1
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Storozhuk O, Bruekner SR, Paul A, Lebbink JHG, Sixma TK, Friedhoff P. MutL Activates UvrD by Interaction Between the MutL C-terminal Domain and the UvrD 2B Domain. J Mol Biol 2024; 436:168589. [PMID: 38677494 DOI: 10.1016/j.jmb.2024.168589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
UvrD is a helicase vital for DNA replication and quality control processes. In its monomeric state, UvrD exhibits limited helicase activity, necessitating either dimerization or assistance from an accessory protein to efficiently unwind DNA. Within the DNA mismatch repair pathway, MutL plays a pivotal role in relaying the repair signal, enabling UvrD to unwind DNA from the strand incision site up to and beyond the mismatch. Although this interdependence is well-established, the precise mechanism of activation and the specific MutL-UvrD interactions that trigger helicase activity remain elusive. To address these questions, we employed site-specific crosslinking techniques using single-cysteine variants of MutL and UvrD followed by functional assays. Our investigation unveils that the C-terminal domain of MutL not only engages with UvrD but also acts as a self-sufficient activator of UvrD helicase activity on DNA substrates with 3'-single-stranded tails. Especially when MutL is covalently attached to the 2B or 1B domain the tail length can be reduced to a minimal substrate of 5 nucleotides without affecting unwinding efficiency.
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Affiliation(s)
- Olha Storozhuk
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Susanne R Bruekner
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands
| | - Ankon Paul
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Radiotherapy, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
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2
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Keijzer N, Priyanka A, Stijf-Bultsma Y, Fish A, Gersch M, Sixma TK. Variety in the USP deubiquitinase catalytic mechanism. Life Sci Alliance 2024; 7:e202302533. [PMID: 38355287 PMCID: PMC10867860 DOI: 10.26508/lsa.202302533] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The ubiquitin-specific protease (USP) family of deubiquitinases (DUBs) controls cellular ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies. Understanding of the USP active site is primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine, and a third residue (third critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (fourth critical residue) is directly adjacent to this third critical residue. Although both critical residues accommodate catalysis in USP2, these residues have not been comprehensively investigated in other USPs. Here, we quantitatively investigate their roles in five USPs. Although USP7 relies on the third critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40, and USP48, where the fourth critical residue is vital instead. Furthermore, these residues vary in importance for nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. This unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.
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Affiliation(s)
- Niels Keijzer
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anu Priyanka
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yvette Stijf-Bultsma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Alexander Fish
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Titia K Sixma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
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3
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Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 2022; 8:eabo0517. [PMID: 35895815 PMCID: PMC9328677 DOI: 10.1126/sciadv.abo0517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
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Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Xiaohu Guo
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Bruna V. Eckhardt
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kees Vreeken
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Titia K. Sixma
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
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4
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Affiliation(s)
- Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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5
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Dharadhar S, van Dijk WJ, Scheffers S, Fish A, Sixma TK. Insert L1 is a central hub for allosteric regulation of USP1 activity. EMBO Rep 2021; 22:e51749. [PMID: 33619839 PMCID: PMC8024992 DOI: 10.15252/embr.202051749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
During DNA replication, the deubiquitinating enzyme USP1 limits the recruitment of translesion polymerases by removing ubiquitin marks from PCNA to allow specific regulation of the translesion synthesis (TLS) pathway. USP1 activity depends on an allosteric activator, UAF1, and this is tightly controlled. In comparison to paralogs USP12 and USP46, USP1 contains three defined inserts and lacks the second WDR20-mediated activation step. Here we show how inserts L1 and L3 together limit intrinsic USP1 activity and how this is relieved by UAF1. Intriguingly, insert L1 also conveys substrate-dependent increase in USP1 activity through DNA and PCNA interactions, in a process that is independent of UAF1-mediated activation. This study establishes insert L1 as an important regulatory hub within USP1 necessary for both substrate-mediated activity enhancement and allosteric activation upon UAF1 binding.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Serge Scheffers
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
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6
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van Tilburg GBA, Murachelli AG, Fish A, van der Heden van Noort GJ, Ovaa H, Sixma TK. K27-Linked Diubiquitin Inhibits UCHL3 via an Unusual Kinetic Trap. Cell Chem Biol 2020; 28:191-201.e8. [PMID: 33238157 DOI: 10.1016/j.chembiol.2020.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/25/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Functional analysis of lysine 27-linked ubiquitin chains (K27Ub) is difficult due to the inability to make them through enzymatic methods and due to a lack of model tools and substrates. Here we generate a series of ubiquitin (Ub) tools to study how the deubiquitinase UCHL3 responds to K27Ub chains in comparison to lysine 63-linked chains and mono-Ub. From a crystal structure of a complex between UCHL3 and synthetic K27Ub2, we unexpectedly discover that free K27Ub2 and K27Ub2-conjugated substrates are natural inhibitors of UCHL3. Using our Ub tools to profile UCHL3's activity, we generate a quantitative kinetic model of the inhibitory mechanism and we find that K27Ub2 can inhibit UCHL3 covalently, by binding to its catalytic cysteine, and allosterically, by locking its catalytic loop tightly in place. Based on this inhibition mechanism, we propose that UCHL3 and K27Ub chains likely sense and regulate each other in cells.
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Affiliation(s)
- Gabriëlle B A van Tilburg
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Andrea G Murachelli
- Department of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alexander Fish
- Department of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Gerbrand J van der Heden van Noort
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Huib Ovaa
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Titia K Sixma
- Department of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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7
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Martinelli L, Adamopoulos A, Johansson P, Wan PT, Gunnarsson J, Guo H, Boyd H, Zelcer N, Sixma TK. Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate-binding site. J Biol Chem 2020; 295:13570-13583. [PMID: 32727844 PMCID: PMC7521653 DOI: 10.1074/jbc.ra120.014349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/21/2020] [Indexed: 12/31/2022] Open
Abstract
Hepatic abundance of the low-density lipoprotein receptor (LDLR) is a critical determinant of circulating plasma LDL cholesterol levels and hence development of coronary artery disease. The sterol-responsive E3 ubiquitin ligase inducible degrader of the LDLR (IDOL) specifically promotes ubiquitination and subsequent lysosomal degradation of the LDLR and thus controls cellular LDL uptake. IDOL contains an extended N-terminal FERM (4.1 protein, ezrin, radixin, and moesin) domain, responsible for substrate recognition and plasma membrane association, and a second C-terminal RING domain, responsible for the E3 ligase activity and homodimerization. As IDOL is a putative lipid-lowering drug target, we investigated the molecular details of its substrate recognition. We produced and isolated full-length IDOL protein, which displayed high autoubiquitination activity. However, in vitro ubiquitination of its substrate, the intracellular tail of the LDLR, was low. To investigate the structural basis for this, we determined crystal structures of the extended FERM domain of IDOL and multiple conformations of its F3ab subdomain. These reveal the archetypal F1-F2-F3 trilobed FERM domain structure but show that the F3c subdomain orientation obscures the target-binding site. To substantiate this finding, we analyzed the full-length FERM domain and a series of truncated FERM constructs by small-angle X-ray scattering (SAXS). The scattering data support a compact and globular core FERM domain with a more flexible and extended C-terminal region. This flexibility may explain the low activity in vitro and suggests that IDOL may require activation for recognition of the LDLR.
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Affiliation(s)
- Luca Martinelli
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Patrik Johansson
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Paul T Wan
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Jenny Gunnarsson
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Hongwei Guo
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Helen Boyd
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Noam Zelcer
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Amsterdam, the Netherlands.
| | - Titia K Sixma
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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8
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Mardenborough YSN, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada-Vial A, Winterwerp HHK, Sixma TK, Kanaar R, Friedhoff P, Strick TR, Lebbink JHG. The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair. Nucleic Acids Res 2020; 47:11667-11680. [PMID: 31598722 PMCID: PMC6902014 DOI: 10.1093/nar/gkz834] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 11/16/2018] [Revised: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
DNA mismatch repair (MMR) maintains genome stability through repair of DNA replication errors. In Escherichia coli, initiation of MMR involves recognition of the mismatch by MutS, recruitment of MutL, activation of endonuclease MutH and DNA strand incision at a hemimethylated GATC site. Here, we studied the mechanism of communication that couples mismatch recognition to daughter strand incision. We investigated the effect of catalytically-deficient Cas9 as well as stalled RNA polymerase as roadblocks placed on DNA in between the mismatch and GATC site in ensemble and single molecule nanomanipulation incision assays. The MMR proteins were observed to incise GATC sites beyond a roadblock, albeit with reduced efficiency. This residual incision is completely abolished upon shortening the disordered linker regions of MutL. These results indicate that roadblock bypass can be fully attributed to the long, disordered linker regions in MutL and establish that communication during MMR initiation occurs along the DNA backbone.
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Affiliation(s)
| | - Katerina Nitsenko
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Charlie Laffeber
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Camille Duboc
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Enes Sahin
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Audrey Quessada-Vial
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | | | - Titia K Sixma
- Oncode Institute, the Netherlands.,Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Terence R Strick
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.,Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Superieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,Programme "Equipe Labellisée", Ligue Nationale contre le Cancer
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, the Netherlands
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9
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Bhairosing-Kok D, Groothuizen FS, Fish A, Dharadhar S, Winterwerp HHK, Sixma TK. Sharp kinking of a coiled-coil in MutS allows DNA binding and release. Nucleic Acids Res 2019; 47:8888-8898. [PMID: 31372631 PMCID: PMC6895276 DOI: 10.1093/nar/gkz649] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 11/17/2018] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023] Open
Abstract
DNA mismatch repair (MMR) corrects mismatches, small insertions and deletions in DNA during DNA replication. While scanning for mismatches, dimers of MutS embrace the DNA helix with their lever and clamp domains. Previous studies indicated generic flexibility of the lever and clamp domains of MutS prior to DNA binding, but whether this was important for MutS function was unknown. Here, we present a novel crystal structure of DNA-free Escherichia coli MutS. In this apo-structure, the clamp domains are repositioned due to kinking at specific sites in the coiled-coil region in the lever domains, suggesting a defined hinge point. We made mutations at the coiled-coil hinge point. The mutants made to disrupt the helical fold at the kink site diminish DNA binding, whereas those made to increase stability of coiled-coil result in stronger DNA binding. These data suggest that the site-specific kinking of the coiled-coil in the lever domain is important for loading of this ABC-ATPase on DNA.
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Affiliation(s)
- Doreth Bhairosing-Kok
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Flora S Groothuizen
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Shreya Dharadhar
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Herrie H K Winterwerp
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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10
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Abstract
Ubiquitin-specific proteases (USPs) are an important class of deubiquitinating enzymes (DUBs) that carry out critical roles in cellular physiology and are regulated at multiple levels. Quantitative characterization of USP activity is crucial for mechanistic understanding of USP function and regulation. This requires kinetic analysis using in vitro activity assays on minimal and natural substrates with purified proteins. In this chapter we give advice for efficient design of USP constructs and their optimal expression, followed by a series of purification strategies. We then present protocols for studying USP activity quantitatively on minimal and more natural substrates, and we discuss how to include possible regulatory elements such as internal USP domains or external interacting proteins. Lastly, we examine different binding assays for studying USP interactions and discuss how these can be included in full kinetic analyses.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Uckelmann
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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11
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Kim RQ, Geurink PP, Mulder MPC, Fish A, Ekkebus R, El Oualid F, van Dijk WJ, van Dalen D, Ovaa H, van Ingen H, Sixma TK. Kinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity. Nat Commun 2019; 10:231. [PMID: 30651545 PMCID: PMC6335408 DOI: 10.1038/s41467-018-08231-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
USP7 is a highly abundant deubiquitinating enzyme (DUB), involved in cellular processes including DNA damage response and apoptosis. USP7 has an unusual catalytic mechanism, where the low intrinsic activity of the catalytic domain (CD) increases when the C-terminal Ubl domains (Ubl45) fold onto the CD, allowing binding of the activating C-terminal tail near the catalytic site. Here we delineate how the target protein promotes the activation of USP7. Using NMR analysis and biochemistry we describe the order of activation steps, showing that ubiquitin binding is an instrumental step in USP7 activation. Using chemically synthesised p53-peptides we also demonstrate how the correct ubiquitinated substrate increases catalytic activity. We then used transient reaction kinetic modelling to define how the USP7 multistep mechanism is driven by target recognition. Our data show how this pleiotropic DUB can gain specificity for its cellular targets. Deubiquitinating enzymes (DUBs) are critical regulators of cellular processes by removing ubiquitin from specific targets. Here global kinetic modelling reveals the mechanism by which the low intrinsic activity of USP7 is substantially enhanced on a specific physiological target.
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Affiliation(s)
- Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Paul P Geurink
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Monique P C Mulder
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, the Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Duco van Dalen
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Tumor Immunology department, Radboud Institute for Molecular Sciences, Nijmegen, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands. .,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands. .,Bijvoet center, Utrecht University, Utrecht, the Netherlands.
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
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12
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Morrow ME, Morgan MT, Clerici M, Growkova K, Yan M, Komander D, Sixma TK, Simicek M, Wolberger C. Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. EMBO Rep 2018; 19:embr.201745680. [PMID: 30150323 PMCID: PMC6172466 DOI: 10.15252/embr.201745680] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022] Open
Abstract
A common strategy for exploring the biological roles of deubiquitinating enzymes (DUBs) in different pathways is to study the effects of replacing the wild‐type DUB with a catalytically inactive mutant in cells. We report here that a commonly studied DUB mutation, in which the catalytic cysteine is replaced with alanine, can dramatically increase the affinity of some DUBs for ubiquitin. Overexpression of these tight‐binding mutants thus has the potential to sequester cellular pools of monoubiquitin and ubiquitin chains. As a result, cells expressing these mutants may display unpredictable dominant negative physiological effects that are not related to loss of DUB activity. The structure of the SAGA DUB module bound to free ubiquitin reveals the structural basis for the 30‐fold higher affinity of Ubp8C146A for ubiquitin. We show that an alternative option, substituting the active site cysteine with arginine, can inactivate DUBs while also decreasing the affinity for ubiquitin.
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Affiliation(s)
- Marie E Morrow
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael T Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcello Clerici
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ming Yan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michal Simicek
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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13
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Haahr P, Borgermann N, Guo X, Typas D, Achuthankutty D, Hoffmann S, Shearer R, Sixma TK, Mailand N. ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability. Mol Cell 2018; 70:165-174.e6. [PMID: 29576528 DOI: 10.1016/j.molcel.2018.02.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 12/12/2022]
Abstract
Deubiquitylating enzymes (DUBs) enhance the dynamics of the versatile ubiquitin (Ub) code by reversing and regulating cellular ubiquitylation processes at multiple levels. Here we discovered that the uncharacterized human protein ZUFSP (zinc finger with UFM1-specific peptidase domain protein/C6orf113/ZUP1), which has been annotated as a potentially inactive UFM1 protease, and its fission yeast homolog Mug105 define a previously unrecognized class of evolutionarily conserved cysteine protease DUBs. Human ZUFSP selectively interacts with and cleaves long K63-linked poly-Ub chains by means of tandem Ub-binding domains, whereas it displays poor activity toward mono- or di-Ub substrates. In cells, ZUFSP is recruited to and regulates K63-Ub conjugates at genotoxic stress sites, promoting chromosome stability upon replication stress in a manner dependent on its catalytic activity. Our findings establish ZUFSP as a new type of linkage-selective cysteine peptidase DUB with a role in genome maintenance pathways.
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Affiliation(s)
- Peter Haahr
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nikoline Borgermann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Xiaohu Guo
- Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dimitris Typas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Divya Achuthankutty
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Saskia Hoffmann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Robert Shearer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Titia K Sixma
- Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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14
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Uckelmann M, Densham RM, Baas R, Winterwerp HHK, Fish A, Sixma TK, Morris JR. USP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A. Nat Commun 2018; 9:229. [PMID: 29335415 PMCID: PMC5768779 DOI: 10.1038/s41467-017-02653-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
BRCA1-BARD1-catalyzed ubiquitination of histone H2A is an important regulator of the DNA damage response, priming chromatin for repair by homologous recombination. However, no specific deubiquitinating enzymes (DUBs) are known to antagonize this function. Here we identify ubiquitin specific protease-48 (USP48) as a H2A DUB, specific for the C-terminal BRCA1 ubiquitination site. Detailed biochemical analysis shows that an auxiliary ubiquitin, an additional ubiquitin that itself does not get cleaved, modulates USP48 activity, which has possible implications for its regulation in vivo. In cells we reveal that USP48 antagonizes BRCA1 E3 ligase function and in BRCA1-proficient cells loss of USP48 results in positioning 53BP1 further from the break site and in extended resection lengths. USP48 repression confers a survival benefit to cells treated with camptothecin and its activity acts to restrain gene conversion and mutagenic single-strand annealing. We propose that USP48 promotes genome stability by antagonizing BRCA1 E3 ligase function.
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Affiliation(s)
- Michael Uckelmann
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ruth M Densham
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK
| | - Roy Baas
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Herrie H K Winterwerp
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Alexander Fish
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, B15 2TT, UK.
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15
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Kim RQ, Sixma TK. Regulation of USP7: A High Incidence of E3 Complexes. J Mol Biol 2017; 429:3395-3408. [DOI: 10.1016/j.jmb.2017.05.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
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16
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Friedhoff P, Manelyte L, Giron-Monzon L, Winkler I, Groothuizen FS, Sixma TK. Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair. Methods Enzymol 2017; 592:77-101. [PMID: 28668131 DOI: 10.1016/bs.mie.2017.03.025] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
DNA mismatch repair (MMR) is necessary to prevent incorporation of polymerase errors into the newly synthesized DNA strand, as they would be mutagenic. In humans, errors in MMR cause a predisposition to cancer, called Lynch syndrome. The MMR process is performed by a set of ATPases that transmit, validate, and couple information to identify which DNA strand requires repair. To understand the individual steps in the repair process, it is useful to be able to study these large molecular machines structurally and functionally. However, the steps and states are highly transient; therefore, the methods to capture and enrich them are essential. Here, we describe how single-cysteine variants can be used for specific cross-linking and labeling approaches that allow trapping of relevant transient states. Analysis of these defined states in functional and structural studies is instrumental to elucidate the molecular mechanism of this important DNA MMR process.
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Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany.
| | - Laura Manelyte
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Luis Giron-Monzon
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Ines Winkler
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | | | - Titia K Sixma
- Netherlands Cancer Institute, Amsterdam, The Netherlands.
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17
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Abstract
DNA double strand breaks need to be repaired in an organized fashion to preserve genomic integrity. In the organization of faithful repair, histone ubiquitination plays a crucial role. Recent findings suggest an integrated model for DNA repair regulation through site-specific histone ubiquitination and crosstalk to other posttranslational modifications. Here we discuss how site-specific histone ubiquitination is achieved on a molecular level and how different multi-protein complexes work together to integrate different histone ubiquitination states. We propose a model where site-specific H2A ubiquitination organizes the spatio-temporal recruitment of DNA repair factors which will ultimately contribute to DNA repair pathway choice between homologous recombination and non-homologous end joining.
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Affiliation(s)
- Michael Uckelmann
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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18
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Zhou F, Xie F, Jin K, Zhang Z, Clerici M, Gao R, van Dinther M, Sixma TK, Huang H, Zhang L, Ten Dijke P. USP4 inhibits SMAD4 monoubiquitination and promotes activin and BMP signaling. EMBO J 2017; 36:1623-1639. [PMID: 28468752 DOI: 10.15252/embj.201695372] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
SMAD4 is a common intracellular effector for TGF-β family cytokines, but the mechanism by which its activity is dynamically regulated is unclear. We demonstrated that ubiquitin-specific protease (USP) 4 strongly induces activin/BMP signaling by removing the inhibitory monoubiquitination from SMAD4. This modification was triggered by the recruitment of the E3 ligase, SMURF2, to SMAD4 following ligand-induced regulatory (R)-SMAD-SMAD4 complex formation. Whereas the interaction of the negative regulator c-SKI inhibits SMAD4 monoubiquitination, the ligand stimulates the recruitment of SMURF2 to the c-SKI-SMAD2 complex and triggers c-SKI ubiquitination and degradation. Thus, SMURF2 has a role in termination and initiation of TGF-β family signaling. An increase in monoubiquitinated SMAD4 in USP4-depleted mouse embryonic stem cells (mESCs) decreased both the BMP- and activin-induced changes in the embryonic stem cell fate. USP4 sustained SMAD4 activity during activin- and BMP-mediated morphogenic events in early zebrafish embryos. Moreover, zebrafish depleted of USP4 exhibited defective cell migration and slower coordinated cell movement known as epiboly, both of which could be rescued by SMAD4. Therefore, USP4 is a critical determinant of SMAD4 activity.
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Affiliation(s)
- Fangfang Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands.,Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Feng Xie
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Ke Jin
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Zhengkui Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Marcello Clerici
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rui Gao
- Faculty of Basic Medical Sciences, Chonqing Medical University, Chongqing, China
| | - Maarten van Dinther
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Titia K Sixma
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Huizhe Huang
- Faculty of Basic Medical Sciences, Chonqing Medical University, Chongqing, China
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China .,Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
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19
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Dharadhar S, Clerici M, van Dijk WJ, Fish A, Sixma TK. A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme. J Struct Biol 2016; 196:437-447. [PMID: 27650958 PMCID: PMC5131612 DOI: 10.1016/j.jsb.2016.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/14/2016] [Accepted: 09/16/2016] [Indexed: 12/21/2022]
Abstract
Regulation of deubiquitinating enzyme (DUB) activity is an essential step for proper function of cellular ubiquitin signals. UAF1 is a WD40 repeat protein, which binds and activates three important DUBs, USP1, USP12 and USP46. Here, we report the crystal structure of the USP12-Ub/UAF1 complex at a resolution of 2.8Å and of UAF1 at 2.3Å. In the complex we find two potential sites for UAF1 binding, analogous to what was seen in a USP46/UAF1 complex. In line with these observed dual binding states, we show here that USP12/UAF1 complex has 1:2 stoichiometry in solution, with a two-step binding at 4nM and 325nM respectively. Mutagenesis studies show that the fingers sub-domain of USP12 interacts with UAF1 to form the high affinity interface. Our activation studies confirm that the high affinity binding is important for activation while the second UAF1 binding does not affect activation. Nevertheless, we show that this two step binding is conserved in the well-studied USP12 paralog, USP1. Our results highlight the interfaces essential for regulation of USP12 activity and show a conserved second binding of UAF1 which could be important for regulatory functions independent of USP12 activity.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marcello Clerici
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Willem J van Dijk
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Alexander Fish
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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20
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Kim RQ, van Dijk WJ, Sixma TK. Structure of USP7 catalytic domain and three Ubl-domains reveals a connector α-helix with regulatory role. J Struct Biol 2016; 195:11-8. [PMID: 27183903 DOI: 10.1016/j.jsb.2016.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 02/17/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
Ubiquitin conjugation is an important signal in cellular pathways, changing the fate of a target protein, by degradation, relocalisation or complex formation. These signals are balanced by deubiquitinating enzymes (DUBs), which antagonize ubiquitination of specific protein substrates. Because ubiquitination pathways are critically important, DUB activity is often carefully controlled. USP7 is a highly abundant DUB with numerous targets that plays complex roles in diverse pathways, including DNA regulation, p53 stress response and endosomal protein recycling. Full-length USP7 switches between an inactive and an active state, tuned by the positioning of 5 Ubl folds in the C-terminal HUBL domain. The active state requires interaction between the last two Ubls (USP7(45)) and the catalytic domain (USP7(CD)), and this can be promoted by allosteric interaction from the first 3 Ubl domains of USP7 (USP7(123)) interacting with GMPS. Here we study the transition between USP7 states. We provide a crystal structure of USP7(CD123) and show that CD and Ubl123 are connected via an extended charged alpha helix. Mutational analysis is used to determine whether the charge and rigidity of this 'connector helix' are important for full USP7 activity.
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Affiliation(s)
- Robbert Q Kim
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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21
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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22
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Groothuizen FS, Sixma TK. The conserved molecular machinery in DNA mismatch repair enzyme structures. DNA Repair (Amst) 2015; 38:14-23. [PMID: 26796427 DOI: 10.1016/j.dnarep.2015.11.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 07/14/2015] [Revised: 10/05/2015] [Accepted: 11/30/2015] [Indexed: 12/25/2022]
Abstract
The machinery of DNA mismatch repair enzymes is highly conserved in evolution. The process is initiated by recognition of a DNA mismatch, and validated by ATP and the presence of a processivity clamp or a methylation mark. Several events in MMR promote conformational changes that lead to progression of the repair process. Here we discuss functional conformational changes in the MMR proteins and we compare the enzymes to paralogs in other systems.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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23
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Mattiroli F, Uckelmann M, Sahtoe DD, van Dijk WJ, Sixma TK. The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A. Nat Commun 2015; 5:3291. [PMID: 24518117 PMCID: PMC3929782 DOI: 10.1038/ncomms4291] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 01/22/2014] [Indexed: 11/10/2022] Open
Abstract
During DNA damage response, the RING E3 ligase RNF168 ubiquitinates nucleosomal H2A at K13–15. Here we show that the ubiquitination reaction is regulated by its substrate. We define a region on the RING domain important for target recognition and identify the H2A/H2B dimer as the minimal substrate to confer lysine specificity to the RNF168 reaction. Importantly, we find an active role for the substrate in the reaction. H2A/H2B dimers and nucleosomes enhance the E3-mediated discharge of ubiquitin from the E2 and redirect the reaction towards the relevant target, in a process that depends on an intact acidic patch. This active contribution of a region distal from the target lysine provides regulation of the specific K13–15 ubiquitination reaction during the complex signalling process at DNA damage sites. The E3 ubiquitin ligase RNF168 ubiquitinates specific lysines on histone H2A as part of the DNA damage response. Here, the authors show that the acidic patch on the histone H2A/H2B dimer catalyses RNF168-dependent ubiquitination of histone 2A by redirecting ubiquitination activity towards the relevant target lysines.
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Affiliation(s)
- Francesca Mattiroli
- 1] Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands [2] [3]
| | - Michael Uckelmann
- 1] Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands [2]
| | - Danny D Sahtoe
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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24
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Schelpe J, Monté D, Dewitte F, Sixma TK, Rucktooa P. Structure of UBE2Z Enzyme Provides Functional Insight into Specificity in the FAT10 Protein Conjugation Machinery. J Biol Chem 2015; 291:630-9. [PMID: 26555268 PMCID: PMC4705383 DOI: 10.1074/jbc.m115.671545] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 12/05/2022] Open
Abstract
FAT10 conjugation, a post-translational modification analogous to ubiquitination, specifically requires UBA6 and UBE2Z as its activating (E1) and conjugating (E2) enzymes. Interestingly, these enzymes can also function in ubiquitination. We have determined the crystal structure of UBE2Z and report how the different domains of this E2 enzyme are organized. We further combine our structural data with mutational analyses to understand how specificity is achieved in the FAT10 conjugation pathway. We show that specificity toward UBA6 and UBE2Z lies within the C-terminal CYCI tetrapeptide in FAT10. We also demonstrate that this motif slows down transfer rates for FAT10 from UBA6 onto UBE2Z.
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Affiliation(s)
- Julien Schelpe
- From the UMR8576 CNRS-Université de Lille, 50 Avenue de Halley, 59658 Villeneuve d'Ascq, France and
| | - Didier Monté
- From the UMR8576 CNRS-Université de Lille, 50 Avenue de Halley, 59658 Villeneuve d'Ascq, France and
| | - Frédérique Dewitte
- From the UMR8576 CNRS-Université de Lille, 50 Avenue de Halley, 59658 Villeneuve d'Ascq, France and
| | - Titia K Sixma
- Division of Biochemistry and Centre for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Prakash Rucktooa
- From the UMR8576 CNRS-Université de Lille, 50 Avenue de Halley, 59658 Villeneuve d'Ascq, France and Division of Biochemistry and Centre for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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25
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Thorslund T, Ripplinger A, Hoffmann S, Wild T, Uckelmann M, Villumsen B, Narita T, Sixma TK, Choudhary C, Bekker-Jensen S, Mailand N. Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage. Nature 2015; 527:389-93. [DOI: 10.1038/nature15401] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 08/20/2015] [Indexed: 12/22/2022]
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26
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Sixma TK. Trapping a transient state in DNA mismatch repair: the MutS/MutL sliding clamp loads MutL on DNA. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315099830] [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: 11/10/2022] Open
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Groothuizen FS, Winkler I, Cristóvão M, Fish A, Winterwerp HHK, Reumer A, Marx AD, Hermans N, Nicholls RA, Murshudov GN, Lebbink JHG, Friedhoff P, Sixma TK. MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA. eLife 2015; 4:e06744. [PMID: 26163658 PMCID: PMC4521584 DOI: 10.7554/elife.06744] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022] Open
Abstract
To avoid mutations in the genome, DNA replication is generally followed by DNA mismatch repair (MMR). MMR starts when a MutS homolog recognizes a mismatch and undergoes an ATP-dependent transformation to an elusive sliding clamp state. How this transient state promotes MutL homolog recruitment and activation of repair is unclear. Here we present a crystal structure of the MutS/MutL complex using a site-specifically crosslinked complex and examine how large conformational changes lead to activation of MutL. The structure captures MutS in the sliding clamp conformation, where tilting of the MutS subunits across each other pushes DNA into a new channel, and reorientation of the connector domain creates an interface for MutL with both MutS subunits. Our work explains how the sliding clamp promotes loading of MutL onto DNA, to activate downstream effectors. We thus elucidate a crucial mechanism that ensures that MMR is initiated only after detection of a DNA mismatch. DOI:http://dx.doi.org/10.7554/eLife.06744.001 The genetic code of DNA is written using four letters: “A”, “C”, “T”, and “G”. Molecules of DNA form a double helix in which the letters in the two opposing strands pair up in a specific manner—“A” pairs with “T”, and “C” pairs with “G”. A cell must replicate its DNA before it divides, and sometimes the wrong DNA letter can get added into the new DNA strand. If left uncorrected, these mistakes accumulate over time and can eventually harm the cell. As a result, cells have evolved several ways to identify these mistakes and correct them, including one known as “mismatch repair”. Mismatch repair occurs via several stages. The process starts when a protein called MutS comes across a site in the DNA where the letters are mismatched (for example, where an “A” is paired with a “C”, instead of a “T”). MutS can recognize such a mismatch, bind it, and then bind to another molecule called ATP. MutS then changes shape and encircles the DNA like a clamp that can slide along the DNA. Only when it forms this “sliding clamp” state can MutS recruit another protein called MutL. This activity in turn triggers a series of further events that ultimately correct the mismatch. However, it remains poorly understood how MutS forms a clamp around DNA and how and why this state recruits MutL in order to start the repair. To visualize this short-lived intermediate, Groothuizen et al. trapped the relevant complex in the presence of DNA containing a mismatch and then used a technique called X-ray crystallography to determine the three-dimensional structure of MutS bound to MutL. The structure reveals that two copies of MutS tilt across each other and open up a channel, which is large enough to accommodate the DNA. In this manner, MutS is able to form a loose ring around the DNA. The changes in the structure and the movement of the DNA to the new channel were confirmed using another technique, commonly referred to as FRET. Groothuizen et al. observed that the movements in the MutS protein also serve to make the interfaces available that can recognize MutL. If these interfaces were disturbed, MutS and MutL were unable to associate with each other, which resulted in a failure to trigger mismatch repair. Further analysis revealed that that MutL binds to DNA only after MutS has recognised the mismatch and formed a clamp around it. This is the first time that the MutS clamp and the MutS/MutL complex have been visualized, and further work is now needed to understand how MutL triggers other events that ultimately repair the mismatched DNA. DOI:http://dx.doi.org/10.7554/eLife.06744.002
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ines Winkler
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Michele Cristóvão
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Alexander Fish
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Herrie H K Winterwerp
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Annet Reumer
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Andreas D Marx
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Nicolaas Hermans
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center, Rotterdam, Netherlands
| | - Robert A Nicholls
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Garib N Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Joyce H G Lebbink
- Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
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Abstract
Proteolytic enzymes, such as (iso-)peptidases, are potentially hazardous for cells. To neutralize their potential danger, tight control of their activities has evolved. Deubiquitylating enzymes (DUBs) are isopeptidases involved in eukaryotic ubiquitylation. They reverse ubiquitin signals by hydrolyzing ubiquitin adducts, giving them control over all aspects of ubiquitin biology. The importance of DUB function is underscored by their frequent deregulation in human disease, making these enzymes potential drug targets. Here, we review the different layers of DUB enzyme regulation. We discuss how post-translational modification (PTM), regulatory domains within DUBs, and incorporation of DUBs into macromolecular complexes contribute to their activity. We conclude that most DUBs are likely to use a combination of these basic regulatory mechanisms.
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Affiliation(s)
- Danny D Sahtoe
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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Abstract
Two studies in this issue, Kristariyanto et al. (2015) and Michel et al. (2015), describe innovative ways to produce large quantities of atypical K29 and K33 ubiquitin chains and report structures and mechanisms of chain-specific recognition.
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Affiliation(s)
- Michael Uckelmann
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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Sahtoe DD, van Dijk WJ, El Oualid F, Ekkebus R, Ovaa H, Sixma TK. Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G. Mol Cell 2015; 57:887-900. [PMID: 25702870 PMCID: PMC4352763 DOI: 10.1016/j.molcel.2014.12.039] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/16/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022]
Abstract
Deubiquitinating enzymes (DUBs) control vital processes in eukaryotes by hydrolyzing ubiquitin adducts. Their activities are tightly regulated, but the mechanisms remain elusive. In particular, the DUB UCH-L5 can be either activated or inhibited by conserved regulatory proteins RPN13 and INO80G, respectively. Here we show how the DEUBAD domain in RPN13 activates UCH-L5 by positioning its C-terminal ULD domain and crossover loop to promote substrate binding and catalysis. The related DEUBAD domain in INO80G inhibits UCH-L5 by exploiting similar structural elements in UCH-L5 to promote a radically different conformation, and employs molecular mimicry to block ubiquitin docking. In this process, large conformational changes create small but highly specific interfaces that mediate activity modulation of UCH-L5 by altering the affinity for substrates. Our results establish how related domains can exploit enzyme conformational plasticity to allosterically regulate DUB activity. These allosteric sites may present novel insights for pharmaceutical intervention in DUB activity. The RPN13 DEUBAD domain activates UCH-L5 by positioning its CL and ULD domain The INO80G DEUBAD domain inhibits UCH-L5 by blocking ubiquitin binding The FRF hairpin in the DEUBAD domain of INO80G drives UCH-L5 inhibition DEUBAD domains regulate UCH-L5 activity by tuning UCH-L5 substrate affinity
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Affiliation(s)
- Danny D Sahtoe
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Farid El Oualid
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; UbiQ, Science Park 408, 1098XH Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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31
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Mattiroli F, Sixma TK. Lysine-targeting specificity in ubiquitin and ubiquitin-like modification pathways. Nat Struct Mol Biol 2014; 21:308-16. [PMID: 24699079 DOI: 10.1038/nsmb.2792] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/13/2014] [Indexed: 12/19/2022]
Abstract
Ubiquitin and ubiquitin-like modifications are central to virtually all cellular signaling pathways. They occur primarily on lysine residues of target proteins and stimulate a large number of downstream signals. The diversity of these signals depends on the type, location and dynamics of the modification, but the role of the exact site of modification and the selectivity for specific lysines are poorly understood. Here we review the current literature on lysine specificity in these modifications, and we highlight the known signaling mechanisms and the open questions that pose future challenges to ubiquitin research.
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Affiliation(s)
- Francesca Mattiroli
- 1] Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands. [2]
| | - Titia K Sixma
- Division of Biochemistry, Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
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32
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Abstract
The RING-in-between-RING (RBR) E3s are a curious family of ubiquitin E3-ligases, whose mechanism of action is unusual in several ways. Their activities are auto-inhibited, causing a requirement for activation by protein-protein interactions or posttranslational modifications. They catalyse ubiquitin conjugation by a concerted RING/HECT-like mechanism in which the RING1 domain facilitates E2-discharge to directly form a thioester intermediate with a cysteine in RING2. This short-lived, HECT-like intermediate then modifies the target. Uniquely, the RBR ligase HOIP makes use of this mechanism to target the ubiquitin amino-terminus, by presenting the target ubiquitin for modification using its distinctive LDD region.
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Affiliation(s)
- Judith J Smit
- Division of Biochemistry and Cancer Genomics Centre, The Netherlands Cancer InstituteAmsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Centre, The Netherlands Cancer InstituteAmsterdam, The Netherlands
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33
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Monnet J, Quessada-Vial A, Hermans N, Graves E, Winterwerp HH, Friedhoff P, Sixma TK, Lebbink JH, Strick TR. Nicking Single DNA Molecules to Study Initiation of Mismatch Repair. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Stornaiuolo M, De Kloe GE, Rucktooa P, Fish A, van Elk R, Edink ES, Bertrand D, Smit AB, de Esch IJP, Sixma TK. Assembly of a π-π stack of ligands in the binding site of an acetylcholine-binding protein. Nat Commun 2013; 4:1875. [PMID: 23695669 PMCID: PMC3674282 DOI: 10.1038/ncomms2900] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [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: 09/27/2012] [Accepted: 04/17/2013] [Indexed: 12/11/2022] Open
Abstract
Acetylcholine-binding protein is a water-soluble homologue of the extracellular ligand-binding domain of cys-loop receptors. It is used as a structurally accessible prototype for studying ligand binding to these pharmaceutically important pentameric ion channels, in particular to nicotinic acetylcholine receptors, due to conserved binding site residues present at the interface between two subunits. Here we report that an aromatic conjugated small molecule binds acetylcholine-binding protein in an ordered π-π stack of three identical molecules per binding site, two parallel and one antiparallel. Acetylcholine-binding protein stabilizes the assembly of the stack by aromatic contacts. Thanks to the plasticity of its ligand-binding site, acetylcholine-binding protein can accommodate the formation of aromatic stacks of different size by simple loop repositioning and minimal adjustment of the interactions. This type of supramolecular binding provides a novel paradigm in drug design.
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Affiliation(s)
- Mariano Stornaiuolo
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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35
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Smit JJ, van Dijk WJ, El Atmioui D, Merkx R, Ovaa H, Sixma TK. Target specificity of the E3 ligase LUBAC for ubiquitin and NEMO relies on different minimal requirements. J Biol Chem 2013; 288:31728-37. [PMID: 24030825 PMCID: PMC3814767 DOI: 10.1074/jbc.m113.495846] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The ubiquitination of NEMO with linear ubiquitin chains by the E3-ligase LUBAC is important for the activation of the canonical NF-κB pathway. NEMO ubiquitination requires a dual target specificity of LUBAC, priming on a lysine on NEMO and chain elongation on the N terminus of the priming ubiquitin. Here we explore the minimal requirements for these specificities. Effective linear chain formation requires a precise positioning of the ubiquitin N-terminal amine in a negatively charged environment on the top of ubiquitin. Whereas the RBR-LDD region on HOIP is sufficient for targeting the ubiquitin N terminus, the priming lysine modification on NEMO requires catalysis by the RBR domain of HOIL-1L as well as the catalytic machinery of the RBR-LDD domains of HOIP. Consequently, target specificity toward NEMO is determined by multiple LUBAC components, whereas linear ubiquitin chain elongation is realized by a specific interplay between HOIP and ubiquitin.
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36
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Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HHK, Marinus MG, Lebbink JHG, Svergun DI, Friedhoff P, Sixma TK. Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 2013; 41:8166-81. [PMID: 23821665 PMCID: PMC3783165 DOI: 10.1093/nar/gkt582] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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: 01/23/2023] Open
Abstract
The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CancerGenomiCs.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands, European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Biochemistry, Justus Liebig University, Heinrich-Buff Ring 58, D-35392, Giessen, Germany, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA, Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands and Department of Radiation Oncology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands
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37
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38
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Mattiroli F, Vissers JHA, van Dijk WJ, Ikpa P, Citterio E, Vermeulen W, Marteijn JA, Sixma TK. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell 2012; 150:1182-95. [PMID: 22980979 DOI: 10.1016/j.cell.2012.08.005] [Citation(s) in RCA: 458] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/29/2012] [Accepted: 07/09/2012] [Indexed: 01/01/2023]
Abstract
Ubiquitin-dependent signaling during the DNA damage response (DDR) to double-strand breaks (DSBs) is initiated by two E3 ligases, RNF8 and RNF168, targeting histone H2A and H2AX. RNF8 is the first ligase recruited to the damage site, and RNF168 follows RNF8-dependent ubiquitination. This suggests that RNF8 initiates H2A/H2AX ubiquitination with K63-linked ubiquitin chains and RNF168 extends them. Here, we show that RNF8 is inactive toward nucleosomal H2A, whereas RNF168 catalyzes the monoubiquitination of the histones specifically on K13-15. Structure-based mutagenesis of RNF8 and RNF168 RING domains shows that a charged residue determines whether nucleosomal proteins are recognized. We find that K63 ubiquitin chains are conjugated to RNF168-dependent H2A/H2AX monoubiquitination at K13-15 and not on K118-119. Using a mutant of RNF168 unable to target histones but still catalyzing ubiquitin chains at DSBs, we show that ubiquitin chains per se are insufficient for signaling, but RNF168 target ubiquitination is required for DDR.
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Affiliation(s)
- Francesca Mattiroli
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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39
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Hibbert RG, Sixma TK. Intrinsic flexibility of ubiquitin on proliferating cell nuclear antigen (PCNA) in translesion synthesis. J Biol Chem 2012; 287:39216-23. [PMID: 22989887 PMCID: PMC3493961 DOI: 10.1074/jbc.m112.389890] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/29/2012] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin conjugation provides a crucial signaling role in hundreds of cellular pathways; however, a structural understanding of ubiquitinated substrates is lacking. One important substrate is monoubiquitinated PCNA (PCNA-Ub), which signals for recruitment of damage-tolerant polymerases in the translesion synthesis (TLS) pathway of DNA damage avoidance. We use a novel and efficient enzymatic method to produce PCNA-Ub at high yield with a native isopeptide bond and study its Usp1/UAF1-dependent deconjugation. In solution we find that the ubiquitin moiety is flexible relative to the PCNA, with its hydrophobic patch mostly accessible for recruitment of TLS polymerases, which promotes the interaction with polymerase η. The studies are a prototype for the nature of the ubiquitin modification.
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Affiliation(s)
- Richard G. Hibbert
- From the Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K. Sixma
- From the Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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40
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Smit JJ, Monteferrario D, Noordermeer SM, van Dijk WJ, van der Reijden BA, Sixma TK. The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension. EMBO J 2012; 31:3833-44. [PMID: 22863777 PMCID: PMC3463842 DOI: 10.1038/emboj.2012.217] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [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: 02/29/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Like Parkin, the linear ubiquitin chain assembly complex LUBAC functions as a RING/HECT-hybrid ubiquitin ligase, but includes a unique extension that dictates linear ubiquitin linkage specificity. Activation of the NF-κB pathway requires the formation of Met1-linked ‘linear' ubiquitin chains on NEMO, which is catalysed by the Linear Ubiquitin Chain Assembly Complex (LUBAC) E3 consisting of HOIP, HOIL-1L and Sharpin. Here, we show that both LUBAC catalytic activity and LUBAC specificity for linear ubiquitin chain formation are embedded within the RING-IBR-RING (RBR) ubiquitin ligase subunit HOIP. Linear ubiquitin chain formation by HOIP proceeds via a two-step mechanism involving both RING and HECT E3-type activities. RING1-IBR catalyses the transfer of ubiquitin from the E2 onto RING2, to transiently form a HECT-like covalent thioester intermediate. Next, the ubiquitin is transferred from HOIP onto the N-terminus of a target ubiquitin. This transfer is facilitated by a unique region in the C-terminus of HOIP that we termed ‘Linear ubiquitin chain Determining Domain' (LDD), which may coordinate the acceptor ubiquitin. Consistent with this mechanism, the RING2-LDD region was found to be important for NF-κB activation in cellular assays. These data show how HOIP combines a general RBR ubiquitin ligase mechanism with unique, LDD-dependent specificity for producing linear ubiquitin chains.
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Affiliation(s)
- Judith J Smit
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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41
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Rucktooa P, Haseler CA, van Elk R, Smit AB, Gallagher T, Sixma TK. Structural characterization of binding mode of smoking cessation drugs to nicotinic acetylcholine receptors through study of ligand complexes with acetylcholine-binding protein. J Biol Chem 2012; 287:23283-93. [PMID: 22553201 PMCID: PMC3390607 DOI: 10.1074/jbc.m112.360347] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [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: 11/06/2022] Open
Abstract
Smoking cessation is an important aim in public health worldwide as tobacco smoking causes many preventable deaths. Addiction to tobacco smoking results from the binding of nicotine to nicotinic acetylcholine receptors (nAChRs) in the brain, in particular the α4β2 receptor. One way to aid smoking cessation is by the use of nicotine replacement therapies or partial nAChR agonists like cytisine or varenicline. Here we present the co-crystal structures of cytisine and varenicline in complex with Aplysia californica acetylcholine-binding protein and use these as models to investigate binding of these ligands binding to nAChRs. This analysis of the binding properties of these two partial agonists provides insight into differences with nicotine binding to nAChRs. A mutational analysis reveals that the residues conveying subtype selectivity in nAChRs reside on the binding site complementary face and include features extending beyond the first shell of contacting residues.
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Affiliation(s)
- Prakash Rucktooa
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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42
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Nacerddine K, Beaudry JB, Ginjala V, Westerman B, Mattiroli F, Song JY, van der Poel H, Ponz OB, Pritchard C, Cornelissen-Steijger P, Zevenhoven J, Tanger E, Sixma TK, Ganesan S, van Lohuizen M. Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest 2012; 122:1920-32. [PMID: 22505453 DOI: 10.1172/jci57477] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 02/29/2012] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer (PCa) is a major lethal malignancy in men, but the molecular events and their interplay underlying prostate carcinogenesis remain poorly understood. Epigenetic events and the upregulation of polycomb group silencing proteins including Bmi1 have been described to occur during PCa progression. Here, we found that conditional overexpression of Bmi1 in mice induced prostatic intraepithelial neoplasia, and elicited invasive adenocarcinoma when combined with PTEN haploinsufficiency. In addition, Bmi1 and the PI3K/Akt pathway were coactivated in a substantial fraction of human high-grade tumors. We found that Akt mediated Bmi1 phosphorylation, enhancing its oncogenic potential in an Ink4a/Arf-independent manner. This process also modulated the DNA damage response and affected genomic stability. Together, our findings demonstrate the etiological role of Bmi1 in PCa, unravel an oncogenic collaboration between Bmi1 and the PI3K/Akt pathway, and provide mechanistic insights into the modulation of Bmi1 function by phosphorylation during prostate carcinogenesis.
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Affiliation(s)
- Karim Nacerddine
- Division of Molecular Genetics and Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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43
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Mallette FA, Mattiroli F, Cui G, Young LC, Hendzel MJ, Mer G, Sixma TK, Richard S. RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites. EMBO J 2012; 31:1865-78. [PMID: 22373579 DOI: 10.1038/emboj.2012.47] [Citation(s) in RCA: 268] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/07/2012] [Indexed: 11/09/2022] Open
Abstract
In response to DNA damage, cells initiate complex signalling cascades leading to growth arrest and DNA repair. The recruitment of 53BP1 to damaged sites requires the activation of the ubiquitination cascade controlled by the E3 ubiquitin ligases RNF8 and RNF168, and methylation of histone H4 on lysine 20. However, molecular events that regulate the accessibility of methylated histones, to allow the recruitment of 53BP1 to DNA breaks, are unclear. Here, we show that like 53BP1, the JMJD2A (also known as KDM4A) tandem tudor domain binds dimethylated histone H4K20; however, JMJD2A is degraded by the proteasome following the DNA damage in an RNF8-dependent manner. We demonstrate that JMJD2A is ubiquitinated by RNF8 and RNF168. Moreover, ectopic expression of JMJD2A abrogates 53BP1 recruitment to DNA damage sites, indicating a role in antagonizing 53BP1 for methylated histone marks. The combined knockdown of JMJD2A and JMJD2B significantly rescued the ability of RNF8- and RNF168-deficient cells to form 53BP1 foci. We propose that the RNF8-dependent degradation of JMJD2A regulates DNA repair by controlling the recruitment of 53BP1 at DNA damage sites.
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Affiliation(s)
- Frédérick A Mallette
- Terry Fox Molecular Oncology Group and the Bloomfield Center for Research on Aging, Sir Mortimer B. Davis Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, Québec, Canada
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44
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Osipov AV, Rucktooa P, Kasheverov IE, Filkin SY, Starkov VG, Andreeva TV, Sixma TK, Bertrand D, Utkin YN, Tsetlin VI. Dimeric α-cobratoxin X-ray structure: localization of intermolecular disulfides and possible mode of binding to nicotinic acetylcholine receptors. J Biol Chem 2012; 287:6725-34. [PMID: 22223648 DOI: 10.1074/jbc.m111.322313] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In Naja kaouthia cobra venom, we have earlier discovered a covalent dimeric form of α-cobratoxin (αCT-αCT) with two intermolecular disulfides, but we could not determine their positions. Here, we report the αCT-αCT crystal structure at 1.94 Å where intermolecular disulfides are identified between Cys(3) in one protomer and Cys(20) of the second, and vice versa. All remaining intramolecular disulfides, including the additional bridge between Cys(26) and Cys(30) in the central loops II, have the same positions as in monomeric α-cobratoxin. The three-finger fold is essentially preserved in each protomer, but the arrangement of the αCT-αCT dimer differs from those of noncovalent crystallographic dimers of three-finger toxins (TFT) or from the κ-bungarotoxin solution structure. Selective reduction of Cys(26)-Cys(30) in one protomer does not affect the activity against the α7 nicotinic acetylcholine receptor (nAChR), whereas its reduction in both protomers almost prevents α7 nAChR recognition. On the contrary, reduction of one or both Cys(26)-Cys(30) disulfides in αCT-αCT considerably potentiates inhibition of the α3β2 nAChR by the toxin. The heteromeric dimer of α-cobratoxin and cytotoxin has an activity similar to that of αCT-αCT against the α7 nAChR and is more active against α3β2 nAChRs. Our results demonstrate that at least one Cys(26)-Cys(30) disulfide in covalent TFT dimers, similar to the monomeric TFTs, is essential for their recognition by α7 nAChR, although it is less important for interaction of covalent TFT dimers with the α3β2 nAChR.
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Affiliation(s)
- Alexey V Osipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, Moscow 117997, Russia
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45
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Faesen AC, Dirac AMG, Shanmugham A, Ovaa H, Perrakis A, Sixma TK. Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase. Mol Cell 2011; 44:147-59. [PMID: 21981925 DOI: 10.1016/j.molcel.2011.06.034] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 06/06/2011] [Accepted: 06/29/2011] [Indexed: 02/03/2023]
Abstract
The ubiquitin-specific protease USP7/HAUSP regulates p53 and MDM2 levels, and cellular localization of FOXO4 and PTEN, and hence is critically important for their role in cellular processes. Here we show how the 64 kDa C-terminal region of USP7 can positively regulate deubiquitinating activity. We present the crystal structure of this USP7/HAUSP ubiquitin-like domain (HUBL) comprised of five ubiquitin-like (Ubl) domains organized in 2-1-2 Ubl units. The last di-Ubl unit, HUBL-45, is sufficient to activate USP7, through binding to a "switching" loop in the catalytic domain, which promotes ubiquitin binding and increases activity 100-fold. This activation can be enhanced allosterically by the metabolic enzyme GMPS. It binds to the first three Ubl domains (HUBL-123) and hyperactivates USP7 by stabilization of the HUBL-45-dependent active state.
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Affiliation(s)
- Alex C Faesen
- Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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46
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Akdemir A, Rucktooa P, Jongejan A, Elk RV, Bertrand S, Sixma TK, Bertrand D, Smit AB, Leurs R, de Graaf C, de Esch IJ. Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors. Bioorg Med Chem 2011; 19:6107-19. [DOI: 10.1016/j.bmc.2011.08.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 12/22/2022]
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Monti MC, Cohen SX, Fish A, Winterwerp HHK, Barendregt A, Friedhoff P, Perrakis A, Heck AJR, Sixma TK, van den Heuvel RHH, Lebbink JHG. Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS. Nucleic Acids Res 2011; 39:8052-64. [PMID: 21737427 PMCID: PMC3185415 DOI: 10.1093/nar/gkr498] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates.
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Affiliation(s)
- Maria Chiara Monti
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Serge X. Cohen
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexander Fish
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herrie H. K. Winterwerp
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Friedhoff
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anastassis Perrakis
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
- *To whom correspondence should be addressed. Tel: +31 10 7043604; Fax +31 10 7044747;
| | - Titia K. Sixma
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert H. H. van den Heuvel
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joyce H. G. Lebbink
- Biomolecular Mass Spectrometry and Proteomics Group, and Center for Biomedical Genetics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Institut für Biochemie FB 08, Justus-Liebig-Universität, D-35392 Giessen, Germany and Department of Cell Biology and Genetics, Cancer Genomics Center and Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
- *To whom correspondence should be addressed. Tel: +31 10 7043604; Fax +31 10 7044747;
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Winkler I, Marx AD, Lariviere D, Manelyte L, Giron-Monzon L, Heinze RJ, Cristovao M, Reumer A, Curth U, Sixma TK, Friedhoff P. Chemical trapping of the dynamic MutS-MutL complex formed in DNA mismatch repair in Escherichia coli. J Biol Chem 2011. [DOI: 10.1074/jbc.a110.187641] [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: 11/06/2022] Open
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Huang A, Hibbert RG, de Jong RN, Das D, Sixma TK, Boelens R. Symmetry and asymmetry of the RING-RING dimer of Rad18. J Mol Biol 2011; 410:424-35. [PMID: 21549715 DOI: 10.1016/j.jmb.2011.04.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 04/14/2011] [Accepted: 04/20/2011] [Indexed: 01/08/2023]
Abstract
The human ubiquitin-conjugating enzyme Rad6 (E2), with ubiquitin ligase enzyme Rad18 (RING E3), monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Here, we determine the structure of the homodimeric Rad18 RING domains by X-ray crystallography and classify it to RING-RING dimers that dimerize through helices adjacent to the RING domains and through the canonical RING domains. Using NMR spectroscopy and site-directed mutagenesis, we demonstrate that the Rad6b binding site, for the Rad18 RING domain, strongly resembles that of other E2/E3 RING/U-box complexes. We show that the homodimeric Rad18 RING domain can recruit two Rad6b E2 enzymes, whereas the full-length Rad18 homodimer binds only to a single Rad6b molecule. Such asymmetry is a common feature of RING-RING heterodimers and has been observed for the CHIP U-box homodimer. We propose that asymmetry may be a common feature of dimeric RING E3 ligases.
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Affiliation(s)
- Anding Huang
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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50
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Winkler I, Marx AD, Lariviere D, Heinze RJ, Cristovao M, Reumer A, Curth U, Sixma TK, Friedhoff P. Chemical trapping of the dynamic MutS-MutL complex formed in DNA mismatch repair in Escherichia coli. J Biol Chem 2011; 286:17326-37. [PMID: 21454657 DOI: 10.1074/jbc.m110.187641] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ternary complex comprising MutS, MutL, and DNA is a key intermediate in DNA mismatch repair. We used chemical cross-linking and fluorescence resonance energy transfer (FRET) to study the interaction between MutS and MutL and to shed light onto the structure of this complex. Via chemical cross-linking, we could stabilize this dynamic complex and identify the structural features of key events in DNA mismatch repair. We could show that in the complex between MutS and MutL the mismatch-binding and connector domains of MutS are in proximity to the N-terminal ATPase domain of MutL. The DNA- and nucleotide-dependent complex formation could be monitored by FRET using single cysteine variants labeled in the connector domain of MutS and the transducer domain of MutL, respectively. In addition, we could trap MutS after an ATP-induced conformational change by an intramolecular cross-link between Cys-93 of the mismatch-binding domain and Cys-239 of the connector domain.
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Affiliation(s)
- Ines Winkler
- Institute for Biochemistry, FB 08, Justus Liebig University, D-35392 Giessen, Germany
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