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Barzak FM, Lu A, Geltzeiler AR, Ledgerwood EC, Chung WK, Day CL. A novel RNF125 variant associated with Tenorio syndrome alters ubiquitin chain binding. Clin Genet 2024; 105:254-261. [PMID: 37986019 DOI: 10.1111/cge.14457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
A key signalling pathway required for clearance of viruses from host cells relies on the receptor protein, retinoic acid-inducible gene I (RIG-I). The activity of RIG-I is tightly controlled, and once bound to viral dsRNA, addition of lysine 63-linked ubiquitin chains activates signalling. Meanwhile, the addition of lysine 48-linked ubiquitin chains to RIG-I is required to terminate signalling when the infection has been resolved. Really interesting new gene (RING) finger protein 125 (RNF125) is the E3 ligase responsible for addition of the ubiquitin chains that terminate signalling, with disruption of its function associated with Tenorio syndrome. Here we describe a novel RNF125 gene variant in an individual with clinical symptoms including intellectual disability, macrocephaly and congenital heart disease, consistent with Tenorio syndrome. The newly identified Tenorio syndrome-associated variant [(NM_017831.4):c.670G>C p.Glu224Gln] is the first to be found in the ubiquitin interaction motif (UIM) of RNF125. While the E3 ligase activity of this RNF125 variant is retained, it has an impaired ability to interact with lysine 63-linked ubiquitin chains. The function of the UIM in RNF125 is uncertain; however, this study suggests that the UIM binds lysine 63-linked ubiquitin chains, and that this interaction is required for the normal function of RNF125.
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Affiliation(s)
- Fareeda M Barzak
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anita Lu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alexa R Geltzeiler
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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2
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Middleton AJ, Barzak FM, Fokkens TJ, Nguyen K, Day CL. Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation. Structure 2023; 31:1208-1219.e5. [PMID: 37541247 DOI: 10.1016/j.str.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 03/19/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023]
Abstract
Inflammation is essential for healthy immune function, wound healing, and resolution of infection. RIG-I is a key RNA sensor that initiates an immune response, with activation and termination of RIG-I signaling reliant on its modification with ubiquitin. The RING E3 ubiquitin ligase, RNF125, has a critical role in the attenuation of RIG-I signaling, yet it is not known how RNF125 promotes ubiquitin transfer or how its activity is regulated. Here we show that the E3 ligase activity of RNF125 relies on the first zinc finger (ZF1) as well as the RING domain. Surprisingly, ZF1 helps recruit the E2, while residues N-terminal to the RING domain appear to activate the E2∼Ub conjugate. These discoveries help explain how RNF125 brings about the termination of RIG-I dependent inflammatory responses, and help account for the contribution of RNF125 to disease. This study also reveals a new role for ZF domains in E3 ligases.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Fareeda M Barzak
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Thornton J Fokkens
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Khanh Nguyen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
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3
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Mace PD, Day CL. A massive machine regulates cell death. Science 2023; 379:1093-1094. [PMID: 36927032 DOI: 10.1126/science.adg9605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Structural analysis reveals how the decision to induce apoptotic cell death is regulated.
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Affiliation(s)
- Peter D Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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4
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Das A, Foglizzo M, Padala P, Zhu J, Day CL. TRAF trimers form immune signalling networks via RING domain dimerization. FEBS Lett 2022; 597:1213-1224. [PMID: 36310378 DOI: 10.1002/1873-3468.14530] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 08/11/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 12/13/2022]
Abstract
For many inflammatory cytokines, the response elicited is dependent on the recruitment of the tumour necrosis factor receptor-associated factor (TRAF) family of adaptor proteins. All TRAF proteins have a trimeric C-terminal TRAF domain, while at the N-terminus most TRAFs have a RING domain that forms dimers. The symmetry mismatch of the N- and C-terminal halves of TRAF proteins means that when receptors cluster, it is presumed that RING dimers connect TRAF trimers to form a network. Here, using purified TRAF6 proteins, we provide direct evidence in support of this model, and we show that TRAF6 trimers bind Lys63-linked ubiquitin chains to promote their processive assembly. This study provides critical evidence in support of TRAF trimers as key players in signalling.
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Affiliation(s)
- Anubrita Das
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Martina Foglizzo
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Prasanth Padala
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jingyi Zhu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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5
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Paluda A, Middleton AJ, Rossig C, Mace PD, Day CL. Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C. Nat Commun 2022; 13:1181. [PMID: 35246518 PMCID: PMC8897509 DOI: 10.1038/s41467-022-28782-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
A large family of E3 ligases that contain both substrate recruitment and RING domains confer specificity within the ubiquitylation cascade. Regulation of RING E3s depends on modulating their ability to stabilise the RING bound E2~ubiquitin conjugate in the activated (or closed) conformation. Here we report the structure of the Ark2C RING bound to both a regulatory ubiquitin molecule and an activated E2~ubiquitin conjugate. The structure shows that the RING domain and non-covalently bound ubiquitin molecule together make contacts that stabilise the activated conformation of the conjugate, revealing why ubiquitin is a key regulator of Ark2C activity. We also identify a charged loop N-terminal to the RING domain that enhances activity by interacting with both the regulatory ubiquitin and ubiquitin conjugated to the E2. In addition, the structure suggests how Lys48-linked ubiquitin chains might be assembled by Ark2C and UbcH5b. Together this study identifies features common to RING E3s, as well elements that are unique to Ark2C and related E3s, which enhance assembly of ubiquitin chains. Attachment of ubiquitin to proteins is tightly regulated and controls many signalling pathways. Here, the authors show that addition of ubiquitin by the RING E3 ligases Arkadia and Ark2C is enhanced by ubiquitin and a charged loop that precedes the RING domain.
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Affiliation(s)
- Andrej Paluda
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.,TMDU Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Adam J Middleton
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Claudia Rossig
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Catherine L Day
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.
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Middleton AJ, Teyra J, Zhu J, Sidhu SS, Day CL. Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k. ACS Chem Biol 2021; 16:1745-1756. [PMID: 34397214 DOI: 10.1021/acschembio.1c00445] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Transfer of ubiquitin to substrate proteins regulates most processes in eukaryotic cells. E2 enzymes are a central component of the ubiquitin machinery, and generally determine the type of ubiquitin signal generated and thus the ultimate fate of substrate proteins. The E2, Ube2k, specifically builds degradative ubiquitin chains on diverse substrates. Here we have identified protein-based reagents, called ubiquitin variants (UbVs), that bind tightly and specifically to Ube2k. Crystal structures reveal that the UbVs bind to the E2 enzyme at a hydrophobic cleft that is distinct from the active site and previously identified ubiquitin binding sites. We demonstrate that the UbVs are potent inhibitors of Ube2k and block both ubiquitin charging of the E2 enzyme and E3-catalyzed ubiquitin transfer. The binding site of the UbVs suggests they directly clash with the ubiquitin activating enzyme, while potentially disrupting interactions with E3 ligases via allosteric effects. Our data reveal the first protein-based inhibitors of Ube2k and unveil a hydrophobic groove that could be an effective target for inhibiting Ube2k and other E2 enzymes.
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Affiliation(s)
- Adam J. Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Joan Teyra
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jingyi Zhu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Sachdev S. Sidhu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Catherine L. Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
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McGregor R, Whitcombe AL, Sheen CR, Dickson JM, Day CL, Carlton LH, Sharma P, Lott JS, Koch B, Bennett J, Baker MG, Ritchie SR, Fox-Lewis S, Morpeth SC, Taylor SL, Roberts SA, Webb RH, Moreland NJ. Collaborative networks enable the rapid establishment of serological assays for SARS-CoV-2 during nationwide lockdown in New Zealand. PeerJ 2020; 8:e9863. [PMID: 32953275 PMCID: PMC7474877 DOI: 10.7717/peerj.9863] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Serological assays that detect antibodies to SARS-CoV-2 are critical for determining past infection and investigating immune responses in the COVID-19 pandemic. We established ELISA-based immunoassays using locally produced antigens when New Zealand went into a nationwide lockdown and the supply chain of diagnostic reagents was a widely held domestic concern. The relationship between serum antibody binding measured by ELISA and neutralising capacity was investigated using a surrogate viral neutralisation test (sVNT). METHODS A pre-pandemic sera panel (n = 113), including respiratory infections with symptom overlap with COVID-19, was used to establish assay specificity. Sera from PCR‑confirmed SARS-CoV-2 patients (n = 21), and PCR-negative patients with respiratory symptoms suggestive of COVID-19 (n = 82) that presented to the two largest hospitals in Auckland during the lockdown period were included. A two-step IgG ELISA based on the receptor binding domain (RBD) and spike protein was adapted to determine seropositivity, and neutralising antibodies that block the RBD/hACE‑2 interaction were quantified by sVNT. RESULTS The calculated cut-off (>0.2) in the two-step ELISA maximised specificity by classifying all pre-pandemic samples as negative. Sera from all PCR-confirmed COVID-19 patients were classified as seropositive by ELISA ≥7 days after symptom onset. There was 100% concordance between the two-step ELISA and the sVNT with all 7+ day sera from PCR‑confirmed COVID-19 patients also classified as positive with respect to neutralising antibodies. Of the symptomatic PCR-negative cohort, one individual with notable travel history was classified as positive by two-step ELISA and sVNT, demonstrating the value of serology in detecting prior infection. CONCLUSIONS These serological assays were established and assessed at a time when human activity was severely restricted in New Zealand. This was achieved by generous sharing of reagents and technical expertise by the international scientific community, and highly collaborative efforts of scientists and clinicians across the country. The assays have immediate utility in supporting clinical diagnostics, understanding transmission in high-risk cohorts and underpinning longer‑term 'exit' strategies based on effective vaccines and therapeutics.
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Affiliation(s)
- Reuben McGregor
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
| | - Alana L. Whitcombe
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
| | - Campbell R. Sheen
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - James M. Dickson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Catherine L. Day
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lauren H. Carlton
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Prachi Sharma
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - J. Shaun Lott
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Barbara Koch
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - Julie Bennett
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Michael G. Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Stephen R. Ritchie
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Infectious Diseases Department, Auckland City Hospital, Auckland, New Zealand
| | - Shivani Fox-Lewis
- Department of Microbiology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | | | | | - Sally A. Roberts
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
- Department of Microbiology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Rachel H. Webb
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Starship Children’s Hospital, Auckland, New Zealand
| | - Nicole J. Moreland
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand
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8
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Middleton AJ, Day CL. Ubiquitin Variant Inhibitors Meet the Deubiquitinase USP15. Structure 2019; 27:564-565. [PMID: 30943387 DOI: 10.1016/j.str.2019.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Deubiquitinases (DUBs) are important regulators of cellular function and selective inhibitors are required to reveal their biological role and therapeutic potential. In this issue of Structure, Teyra et al. (2019) report the development of DUB USP15 inhibitors that provide a starting point for the analysis of USP15 function.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
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9
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Abstract
The Really Interesting New Gene (RING) Finger protein 11 (RNF11) is a subunit of the A20 ubiquitin-editing complex that ensures the transient nature of inflammatory responses. Although the role of RNF11 as a negative regulator of NF-κB signalling is well-documented, the molecular mechanisms that underpin this function are poorly understood. Here, we show that RNF11 binds both Ubc13 and the Ubc13~ubiquitin conjugate tightly and with similar affinity, but has minimal E3 ligase activity. Remarkably, RNF11 appears to bind Ubc13 so tightly that it outcompetes the E1 and an active E3 ligase. As a consequence, RNF11 may regulate the activity of E3s that rely on Ubc13 for ubiquitin chain assembly by limiting the availability of Ubc13 and its conjugate.
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Affiliation(s)
- Rhesa Budhidarmo
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jingyi Zhu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Adam J Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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10
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Middleton AJ, Budhidarmo R, Das A, Zhu J, Foglizzo M, Mace PD, Day CL. The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1. Nat Commun 2017; 8:1788. [PMID: 29176576 PMCID: PMC5702613 DOI: 10.1038/s41467-017-01665-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/06/2017] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin chains linked through lysine63 (K63) play a critical role in inflammatory signalling. Following ligand engagement of immune receptors, the RING E3 ligase TRAF6 builds K63-linked chains together with the heterodimeric E2 enzyme Ubc13-Uev1A. Dimerisation of the TRAF6 RING domain is essential for the assembly of K63-linked ubiquitin chains. Here, we show that TRAF6 RING dimers form a catalytic complex where one RING interacts with a Ubc13~Ubiquitin conjugate, while the zinc finger 1 (ZF1) domain and linker-helix of the opposing monomer contact ubiquitin. The RING dimer interface is conserved across TRAFs and we also show that TRAF5–TRAF6 heterodimers form. Importantly, TRAF5 can provide ZF1, enabling ubiquitin transfer from a TRAF6-bound Ubc13 conjugate. Our study explains the dependence of activity on TRAF RING dimers, and suggests that both homo- and heterodimers mediated by TRAF RING domains have the capacity to synthesise ubiquitin chains. TRAF6 is a RING E3 ligase that builds Lys63-linked ubiquitin chains. Here, the authors present the crystal structure of TRAF6 bound to the Ubc13~Ub conjugate, which, together with biochemical assays, reveals the role of the zinc finger domains and why RING dimerisation is required for TRAF6 activity.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Rhesa Budhidarmo
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Anubrita Das
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Jingyi Zhu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Martina Foglizzo
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Peter D Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.
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11
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Feltham RL, Moulin M, Vince JE, Mace PD, Wong WWL, Anderton H, Day CL, Vaux DL, Silke J. Tumor necrosis factor (TNF) signaling, but not TWEAK (TNF-like weak inducer of apoptosis)-triggered cIAP1 (cellular inhibitor of apoptosis protein 1) degradation, requires cIAP1 RING dimerization and E2 binding. J Biol Chem 2017; 292:14310. [PMID: 28842477 DOI: 10.1074/jbc.a109.087635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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12
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Wright JD, Mace PD, Day CL. Noncovalent Ubiquitin Interactions Regulate the Catalytic Activity of Ubiquitin Writers. Trends Biochem Sci 2016; 41:924-937. [PMID: 27614784 DOI: 10.1016/j.tibs.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Covalent modification of substrate proteins with ubiquitin is the end result of an intricate network of protein-protein interactions. The inherent ability of the E1, E2, and E3 proteins of the ubiquitylation cascade (the ubiquitin writers) to interact with ubiquitin facilitates this process. Importantly, contact between ubiquitin and the E2/E3 writers is required for catalysis and the assembly of chains of a given linkage. However, ubiquitin is also an activator of ubiquitin-writing enzymes, with many recent studies highlighting the ability of ubiquitin to regulate activity and substrate modification. Here, we review the interactions between ubiquitin-writing enzymes and regulatory ubiquitin molecules that promote activity, and highlight the potential of these interactions to promote processive ubiquitin transfer.
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Affiliation(s)
- Joshua D Wright
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand; The Francis Crick Institute, London NW1 1AT, UK
| | - Peter D Mace
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.
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13
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Foglizzo M, Middleton AJ, Day CL. Structure and Function of the RING Domains of RNF20 and RNF40, Dimeric E3 Ligases that Monoubiquitylate Histone H2B. J Mol Biol 2016; 428:4073-4086. [PMID: 27569044 DOI: 10.1016/j.jmb.2016.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/01/2016] [Accepted: 07/26/2016] [Indexed: 01/20/2023]
Abstract
Monoubiquitylation of histone H2B is a post-translational mark that plays key roles in regulation of transcription and genome stability. In humans, attachment of ubiquitin to lysine 120 of histone H2B depends on the activity of the E2 ubiquitin-conjugating enzyme, Ube2B, and the really interesting new gene (RING) E3 ligases, RING finger protein (RNF) 20 and RNF40. To better understand the molecular basis of this modification, we have solved the crystal structure of the RNF20 RING domain and show that it is a homodimer that specifically interacts with the Ube2B~Ub conjugate. By mutating residues at the E3-E2 and E3-ubiquitin interfaces, we identify key contacts required for interaction of the RNF20 RING domain with the Ube2B~Ub conjugate. These mutants were used to generate a structure-based model of the RNF20-Ube2B~Ub complex that reveals differences from other RING-E2~Ub complexes, and suggests how the RNF20-Ube2B~Ub complex might interact with its nucleosomal substrate. Additionally, we show that the RING domains of RNF20 and RNF40 can form a stable heterodimer that is active. Together, our studies provide new insights into the mechanisms that regulate RNF20-mediated ubiquitin transfer from Ube2B.
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Affiliation(s)
- Martina Foglizzo
- Biochemistry Department, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Adam J Middleton
- Biochemistry Department, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Biochemistry Department, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
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14
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Abstract
The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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15
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Abstract
Members of the inhibitor of apoptosis (IAP) family are characterised by the presence of at least one baculoviral IAP repeat (BIR) domain. However, during the course of evolution, other globular modules have been adopted to perform distinct functions. Consequently, the IAP family is now recognised as consisting of members that perform critical functions in different aspects of cellular regulation. In this review, the structural diversity present within the IAP protein family is presented. Known structures of individual domains are discussed and their properties are described in light of recent data. In particular the plasticity of BIR domains and their ability to accommodate different binding partners is highlighted, as well as the importance of communication between the domains in regulating the covalent attachment of ubiquitin.
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Affiliation(s)
- Rhesa Budhidarmo
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
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16
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Abstract
The cellular inhibitor of apoptosis (cIAP) proteins are essential RING E3 ubiquitin ligases that regulate apoptosis and inflammatory responses. cIAPs contain a ubiquitin-associated (UBA) domain that binds ubiquitin and is implicated in the regulation of cell survival and proteasomal degradation. Here we show that mutation of the MGF and LL motifs in the UBA domain of cIAP1 caused unfolding and increased cIAP1 multimonoubiquitylation. By developing a UBA mutant that disrupted ubiquitin binding but not the structure of the UBA domain, we found that the UBA domain enhances cIAP1 and cIAP2 ubiquitylation. We demonstrate that the UBA domain binds to the UbcH5b∼Ub conjugate, and this promotes RING domain-dependent monoubiquitylation. This study establishes ubiquitin-binding modules, such as the UBA domain, as important regulatory modules that can fine tune the activity of E3 ligases.
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Affiliation(s)
- Rhesa Budhidarmo
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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17
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Condon SM, Mitsuuchi Y, Deng Y, LaPorte MG, Rippin SR, Haimowitz T, Alexander MD, Kumar PT, Hendi MS, Lee YH, Benetatos CA, Yu G, Kapoor GS, Neiman E, Seipel ME, Burns JM, Graham MA, McKinlay MA, Li X, Wang J, Shi Y, Feltham R, Bettjeman B, Cumming MH, Vince JE, Khan N, Silke J, Day CL, Chunduru SK. Birinapant, a smac-mimetic with improved tolerability for the treatment of solid tumors and hematological malignancies. J Med Chem 2014; 57:3666-77. [PMID: 24684347 DOI: 10.1021/jm500176w] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Birinapant (1) is a second-generation bivalent antagonist of IAP proteins that is currently undergoing clinical development for the treatment of cancer. Using a range of assays that evaluated cIAP1 stability and oligomeric state, we demonstrated that 1 stabilized the cIAP1-BUCR (BIR3-UBA-CARD-RING) dimer and promoted autoubiquitylation of cIAP1 in vitro. Smac-mimetic 1-induced loss of cIAPs correlated with inhibition of TNF-mediated NF-κB activation, caspase activation, and tumor cell killing. Many first-generation Smac-mimetics such as compound A (2) were poorly tolerated. Notably, animals that lack functional cIAP1, cIAP2, and XIAP are not viable, and 2 mimicked features of triple IAP knockout cells in vitro. The improved tolerability of 1 was associated with (i) decreased potency against cIAP2 and affinity for XIAP BIR3 and (ii) decreased ability to inhibit XIAP-dependent signaling pathways. The P2' position of 1 was critical to this differential activity, and this improved tolerability has allowed 1 to proceed into clinical studies.
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Affiliation(s)
- Stephen M Condon
- TetraLogic Pharmaceuticals, Inc. , 343 Phoenixville Pike, Malvern, Pennsylvania 19355, United States
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18
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Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, Cook GM. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Mol Microbiol 2014; 91:950-64. [PMID: 24444429 DOI: 10.1111/mmi.12507] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2013] [Indexed: 11/30/2022]
Abstract
Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5 Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.
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Affiliation(s)
- Adam Heikal
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
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19
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Middleton AJ, Budhidarmo R, Day CL. Use of E2~Ubiquitin Conjugates for the Characterization of Ubiquitin Transfer by RING E3 Ligases Such as the Inhibitor of Apoptosis Proteins. Methods Enzymol 2014; 545:243-63. [DOI: 10.1016/b978-0-12-801430-1.00010-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Lutwama F, Kagina BM, Wajja A, Waiswa F, Mansoor N, Kirimunda S, Hughes EJ, Kiwanuka N, Joloba ML, Musoke P, Scriba TJ, Mayanja-Kizza H, Day CL, Hanekom WA. Distinct T-cell responses when BCG vaccination is delayed from birth to 6 weeks of age in Ugandan infants. J Infect Dis 2013; 209:887-97. [PMID: 24179111 DOI: 10.1093/infdis/jit570] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 12/15/2022] Open
Abstract
BACKGROUND In Uganda, the tuberculosis vaccine BCG is administered on the first day of life. Infants delivered at home receive BCG vaccine at their first healthcare facility visit at 6 weeks of age. Our aim was to determine the effect of this delay in BCG vaccination on the induced immune response. METHODS We assessed CD4(+) and CD8(+) T-cell responses with a 12-hour whole-blood intracellular cytokine/cytotoxic marker assay, and with a 6-day proliferation assay. RESULTS We enrolled 92 infants: 50 had received BCG vaccine at birth and 42 at 6 weeks of age. Birth vaccination was associated with (1) greater induction of CD4(+) and CD8(+) T cells expressing either interferon γ (IFN-γ) alone or IFN-γ together with perforin and (2) induction of proliferating cells that had greater capacity to produce IFN-γ, tumor necrosis factor α (TNF-α), and interleukin 2 together, compared with delayed vaccination. CONCLUSIONS Distinct patterns of T-cell induction occurred when BCG vaccine was given at birth and at 6 weeks of age. We propose that this diversity might impact protection against tuberculosis. Our results differ from those of studies of delayed BCG vaccination in South Africa and the Gambia, suggesting that geographical and population heterogeneity may affect the BCG vaccine-induced T-cell response.
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Affiliation(s)
- F Lutwama
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine
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21
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Schumacher FR, Wilson G, Day CL. The N-terminal extension of UBE2E ubiquitin-conjugating enzymes limits chain assembly. J Mol Biol 2013; 425:4099-111. [PMID: 23871895 DOI: 10.1016/j.jmb.2013.06.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/18/2013] [Accepted: 06/25/2013] [Indexed: 11/24/2022]
Abstract
Protein ubiquitylation depends upon the concerted action of ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). All E2s have a conserved ubiquitin-conjugating (UBC) domain but many have variable extensions N- and C-terminal to the UBC domain. For many E2s, the function of the extension is not well understood. Here, we show that the N-terminal extension of the UBE2E proteins regulates formation of polyubiquitin chains by the processive UBC domain. Target proteins are therefore monoubiquitylated by full-length UBE2E, whereas the UBC domain alone polyubiquitylates proteins. Although the N-terminal extension of UBE2E1 is largely disordered in solution, these residues have a critical role in limiting chain building, and when fused to the highly processive E2, UBE2D2, ubiquitylation is limited. For some E2s, interaction of ubiquitin with the 'backside' of the UBC domain promotes polyubiquitylation. However, interaction of ubiquitin with the backside of the UBC domain of UBE2E1 does not appear to be important for processivity. This study underscores the importance of studying full-length E2 proteins and not just the highly conserved core domain.
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22
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Feltham R, Bettjeman B, Budhidarmo R, Mace PD, Shirley S, Condon SM, Chunduru SK, McKinlay MA, Vaux DL, Silke J, Day CL. Smac mimetics activate the E3 ligase activity of cIAP1 protein by promoting RING domain dimerization. J Biol Chem 2011; 286:17015-28. [PMID: 21393245 DOI: 10.1074/jbc.m111.222919] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The inhibitor of apoptosis (IAP) proteins are important ubiquitin E3 ligases that regulate cell survival and oncogenesis. The cIAP1 and cIAP2 paralogs bear three N-terminal baculoviral IAP repeat (BIR) domains and a C-terminal E3 ligase RING domain. IAP antagonist compounds, also known as Smac mimetics, bind the BIR domains of IAPs and trigger rapid RING-dependent autoubiquitylation, but the mechanism is unknown. We show that RING dimerization is essential for the E3 ligase activity of cIAP1 and cIAP2 because monomeric RING mutants could not interact with the ubiquitin-charged E2 enzyme and were resistant to Smac mimetic-induced autoubiquitylation. Unexpectedly, the BIR domains inhibited cIAP1 RING dimerization, and cIAP1 existed predominantly as an inactive monomer. However, addition of either mono- or bivalent Smac mimetics relieved this inhibition, thereby allowing dimer formation and promoting E3 ligase activation. In contrast, the cIAP2 dimer was more stable, had higher intrinsic E3 ligase activity, and was not highly activated by Smac mimetics. These results explain how Smac mimetics promote rapid destruction of cIAP1 and suggest mechanisms for activating cIAP1 in other pathways.
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Affiliation(s)
- Rebecca Feltham
- Department of Biochemistry, La Trobe University, Victoria 3086, Australia
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23
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Affiliation(s)
- Gilles J P Rautureau
- Division of Structural Biology, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
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24
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Risk JM, Laurie RE, Macknight RC, Day CL. FRIGIDA and related proteins have a conserved central domain and family specific N- and C- terminal regions that are functionally important. Plant Mol Biol 2010; 73:493-505. [PMID: 20405310 DOI: 10.1007/s11103-010-9635-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 04/05/2010] [Indexed: 05/08/2023]
Abstract
Arabidopsis accessions are either winter-annuals, which require cold winter temperatures for spring flowering, or rapid-cycling summer annuals. Typically, winter annual accessions have functional FRIGIDA (FRI) and FRIGIDA-LIKE 1 (FRL1) proteins that promote high expression of FLOWERING LOCUS C (FLC), which prevents flowering until after winter. In contrast, many rapid-cycling accessions have low FLC levels because FRI is inactive. Using biochemical, functional and bioinformatic approaches, we show that FRI and FRL1 contain a stable, central domain that is conserved across the FRI superfamily. This core domain is monomeric in solution and primarily alpha-helical. We analysed the ability of several FRI deletion constructs to function in Arabidopsis plants. Our findings suggest that the C-terminus, which is predicted to be disordered, is required for FRI to promote FLC expression and may mediate protein:protein interactions. The contribution of the FRI N-terminus appears to be limited, as constructs missing these residues retained significant activity when expressed at high levels. The important N- and C-terminal regions differ between members of the FRI superfamily and sequence analysis identified five FRI families with distinct expression patterns in Arabidopsis, suggesting the families have separate biological roles.
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Affiliation(s)
- Joanna M Risk
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
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25
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Mace PD, Smits C, Vaux DL, Silke J, Day CL. Asymmetric recruitment of cIAPs by TRAF2. J Mol Biol 2010; 400:8-15. [PMID: 20447407 DOI: 10.1016/j.jmb.2010.04.055] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 04/23/2010] [Accepted: 04/27/2010] [Indexed: 01/01/2023]
Abstract
Cellular inhibitor of apoptosis protein (cIAP) 1 and cIAP2 set the balance between transcription factor and apoptosis signaling downstream of tumor necrosis factor (TNF) receptor superfamily members by acting as ubiquitin E3 ligases for substrates that are part of the TNF receptor complex. To fulfill this role, cIAPs must be recruited to the receptor complex by TNF-receptor-associated factor (TRAF) 2. In this study, we reconstituted the complex between baculoviral IAP repeat (BIR) 1 of cIAP1 and the coiled-coil region of TRAF2, solved the structure of BIR1 from cIAP1, and mapped key binding residues on each molecule using mutagenesis. Biophysical analysis indicates that a single BIR1 domain binds the trimeric TRAF2 coiled-coil domain. This suggests that only one IAP molecule binds to each TRAF trimer and makes it likely that the dimeric cIAPs crosslink two TRAF trimers.
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Affiliation(s)
- Peter D Mace
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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26
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Feltham R, Moulin M, Vince JE, Mace PD, Wong WWL, Anderton H, Day CL, Vaux DL, Silke J. Tumor necrosis factor (TNF) signaling, but not TWEAK (TNF-like weak inducer of apoptosis)-triggered cIAP1 (cellular inhibitor of apoptosis protein 1) degradation, requires cIAP1 RING dimerization and E2 binding. J Biol Chem 2010; 285:17525-36. [PMID: 20356846 DOI: 10.1074/jbc.m109.087635] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellular inhibitor of apoptosis (cIAP) proteins, cIAP1 and cIAP2, are important regulators of tumor necrosis factor (TNF) superfamily (SF) signaling and are amplified in a number of tumor types. They are targeted by IAP antagonist compounds that are undergoing clinical trials. IAP antagonist compounds trigger cIAP autoubiquitylation and degradation. The TNFSF member TWEAK induces lysosomal degradation of TRAF2 and cIAPs, leading to elevated NIK levels and activation of non-canonical NF-kappaB. To investigate the role of the ubiquitin ligase RING domain of cIAP1 in these pathways, we used cIAP-deleted cells reconstituted with cIAP1 point mutants designed to interfere with the ability of the RING to dimerize or to interact with E2 enzymes. We show that RING dimerization and E2 binding are required for IAP antagonists to induce cIAP1 degradation and protect cells from TNF-induced cell death. The RING functions of cIAP1 are required for full TNF-induced activation of NF-kappaB, however, delayed activation of NF-kappaB still occurs in cIAP1 and -2 double knock-out cells. The RING functions of cIAP1 are also required to prevent constitutive activation of non-canonical NF-kappaB by targeting NIK for proteasomal degradation. However, in cIAP double knock-out cells TWEAK was still able to increase NIK levels demonstrating that NIK can be regulated by cIAP-independent pathways. Finally we show that, unlike IAP antagonists, TWEAK was able to induce degradation of cIAP1 RING mutants. These results emphasize the critical importance of the RING of cIAP1 in many signaling scenarios, but also demonstrate that in some pathways RING functions are not required.
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Affiliation(s)
- Rebecca Feltham
- Department of Biochemistry, La Trobe University, Victoria 3086, Australia
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27
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Manning JA, Shalini S, Risk JM, Day CL, Kumar S. A direct interaction with NEDD1 regulates gamma-tubulin recruitment to the centrosome. PLoS One 2010; 5:e9618. [PMID: 20224777 PMCID: PMC2835750 DOI: 10.1371/journal.pone.0009618] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 02/17/2010] [Indexed: 01/01/2023] Open
Abstract
The centrosome is the primary microtubule organizing centre of the cell. γ-tubulin is a core component of the centrosome and is required for microtubule nucleation and centrosome function. The recruitment of γ-tubulin to centrosomes is mediated by its interaction with NEDD1, a WD40-repeat containing protein. Here we demonstrate that NEDD1 is likely to be oligomeric in vivo and binds directly to γ-tubulin through a small region of just 62 residues at the carboxyl-terminus of the protein. This carboxyl-terminal domain that binds γ-tubulin has a helical structure and is a stable tetramer in solution. Mutation of residues in NEDD1 that disrupt binding to γ-tubulin result in a mis-localization of γ-tubulin away from the centrosome. Hence, this study defines the binding site on NEDD1 that is required for its interaction with γ-tubulin, and shows that this interaction is required for the correct localization of γ-tubulin.
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Affiliation(s)
- Jantina A. Manning
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Sonia Shalini
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Joanna M. Risk
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Catherine L. Day
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sharad Kumar
- Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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28
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Vince JE, Pantaki D, Feltham R, Mace PD, Cordier SM, Schmukle AC, Davidson AJ, Callus BA, Wong WWL, Gentle IE, Carter H, Lee EF, Walczak H, Day CL, Vaux DL, Silke J. TRAF2 must bind to cellular inhibitors of apoptosis for tumor necrosis factor (tnf) to efficiently activate nf-{kappa}b and to prevent tnf-induced apoptosis. J Biol Chem 2009; 284:35906-15. [PMID: 19815541 PMCID: PMC2791019 DOI: 10.1074/jbc.m109.072256] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Indexed: 12/22/2022] Open
Abstract
Tumor necrosis factor (TNF) receptor-associated factor-2 (TRAF2) binds to cIAP1 and cIAP2 (cIAP1/2) and recruits them to the cytoplasmic domain of several members of the TNF receptor (TNFR) superfamily, including the TNF-TNFR1 ligand-receptor complex. Here, we define a cIAP1/2-interacting motif (CIM) within the TRAF-N domain of TRAF2, and we use TRAF2 CIM mutants to determine the role of TRAF2 and cIAP1/2 individually, and the TRAF2-cIAP1/2 interaction, in TNFR1-dependent signaling. We show that both the TRAF2 RING domain and the TRAF2 CIM are required to regulate NF-kappaB-inducing kinase stability and suppress constitutive noncanonical NF-kappaB activation. Conversely, following TNFR1 stimulation, cells bearing a CIM-mutated TRAF2 showed reduced canonical NF-kappaB activation and TNF-induced RIPK1 ubiquitylation. Remarkably, the RING domain of TRAF2 was dispensable for these functions. However, like the TRAF2 CIM, the RING domain of TRAF2 was required for protection against TNF-induced apoptosis. These results show that TRAF2 has anti-apoptotic signaling roles in addition to promoting NF-kappaB signaling and that efficient activation of NF-kappaB by TNFR1 requires the recruitment of cIAP1/2 by TRAF2.
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Affiliation(s)
- James E. Vince
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Delara Pantaki
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Rebecca Feltham
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Peter D. Mace
- the Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Stephanie M. Cordier
- the Department of Immunology, Tumour Immunology Unit, Division of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom, and
| | - Anna C. Schmukle
- the Department of Immunology, Tumour Immunology Unit, Division of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom, and
| | - Angelina J. Davidson
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Bernard A. Callus
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Wendy Wei-Lynn Wong
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Ian E. Gentle
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Holly Carter
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - Erinna F. Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Henning Walczak
- the Department of Immunology, Tumour Immunology Unit, Division of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom, and
| | - Catherine L. Day
- the Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - David L. Vaux
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
| | - John Silke
- From the Department of Biochemistry, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
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29
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Dewson G, Kratina T, Czabotar P, Day CL, Adams JM, Kluck RM. Bak activation for apoptosis involves oligomerization of dimers via their alpha6 helices. Mol Cell 2009; 36:696-703. [PMID: 19941828 DOI: 10.1016/j.molcel.2009.11.008] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Revised: 06/20/2009] [Accepted: 11/02/2009] [Indexed: 11/16/2022]
Abstract
A pivotal step toward apoptosis is oligomerization of the Bcl-2 relative Bak. We recently reported that its oligomerization initiates by insertion of an exposed BH3 domain into the groove of another Bak monomer. We now report that the resulting BH3:groove dimers can be converted to the larger oligomers that permeabilize mitochondria by an interface between alpha6 helices. Cysteine residues placed in alpha6 could be crosslinked only after apoptotic signaling. Cysteines placed at both interfaces established that the BH3:groove dimer is symmetric and that the alpha6:alpha6 interface can link these dimers into homo-oligomers containing at least 18 Bak molecules. A putative zinc-binding site in alpha6 was not required to form the alpha6:alpha6 interface, and its mutation in full-length Bak did not affect Bak conformation, oligomerization, or function. We conclude that alpha6:alpha6 interaction occurs during Bak oligomerization and proapoptotic function, but we find no evidence that zinc binding to that interface regulates apoptosis.
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Affiliation(s)
- Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Parkville Victoria, Australia
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30
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Mabbitt PD, Rautureau GJP, Day CL, Wilbanks SM, Eaton-Rye JJ, Hinds MG. Solution Structure of Psb27 from Cyanobacterial Photosystem II,. Biochemistry 2009; 48:8771-3. [DOI: 10.1021/bi901309c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter D. Mabbitt
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | | | - Catherine L. Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Sigurd M. Wilbanks
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | | | - Mark G. Hinds
- Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
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31
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Risk JM, Day CL, Macknight RC. Reevaluation of abscisic acid-binding assays shows that G-Protein-Coupled Receptor2 does not bind abscisic Acid. Plant Physiol 2009; 150:6-11. [PMID: 19286934 PMCID: PMC2675752 DOI: 10.1104/pp.109.135749] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 02/04/2009] [Indexed: 05/20/2023]
Affiliation(s)
- Joanna M Risk
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
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32
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Mace PD, Shirley S, Day CL. Assembling the building blocks: structure and function of inhibitor of apoptosis proteins. Cell Death Differ 2009; 17:46-53. [DOI: 10.1038/cdd.2009.45] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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33
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Mace PD, Linke K, Feltham R, Schumacher FR, Smith CA, Vaux DL, Silke J, Day CL. Structures of the cIAP2 RING domain reveal conformational changes associated with ubiquitin-conjugating enzyme (E2) recruitment. J Biol Chem 2008; 283:31633-40. [PMID: 18784070 DOI: 10.1074/jbc.m804753200] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inhibitor of apoptosis (IAP) proteins are key negative regulators of cell death that are highly expressed in many cancers. Cell death caused by antagonists that bind to IAP proteins is associated with their ubiquitylation and degradation. The RING domain at the C terminus of IAP proteins is pivotal. Here we report the crystal structures of the cIAP2 RING domain homodimer alone, and bound to the ubiquitin-conjugating (E2) enzyme UbcH5b. These structures show that small changes in the RING domain accompany E2 binding. By mutating residues at the E2-binding surface, we show that autoubiquitylation is required for regulation of IAP abundance. Dimer formation is also critical, and mutation of a single C-terminal residue abrogated dimer formation and E3 ligase activity was diminished. We further demonstrate that disruption of E2 binding, or dimerization, stabilizes IAP proteins against IAP antagonists in vivo.
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Affiliation(s)
- Peter D Mace
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
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Day CL, Smits C, Fan FC, Lee EF, Fairlie WD, Hinds MG. Structure of the BH3 domains from the p53-inducible BH3-only proteins Noxa and Puma in complex with Mcl-1. J Mol Biol 2008; 380:958-71. [PMID: 18589438 DOI: 10.1016/j.jmb.2008.05.071] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/29/2008] [Accepted: 05/29/2008] [Indexed: 02/02/2023]
Abstract
Pro-survival proteins in the B-cell lymphoma-2 (Bcl-2) family have a defined specificity profile for their cell death-inducing BH3-only antagonists. Solution structures of myeloid cell leukaemia-1 (Mcl-1) in complex with the BH3 domains from Noxa and Puma, two proteins regulated by the tumour suppressor p53, show that they bind as amphipathic alpha-helices in the same hydrophobic groove of Mcl-1, using conserved residues for binding. Thermodynamic parameters for the interaction of Noxa, Puma and the related BH3 domains of Bmf, Bim, Bid and Bak with Mcl-1 were determined by calorimetry. These unstructured BH3 domains bind Mcl-1 with affinities that span 3 orders of magnitude, and binding is an enthalpically driven and entropy-enthalpy-compensated process. Alanine scanning analysis of Noxa demonstrated that only a subset of residues is required for interaction with Mcl-1, and these residues are localised to a short highly conserved sequence motif that defines the BH3 domain. Chemical shift mapping of Mcl-1:BH3 complexes showed that Mcl-1 engages all BH3 ligands in a similar way and that, in addition to changes in the immediate vicinity of the binding site, small molecule-wide structural adjustments accommodate ligand binding. Our studies show that unstructured peptides, such as the BH3 domains, behave like their structured counterparts and can bind tightly and selectively in an enthalpically driven process.
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Affiliation(s)
- Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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Linke K, Mace PD, Smith CA, Vaux DL, Silke J, Day CL. Structure of the MDM2/MDMX RING domain heterodimer reveals dimerization is required for their ubiquitylation in trans. Cell Death Differ 2008; 15:841-8. [PMID: 18219319 DOI: 10.1038/sj.cdd.4402309] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
MDM2, a ubiquitin E3-ligase of the RING family, has a key role in regulating p53 abundance. During normal non-stress conditions p53 is targeted for degradation by MDM2. MDM2 can also target itself and MDMX for degradation. MDMX is closely related to MDM2 but the RING domain of MDMX does not possess intrinsic E3-ligase activity. Instead, MDMX regulates p53 abundance by modulating the levels and activity of MDM2. Dimerization, mediated by the conserved C-terminal RING domains of both MDM2 and MDMX, is critical to this activity. Here we report the crystal structure of the MDM2/MDMX RING domain heterodimer and map residues required for functional interaction with the E2 (UbcH5b). In both MDM2 and MDMX residues C-terminal to the RING domain have a key role in dimer formation. In addition we show that these residues are part of an extended surface that is essential for ubiquitylation in trans. This study provides a molecular basis for understanding how heterodimer formation leads to stabilization of MDM2, yet degradation of p53, and suggests novel targets for therapeutic intervention.
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Affiliation(s)
- K Linke
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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36
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Hinds MG, Day CL. Solution structure of Mcl‐1 and its complexes. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a638-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mark G. Hinds
- Structural BiologyWalter and Eliza Hall Institute of Medical Research1G Royal ParadeParkville3050Australia
| | - Catherine L. Day
- Biochemistry DepartmentOtago UniversityCumberland StreetDunedinNew Zealand
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Czabotar PE, Lee EF, van Delft MF, Day CL, Smith BJ, Huang DCS, Fairlie WD, Hinds MG, Colman PM. Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proc Natl Acad Sci U S A 2007; 104:6217-22. [PMID: 17389404 PMCID: PMC1851040 DOI: 10.1073/pnas.0701297104] [Citation(s) in RCA: 361] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is held in check by prosurvival proteins of the Bcl-2 family. The distantly related BH3-only proteins bind to and antagonize them, thereby promoting apoptosis. Whereas binding of the BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1 degradation by the proteasome, binding of another BH3-only ligand, Bim, elevates Mcl-1 protein levels. We compared the three-dimensional structures of the complexes formed between BH3 peptides of both Bim and Noxa, and we show that a discrete C-terminal sequence of the Noxa BH3 is necessary to instigate Mcl-1 degradation.
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Affiliation(s)
- Peter E. Czabotar
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Erinna F. Lee
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia; and
| | - Mark F. van Delft
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia; and
| | - Catherine L. Day
- Department of Biochemistry, University of Otago, Dunedin 9001, New Zealand
| | - Brian J. Smith
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - David C. S. Huang
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - W. Douglas Fairlie
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Mark G. Hinds
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Peter M. Colman
- *The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
- To whom correspondence should be addressed. E-mail:
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van Delft MF, Wei AH, Mason KD, Vandenberg CJ, Chen L, Czabotar PE, Willis SN, Scott CL, Day CL, Cory S, Adams JM, Roberts AW, Huang DC. The BH3 mimetic ABT-737 targets selective Bcl-2 proteins and efficiently induces apoptosis via Bak/Bax if Mcl-1 is neutralized. Cancer Cell 2006; 10:389-99. [PMID: 17097561 PMCID: PMC2953559 DOI: 10.1016/j.ccr.2006.08.027] [Citation(s) in RCA: 908] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 06/28/2006] [Accepted: 08/24/2006] [Indexed: 10/23/2022]
Abstract
Since apoptosis is impaired in malignant cells overexpressing prosurvival Bcl-2 proteins, drugs mimicking their natural antagonists, BH3-only proteins, might overcome chemoresistance. Of seven putative BH3 mimetics tested, only ABT-737 triggered Bax/Bak-mediated apoptosis. Despite its high affinity for Bcl-2, Bcl-x(L), and Bcl-w, many cell types proved refractory to ABT-737. We show that this resistance reflects ABT-737's inability to target another prosurvival relative, Mcl-1. Downregulation of Mcl-1 by several strategies conferred sensitivity to ABT-737. Furthermore, enforced Mcl-1 expression in a mouse lymphoma model conferred resistance. In contrast, cells overexpressing Bcl-2 remained highly sensitive to ABT-737. Hence, ABT-737 should prove efficacious in tumors with low Mcl-1 levels, or when combined with agents that inactivate Mcl-1, even to treat those tumors that overexpress Bcl-2.
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MESH Headings
- Animals
- Apoptosis
- Biphenyl Compounds/metabolism
- Biphenyl Compounds/pharmacology
- Biphenyl Compounds/therapeutic use
- Cells, Cultured
- Cytokines/metabolism
- Disease Models, Animal
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Myeloid Cell Leukemia Sequence 1 Protein
- Neoplasm Proteins/metabolism
- Nitrophenols/metabolism
- Nitrophenols/pharmacology
- Nitrophenols/therapeutic use
- Piperazines/metabolism
- Piperazines/pharmacology
- Piperazines/therapeutic use
- Protein Structure, Tertiary
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/chemistry
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- RNA Interference
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sulfonamides/metabolism
- Sulfonamides/pharmacology
- Sulfonamides/therapeutic use
- bcl-2 Homologous Antagonist-Killer Protein/genetics
- bcl-2 Homologous Antagonist-Killer Protein/metabolism
- bcl-2-Associated X Protein/chemistry
- bcl-2-Associated X Protein/genetics
- bcl-2-Associated X Protein/metabolism
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Affiliation(s)
- Mark F. van Delft
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew H. Wei
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Kylie D. Mason
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Lin Chen
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Peter E. Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Simon N. Willis
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Catherine L. Day
- Biochemistry Department, University of Otago, Dunedin 9001, New Zealand
| | - Suzanne Cory
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Jerry M. Adams
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Andrew W. Roberts
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - David C.S. Huang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
- Correspondence: David Huang, Ph - +61 3 9345 2555, Fax: +61 3 9347 0852, E-mail:
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Hinds MG, Smits C, Fredericks-Short R, Risk JM, Bailey M, Huang DCS, Day CL. Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets. Cell Death Differ 2006; 14:128-36. [PMID: 16645638 DOI: 10.1038/sj.cdd.4401934] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
All BH3-only proteins, key initiators of programmed cell death, interact tightly with multiple binding partners and have sequences of low complexity, properties that are the hallmark of intrinsically unstructured proteins (IUPs). We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured. When Bim binds and inactivates prosurvival proteins, most residues remain disordered, only the BH3 element becomes structured, and the short alpha-helical molecular recognition element can be considered to behave as a 'bead on a string'. Coupled folding and binding is typical of many IUPs that have important signaling roles, such as BH3-only proteins, as the inherent structural plasticity favors interaction with multiple targets. This understanding offers promise for the development of BH3 mimetics, as multiple modes of binding are tolerated.
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Affiliation(s)
- M G Hinds
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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40
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Silke J, Kratina T, Chu D, Ekert PG, Day CL, Pakusch M, Huang DCS, Vaux DL. Determination of cell survival by RING-mediated regulation of inhibitor of apoptosis (IAP) protein abundance. Proc Natl Acad Sci U S A 2005; 102:16182-7. [PMID: 16263936 PMCID: PMC1283416 DOI: 10.1073/pnas.0502828102] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [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] [Received: 04/06/2005] [Indexed: 11/18/2022] Open
Abstract
Inhibitor of apoptosis (IAP) proteins, which bind to caspases via their baculoviral IAP repeat domains, also bear RING domains that enable them to promote ubiquitylation of themselves and other interacting proteins. Here we show that the RING domain of cIAP1 allows it to bind directly to the RING of X-linked IAP, causing its ubiquitylation and degradation by the proteasome, thus revealing a mechanism by which IAPs can regulate their abundance. Expression of a construct containing the RING of cellular IAP1 was able to deplete melanoma cells of endogenous X-linked IAP, promoted apoptosis, and also markedly reduced their clonogenicity when treated with cisplatin. Cross control of protein levels by RING domains may therefore enable their levels to be manipulated therapeutically.
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Affiliation(s)
- John Silke
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.
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41
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Hinds MG, Day CL. Regulation of apoptosis: uncovering the binding determinants. Curr Opin Struct Biol 2005; 15:690-9. [PMID: 16263267 DOI: 10.1016/j.sbi.2005.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 08/17/2005] [Accepted: 10/18/2005] [Indexed: 12/17/2022]
Abstract
Eukaryotic cells use complex networks of signal transduction proteins to make decisions about whether to differentiate, grow or die. In the case of apoptosis, which is responsible for the programmed death of unwanted or damaged cells in multicellular organisms, recent structural, biochemical and cell-based assays have enhanced our understanding of the mechanisms by which some of the key proteins regulate this process. These studies have highlighted a critical role for conformational change and the regulated formation of specific complexes that can either inhibit or stimulate apoptosis. In some cases, it is still not clear what distinguishes inhibitory from activating complexes, but the value of a structural understanding is highlighted by the success of recent structure-based drug discovery programs that have targeted these complexes.
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Affiliation(s)
- Mark G Hinds
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia
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42
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Chen L, Willis SN, Wei A, Smith BJ, Fletcher JI, Hinds MG, Colman PM, Day CL, Adams JM, Huang DCS. Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function. Mol Cell 2005; 17:393-403. [PMID: 15694340 DOI: 10.1016/j.molcel.2004.12.030] [Citation(s) in RCA: 1413] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Revised: 09/22/2004] [Accepted: 12/09/2004] [Indexed: 02/08/2023]
Abstract
Apoptosis is initiated when Bcl-2 and its prosurvival relatives are engaged by proapoptotic BH3-only proteins via interaction of its BH3 domain with a groove on the Bcl-2-like proteins. These interactions have been considered promiscuous, but our analysis of the affinity of eight BH3 peptides for five Bcl-2-like proteins has revealed that the interactions vary over 10,000-fold in affinity, and accordingly, only certain protein pairs associate inside cells. Bim and Puma potently engaged all the prosurvival proteins comparably. Bad, however, bound tightly to Bcl-2, Bcl-xL, and Bcl-w but only weakly to A1 and not to Mcl-1. Strikingly, Noxa bound only Mcl-1 and A1. In accord with their complementary binding, Bad and Noxa cooperated to induce potent killing. The results suggest that apoptosis relies on selective interactions between particular subsets of these proteins and that it should be feasible to discover BH3-mimetic drugs that inactivate specific prosurvival targets.
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Affiliation(s)
- Lin Chen
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3050, Australia
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43
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Day CL, Chen L, Richardson SJ, Harrison PJ, Huang DCS, Hinds MG. Solution Structure of Prosurvival Mcl-1 and Characterization of Its Binding by Proapoptotic BH3-only Ligands. J Biol Chem 2005; 280:4738-44. [PMID: 15550399 DOI: 10.1074/jbc.m411434200] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The B cell lymphoma-2 (Bcl-2) homologs myeloid cell leukemia-1 (Mcl-1) and A1 are prosurvival factors that selectively bind a subset of proapoptotic Bcl homology (BH) 3-only proteins. To investigate the molecular basis of the selectivity, we determined the solution structure of the C-terminal Bcl-2-like domain of Mcl-1. This domain shares features expected of a prosurvival Bcl-2 protein, having a helical fold centered on a core hydrophobic helix and a surface-exposed hydrophobic groove for binding its cognate partners. A number of residues in the binding groove differentiate Mcl-1 from its homologs, and in contrast to other Bcl-2 homologs, Mcl-1 has a binding groove in a conformation intermediate between the open structures characterized by peptide complexes and the closed state observed in unliganded structures. Mutagenesis of potential binding site residues was used to probe the contributions of groove residues to the binding properties of Mcl-1. Although mutations in Mcl-1 had little impact on binding, a single mutation in the BH3-only ligand Bad enabled it to bind both Mcl-1 and A1 while retaining its binding to Bcl-2, Bcl-xL, and Bcl-w. Elucidating the selective action of certain BH3-only ligands is required for delineating their mode of action and will aid the search for effective BH3-mimetic drugs.
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Affiliation(s)
- Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin 9001, New Zealand
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44
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Day CL, Puthalakath H, Skea G, Strasser A, Barsukov I, Lian LY, Huang DCS, Hinds MG. Localization of dynein light chains 1 and 2 and their pro-apoptotic ligands. Biochem J 2004; 377:597-605. [PMID: 14561217 PMCID: PMC1223895 DOI: 10.1042/bj20031251] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 10/10/2003] [Accepted: 10/15/2003] [Indexed: 11/17/2022]
Abstract
The dynein and myosin V motor complexes are multi-protein structures that function to transport molecules and organelles within the cell. DLC (dynein light-chain) proteins, found as components of both dynein and myosin V motor complexes, connect the complexes to their cargoes. One of the roles of these motor complexes is to selectively sequester the pro-apoptotic 'BH3-only' (Bcl-2 homology 3-only) proteins, Bim (Bcl-2-interacting mediator of cell death) and Bmf (Bcl-2-modifying factor), and so regulate their cell death-inducing function. In vivo DLC2 is found exclusively as a component of the myosin V motor complex and Bmf binds DLC2 selectively. On the other hand, Bim interacts with DLC1 (LC8), an integral component of the dynein motor complex. The two DLCs share 93% sequence identity yet show unambiguous in vivo specificity for their respective BH3-only ligands. To investigate this specificity the three-dimensional solution structure of DLC2 was elucidated using NMR spectroscopy. In vitro structural and mutagenesis studies show that Bmf and Bim have identical binding characteristics to recombinant DLC2 or DLC1. Thus the selectivity shown by Bmf and Bim for binding DLC1 or DLC2, respectively, does not reside in their DLC-binding domains. Remarkably, mutational analysis of DLC1 and DLC2 indicates that a single surface residue (residue 41) determines the specific localization of DLCs with their respective motor complexes. These results suggest a molecular mechanism for the specific compartmentalization of DLCs and their pro-apoptotic cargoes and implicate other protein(s) in defining the specificity between the cargoes and the DLC proteins.
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Affiliation(s)
- Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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45
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Affiliation(s)
- Simon Willis
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
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46
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Wilson-Annan J, O'Reilly LA, Crawford SA, Hausmann G, Beaumont JG, Parma LP, Chen L, Lackmann M, Lithgow T, Hinds MG, Day CL, Adams JM, Huang DCS. Proapoptotic BH3-only proteins trigger membrane integration of prosurvival Bcl-w and neutralize its activity. J Cell Biol 2003; 162:877-87. [PMID: 12952938 PMCID: PMC2172834 DOI: 10.1083/jcb.200302144] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Prosurvival Bcl-2-like proteins, like Bcl-w, are thought to function on organelles such as the mitochondrion and to be targeted to them by their hydrophobic COOH-terminal domain. We unexpectedly found, however, that the membrane association of Bcl-w was enhanced during apoptosis. In healthy cells, Bcl-w was loosely attached to the mitochondrial membrane, but it was converted into an integral membrane protein by cytotoxic signals that induce binding of BH3-only proteins, such as Bim, or by the addition of BH3 peptides to lysates. As the structure of Bcl-w has revealed that its COOH-terminal domain occupies the hydrophobic groove where BH3 ligands bind, displacement of that domain by a BH3 ligand would displace the hydrophobic COOH-terminal residues, allowing their insertion into the membrane. To determine whether BH3 ligation is sufficient to induce the enhanced membrane affinity, or to render Bcl-w proapoptotic, we mimicked their complex by tethering the Bim BH3 domain to the NH2 terminus of Bcl-w. The chimera indeed bound avidly to membranes, in a fashion requiring the COOH-terminal domain, but neither promoted nor inhibited apoptosis. These results suggest that ligation of a proapoptotic BH3-only protein alters the conformation of Bcl-w, enhances membrane association, and neutralizes its survival function.
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Affiliation(s)
- Julie Wilson-Annan
- Walter and Eliza Hall Institute of Medical Research, Victoria 3050, Australia
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47
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Hinds MG, Lackmann M, Skea GL, Harrison PJ, Huang DCS, Day CL. The structure of Bcl-w reveals a role for the C-terminal residues in modulating biological activity. EMBO J 2003; 22:1497-507. [PMID: 12660157 PMCID: PMC152889 DOI: 10.1093/emboj/cdg144] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pro-survival Bcl-2-related proteins, critical regulators of apoptosis, contain a hydrophobic groove targeted for binding by the BH3 domain of the pro-apoptotic BH3-only proteins. The solution structure of the pro-survival protein Bcl-w, presented here, reveals that the binding groove is not freely accessible as predicted by previous structures of pro-survival Bcl-2-like molecules. Unexpectedly, the groove appears to be occluded by the C-terminal residues. Binding and kinetic data suggest that the C-terminal residues of Bcl-w and Bcl-x(L) modulate pro-survival activity by regulating ligand access to the groove. Binding of the BH3-only proteins, critical for cell death initiation, is likely to displace the hydrophobic C-terminal region of Bcl-w and Bcl-x(L). Moreover, Bcl-w does not act only by sequestering the BH3-only proteins. There fore, pro-survival Bcl-2-like molecules probably control the activation of downstream effectors by a mechanism that remains to be elucidated.
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Affiliation(s)
- Mark G Hinds
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
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Tikoo A, O'Reilly L, Day CL, Verhagen AM, Pakusch M, Vaux DL. Tissue distribution of Diablo/Smac revealed by monoclonal antibodies. Cell Death Differ 2002; 9:710-6. [PMID: 12058276 DOI: 10.1038/sj.cdd.4401031] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2001] [Revised: 01/22/2002] [Accepted: 01/23/2002] [Indexed: 11/08/2022] Open
Abstract
Diablo/Smac is a mammalian pro-apoptotic protein that can antagonize the inhibitor of apoptosis proteins (IAPs). We have produced monoclonal antibodies specific for Diablo and have used these to examine its tissue distribution and subcellular localization in healthy and apoptotic cells. Diablo could be detected in a wide range of mouse tissues including liver, kidney, lung, intestine, pancreas and testes by Western blot analysis. Immunohistochemical analysis found Diablo to be most abundant in the germinal cells of the testes, the parenchymal cells of the liver and the tubule cells of the kidney. In support of previous subcellular localization analysis, Diablo was present within the mitochondria of healthy cells, but released into the cytosol following the induction of apoptosis by UV.
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Affiliation(s)
- A Tikoo
- The Walter and Eliza Hall Institute of Medical Research, Post Office Royal Melbourne Hospital, VIC 3050, Australia.
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Jameson GB, Anderson BF, Breyer WA, Day CL, Tweedie JW, Baker EN. Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form. Acta Crystallogr D Biol Crystallogr 2002; 58:955-62. [PMID: 12037297 DOI: 10.1107/s0907444902005127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2002] [Accepted: 03/19/2002] [Indexed: 11/10/2022]
Abstract
Human lactoferrin is an iron-binding protein with a bilobal structure. Each lobe contains a high-affinity binding site for a single Fe(3+) ion and an associated CO(3)(2-) ion. Although iron binds very tightly, it can be released at low pH, with an accompanying conformational change in which the two domains move apart. The Arg121Asp (R121D) mutant of the N-lobe half-molecule of human lactoferrin was constructed in order to test whether the Asp121 side chain could substitute for the CO(3)(2-) ion at the iron-binding site. The R121D mutant protein was crystallized in its apo form as it lost iron during crystallization. The crystals were also merohedrally twinned, with a twin fraction close to 0.5. Starting from the initial molecular-replacement solution [Breyer et al. (1999), Acta Cryst. D55, 129-138], the structure has been refined at 3.0 A resolution to an R factor of 13.9% (R(free) of 19.9%). Despite the moderate resolution, the high solvent content and non-crystallographic symmetry contributed to electron-density maps of excellent quality. Weakened iron binding by the R121D mutant is explained by occlusion of the anion-binding site by the Asp side chain. The opening of the two domains in the apoR121D structure (a rotation of 54 degrees ) closely matches that of the N-lobe in full-length lactoferrin, showing that the extent of the conformational change depends on properties inherent to the N-lobe. Differences in the C-terminal portion of the N-lobe (residues 321-332) for apoR121D relative to the closed wild-type iron-bound structure point to the importance of this region in stabilizing the open form.
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Affiliation(s)
- Geoffrey B Jameson
- Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand
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Abstract
Initially identified as proteases, members of the HtrA/DegP family of proteins have also been shown to act as chaperones in bacteria, and more recently implicated, as regulators of apoptosis in mammals. Two new structures of mammalian HtrA2 and E. coli DegP provide insights into the origin of this plurality of function.
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Affiliation(s)
- Catherine L Day
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, New Zealand
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