1
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Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G. Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol Cell 2024; 84:1304-1320.e16. [PMID: 38382526 PMCID: PMC10997478 DOI: 10.1016/j.molcel.2024.01.022] [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: 09/13/2023] [Revised: 12/07/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.
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Affiliation(s)
- Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Holly A Byers
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Spencer Hill
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Trent Hinkle
- Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | | | | | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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2
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Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G. Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Nat Struct Mol Biol 2024; 31:378-389. [PMID: 38326650 PMCID: PMC10873206 DOI: 10.1038/s41594-023-01206-1] [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: 08/07/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024]
Abstract
E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.
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Affiliation(s)
- Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Chutima Rattanasopa
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Samuel Maiwald
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David T Krist
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Gary Kleiger
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA.
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3
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Purser N, Tripathi-Giesgen I, Li J, Scott DC, Horn-Ghetko D, Baek K, Schulman BA, Alpi AF, Kleiger G. Catalysis of non-canonical protein ubiquitylation by the ARIH1 ubiquitin ligase. Biochem J 2023; 480:1817-1831. [PMID: 37870100 PMCID: PMC10657180 DOI: 10.1042/bcj20230373] [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: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Protein ubiquitylation typically involves isopeptide bond formation between the C-terminus of ubiquitin to the side-chain amino group on Lys residues. However, several ubiquitin ligases (E3s) have recently been identified that ubiquitylate proteins on non-Lys residues. For instance, HOIL-1 belongs to the RING-in-between RING (RBR) class of E3s and has an established role in Ser ubiquitylation. Given the homology between HOIL-1 and ARIH1, an RBR E3 that functions with the large superfamily of cullin-RING E3 ligases (CRLs), a biochemical investigation was undertaken, showing ARIH1 catalyzes Ser ubiquitylation to CRL-bound substrates. However, the efficiency of ubiquitylation was exquisitely dependent on the location and chemical environment of the Ser residue within the primary structure of the substrate. Comprehensive mutagenesis of the ARIH1 Rcat domain identified residues whose mutation severely impacted both oxyester and isopeptide bond formation at the preferred site for Ser ubiquitylation while only modestly affecting Lys ubiquitylation at the physiological site. The results reveal dual isopeptide and oxyester protein ubiquitylation activities of ARIH1 and set the stage for physiological investigations into this function of emerging importance.
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Affiliation(s)
- Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Daniel C. Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Arno F. Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
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4
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Baek K, Scott DC, Henneberg LT, King MT, Mann M, Schulman BA. Systemwide disassembly and assembly of SCF ubiquitin ligase complexes. Cell 2023; 186:2492. [PMID: 37236156 DOI: 10.1016/j.cell.2023.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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5
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Baek K, Scott DC, Henneberg LT, King MT, Mann M, Schulman BA. Systemwide disassembly and assembly of SCF ubiquitin ligase complexes. Cell 2023; 186:1895-1911.e21. [PMID: 37028429 PMCID: PMC10156175 DOI: 10.1016/j.cell.2023.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 12/08/2022] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 04/09/2023]
Abstract
Cells respond to environmental cues by remodeling their inventories of multiprotein complexes. Cellular repertoires of SCF (SKP1-CUL1-F box protein) ubiquitin ligase complexes, which mediate much protein degradation, require CAND1 to distribute the limiting CUL1 subunit across the family of ∼70 different F box proteins. Yet, how a single factor coordinately assembles numerous distinct multiprotein complexes remains unknown. We obtained cryo-EM structures of CAND1-bound SCF complexes in multiple states and correlated mutational effects on structures, biochemistry, and cellular assays. The data suggest that CAND1 clasps idling catalytic domains of an inactive SCF, rolls around, and allosterically rocks and destabilizes the SCF. New SCF production proceeds in reverse, through SKP1-F box allosterically destabilizing CAND1. The CAND1-SCF conformational ensemble recycles CUL1 from inactive complexes, fueling mixing and matching of SCF parts for E3 activation in response to substrate availability. Our data reveal biogenesis of a predominant family of E3 ligases, and the molecular basis for systemwide multiprotein complex assembly.
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Affiliation(s)
- Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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6
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Scott DC, King MT, Baek K, Gee CT, Kalathur R, Li J, Purser N, Nourse A, Chai SC, Vaithiyalingam S, Chen T, Lee RE, Elledge SJ, Kleiger G, Schulman BA. E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity. Mol Cell 2023; 83:770-786.e9. [PMID: 36805027 PMCID: PMC10080726 DOI: 10.1016/j.molcel.2023.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023]
Abstract
E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2KLHDC2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2KLHDC2. Without substrate, neddylated CRL2KLHDC2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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Nardone C, Palanski BA, Scott DC, Timms RT, Barber KW, Gu X, Mao A, Leng Y, Watson EV, Schulman BA, Cole PA, Elledge SJ. A central role for regulated protein stability in the control of TFE3 and MITF by nutrients. Mol Cell 2023; 83:57-73.e9. [PMID: 36608670 PMCID: PMC9908011 DOI: 10.1016/j.molcel.2022.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 07/18/2022] [Revised: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023]
Abstract
The TFE3 and MITF master transcription factors maintain metabolic homeostasis by regulating lysosomal, melanocytic, and autophagy genes. Previous studies posited that their cytosolic retention by 14-3-3, mediated by the Rag GTPases-mTORC1, was key for suppressing transcriptional activity in the presence of nutrients. Here, we demonstrate using mammalian cells that regulated protein stability plays a fundamental role in their control. Amino acids promote the recruitment of TFE3 and MITF to the lysosomal surface via the Rag GTPases, activating an evolutionarily conserved phospho-degron and leading to ubiquitination by CUL1β-TrCP and degradation. Elucidation of the minimal functional degron revealed a conserved alpha-helix required for interaction with RagA, illuminating the molecular basis for a severe neurodevelopmental syndrome caused by missense mutations in TFE3 within the RagA-TFE3 interface. Additionally, the phospho-degron is recurrently lost in TFE3 genomic translocations that cause kidney cancer. Therefore, two divergent pathologies converge on the loss of protein stability regulation by nutrients.
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Affiliation(s)
- Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brad A Palanski
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Karl W Barber
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Aoyue Mao
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Emma V Watson
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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8
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Kim HS, Hammill JT, Scott DC, Chen Y, Rice AL, Pistel W, Singh B, Schulman BA, Guy RK. Improvement of Oral Bioavailability of Pyrazolo-Pyridone Inhibitors of the Interaction of DCN1/2 and UBE2M. J Med Chem 2021; 64:5850-5862. [PMID: 33945681 PMCID: PMC8159160 DOI: 10.1021/acs.jmedchem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Indexed: 11/30/2022]
Abstract
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The cullin-RING ubiquitin ligases (CRLs) are ubiquitin E3 enzymes that play a key role
in controlling proteasomal degradation and are activated by neddylation. We previously
reported inhibitors that target CRL activation by disrupting the interaction of
defective in cullin neddylation 1 (DCN1), a CRL neddylation co-E3, and UBE2M, a
neddylation E2. Our first-generation inhibitors possessed poor oral bioavailability and
fairly rapid clearance that hindered the study of acute inhibition of DCN-controlled CRL
activity in vivo. Herein, we report studies to improve the pharmacokinetic performance
of the pyrazolo-pyridone inhibitors. The current best inhibitor, 40,
inhibits the interaction of DCN1 and UBE2M, blocks NEDD8 transfer in biochemical assays,
thermally stabilizes cellular DCN1, and inhibits anchorage-independent growth in a DCN1
amplified squamous cell carcinoma cell line. Additionally, we demonstrate that a single
oral 50 mg/kg dose sustains plasma exposures above the biochemical IC90 for
24 h in mice.
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Affiliation(s)
- Ho Shin Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Jared T Hammill
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yizhe Chen
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Amy L Rice
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
| | - William Pistel
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
| | - Bhuvanesh Singh
- Department of Surgery, Laboratory of Epithelial Cancer Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - R Kiplin Guy
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40508, United States
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9
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Horn-Ghetko D, Krist DT, Prabu JR, Baek K, Mulder MPC, Klügel M, Scott DC, Ovaa H, Kleiger G, Schulman BA. Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Nature 2021; 590:671-676. [PMID: 33536622 PMCID: PMC7904520 DOI: 10.1038/s41586-021-03197-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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] [Received: 05/21/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023]
Abstract
E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates1,2. However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies3-7. Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation.
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Affiliation(s)
- Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David T Krist
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Carle Illinois College of Medicine, Champaign, IL, USA
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Monique P C Mulder
- Oncode Institute, Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maren Klügel
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel C Scott
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Huib Ovaa
- Oncode Institute, Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
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10
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Xu P, Scott DC, Xu B, Yao Y, Feng R, Cheng L, Mayberry K, Wang YD, Bi W, Palmer LE, King MT, Wang H, Li Y, Fan Y, Alpi AF, Li C, Peng J, Papizan J, Pruett-Miller SM, Spallek R, Bassermann F, Cheng Y, Schulman BA, Weiss MJ. FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. Blood 2021; 137:155-167. [PMID: 33156908 PMCID: PMC7820877 DOI: 10.1182/blood.2020007809] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 06/23/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
The histone mark H3K27me3 and its reader/writer polycomb repressive complex 2 (PRC2) mediate widespread transcriptional repression in stem and progenitor cells. Mechanisms that regulate this activity are critical for hematopoietic development but are poorly understood. Here we show that the E3 ubiquitin ligase F-box only protein 11 (FBXO11) relieves PRC2-mediated repression during erythroid maturation by targeting its newly identified substrate bromo adjacent homology domain-containing 1 (BAHD1), an H3K27me3 reader that recruits transcriptional corepressors. Erythroblasts lacking FBXO11 are developmentally delayed, with reduced expression of maturation-associated genes, most of which harbor bivalent histone marks at their promoters. In FBXO11-/- erythroblasts, these gene promoters bind BAHD1 and fail to recruit the erythroid transcription factor GATA1. The BAHD1 complex interacts physically with PRC2, and depletion of either component restores FBXO11-deficient erythroid gene expression. Our studies identify BAHD1 as a novel effector of PRC2-mediated repression and reveal how a single E3 ubiquitin ligase eliminates PRC2 repression at many developmentally poised bivalent genes during erythropoiesis.
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Affiliation(s)
| | | | - Beisi Xu
- Department of Computational Biology
| | | | | | | | | | | | | | | | | | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Junmin Peng
- Department of Structural Biology
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN
- Department of Development Neurobiology
| | | | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, and
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN; and
| | - Ria Spallek
- Department of Medicine III and
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Florian Bassermann
- Department of Medicine III and
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Yong Cheng
- Department of Hematology
- Department of Computational Biology
| | - Brenda A Schulman
- Department of Structural Biology
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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11
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Baek K, Scott DC, Schulman BA. NEDD8 and ubiquitin ligation by cullin-RING E3 ligases. Curr Opin Struct Biol 2020; 67:101-109. [PMID: 33160249 DOI: 10.1016/j.sbi.2020.10.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023]
Abstract
RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s - including the cullin-RING ligase family - are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms - interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners - directing cullin-RING E3-E2 enzyme active sites to modify their specific targets.
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Affiliation(s)
- Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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12
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Majumdar A, Trinh V, Moore KJ, Smallwood CR, Kumar A, Yang T, Scott DC, Long NJ, Newton SM, Klebba PE. Conformational rearrangements in the N-domain of Escherichia coli FepA during ferric enterobactin transport. J Biol Chem 2020; 295:4974-4984. [PMID: 32098871 DOI: 10.1074/jbc.ra119.011850] [Citation(s) in RCA: 7] [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: 11/26/2019] [Revised: 02/14/2020] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli outer membrane receptor FepA transports ferric enterobactin (FeEnt) by an energy- and TonB-dependent, but otherwise a mechanistically undetermined process involving its internal 150-residue N-terminal globular domain (N-domain). We genetically introduced pairs of Cys residues in different regions of the FepA tertiary structure, with the potential to form disulfide bonds. These included Cys pairs on adjacent β-strands of the N-domain (intra-N) and Cys pairs that bridged the external surface of the N-domain to the interior of the C-terminal transmembrane β-barrel (inter-N-C). We characterized FeEnt uptake by these mutants with siderophore nutrition tests, [59Fe]Ent binding and uptake experiments, and fluorescence decoy sensor assays. The three methods consistently showed that the intra-N disulfide bonds, which restrict conformational motion within the N-domain, prevented FeEnt uptake, whereas most inter-N-C disulfide bonds did not prevent FeEnt uptake. These outcomes indicate that conformational rearrangements must occur in the N terminus of FepA during FeEnt transport. They also argue against disengagement of the N-domain out of the channel as a rigid body and suggest instead that it remains within the transmembrane pore as FeEnt enters the periplasm.
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Affiliation(s)
- Aritri Majumdar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Vy Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Kyle J Moore
- Department of Chemistry, Physics and Engineering, Cameron University, Lawton, Oklahoma 73505
| | | | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Daniel C Scott
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Noah J Long
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Salete M Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
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13
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Hill S, Reichermeier K, Scott DC, Samentar L, Coulombe-Huntington J, Izzi L, Tang X, Ibarra R, Bertomeu T, Moradian A, Sweredoski MJ, Caberoy N, Schulman BA, Sicheri F, Tyers M, Kleiger G. Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways. eLife 2019; 8:e51163. [PMID: 31868589 PMCID: PMC6975927 DOI: 10.7554/elife.51163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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] [Received: 08/17/2019] [Accepted: 12/22/2019] [Indexed: 12/24/2022] Open
Abstract
The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylation in vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-dependent ubiquitylation reactions with physiological enzyme concentrations, mass spectrometry was employed to estimate E2 and E3 levels in cells. In combination with UBE2R1/2, the E2 UBE2D3 and the E3 ARIH1 both promoted SCF-mediated polyubiquitylation in a substrate-specific fashion. Unexpectedly, UBE2R2 alone had negligible ubiquitylation activity at physiological concentrations and the ablation of UBE2R1/2 had no effect on the stability of SCF substrates in cells. A genome-wide CRISPR screen revealed that an additional E2 enzyme, UBE2G1, buffers against the loss of UBE2R1/2. UBE2G1 had robust in vitro chain extension activity with SCF, and UBE2G1 knockdown in cells lacking UBE2R1/2 resulted in stabilization of the SCF substrates p27 and CYCLIN E as well as the CUL2-RING ligase substrate HIF1α. The results demonstrate the human SCF enzyme system is diversified by association with multiple catalytic enzyme partners.
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Affiliation(s)
- Spencer Hill
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Kurt Reichermeier
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Department of Discovery ProteomicsGenentech IncSouth San FranciscoUnited States
- Department of Discovery OncologyGenentech IncSouth San FranciscoUnited States
| | - Daniel C Scott
- Department of Structural BiologySt Jude Children's Research HospitalMemphisUnited States
| | - Lorena Samentar
- School of Life SciencesUniversity of NevadaLas VegasUnited States
- University of the PhilippinesIloiloPhilippines
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Luisa Izzi
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Rebeca Ibarra
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Nora Caberoy
- School of Life SciencesUniversity of NevadaLas VegasUnited States
| | - Brenda A Schulman
- Max Planck Institute of Biochemistry, Molecular Machines and SignalingMartinsriedGermany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Gary Kleiger
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
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14
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Kim HS, Hammill JT, Scott DC, Chen Y, Min J, Rector J, Singh B, Schulman BA, Guy RK. Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation. J Med Chem 2019; 62:8429-8442. [PMID: 31465221 DOI: 10.1021/acs.jmedchem.9b00410] [Citation(s) in RCA: 13] [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: 12/14/2022]
Abstract
Chemical control of cullin neddylation is attracting increased attention based largely on the successes of the NEDD8-activating enzyme (E1) inhibitor pevonedistat. Recently reported chemical probes enable selective and time-dependent inhibition of downstream members of the neddylation trienzymatic cascade including the co-E3, DCN1. In this work, we report the optimization of a novel class of small molecule inhibitors of the DCN1-UBE2M interaction. Rational X-ray co-structure enabled optimization afforded a 25-fold improvement in potency relative to the initial screening hit. The potency gains are largely attributed to additional hydrophobic interactions mimicking the N-terminal acetyl group that drives binding of UBE2M to DCN1. The compounds inhibit the protein-protein interaction, block NEDD8 transfer in biochemical assays, engage DCN1 in cells, and selectively reduce the steady-state neddylation of Cul1 and Cul3 in two squamous carcinoma cell lines harboring DCN1 amplification.
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Affiliation(s)
- Ho Shin Kim
- Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Jared T Hammill
- Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Daniel C Scott
- Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States
| | - Yizhe Chen
- Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States
| | - Jonah Rector
- Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Bhuvanesh Singh
- Department of Surgery, Laboratory of Epithelial Cancer Biology , Memorial Sloan Kettering Cancer Center , New York New York 10065 , United States
| | - Brenda A Schulman
- Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States.,Department of Molecular Machines and Signaling , Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - R Kiplin Guy
- Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States
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15
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Abstract
Many fundamental discoveries in ubiquitin-proteasome research have relied on reconstitution of activities from purified or recombinantly expressed components. These include landmark discoveries of E1-E2-E3 mechanisms, in which ubiquitin (UB) is initially activated and then covalently shuttled between enzyme active sites and ultimately ligated to substrate or substrate-linked UBs during polyubiquitination. However, recent studies have unearthed enormous variations on the E1-E2-E3 theme; for example, one E3 may employ two distinct E2s, or two different E3s may act in a single assembly or in series, to prime substrates directly with UB and subsequently decorate them with myriad types of polyubiquitin chains. To dissect this complexity, it can be helpful to monitor specific UB transfer reactions in isolation, rather than the end-point products formed upon mixing all enzymes in a cascade. Pulse-chase assays enable observation of a single reaction step and also allow one to differentially label UBs carried by different enzymes within the same tube. In such assays, the "pulse" reaction generates a thioester-linked enzyme~UB intermediate, while the "chase" monitors UB transfer to downstream components over time. Here, we describe pulse-chase assays for detecting fluorescent-UB in E2~UB intermediates. These assays enable direct assessment of particular ligation reactions, alone and in combination, to explore roles of multiple enzymatic cascades in the same tube. We anticipate this technique can be adapted to many different E2s, as well as thioester-forming E3s, to dissect ubiquitination by many distinct enzyme cascades.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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16
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Abstract
Summary
Echis carinatus venom contains proteases capable of activating both normal and descarboxy prothrombin. We showed this venom (Sigma) principally activates prothrombin with almost no factor X activation. Echis time in combination with prothrombin time can predict vitamin K responsiveness since the Echis time is usually normal in the presence of descarboxy prothrombin associated with vitamin K deficiency.38 patients with abnormal routine prothrombin times (PT) had both coagulant and immunogenic factor II assays along with Echis times done before and after vitamin K. Of 22 patients responding to vitamin K, based on correction of PT, 21 had normal initial Echis times and of 16 not responding, 11 had abnormal Echis times, giving a sensitivity of 95.4% and specificity of 68.8% for vitamin K responsiveness. 90% of patients with a PT/Echis time ratio <1.3 and a prolonged Echis time did not correct their PTs with vitamin K therapy.The 5 non-responders with normal Echis times all showed normal initial coagulant and antigenic prothrombin, but 3 had low F V and/or F VII.
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Affiliation(s)
- C Solano
- The Haematology Department, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - R G Cobcroft
- The Haematology Department, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - D C Scott
- The Haematology Department, Princess Alexandra Hospital, Brisbane, Queensland, Australia
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17
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Thomas Y, Scott DC, Kristariyanto YA, Rinehart J, Clark K, Cohen P, Kurz T. The NEDD8 E3 ligase DCNL5 is phosphorylated by IKK alpha during Toll-like receptor activation. PLoS One 2018; 13:e0199197. [PMID: 29958295 PMCID: PMC6025869 DOI: 10.1371/journal.pone.0199197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/01/2018] [Indexed: 11/19/2022] Open
Abstract
The activity of Cullin-RING ubiquitin E3 ligases (CRL) is regulated by NEDD8 modification. DCN-like proteins promote Cullin neddylation as scaffold-like E3s. One DCNL, DCNL5, is highly expressed in immune tissue. Here, we provide evidence that DCNL5 may be involved in innate immunity, as it is a direct substrate of the kinase IKKα during immune signalling. We find that upon activation of Toll-like receptors, DCNL5 gets rapidly and transiently phosphorylated on a specific N-terminal serine residue (S41). This phosphorylation event is specifically mediated by IKKα and not IKKβ. Our data for the first time provides evidence that DCNL proteins are post-translationally modified in an inducible manner. Our findings also provide the first example of a DCNL member as a kinase substrate in a signalling pathway, indicating that the activity of at least some DCNLs may be regulated.
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Affiliation(s)
- Yann Thomas
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel C. Scott
- Department of Structural Biology, Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yosua Adi Kristariyanto
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, Connecticut, United States of America
- Systems Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Kristopher Clark
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Philip Cohen
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Thimo Kurz
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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18
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Hammill JT, Scott DC, Min J, Connelly MC, Holbrook G, Zhu F, Matheny A, Yang L, Singh B, Schulman BA, Guy RK. Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. J Med Chem 2018; 61:2680-2693. [PMID: 29547696 DOI: 10.1021/acs.jmedchem.7b01277] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We previously discovered and validated a class of piperidinyl ureas that regulate defective in cullin neddylation 1 (DCN1)-dependent neddylation of cullins. Here, we report preliminary structure-activity relationship studies aimed at advancing our high-throughput screen hit into a tractable tool compound for dissecting the effects of acute DCN1-UBE2M inhibition on the NEDD8/cullin pathway. Structure-enabled optimization led to a 100-fold increase in biochemical potency and modestly increased solubility and permeability as compared to our initial hit. The optimized compounds inhibit the DCN1-UBE2M protein-protein interaction in our TR-FRET binding assay and inhibit cullin neddylation in our pulse-chase NEDD8 transfer assay. The optimized compounds bind to DCN1 and selectively reduce steady-state levels of neddylated CUL1 and CUL3 in a squamous cell carcinoma cell line. Ultimately, we anticipate that these studies will identify early lead compounds for clinical development for the treatment of lung squamous cell carcinomas and other cancers.
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Affiliation(s)
- Jared T Hammill
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Daniel C Scott
- Howard Hughes Medical Institute , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States.,Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Jaeki Min
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Michele C Connelly
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Gloria Holbrook
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Fangyi Zhu
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Amy Matheny
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Lei Yang
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Bhuvanesh Singh
- Department of Surgery, Laboratory of Epithelial Cancer Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 United States
| | - Brenda A Schulman
- Howard Hughes Medical Institute , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States.,Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - R Kiplin Guy
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
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19
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Hammill JT, Bhasin D, Scott DC, Min J, Chen Y, Lu Y, Yang L, Kim HS, Connelly MC, Hammill C, Holbrook G, Jeffries C, Singh B, Schulman BA, Guy RK. Discovery of an Orally Bioavailable Inhibitor of Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. J Med Chem 2018; 61:2694-2706. [PMID: 29547693 DOI: 10.1021/acs.jmedchem.7b01282] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We previously reported the discovery, validation, and structure-activity relationships of a series of piperidinyl ureas that potently inhibit the DCN1-UBE2M interaction. We demonstrated that compound 7 inhibits both the DCN1-UBE2M protein-protein interaction and DCN1-mediated cullin neddylation in biochemical assays and reduces levels of steady-state cullin neddylation in a squamous carcinoma cell line harboring DCN1 amplification. Although compound 7 exhibits good solubility and permeability, it is rapidly metabolized in microsomal models (CLint = 170 mL/min/kg). This work lays out the discovery of an orally bioavailable analogue, NAcM-OPT (67). Compound 67 retains the favorable biochemical and cellular activity of compound 7 but is significantly more stable both in vitro and in vivo. Compound 67 is orally bioavailable, well tolerated in mice, and currently used to study the effects of acute pharmacologic inhibition of the DCN1-UBE2M interaction on the NEDD8/CUL pathway.
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Affiliation(s)
- Jared T Hammill
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Deepak Bhasin
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Daniel C Scott
- Howard Hughes Medical Institute , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States.,Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Jaeki Min
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Yizhe Chen
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Yan Lu
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Lei Yang
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Ho Shin Kim
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Michele C Connelly
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Courtney Hammill
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Gloria Holbrook
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Cynthia Jeffries
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - Bhuvanesh Singh
- Department of Surgery, Laboratory of Epithelial Cancer Biology , Memorial Sloan Kettering Cancer Center , New York , New York , 10065 United States
| | - Brenda A Schulman
- Howard Hughes Medical Institute , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States.,Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
| | - R Kiplin Guy
- Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States
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20
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Abstract
Liu et al. (2018) report a mathematical model predicting how the cellular repertoire of SCF E3 ligases is assembled by "adaptive exchange on demand," with the limited pool of CUL1 scanning the vast sea of F-box proteins for those with substrates demanding ubiquitylation.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried bei München, Germany.
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21
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Scott DC, Hammill JT, Min J, Rhee DY, Connelly M, Sviderskiy VO, Bhasin D, Chen Y, Ong SS, Chai SC, Goktug AN, Huang G, Monda JK, Low J, Kim HS, Paulo JA, Cannon JR, Shelat AA, Chen T, Kelsall IR, Alpi AF, Pagala V, Wang X, Peng J, Singh B, Harper JW, Schulman BA, Guy RK. Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase. Nat Chem Biol 2017; 13:850-857. [PMID: 28581483 PMCID: PMC5577376 DOI: 10.1038/nchembio.2386] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 09/21/2016] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
Abstract
N-terminal acetylation is an abundant modification influencing protein functions. Since ≈80% of mammalian cytosolic proteins are N-terminally acetylated, this potentially represents an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions, suggesting it may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation-dependent interaction between an E2 conjugating enzyme (UBE2M, aka UBC12) and DCN1 (aka DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl amide binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress the anchorage-independent growth of a cell line harboring DCN1 amplification. Overall, the data demonstrate that N-terminal acetyl-dependent protein interactions are druggable targets, and provide insights into targeting multiprotein E2–E3 ligases.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jared T Hammill
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michele Connelly
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Vladislav O Sviderskiy
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deepak Bhasin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yizhe Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Su-Sien Ong
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Asli N Goktug
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guochang Huang
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Julie K Monda
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ho Shin Kim
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joe R Cannon
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ian R Kelsall
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Vishwajeeth Pagala
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xusheng Wang
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bhuvanesh Singh
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - R Kip Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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22
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Scott DC, Sviderskiy VO, Monda JK, Lydeard JR, Cho SE, Harper JW, Schulman BA. Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8. Cell 2014; 157:1671-84. [PMID: 24949976 DOI: 10.1016/j.cell.2014.04.037] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/16/2014] [Accepted: 04/21/2014] [Indexed: 12/29/2022]
Abstract
Most E3 ligases use a RING domain to activate a thioester-linked E2∼ubiquitin-like protein (UBL) intermediate and promote UBL transfer to a remotely bound target protein. Nonetheless, RING E3 mechanisms matching a specific UBL and acceptor lysine remain elusive, including for RBX1, which mediates NEDD8 ligation to cullins and >10% of all ubiquitination. We report the structure of a trapped RING E3-E2∼UBL-target intermediate representing RBX1-UBC12∼NEDD8-CUL1-DCN1, which reveals the mechanism of NEDD8 ligation and how a particular UBL and acceptor lysine are matched by a multifunctional RING E3. Numerous mechanisms specify cullin neddylation while preventing noncognate ubiquitin ligation. Notably, E2-E3-target and RING-E2∼UBL modules are not optimized to function independently, but instead require integration by the UBL and target for maximal reactivity. The UBL and target regulate the catalytic machinery by positioning the RING-E2∼UBL catalytic center, licensing the acceptor lysine, and influencing E2 reactivity, thereby driving their specific coupling by a multifunctional RING E3.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vladislav O Sviderskiy
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Julie K Monda
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John R Lydeard
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shein Ei Cho
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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23
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Monda JK, Scott DC, Miller DJ, Lydeard J, King D, Harper JW, Bennett EJ, Schulman BA. Structural conservation of distinctive N-terminal acetylation-dependent interactions across a family of mammalian NEDD8 ligation enzymes. Structure 2013; 21:42-53. [PMID: 23201271 PMCID: PMC3786212 DOI: 10.1016/j.str.2012.10.013] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/20/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
Little is known about molecular recognition of acetylated N termini, despite prevalence of this modification among eukaryotic cytosolic proteins. We report that the family of human DCN-like (DCNL) co-E3s, which promote ligation of the ubiquitin-like protein NEDD8 to cullin targets, recognizes acetylated N termini of the E2 enzymes UBC12 and UBE2F. Systematic biochemical and biophysical analyses reveal 40- and 10-fold variations in affinities among different DCNL-cullin and DCNL-E2 complexes, contributing to varying efficiencies of different NEDD8 ligation cascades. Structures of DCNL2 and DCNL3 complexes with N-terminally acetylated peptides from UBC12 and UBE2F illuminate a common mechanism by which DCNL proteins recognize N-terminally acetylated E2s and how selectivity for interactions dependent on N-acetyl-methionine are established through side chains recognizing distal residues. Distinct preferences of UBC12 and UBE2F peptides for inhibiting different DCNLs, including the oncogenic DCNL1 protein, suggest it may be possible to develop small molecules blocking specific N-acetyl-methionine-dependent protein interactions.
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Affiliation(s)
- Julie K. Monda
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Daniel C. Scott
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - Darcie J. Miller
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105
| | - John Lydeard
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - David King
- HHMI Mass Spectrometry Laboratory, University of California, Berkeley CA 94720
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston MA 02115
| | - Eric J. Bennett
- Department of Cell Biology, Harvard Medical School, Boston MA 02115,Division of Biological Sciences, University of California San Diego, La Jolla CA 92093
| | - Brenda A. Schulman
- Department of Structural Biology and Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis TN, 38105,Department of Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis TN, 38105
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24
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Enchev RI, Scott DC, da Fonseca PCA, Schreiber A, Monda JK, Schulman BA, Peter M, Morris EP. Structural basis for a reciprocal regulation between SCF and CSN. Cell Rep 2012; 2:616-27. [PMID: 22959436 DOI: 10.1016/j.celrep.2012.08.019] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 08/24/2012] [Accepted: 08/24/2012] [Indexed: 10/27/2022] Open
Abstract
Skp1-Cul1-Fbox (SCF) E3 ligases are activated by ligation to the ubiquitin-like protein Nedd8, which is reversed by the deneddylating Cop9 signalosome (CSN). However, CSN also promotes SCF substrate turnover through unknown mechanisms. Through biochemical and electron microscopy analyses, we determined molecular models of CSN complexes with SCF(Skp2/Cks1) and SCF(Fbw7) and found that CSN occludes both SCF functional sites-the catalytic Rbx1-Cul1 C-terminal domain and the substrate receptor. Indeed, CSN binding prevents SCF interactions with E2 enzymes and a ubiquitination substrate, and it inhibits SCF-catalyzed ubiquitin chain formation independent of deneddylation. Importantly, CSN prevents neddylation of the bound cullin, unless binding of a ubiquitination substrate triggers SCF dissociation and neddylation. Taken together, the results provide a model for how reciprocal regulation sensitizes CSN to the SCF assembly state and inhibits a catalytically competent SCF until a ubiquitination substrate drives its own degradation by displacing CSN, thereby promoting cullin neddylation and substrate ubiquitination.
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Affiliation(s)
- Radoslav I Enchev
- ETH-Zurich, Institute of Biochemistry, Department of Biology, Zurich, Switzerland
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25
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Chaurushiya MS, Lilley CE, Aslanian A, Meisenhelder J, Scott DC, Landry S, Ticau S, Boutell C, Yates JR, Schulman BA, Hunter T, Weitzman MD. Viral E3 ubiquitin ligase-mediated degradation of a cellular E3: viral mimicry of a cellular phosphorylation mark targets the RNF8 FHA domain. Mol Cell 2012; 46:79-90. [PMID: 22405594 DOI: 10.1016/j.molcel.2012.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 05/13/2011] [Revised: 09/19/2011] [Accepted: 01/27/2012] [Indexed: 01/22/2023]
Abstract
Viral hijacking of cellular processes relies on the ability to mimic the structure or function of cellular proteins. Many viruses encode ubiquitin ligases to facilitate infection, although the mechanisms by which they select their substrates are often unknown. The Herpes Simplex Virus type-1-encoded E3 ubiquitin ligase, ICP0, promotes infection through degradation of cellular proteins, including the DNA damage response E3 ligases RNF8 and RNF168. Here we describe a mechanism by which this viral E3 hijacks a cellular phosphorylation-based targeting strategy to degrade RNF8. By mimicking a cellular phosphosite, ICP0 binds RNF8 via the RNF8 forkhead associated (FHA) domain. Phosphorylation of ICP0 T67 by CK1 recruits RNF8 for degradation and thereby promotes viral transcription, replication, and progeny production. We demonstrate that this mechanism may constitute a broader viral strategy to target other cellular factors, highlighting the importance of this region of the ICP0 protein in countering intrinsic antiviral defenses.
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Affiliation(s)
- Mira S Chaurushiya
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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26
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Abstract
Although many eukaryotic proteins are amino (N)-terminally acetylated, structural mechanisms by which N-terminal acetylation mediates protein interactions are largely unknown. Here, we found that N-terminal acetylation of the E2 enzyme, Ubc12, dictates distinctive E3-dependent ligation of the ubiquitin-like protein Nedd8 to Cul1. Structural, biochemical, biophysical, and genetic analyses revealed how complete burial of Ubc12's N-acetyl-methionine in a hydrophobic pocket in the E3, Dcn1, promotes cullin neddylation. The results suggest that the N-terminal acetyl both directs Ubc12's interactions with Dcn1 and prevents repulsion of a charged N terminus. Our data provide a link between acetylation and ubiquitin-like protein conjugation and define a mechanism for N-terminal acetylation-dependent recognition.
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Affiliation(s)
- Daniel C Scott
- Structural Biology Department, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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27
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Schulman BA, Duda DM, Kamadurai HB, Souphron J, Scott DC, Monda JK, Olszewski J, Calabrese MF. Structural Studies of Ubiquitin and Ubiquitin-Like Protein Transfer Cascades. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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28
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Duda DM, Scott DC, Calabrese MF, Zimmerman ES, Zheng N, Schulman BA. Structural regulation of cullin-RING ubiquitin ligase complexes. Curr Opin Struct Biol 2011; 21:257-64. [PMID: 21288713 DOI: 10.1016/j.sbi.2011.01.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 01/05/2011] [Accepted: 01/06/2011] [Indexed: 01/19/2023]
Abstract
Cullin-RING ligases (CRLs) compose the largest class of E3 ubiquitin ligases. CRLs are modular, multisubunit enzymes, comprising interchangeable substrate receptors dedicated to particular Cullin-RING catalytic cores. Recent structural studies have revealed numerous ways in which CRL E3 ligase activities are controlled, including multimodal E3 ligase activation by covalent attachment of the ubiquitin-like protein NEDD8, inhibition of CRL assembly/activity by CAND1, and several mechanisms of regulated substrate recruitment. These features highlight the potential for CRL activities to be tuned in responses to diverse cellular cues, and for modulating CRL functions through small-molecule agonists or antagonists. As the second installment of a two-review series, this article focuses on recent structural studies advancing our knowledge of how CRL activities are regulated.
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Affiliation(s)
- David M Duda
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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29
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Scott DC, Monda JK, Grace CRR, Duda DM, Kriwacki RW, Kurz T, Schulman BA. A dual E3 mechanism for Rub1 ligation to Cdc53. Mol Cell 2010; 39:784-96. [PMID: 20832729 DOI: 10.1016/j.molcel.2010.08.030] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 07/29/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
In ubiquitin-like protein (UBL) cascades, a thioester-linked E2∼UBL complex typically interacts with an E3 enzyme for UBL transfer to the target. Here we demonstrate a variant mechanism, whereby the E2 Ubc12 functions with two E3s, Hrt1 and Dcn1, for ligation of the UBL Rub1 to Cdc53's WHB subdomain. Hrt1 functions like a conventional RING E3, with its N terminus recruiting Cdc53 and C-terminal RING activating Ubc12∼Rub1. Dcn1's "potentiating neddylation" domain (Dcn1(P)) acts as an additional E3, reducing nonspecific Hrt1-mediated Ubc12∼Rub1 discharge and directing Ubc12's active site to Cdc53. Crystal structures of Dcn1(P)-Cdc53(WHB) and Ubc12 allow modeling of a catalytic complex, supported by mutational data. We propose that Dcn1's interactions with both Cdc53 and Ubc12 would restrict the otherwise flexible Hrt1 RING-bound Ubc12∼Rub1 to a catalytically competent orientation. Our data reveal mechanisms by which two E3s function synergistically to promote UBL transfer from one E2 to a target.
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Affiliation(s)
- Daniel C Scott
- Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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30
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Kamadurai HB, Souphron J, Scott DC, Duda DM, Miller DJ, Stringer D, Piper RC, Schulman BA. Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol Cell 2010; 36:1095-102. [PMID: 20064473 DOI: 10.1016/j.molcel.2009.11.010] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 09/01/2009] [Accepted: 09/23/2009] [Indexed: 01/25/2023]
Abstract
In E1-E2-E3 ubiquitin (Ub) conjugation cascades, the E2 first forms a transient E2 approximately Ub covalent complex and then interacts with an E3 for Ub transfer. For cascades involving E3s in the HECT class, Ub is transferred from an associated E2 to the acceptor cysteine in the HECT domain C lobe. To gain insights into this process, we determined the crystal structure of a complex between the HECT domain of NEDD4L and the E2 UbcH5B bearing a covalently linked Ub at its active site (UbcH5B approximately Ub). Noncovalent interactions between UbcH5B and the HECT N lobe and between Ub and the HECT domain C lobe lead to an overall compact structure, with the Ub C terminus sandwiched between UbcH5B and HECT domain active sites. The structure suggests a model for E2-to-HECT Ub transfer, in which interactions between a donor Ub and an acceptor domain constrain upstream and downstream enzymes for conjugation.
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Affiliation(s)
- Hari B Kamadurai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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31
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Huang DT, Ayrault O, Hunt HW, Taherbhoy AM, Duda DM, Scott DC, Borg LA, Neale G, Murray PJ, Roussel MF, Schulman BA. E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification. Mol Cell 2009; 33:483-95. [PMID: 19250909 DOI: 10.1016/j.molcel.2009.01.011] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [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: 09/09/2008] [Revised: 12/04/2008] [Accepted: 01/09/2009] [Indexed: 11/17/2022]
Abstract
Ubiquitin and ubiquitin-like proteins (UBLs) are directed to targets by cascades of E1, E2, and E3 enzymes. The largest ubiquitin E3 subclass consists of cullin-RING ligases (CRLs), which contain one each of several cullins (CUL1, -2, -3, -4, or -5) and RING proteins (RBX1 or -2). CRLs are activated by ligation of the UBL NEDD8 to a conserved cullin lysine. How is cullin NEDD8ylation specificity established? Here we report that, like UBE2M (also known as UBC12), the previously uncharacterized E2 UBE2F is a NEDD8-conjugating enzyme in vitro and in vivo. Biochemical and structural analyses indicate how plasticity of hydrophobic E1-E2 interactions and E1 conformational flexibility allow one E1 to charge multiple E2s. The E2s have distinct functions, with UBE2M/RBX1 and UBE2F/RBX2 displaying different target cullin specificities. Together, these studies reveal the molecular basis for and functional importance of hierarchical expansion of the NEDD8 conjugation system in establishing selective CRL activation.
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Affiliation(s)
- Danny T Huang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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32
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Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 2008; 134:995-1006. [PMID: 18805092 PMCID: PMC2628631 DOI: 10.1016/j.cell.2008.07.022] [Citation(s) in RCA: 599] [Impact Index Per Article: 37.4] [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: 03/10/2008] [Revised: 06/23/2008] [Accepted: 07/15/2008] [Indexed: 01/07/2023]
Abstract
Cullin-RING ligases (CRLs) comprise the largest ubiquitin E3 subclass, in which a central cullin subunit links a substrate-binding adaptor with an E2-binding RING. Covalent attachment of the ubiquitin-like protein NEDD8 to a conserved C-terminal domain (ctd) lysine stimulates CRL ubiquitination activity and prevents binding of the inhibitor CAND1. Here we report striking conformational rearrangements in the crystal structure of NEDD8~Cul5(ctd)-Rbx1 and SAXS analysis of NEDD8~Cul1(ctd)-Rbx1 relative to their unmodified counterparts. In NEDD8ylated CRL structures, the cullin WHB and Rbx1 RING subdomains are dramatically reoriented, eliminating a CAND1-binding site and imparting multiple potential catalytic geometries to an associated E2. Biochemical analyses indicate that the structural malleability is important for both CRL NEDD8ylation and subsequent ubiquitination activities. Thus, our results point to a conformational control of CRL activity, with ligation of NEDD8 shifting equilibria to disfavor inactive CAND1-bound closed architectures, and favor dynamic, open forms that promote polyubiquitination.
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Affiliation(s)
- David M. Duda
- Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Laura A. Borg
- Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Daniel C. Scott
- Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Harold W. Hunt
- Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Brenda A. Schulman
- Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Correspondence: St. Jude Children’s Research Hospital, MS #311, Memphis, TN 38105, Phone: 901-495-5147, e-mail:
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33
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Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are identified and degraded by the ER-associated degradation pathway (ERAD), a component of ER quality control. In ERAD, misfolded proteins are removed from the ER by retrotranslocation into the cytosol where they are degraded by the ubiquitin-proteasome system. The identity of the specific protein components responsible for retrotranslocation remains controversial, with the potential candidates being Sec61p, Der1p, and Doa10. We show that the cytoplasmic N-terminal domain of a short-lived transmembrane ERAD substrate is exposed to the lumen of the ER during the degradation process. The addition of N-linked glycan to the N terminus of the substrate is prevented by mutation of a specific cysteine residue of Sec61p, as well as a specific cysteine residue of the substrate protein. We show that the substrate protein forms a disulfide-linked complex to Sec61p, suggesting that at least part of the retrotranslocation process involves Sec61p.
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Affiliation(s)
- Daniel C Scott
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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34
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Ma L, Kaserer W, Annamalai R, Scott DC, Jin B, Jiang X, Xiao Q, Maymani H, Massis LM, Ferreira LCS, Newton SMC, Klebba PE. Evidence of ball-and-chain transport of ferric enterobactin through FepA. J Biol Chem 2006; 282:397-406. [PMID: 17056600 PMCID: PMC2398697 DOI: 10.1074/jbc.m605333200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [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: 11/06/2022] Open
Abstract
The Escherichia coli iron transporter, FepA, has a globular N terminus that resides within a transmembrane beta-barrel formed by its C terminus. We engineered 25 cysteine substitution mutations at different locations in FepA and modified their sulfhydryl side chains with fluorescein maleimide in live cells. The reactivity of the Cys residues changed, sometimes dramatically, during the transport of ferric enterobactin, the natural ligand of FepA. Patterns of Cys susceptibility reflected energy- and TonB-dependent motion in the receptor protein. During transport, a residue on the normally buried surface of the N-domain was labeled by fluorescein maleimide in the periplasm, providing evidence that the transport process involves expulsion of the globular domain from the beta-barrel. Porin deficiency much reduced the fluoresceination of this site, confirming the periplasmic labeling route. These data support the previously proposed, but never demonstrated, ball-and-chain theory of membrane transport. Functional complementation between a separately expressed N terminus and C-terminal beta-barrel domain confirmed the feasibility of this mechanism.
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Affiliation(s)
- Li Ma
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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Abstract
Using a lysine-specific cleavable cross-linking reagent ethylene glycolbis(sulfosuccimidylsuccinate) (Sulfo-EGS), we studied conformational motion in the surface loops of Escherichia coli FepA during its transport of the siderophore ferric enterobactin. Site-directed mutagenesis determined that Sulfo-EGS reacted with two lysines, K332 and K483, and at least two other unidentified Lys residues in the surface loops of the outer membrane protein. The reagent cross-linked K483 in FepA L7 to either K332 in L5, forming a product that we designated band 1, or to the major outer membrane proteins OmpF, OmpC, and OmpA, forming band 2. Ferric enterobactin binding to FepA did not prevent modification of K483 by Sulfo-EGS but blocked its cross-linking to OmpF/C and OmpA and reduced its coupling to K332. These data show that the loops of FepA undergo conformational changes in vivo, with an approximate magnitude of 15 A, from a ligand-free open state to a ligand-bound closed state. The coupling of FepA L7 to OmpF, OmpC, or OmpA was TonB independent and was unaffected by the uncouplers CCCP (carbonyl cyanide m-chlorophenylhydrazone) and DNP (2,4-dinitrophenol) but completely inhibited by cyanide.
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Affiliation(s)
- Daniel C Scott
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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Affiliation(s)
- D C Scott
- The Procter & Gamble Company, Health Care Research Center, Mason, Ohio 45040, USA.
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Abstract
The ferric siderophore transporters of the Gram-negative bacterial outer membrane manifest a unique architecture: Their N termini fold into a globular domain that lodges within, and physically obstructs, a transmembrane porin beta-barrel formed by their C termini. We exchanged and deleted the N termini of two such siderophore receptors, FepA and FhuA, which recognize and transport ferric enterobactin and ferrichrome, respectively. The resultant chimeric proteins and empty beta-barrels avidly bound appropriate ligands, including iron complexes, protein toxins, and viruses. Thus, the ability to recognize and discriminate these molecules fully originates in the transmembrane beta-barrel domain. Both the hybrid and the deletion proteins also transported the ferric siderophore that they bound. The FepA constructs showed less transport activity than wild type receptor protein, but the FhuA constructs functioned with turnover numbers that were equivalent to wild type. The mutant proteins displayed the full range of transport functionalities, despite their aberrant or missing N termini, confirming (Braun, M., Killmann, H., and Braun, V. (1999) Mol. Microbiol. 33, 1037-1049) that the globular domain within the pore is dispensable to the siderophore internalization reaction, and when present, acts without specificity during solute uptake. These and other data suggest a transport process in which siderophore receptors undergo multiple conformational states that ultimately expel the N terminus from the channel concomitant with solute internalization.
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Affiliation(s)
- D C Scott
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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Webster CR, Flesch GJ, Scott DC, Swanson JE, May RD, Woodward WS, Gmachl C, Capasso F, Sivco DL, Baillargeon JN, Hutchinson AL, Cho AY. Quantum-cascade laser measurements of stratospheric methane and nitrous oxide. Appl Opt 2001; 40:321-326. [PMID: 18357003 DOI: 10.1364/ao.40.000321] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A tunable quantum-cascade (QC) laser has been flown on NASA's ER-2 high-altitude aircraft to produce the first atmospheric gas measurements with this newly invented device, an important milestone in the QC laser's future planetary, industrial, and commercial applications. Using a cryogenically cooled QC laser during a series of 20 aircraft flights beginning in September 1999 and extending through March 2000, we took measurements of methane (CH(4)) and nitrous oxide (N(2)O) gas up to ~20 km in the stratosphere over North America, Scandinavia, and Russia. The QC laser operating near an 8-mum wavelength was produced by the groups of Capasso and Cho of Bell Laboratories, Lucent Technologies, where QC lasers were invented in 1994. Compared with its companion lead salt diode lasers that were also flown on these flights, the single-mode QC laser cooled to 82 K and produced higher output power (10 mW), narrower laser linewidth (17 MHz), increased measurement precision (a factor of 3), and better spectral stability (~0.1 cm(-1) K). The sensitivity of the QC laser channel was estimated to correspond to a minimum-detectable mixing ratio for methane of approximately 2 parts per billion by volume.
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Sprencel C, Cao Z, Qi Z, Scott DC, Montague MA, Ivanoff N, Xu J, Raymond KM, Newton SM, Klebba PE. Binding of ferric enterobactin by the Escherichia coli periplasmic protein FepB. J Bacteriol 2000; 182:5359-64. [PMID: 10986237 PMCID: PMC110977 DOI: 10.1128/jb.182.19.5359-5364.2000] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [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: 11/20/2022] Open
Abstract
The periplasmic protein FepB of Escherichia coli is a component of the ferric enterobactin transport system. We overexpressed and purified the binding protein 23-fold from periplasmic extracts by ammonium sulfate precipitation and chromatographic methods, with a yield of 20%, to a final specific activity of 15,500 pmol of ferric enterobactin bound/mg. Periplasmic fluid from cells overexpressing the binding protein adsorbed catecholate ferric siderophores with high affinity: in a gel filtration chromatography assay the K(d) of the ferric enterobactin-FepB binding reaction was approximately 135 nM. Intrinsic fluorescence measurements of binding by the purified protein, which were more accurate, showed higher affinity for both ferric enterobactin (K(d) = 30 nM) and ferric enantioenterobactin (K(d) = 15 nM), the left-handed stereoisomer of the natural E. coli siderophore. Purified FepB also adsorbed the apo-siderophore, enterobactin, with comparable affinity (K(d) = 60 nM) but did not bind ferric agrobactin. Polyclonal rabbit antisera and mouse monoclonal antibodies raised against nearly homogeneous preparations of FepB specifically recognized it in solid-phase immunoassays. These sera enabled the measurement of the FepB concentration in vivo when expressed from the chromosome (4,000 copies/cell) or from multicopy plasmids (>100,000 copies/cell). Overexpression of the binding protein did not enhance the overall affinity or rate of ferric enterobactin transport, supporting the conclusion that the rate-limiting step of ferric siderophore uptake through the cell envelope is passage through the outer membrane.
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Affiliation(s)
- C Sprencel
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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Scott DC, Herman RL, Webster CR, May RD, Flesch GJ, Moyer EJ. Airborne laser infrared absorption spectrometer (ALIAS-II) for in situ atmospheric measurements of N2O, CH4, CO, HCl, and NO2 from balloon or remotely piloted aircraft platforms. Appl Opt 1999; 38:4609-4622. [PMID: 18323948 DOI: 10.1364/ao.38.004609] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Airborne Laser Infrared Absorption Spectrometer II (ALIAS-II) is a lightweight, high-resolution (0.0003-cm(-1)), scanning, mid-infrared absorption spectrometer based on cooled (80 K) lead-salt tunable diode laser sources. It is designed to make in situ measurements in the lower and middle stratosphere on either a balloon platform or high-altitude remotely piloted aircraft. Chemical species that can be measured precisely include long-lived tracers N(2)O and CH(4), the shorter-lived tracer CO, and chemically active species HCl and NO(2). Advances in electronic instrumentation developed for ALIAS-I, with the experience of more than 250 flights on board NASA's ER-2 aircraft, have been implemented in ALIAS-II. The two-channel spectrometer features an open cradle, multipass absorption cell to ensure minimal contamination from inlet and surfaces. Time resolution of the instrument is <or=3 s, allowing rapid in situ measurements with excellent spatial resolution. ALIAS-II has completed successful balloon flights from New Mexico, Alaska, and Brazil providing CH(4) and N(2)O vertical profiles in the tropics, mid-latitudes, and high northern latitudes up to altitudes of 32 km.
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Affiliation(s)
- D C Scott
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA.
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Abstract
The siderophore ferric enterobactin enters Escherichia coli through the outer membrane (OM) porin FepA, which contains an aqueous transmembrane channel that is normally occluded by other parts of the protein. After binding the siderophore at a site within the surface loops, FepA undergoes conformational changes that promote ligand internalization. We assessed the participation of different loops in ligand recognition and uptake by creating and analysing a series of deletions. We genetically engineered 26 mutations that removed 9-75 amino acids from nine loops and two buried regions of the OM protein. The mutations had various effects on the uptake reaction, which we discerned by comparing the substrate concentrations of half-maximal binding (Kd) and uptake (Km): every loop deletion affected siderophore transport kinetics, decreasing or eliminating binding affinity and transport efficiency. We classified the mutations in three groups on the basis of their slight, strong or complete inhibition of the rate of ferric enterobactin transport across the OM. Finally, characterization of the FepA mutants revealed that prior experiments underestimated the affinity of FepA for ferric enterobactin: the interaction between the protein and the ferric siderophore is so avid (Kd < 0.2 nM) that FepA tolerated the large reductions in affinity that some loop deletions caused without loss of uptake functionality. That is, like other porins, many of the loops of FepA are superficially dispensable: ferric enterobactin transport occurred without them, at levels that allowed bacterial growth.
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Affiliation(s)
- S M Newton
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA
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Lewis ME, Scott DC, Baranoski MV, Buchanan JA, Griffith EE. Prototypes of intrafamily homicide and serious assault among insanity acquittees. J Am Acad Psychiatry Law 1998; 26:37-48. [PMID: 9554708] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Public concern with societal violence is intensified when persons who have been found not guilty by reason of insanity (NGRI) of having committed a homicide or serious assault are returned to the community. Successful management of such acquittees in the community requires a sophisticated understanding of the person and the illness within the larger context of the violent incident, the family, the community, and the culture. In this article, we present an analysis of psychotic violence within a family context. A qualitative study of 64 subjects who were found NGRI of killing or seriously injuring a family member resulted in four prototypes of intrafamilial homicide/assault: Till Death Us Do Part; Overwhelming Burden, Elimination of the Limit Setter; and Family-Focused Delusional Killing. The prototypes are presented as a model for developing management strategies both for future risk assessment and for successful transition of the insanity acquittee into the community.
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Affiliation(s)
- M E Lewis
- Psychiatric Security Review Board, State of Connecticut, USA
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Solano C, Hogg AL, Saal RJ, Scott DC, Cobcroft RG. The use of two different APC resistance assay systems provides optimal sensitivity and specificity for diagnosing genetic APC resistance. Blood Coagul Fibrinolysis 1997; 8:268-73. [PMID: 9282790 DOI: 10.1097/00001721-199707000-00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 02/05/2023]
Abstract
We compared the performance characteristics of a commercial dilute Russell's viper venom (DRVV)-based APC resistance assay (Gradipore PC Impedance Test) to a routinely utilized commercial APTT based assay (Coatest APC Resistance Assay). The DRVV based assay offers improved sensitivity and specificity for the factor V Leiden mutation. However, the routine use of both assays provides optimum reliability for diagnosis of genetic APC resistance. Our results suggest that when both tests are either positive or negative, DNA analysis is unnecessary. Interference by lupus anticoagulants is dramatically minimized by the phospholipid rich DRVV reagent used in the assay and it is insensitive to high factor VIII activity. Additionally, discrepant functional assay results allow identification of patients who may have an acquired APC resistant phenotype.
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Affiliation(s)
- C Solano
- Haematology Department, Princess Alexandra Hospital, Wooloongabba, Queensland, Australia
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44
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Abstract
A sensitive PCR-based method was developed to produce B-cell clonogenic probes without the need for sequencing and specific oligonucleotide synthesis. Specificity and sensitivity were assessed and found to be comparable to that achieved using established methods. Possible applications include the detection of MRD, bone marrow involvement with lymphoma, and the contamination of autologous bone marrow or peripheral blood progenitor cell harvests with malignant cells carrying IgH rearrangements.
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Affiliation(s)
- R J Saal
- Department of Haematology, University of Queensland, Princess Alexandra Hospital, Brisbane, Australia
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Olson BR, Scott DC, Wetsel WC, Elliot SJ, Tomic M, Stojilkovic S, Nieman LK, Wray S. Effects of insulin-like growth factors I and II and insulin on the immortalized hypothalamic GTI-7 cell line. Neuroendocrinology 1995; 62:155-65. [PMID: 8584115 DOI: 10.1159/000127000] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Insulin and insulin-like growth factor I (IGF-I) participate in energy metabolism, regulate cellular growth and differentiation, and are thought to act locally in a paracrine manner through specific receptors. Systemic levels of these peptides in humans and primates are directly associated with levels of activity of the reproductive axis. To date, it is unclear whether these peptides participate in reproductive function by acting at the level of the GnRH neuron. In this study we examined the effects of IGF-I, IGF-II and insulin on immortalized GnRH-secreting neurons, the GTI-7 cell line. The GTI-7 cells expressed all three members of the insulin receptor family as determined by analysis of 125I-IGF-I, 125I-IGF-II and 125I-insulin binding sites. Insulin receptors bound insulin, IGF-II and IGF-I with a ratio of potency of 1:5:20. IGF-I and IGF-II receptors bound both IGF-I and IGF-II. The ratio of potency of IGF-I/IGF-II was 1:5 for the IGF-I receptor and 100:1 for the IGF-II receptor. The binding characteristics of the growth factors at 22 degrees C suggested the possibility that these cells may secrete IGF binding proteins. To ensure that changes in GnRH levels in the media were due to secretion and not to changes in cell number, the mitogenic effect of these peptides on GTI cells was evaluated. Both insulin and IGF-I were strong mitogens (48-hour incubation), restoring cell number to that of serum-replete cultures at a dose of 0.1 ng/ml. A 100-fold higher dose of IGF-II was required to produce a similar level of mitogenicity, implicating an action through the IGF-I and/or insulin receptor. Due to these mitogenic effects, the effect of insulin, IGF-I and IGF-II on GnRH secretion was studied after short-term exposure. Insulin and IGF-I did not affect GnRH secretion, but IGF-II had a biphasic effect on GnRH release after 2 h of incubation (a maximum stimulatory effect occurred with a 0.1 ng/ml dose). In order to examine the signal transduction mechanism, the role of cytoplasmic calcium mobilization in IGF-II-induced GnRH secretion was examined in single cells using calcium imaging. The effect of IGF-II on GnRH secretion appeared to operate via a calcium-independent mechanism. The studies document an insulin/IGF system in the GTI-7 neuronal cell line and show that insulin and IGFs can exert direct effects on the immortalized GnRH neurons.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- B R Olson
- Developmental Endocrinology, Endocrinology and Reproduction, National Institutes of Health, Bethesda, MD 20892-1862, USA
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Abstract
Pseudohypoparathyroidism type Ia (PHP type Ia) is associated with several endocrinopathies. We describe two siblings with PHP type Ia, hypothyroidism and growth hormone deficiency (GHD). To our knowledge, these patients are the first to have PHP type Ia and GHD. The defect which is most likely responsible for the three endocrinopathies is a deficiency of the stimulatory guanine nucleotide-binding regulatory protein, Gs.
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Affiliation(s)
- D C Scott
- Department of Pediatrics, Georgetown University School of Medicine, Washington, D.C., USA
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Bonitz M, Scott DC, Binder R, Koch SW. Nonlinear carrier-plasmon interaction in a one-dimensional quantum plasma. Phys Rev B Condens Matter 1994; 50:15095-15098. [PMID: 9975859 DOI: 10.1103/physrevb.50.15095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Abstract
The large-scale production of lymphocytes in the bone marrow reflects a delicate balance between positive and negative regulatory signals. For instance, interleukin 7 (IL-7) provides a positive signal, and appears to be both essential and limiting in the mouse. However, much less is understood concerning the negative molecular signals that may limit the output of lymphocytes. Here, Paul Kincade and colleagues discuss how a chance observation with pregnant mice revealed that sex steroids can act as negative regulators of B lymphopoiesis, and may do so under normal steady-state conditions.
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Affiliation(s)
- P W Kincade
- Oklahoma Medical Research Foundation, Oklahoma City 73104
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Bonitz M, Binder R, Scott DC, Koch SW, Kremp D. Theory of plasmons in quasi-one-dimensional degenerate plasmas. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1994; 49:5535-5545. [PMID: 9961879 DOI: 10.1103/physreve.49.5535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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