the corresponding residues from Ube2g1 (Tyr-102-Gly-103-Tyr-104) increased Lys-48-ubiquitylation activity and ubiquitin binding. Two E2∼UB thioester mimics (oxyester and disulfide) were prepared to characterize the ubiquitin binding activity of the acidic loop. The oxyester but not the disulfide derivative was found to be a functional equivalent of the E2∼UB thioester. The ubiquitin moiety of the Ube2r1C(C93S)-[(15)N]UB(K48R) oxyester displayed two-state conformational exchange, whereas the Ube2r1C(C93S/YGY)-[(15)N]UB(K48R) oxyester showed predominantly one state. Together with NMR studies that compared UB(K48R) oxyesters of the wild-type and the acidic loop mutant (Y102G/Y104G) forms of Ube2g1, in vitro ubiquitylation assays with various mutation forms of the E2s revealed how the intramolecular interaction between the acidic loop and the attached donor ubiquitin regulates Lys-48-ubiquitylation activity.
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Affiliation(s)
- Yun-Seok Choi
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Yun-Ju Lee
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Seo-Yeon Lee
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Lei Shi
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, and
| | - Jung-Hye Ha
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea
| | - Hae-Kap Cheong
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Chaejoon Cheong
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Kyoung-Seok Ryu
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea,
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Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem 2014; 290:3308-32. [PMID: 25451919 DOI: 10.1074/jbc.m114.611525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CYP3A4 is an abundant and catalytically dominant human liver endoplasmic reticulum-anchored cytochrome P450 enzyme engaged in the biotransformation of endo- and xenobiotics, including >50% of clinically relevant drugs. Alterations of CYP3A4 protein turnover can influence clinically relevant drug metabolism and bioavailability and drug-drug interactions. This CYP3A4 turnover involves endoplasmic reticulum-associated degradation via the ubiquitin (Ub)-dependent 26 S proteasomal system that relies on two highly complementary E2 Ub-conjugating-E3 Ub-ligase (UBC7-gp78 and UbcH5a-C terminus of Hsc70-interacting protein (CHIP)-Hsc70-Hsp40) complexes, as well as protein kinases (PK) A and C. We have documented that CYP3A4 Ser/Thr phosphorylation (Ser(P)/Thr(P)) by PKA and/or PKC accelerates/enhances its Lys ubiquitination by either of these E2-E3 systems. Intriguingly, CYP3A4 Ser(P)/Thr(P) and ubiquitinated Lys residues reside within the cytosol-accessible surface loop and/or conformationally assembled acidic Asp/Glu clusters, leading us to propose that such post-translational Ser/Thr protein phosphorylation primes CYP3A4 for ubiquitination. Herein, this possibility was examined through various complementary approaches, including site-directed mutagenesis, chemical cross-linking, peptide mapping, and LC-MS/MS analyses. Our findings reveal that such CYP3A4 Asp/Glu/Ser(P)/Thr(P) surface clusters are indeed important for its intermolecular electrostatic interactions with each of these E2-E3 subcomponents. By imparting additional negative charge to these Asp/Glu clusters, such Ser/Thr phosphorylation would generate P450 phosphodegrons for molecular recognition by the E2-E3 complexes, thereby controlling the timing of CYP3A4 ubiquitination and endoplasmic reticulum-associated degradation. Although the importance of phosphodegrons in the CHIP targeting of its substrates is known, to our knowledge this is the first example of phosphodegron involvement in gp78-substrate recruitment, an important step in CYP3A4 proteasomal degradation.
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Affiliation(s)
- YongQiang Wang
- From the Departments of Cellular and Molecular Pharmacology
| | - Sung-Mi Kim
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Yi Liu
- From the Departments of Cellular and Molecular Pharmacology
| | | | - Maria Almira Correia
- From the Departments of Cellular and Molecular Pharmacology, Pharmaceutical Chemistry, and Bioengineering and Therapeutic Sciences, The Liver Center, University of California at San Francisco, San Francisco, California 94158-2517
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Koenig PA, Nicholls PK, Schmidt FI, Hagiwara M, Maruyama T, Frydman GH, Watson N, Page DC, Ploegh HL. The E2 ubiquitin-conjugating enzyme UBE2J1 is required for spermiogenesis in mice. J Biol Chem 2014; 289:34490-502. [PMID: 25320092 DOI: 10.1074/jbc.m114.604132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ER-resident proteins destined for degradation are dislocated into the cytosol by components of the ER quality control machinery for proteasomal degradation. Dislocation substrates are ubiquitylated in the cytosol by E2 ubiquitin-conjugating/E3 ligase complexes. UBE2J1 is one of the well-characterized E2 enzymes that participate in this process. However, the physiological function of Ube2j1 is poorly defined. We find that Ube2j1(-/-) mice have reduced viability and fail to thrive early after birth. Male Ube2j1(-/-) mice are sterile due to a defect in late spermatogenesis. Ultrastructural analysis shows that removal of the cytoplasm is incomplete in Ube2j1(-/-) elongating spermatids, compromising the release of mature elongate spermatids into the lumen of the seminiferous tubule. Our findings identify an essential function for the ubiquitin-proteasome-system in spermiogenesis and define a novel, non-redundant physiological function for the dislocation step of ER quality control.
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Affiliation(s)
- Paul-Albert Koenig
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Peter K Nicholls
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Florian I Schmidt
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Masatoshi Hagiwara
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Takeshi Maruyama
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Galit H Frydman
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Nicki Watson
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - David C Page
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, and Howard Hughes Medical Institute, Cambridge, Massachusetts 02142
| | - Hidde L Ploegh
- From the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, and
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Gavin JM, Hoar K, Xu Q, Ma J, Lin Y, Chen J, Chen W, Bruzzese FJ, Harrison S, Mallender WD, Bump NJ, Sintchak MD, Bence NF, Li P, Dick LR, Gould AE, Chen JJ. Mechanistic study of Uba5 enzyme and the Ufm1 conjugation pathway. J Biol Chem 2014; 289:22648-22658. [PMID: 24966333 PMCID: PMC4132772 DOI: 10.1074/jbc.m114.573972] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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.
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Affiliation(s)
- James M Gavin
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139.
| | - Kara Hoar
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Qing Xu
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jingya Ma
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Yafang Lin
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jiejin Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Wei Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Frank J Bruzzese
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Sean Harrison
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - William D Mallender
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Nancy J Bump
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Michael D Sintchak
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Neil F Bence
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Ping Li
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Lawrence R Dick
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Alexandra E Gould
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139
| | - Jesse J Chen
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, Massachusetts 02139.
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