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Zhang X, Huo C, Liu Y, Su R, Zhao Y, Li Y. Mechanism and Disease Association With a Ubiquitin Conjugating E2 Enzyme: UBE2L3. Front Immunol 2022; 13:793610. [PMID: 35265070 PMCID: PMC8899012 DOI: 10.3389/fimmu.2022.793610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Ubiquitin conjugating enzyme E2 is an important component of the post-translational protein ubiquitination pathway, which mediates the transfer of activated ubiquitin to substrate proteins. UBE2L3, also called UBcH7, is one of many E2 ubiquitin conjugating enzymes that participate in the ubiquitination of many substrate proteins and regulate many signaling pathways, such as the NF-κB, GSK3β/p65, and DSB repair pathways. Studies on UBE2L3 have found that it has an abnormal expression in many diseases, mainly immune diseases, tumors and Parkinson's disease. It can also promote the occurrence and development of these diseases. Resultantly, UBE2L3 may become an important target for some diseases. Herein, we review the structure of UBE2L3, and its mechanism in diseases, as well as diseases related to UBE2L3 and discuss the related challenges.
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Affiliation(s)
- Xiaoxia Zhang
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Chengdong Huo
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yating Liu
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Ruiliang Su
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yang Zhao
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yumin Li
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
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Birkou M, Chasapis CT, Marousis KD, Loutsidou AK, Bentrop D, Lelli M, Herrmann T, Carthy JM, Episkopou V, Spyroulias GA. A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity. J Mol Biol 2017; 429:2373-2386. [PMID: 28647409 DOI: 10.1016/j.jmb.2017.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022]
Abstract
Arkadia (Rnf111) is an E3 ubiquitin ligase that plays a central role in the amplification of transforming growth factor beta (TGF-β) signaling responses by targeting for degradation the negative regulators of the pathway, Smad6 and Smad7, and the nuclear co-repressors Ski and Skil (SnoN). Arkadia's function in vivo depends on the really interesting new gene (RING)-H2 interaction with the E2 enzyme UbcH5b in order to ligate ubiquitin chains on its substrates. A conserved tryptophan (W972) in the C-terminal α-helix is widely accepted as essential for E2 recruitment and interaction and thus also for E3 enzymatic activity. The present NMR-driven study provides an atomic-level investigation of the structural and dynamical properties of two W972 Arkadia RING mutants, attempting to illuminate for the first time the differences between a functional and a nonfunctional mutant W972A and W972R, respectively. A TGF-β-responsive promoter driving luciferase was used to assay for Arkadia function in vivo. These experiments showed that the Arkadia W972A mutant has the same activity as wild-type (WT) Arkadia in enhancing TGF-β signaling responses, while W972R does not. Only minor structural differences exist between the W972A RING domain and WT-RING. In contrast, the W972R mutant hardly interacts with E2. The loss of function correlates with structural changes in the C-terminal α-helix and an increase in the distance between the Zn(II) ions. Our data show that the position occupied by W972 within WT Arkadia is critical for the function of RING and that it depends on the nature of the residue at this position.
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Affiliation(s)
- Maria Birkou
- Department of Pharmacy, University of Patras, GR-26504 Patras, Greece
| | | | | | | | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Moreno Lelli
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Jonathon M Carthy
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK
| | - Vasso Episkopou
- Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes, London W12 0NN, UK.
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A comprehensive computational study on pathogenic mis-sense mutations spanning the RING2 and REP domains of Parkin protein. Gene 2017; 610:49-58. [PMID: 28189762 DOI: 10.1016/j.gene.2017.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/17/2017] [Accepted: 02/06/2017] [Indexed: 11/23/2022]
Abstract
Various mutations in PARK2 gene, which encodes the protein parkin, are significantly associated with the onset of autosomal recessive juvenile Parkinson (ARJP) in neuronal cells. Parkin is a multi domain protein, the N-terminal part contains the Ubl and the C-terminal part consists of four zinc coordinating domains, viz., RING0, RING1, in between ring (IBR) and RING2. Disease mutations are spread over all the domains of Parkin, although mutations in some regions may affect the functionality of Parkin more adversely. The mutations in the RING2 domain are seen to abolish the neuroprotective E3 ligase activity of Parkin. In this current work, we carried out detailed in silico analysis to study the extent of pathogenicity of mutations spanning the Parkin RING2 domain and the adjoining REP region by SIFT, Mutation Accessor, PolyPhen2, SNPs and GO, GV/GD and I-mutant. To study the structural and functional implications of these mutations on RING2-REP domain of Parkin, we studied the solvent accessibility (SASA/RSA), hydrophobicity, intra-molecular hydrogen bonding profile and domain analysis by various computational tools. Finally, we analysed the interaction energy profiles of the mutants and compared them to the wild type protein using Discovery studio 2.5. By comparing the various analyses it could be safely concluded that except P437L and A379V mutations, all other mutations were potentially deleterious affecting various structural aspects of RING2 domain architecture. This study is based purely on computational approach which has the potential to identify disease mutations and the information could further be used in treatment of diseases and prognosis.
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Dove KK, Stieglitz B, Duncan ED, Rittinger K, Klevit RE. Molecular insights into RBR E3 ligase ubiquitin transfer mechanisms. EMBO Rep 2016; 17:1221-35. [PMID: 27312108 PMCID: PMC4967960 DOI: 10.15252/embr.201642641] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/24/2016] [Indexed: 12/30/2022] Open
Abstract
RING-in-between-RING (RBR) ubiquitin (Ub) ligases are a distinct class of E3s, defined by a RING1 domain that binds E2 Ub-conjugating enzyme and a RING2 domain that contains an active site cysteine similar to HECT-type E3s. Proposed to function as RING/HECT hybrids, details regarding the Ub transfer mechanism used by RBRs have yet to be defined. When paired with RING-type E3s, E2s perform the final step of Ub ligation to a substrate. In contrast, when paired with RBR E3s, E2s must transfer Ub onto the E3 to generate a E3~Ub intermediate. We show that RBRs utilize two strategies to ensure transfer of Ub from the E2 onto the E3 active site. First, RING1 domains of HHARI and RNF144 promote open E2~Ubs. Second, we identify a Ub-binding site on HHARI RING2 important for its recruitment to RING1-bound E2~Ub. Mutations that ablate Ub binding to HHARI RING2 also decrease RBR ligase activity, consistent with RING2 recruitment being a critical step for the RBR Ub transfer mechanism. Finally, we demonstrate that the mechanism defined here is utilized by a variety of RBRs.
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Affiliation(s)
- Katja K Dove
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Benjamin Stieglitz
- Mill Hill LaboratoryThe Francis Crick InstituteLondonUK,Present address: Department of Chemistry and BiochemistrySchool of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Emily D Duncan
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Rachel E Klevit
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
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Cui W, Sun M, Galeva N, Williams TD, Azuma Y, Staudinger JL. SUMOylation and Ubiquitylation Circuitry Controls Pregnane X Receptor Biology in Hepatocytes. Drug Metab Dispos 2015; 43:1316-25. [PMID: 26063058 DOI: 10.1124/dmd.115.065201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Several nuclear receptor (NR) superfamily members are known to be the molecular target of either the small ubiquitin-related modifier (SUMO) or ubiquitin-signaling pathways. However, little is currently known regarding how these two post-translational modifications interact to control NR biology. We show that SUMO and ubiquitin circuitry coordinately modifies the pregnane X receptor (PXR, NR1I2) to play a key role in regulating PXR protein stability, transactivation capacity, and transcriptional repression. The SUMOylation and ubiquitylation of PXR is increased in a ligand- and tumor necrosis factor alpha -: dependent manner in hepatocytes. The SUMO-E3 ligase enzymes protein inhibitor of activated signal transducer and activator of transcription-1 (STAT1) STAT-1 (PIAS1) and protein inhibitor of activated STAT Y (PIASy) drive high levels of PXR SUMOylation. Expression of protein inhibitor of activated stat 1 selectively increases SUMO(3)ylation as well as PXR-mediated induction of cytochrome P450, family 3, subfamily A and the xenobiotic response. The PIASy-mediated SUMO(1)ylation imparts a transcriptionally repressive function by ameliorating interaction of PXR with coactivator protein peroxisome proliferator-activated receptor gamma coactivator-1-alpha. The SUMO modification of PXR is effectively antagonized by the SUMO protease sentrin protease (SENP) 2, whereas SENP3 and SENP6 proteases are highly active in the removal of SUMO2/3 chains. The PIASy-mediated SUMO(1)ylation of PXR inhibits ubiquitin-mediated degradation of this important liver-enriched NR by the 26S proteasome. Our data reveal a working model that delineates the interactive role that these two post-translational modifications play in reconciling PXR-mediated gene activation of the xenobiotic response versus transcriptional repression of the proinflammatory response in hepatocytes. Taken together, our data reveal that the SUMOylation and ubiquitylation of the PXR interface in a fundamental manner directs its biologic function in the liver in response to xenobiotic or inflammatory stress.
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Affiliation(s)
- Wenqi Cui
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Mengxi Sun
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Nadezhda Galeva
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Todd D Williams
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Yoshiaki Azuma
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Jeff L Staudinger
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
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Raychaudhuri S, Espenshade PJ. Endoplasmic Reticulum Exit of Golgi-resident Defective for SREBP Cleavage (Dsc) E3 Ligase Complex Requires Its Activity. J Biol Chem 2015; 290:14430-40. [PMID: 25918164 DOI: 10.1074/jbc.m114.630863] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Indexed: 01/23/2023] Open
Abstract
Layers of quality control ensure proper protein folding and complex formation prior to exit from the endoplasmic reticulum. The fission yeast Dsc E3 ligase is a Golgi-localized complex required for sterol regulatory element-binding protein (SREBP) transcription factor activation that shows architectural similarity to endoplasmic reticulum-associated degradation E3 ligases. The Dsc E3 ligase consists of five integral membrane proteins (Dsc1-Dsc5) and functionally interacts with the conserved AAA-ATPase Cdc48. Utilizing an in vitro ubiquitination assay, we demonstrated that Dsc1 has ubiquitin E3 ligase activity that requires the E2 ubiquitin-conjugating enzyme Ubc4. Mutations that specifically block Dsc1-Ubc4 interaction prevent SREBP cleavage, indicating that SREBP activation requires Dsc E3 ligase activity. Surprisingly, Golgi localization of the Dsc E3 ligase complex also requires Dsc1 E3 ligase activity. Analysis of Dsc E3 ligase complex formation, glycosylation, and localization indicated that Dsc1 E3 ligase activity is specifically required for endoplasmic reticulum exit of the complex. These results define enzyme activity-dependent sorting as an autoregulatory mechanism for protein trafficking.
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Affiliation(s)
- Sumana Raychaudhuri
- From the Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Peter J Espenshade
- From the Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA, Wells JA, Gygi SP, Schulman BA, Harper JW. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol Cell 2014; 56:360-375. [PMID: 25284222 PMCID: PMC4254048 DOI: 10.1016/j.molcel.2014.09.007] [Citation(s) in RCA: 513] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 01/20/2023]
Abstract
Phosphorylation is often used to promote protein ubiquitylation, yet we rarely understand quantitatively how ligase activation and ubiquitin (UB) chain assembly are integrated with phosphoregulation. Here we employ quantitative proteomics and live-cell imaging to dissect individual steps in the PINK1 kinase-PARKIN UB ligase mitochondrial control pathway disrupted in Parkinson's disease. PINK1 plays a dual role by phosphorylating PARKIN on its UB-like domain and poly-UB chains on mitochondria. PARKIN activation by PINK1 produces canonical and noncanonical UB chains on mitochondria, and PARKIN-dependent chain assembly is required for accumulation of poly-phospho-UB (poly-p-UB) on mitochondria. In vitro, PINK1 directly activates PARKIN's ability to assemble canonical and noncanonical UB chains and promotes association of PARKIN with both p-UB and poly-p-UB. Our data reveal a feedforward mechanism that explains how PINK1 phosphorylation of both PARKIN and poly-UB chains synthesized by PARKIN drives a program of PARKIN recruitment and mitochondrial ubiquitylation in response to mitochondrial damage.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shireen A Sarraf
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David M Duda
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Vladislav O Sviderskiy
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Olszewski
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tiao Xie
- Data and Imaging Analysis Core, Harvard Medical School, Boston, MA 02115, USA
| | | | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brenda A Schulman
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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