1
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Fruhauf S, Pühringer D, Thamhesl M, Fajtl P, Kunz-Vekiru E, Höbartner-Gussl A, Schatzmayr G, Adam G, Damborsky J, Djinovic-Carugo K, Prokop Z, Moll WD. Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS Catal 2024; 14:3392-3410. [PMID: 38449531 PMCID: PMC10913051 DOI: 10.1021/acscatal.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Zearalenone (ZEN) is a mycoestrogenic polyketide produced by Fusarium graminearum and other phytopathogenic members of the genus Fusarium. Contamination of cereals with ZEN is frequent, and hydrolytic detoxification with fungal lactonases has been explored. Here, we report the isolation of a bacterial strain, Rhodococcus erythropolis PFA D8-1, with ZEN hydrolyzing activity, cloning of the gene encoding α/β hydrolase ZenA encoded on the linear megaplasmid pSFRL1, and biochemical characterization of nine homologues. Furthermore, we report site-directed mutagenesis as well as structural analysis of the dimeric ZenARe of R. erythropolis and the more thermostable, tetrameric ZenAScfl of Streptomyces coelicoflavus with and without bound ligands. The X-ray crystal structures not only revealed canonical features of α/β hydrolases with a cap domain including a Ser-His-Asp catalytic triad but also unusual features including an uncommon oxyanion hole motif and a peripheral, short antiparallel β-sheet involved in tetramer interactions. Presteady-state kinetic analyses for ZenARe and ZenAScfl identified balanced rate-limiting steps of the reaction cycle, which can change depending on temperature. Some new bacterial ZEN lactonases have lower KM and higher kcat than the known fungal ZEN lactonases and may lend themselves to enzyme technology development for the degradation of ZEN in feed or food.
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Affiliation(s)
- Sebastian Fruhauf
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
| | - Michaela Thamhesl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Patricia Fajtl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Elisavet Kunz-Vekiru
- Institute
of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology
IFA-Tulln, University of Natural Resources
and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, Tulln 3430, Austria
| | - Andreas Höbartner-Gussl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Gerd Schatzmayr
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Gerhard Adam
- Institute
of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences
Vienna (BOKU), Konrad-Lorenz-Straße
24, Tulln 3430, Austria
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Bld. A13, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Kristina Djinovic-Carugo
- Department
for Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
- European
Molecular Biology Laboratory (EMBL) Grenoble, Grenoble 38000, France
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Bld. A13, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Wulf-Dieter Moll
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
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2
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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3
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Johnson KA. You get what you screen for: Standards for experimental design and data fitting in drug discovery. Methods Enzymol 2023; 690:131-157. [PMID: 37858528 DOI: 10.1016/bs.mie.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A common mantra in drug discovery is that "You get what you screen for." This is not a promise that you will always get an effective drug candidate, but rather a warning that inaccuracies in your protocol for screening will more likely produce a compound that fails to be an effective candidate because it matches the properties of your screen, not the desired features of an ideal lead compound. It is with this in mind that we examine the current protocols for evaluating drug candidates and highlight some deficiencies while pointing the way to better methods. Many of the errors in data fitting can be rectified by abandoning the traditional equation-based data fitting methods and adopting the more rigorous mechanism-based fitting afforded by computer simulation based on numerical integration of rate equations. Using these methods bypasses the errors in judgement in choosing the appropriate equation for data fitting and the approximations required to derive those equations. In this chapter we outline the limitations and systematic errors in conventional methods of data fitting and illustrate the advantages of computer simulation and introduce the methods of analysis.
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Affiliation(s)
- Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.
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4
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Ray S, Dandpat SS, Chatterjee S, Walter NG. Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs. Nucleic Acids Res 2022; 50:8818-8833. [PMID: 35892287 PMCID: PMC9410914 DOI: 10.1093/nar/gkac635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
Noncoding, structured 5′-untranslated regions (5′-UTRs) of bacterial messenger RNAs (mRNAs) can control translation efficiency by forming structures that either recruit or repel the ribosome. Here we exploit a 5′-UTR embedded preQ1-sensing, pseudoknotted translational riboswitch to probe how binding of a small ligand controls recruitment of the bacterial ribosome to the partially overlapping Shine-Dalgarno (SD) sequence. Combining single-molecule fluorescence microscopy with mutational analyses, we find that the stability of 30S ribosomal subunit binding is inversely correlated with the free energy needed to unfold the 5′-UTR during mRNA accommodation into the mRNA binding cleft. Ligand binding to the riboswitch stabilizes the structure to both antagonize 30S recruitment and accelerate 30S dissociation. Proximity of the 5′-UTR and stability of the SD:anti-SD interaction both play important roles in modulating the initial 30S-mRNA interaction. Finally, depletion of small ribosomal subunit protein S1, known to help resolve structured 5′-UTRs, further increases the energetic penalty for mRNA accommodation. The resulting model of rapid standby site exploration followed by gated non-equilibrium unfolding of the 5′-UTR during accommodation provides a mechanistic understanding of how translation efficiency is governed by riboswitches and other dynamic structure motifs embedded upstream of the translation initiation site of bacterial mRNAs.
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Affiliation(s)
- Sujay Ray
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiba S Dandpat
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Surajit Chatterjee
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Dangerfield TL, Kirmizialtin S, Johnson KA. Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase. J Biol Chem 2022; 298:101627. [PMID: 35074426 PMCID: PMC8867116 DOI: 10.1016/j.jbc.2022.101627] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
Faithful replication of genomic DNA by high-fidelity DNA polymerases is crucial for the survival of most living organisms. While high-fidelity DNA polymerases favor canonical base pairs over mismatches by a factor of ∼1 × 105, fidelity is further enhanced several orders of magnitude by a 3′–5′ proofreading exonuclease that selectively removes mispaired bases in the primer strand. Despite the importance of proofreading to maintaining genome stability, it remains much less studied than the fidelity mechanisms employed at the polymerase active site. Here we characterize the substrate specificity for the proofreading exonuclease of a high-fidelity DNA polymerase by investigating the proofreading kinetics on various DNA substrates. The contribution of the exonuclease to net fidelity is a function of the kinetic partitioning between extension and excision. We show that while proofreading of a terminal mismatch is efficient, proofreading a mismatch buried by one or two correct bases is even more efficient. Because the polymerase stalls after incorporation of a mismatch and after incorporation of one or two correct bases on top of a mismatch, the net contribution of the exonuclease is a function of multiple opportunities to correct mistakes. We also characterize the exonuclease stereospecificity using phosphorothioate-modified DNA, provide a homology model for the DNA primer strand in the exonuclease active site, and propose a dynamic structural model for the transfer of DNA from the polymerase to the exonuclease active site based on MD simulations.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA.
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6
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Redhair M, Atkins WM. Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection. Arch Biochem Biophys 2021; 714:109064. [PMID: 34715072 DOI: 10.1016/j.abb.2021.109064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
Ligand-dependent changes in protein conformation are foundational to biology. Historical mechanistic models for substrate-specific proteins are induced fit (IF) and conformational selection (CS), which invoke a change in protein conformation after ligand binds or before ligand binds, respectively. These mechanisms have important, but rarely discussed, functional relevance because IF vs. CS can differentially affect a protein's substrate specificity or promiscuity, and its regulatory properties. The modern view of proteins as conformational ensembles in both ligand free and bound states, together with the realization that most proteins exhibit some substrate promiscuity, demands a deeper interpretation of the historical models and provides an opportunity to improve mechanistic analyses. Here we describe alternative analytical strategies for distinguishing the historical models, including the more complex expanded versions of IF and CS. Functional implications of the different models are described. We provide an alternative perspective based on protein ensembles interacting with ligand ensembles that clarifies how a single protein can 'apparently' exploit different mechanisms for different ligands. Mechanistic information about protein ensembles can be optimized when they are probed with multiple ligands.
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Affiliation(s)
- Michelle Redhair
- Department of Medicinal Chemistry, Box 375610, University of Washington, Seattle, WA, 98177, USA
| | - William M Atkins
- Department of Medicinal Chemistry, Box 375610, University of Washington, Seattle, WA, 98177, USA.
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7
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Hess D, Dockalova V, Kokkonen P, Bednar D, Damborsky J, deMello A, Prokop Z, Stavrakis S. Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Dangerfield TL, Johnson KA. Conformational dynamics during high-fidelity DNA replication and translocation defined using a DNA polymerase with a fluorescent artificial amino acid. J Biol Chem 2020; 296:100143. [PMID: 33273013 PMCID: PMC7857513 DOI: 10.1074/jbc.ra120.016617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/21/2022] Open
Abstract
We address the role of enzyme conformational dynamics in specificity for a high-fidelity DNA polymerase responsible for genome replication. We present the complete characterization of the conformational dynamics during the correct nucleotide incorporation forward and reverse reactions using stopped-flow and rapid-quench methods with a T7 DNA polymerase variant containing a fluorescent unnatural amino acid, (7-hydroxy-4-coumarin-yl) ethylglycine, which provides a signal for enzyme conformational changes. We show that the forward conformational change (>6000 s−1) is much faster than chemistry (300 s−1) while the enzyme opening to allow release of bound nucleotide (1.7 s−1) is much slower than chemistry. These parameters show that the conformational change selects a correct nucleotide for incorporation through an induced-fit mechanism. We also measured conformational changes occurring after chemistry and during pyrophosphorolysis, providing new insights into processive polymerization. Pyrophosphorolysis occurs via a conformational selection mechanism as the pyrophosphate binds to a rare pretranslocation state of the enzyme–DNA complex. Global data fitting was achieved by including experiments in the forward and reverse directions to correlate conformational changes with chemical reaction steps. This analysis provided well-constrained values for nine rate constants to establish a complete free-energy profile including the rates of DNA translocation during processive synthesis. Translocation does not follow Brownian ratchet or power stroke models invoking nucleotide binding as the driving force. Rather, translocation is rapid and thermodynamically favorable after enzyme opening and pyrophosphate release, and it appears to limit the rate of processive synthesis at 4 °C.
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Affiliation(s)
- Tyler L Dangerfield
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, USA.
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9
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Mazurenko S, Stourac J, Kunka A, Nedeljkovic S, Bednar D, Prokop Z, Damborsky J. CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Res 2019; 46:W344-W349. [PMID: 29762722 PMCID: PMC6031030 DOI: 10.1093/nar/gky358] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/24/2018] [Indexed: 01/26/2023] Open
Abstract
Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Sava Nedeljkovic
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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10
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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] [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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