1
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Sander CL, Luu J, Kim K, Furkert D, Jang K, Reichenwallner J, Kang M, Lee HJ, Eger BT, Choe HW, Fiedler D, Ernst OP, Kim YJ, Palczewski K, Kiser PD. Structural evidence for visual arrestin priming via complexation of phosphoinositols. Structure 2022; 30:263-277.e5. [PMID: 34678158 PMCID: PMC8818024 DOI: 10.1016/j.str.2021.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
Visual arrestin (Arr1) terminates rhodopsin signaling by blocking its interaction with transducin. To do this, Arr1 translocates from the inner to the outer segment of photoreceptors upon light stimulation. Mounting evidence indicates that inositol phosphates (InsPs) affect Arr1 activity, but the Arr1-InsP molecular interaction remains poorly defined. We report the structure of bovine Arr1 in a ligand-free state featuring a near-complete model of the previously unresolved C-tail, which plays a crucial role in regulating Arr1 activity. InsPs bind to the N-domain basic patch thus displacing the C-tail, suggesting that they prime Arr1 for interaction with rhodopsin and help direct Arr1 translocation. These structures exhibit intact polar cores, suggesting that C-tail removal by InsP binding is insufficient to activate Arr1. These results show how Arr1 activity can be controlled by endogenous InsPs in molecular detail.
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Affiliation(s)
- Christopher L. Sander
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA,Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Jennings Luu
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA,Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Kiyoung Jang
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | | | - MinSoung Kang
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea,Thin Film Materials Research Center, Korea Research Institute of Chemical Technology (KRICT), 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Ho-Jun Lee
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hui-Woog Choe
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yong Ju Kim
- Department of Lifestyle Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea,Department of Oriental Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Krzysztof Palczewski
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Department of Chemistry and Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA,Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA
| | - Philip D. Kiser
- Department of Ophthalmology and the Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA,Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA,Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA,Lead contact
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2
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Mehrabi P, Bücker R, Bourenkov G, Ginn HM, von Stetten D, Müller-Werkmeister HM, Kuo A, Morizumi T, Eger BT, Ou WL, Oghbaey S, Sarracini A, Besaw JE, Pare-Labrosse O, Meier S, Schikora H, Tellkamp F, Marx A, Sherrell DA, Axford D, Owen RL, Ernst OP, Pai EF, Schulz EC, Miller RJD. Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. Sci Adv 2021; 7:7/12/eabf1380. [PMID: 33731353 PMCID: PMC7968842 DOI: 10.1126/sciadv.abf1380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/28/2021] [Indexed: 05/09/2023]
Abstract
For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Affiliation(s)
- P Mehrabi
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R Bücker
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - G Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Ginn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Müller-Werkmeister
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - T Morizumi
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - B T Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - W-L Ou
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - S Oghbaey
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Sarracini
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - J E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - O Pare-Labrosse
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - S Meier
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - H Schikora
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Tellkamp
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Marx
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D A Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - R L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - O P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E F Pai
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E C Schulz
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J D Miller
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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3
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Besaw JE, Ou WL, Morizumi T, Eger BT, Sanchez Vasquez JD, Chu JHY, Harris A, Brown LS, Miller RJD, Ernst OP. The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants. J Biol Chem 2020; 295:14793-14804. [PMID: 32703899 DOI: 10.1074/jbc.ra120.014118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 04/28/2020] [Revised: 07/14/2020] [Indexed: 01/25/2023] Open
Abstract
Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Juan D Sanchez Vasquez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica H Y Chu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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4
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Mabanglo MF, Leung E, Vahidi S, Seraphim TV, Eger BT, Bryson S, Bhandari V, Zhou JL, Mao YQ, Rizzolo K, Barghash MM, Goodreid JD, Phanse S, Babu M, Barbosa LRS, Ramos CHI, Batey RA, Kay LE, Pai EF, Houry WA. ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol 2019; 2:410. [PMID: 31754640 PMCID: PMC6853987 DOI: 10.1038/s42003-019-0656-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/17/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
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Affiliation(s)
- Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Siavash Vahidi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Thiago V. Seraphim
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | | | - Carlos H. I. Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Lewis E. Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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5
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Bandyopadhyay A, Van Eps N, Eger BT, Rauscher S, Yedidi RS, Moroni T, West GM, Robinson KA, Griffin PR, Mitchell J, Ernst OP. A Novel Polar Core and Weakly Fixed C-Tail in Squid Arrestin Provide New Insight into Interaction with Rhodopsin. J Mol Biol 2018; 430:4102-4118. [PMID: 30120952 DOI: 10.1016/j.jmb.2018.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 12/31/2022]
Abstract
Photoreceptors of the squid Loligo pealei contain a G-protein-coupled receptor (GPCR) signaling system that activates phospholipase C in response to light. Analogous to the mammalian visual system, signaling of the photoactivated GPCR rhodopsin is terminated by binding of squid arrestin (sArr). sArr forms a light-dependent, high-affinity complex with squid rhodopsin, which does not require prior receptor phosphorylation for interaction. This is at odds with classical mammalian GPCR desensitization where an agonist-bound phosphorylated receptor is needed to break stabilizing constraints within arrestins, the so-called "three-element interaction" and "polar core" network, before a stable receptor-arrestin complex can be established. Biophysical and mass spectrometric analysis of the squid rhodopsin-arrestin complex indicates that in contrast to mammalian arrestins, the sArr C-tail is not involved in a stable three-element interaction. We determined the crystal structure of C-terminally truncated sArr that adopts a basal conformation common to arrestins and is stabilized by a series of weak but novel polar core interactions. Unlike mammalian arrestin-1, deletion of the sArr C-tail does not influence kinetic properties of complex formation of sArr with the receptor. Hydrogen-deuterium exchange studies revealed the footprint of the light-activated rhodopsin on sArr. Furthermore, double electron-electron resonance spectroscopy experiments provide evidence that receptor-bound sArr adopts a conformation different from the one known for arrestin-1 and molecular dynamics simulations reveal the residues that account for the weak three-element interaction. Insights gleaned from studying this system add to our general understanding of GPCR-arrestin interaction.
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Affiliation(s)
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| | - Ravikiran S Yedidi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tina Moroni
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Graham M West
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kelly Ann Robinson
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jane Mitchell
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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6
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Broecker J, Eger BT, Ernst OP. Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1933] [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: 11/26/2022] Open
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7
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Oghbaey S, Sarracini A, Ginn HM, Pare-Labrosse O, Kuo A, Marx A, Epp SW, Sherrell DA, Eger BT, Zhong Y, Loch R, Mariani V, Alonso-Mori R, Nelson S, Lemke HT, Owen RL, Pearson AR, Stuart DI, Ernst OP, Mueller-Werkmeister HM, Miller RJD. Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography. Acta Crystallogr D Struct Biol 2016; 72:944-55. [PMID: 27487825 PMCID: PMC5937680 DOI: 10.1107/s2059798316010834] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022] Open
Abstract
The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.
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Affiliation(s)
- Saeed Oghbaey
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Antoine Sarracini
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Olivier Pare-Labrosse
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Alexander Marx
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Sascha W. Epp
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Darren A. Sherrell
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Yinpeng Zhong
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Rolf Loch
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Desy, 22607, Hamburg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Henrik T. Lemke
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Henrike M. Mueller-Werkmeister
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
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8
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Goodreid JD, Janetzko J, Santa Maria JP, Wong KS, Leung E, Eger BT, Bryson S, Pai EF, Gray-Owen SD, Walker S, Houry WA, Batey RA. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J Med Chem 2016; 59:624-46. [PMID: 26818454 DOI: 10.1021/acs.jmedchem.5b01451] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.
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Affiliation(s)
- Jordan D Goodreid
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - John Janetzko
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - John P Santa Maria
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Keith S Wong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Walid A Houry
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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9
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Nishino T, Okamoto K, Kawaguchi Y, Matsumura T, Eger BT, Pai EF, Nishino T. The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase. FEBS J 2015; 282:3075-90. [PMID: 25817260 PMCID: PMC4832347 DOI: 10.1111/febs.13277] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 10/30/2014] [Revised: 03/09/2015] [Accepted: 03/21/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED Mammalian xanthine oxidoreductase can exist in both dehydrogenase and oxidase forms. Conversion between the two is implicated in such diverse processes as lactation, anti-bacterial activity, reperfusion injury and a growing number of diseases. We have constructed a variant of the rat liver enzyme that lacks the carboxy-terminal amino acids 1316-1331; it appears to assume an intermediate form, exhibiting a mixture of dehydrogenase and oxidase activities. The purified variant protein retained ~ 50-70% of oxidase activity even after prolonged dithiothreitol treatment, supporting a previous prediction that the C-terminal region plays a role in the dehydrogenase to oxidase conversion. In the crystal structure of the protein variant, most of the enzyme stays in an oxidase conformation. After 15 min of incubation with a high concentration of NADH, however, the corresponding X-ray structures showed a dehydrogenase-type conformation. On the other hand, disulfide formation between Cys535 and Cys992, which can clearly be seen in the electron density map of the crystal structure of the variant after removal of dithiothreitol, goes in parallel with the complete conversion to oxidase, resulting in structural changes identical to those observed upon proteolytic cleavage of the linker peptide. These results indicate that the dehydrogenase-oxidase transformation occurs rather readily and the insertion of the C-terminal peptide into the active site cavity of its subunit stabilizes the dehydrogenase form. We propose that the intermediate form can be generated (e.g. in endothelial cells) upon interaction of the C-terminal peptide portion of the enzyme with other proteins or the cell membrane. DATABASE Coordinate sets and structure factors for the four crystal structures reported in the present study have been deposited in the Protein Data Bank under the identification numbers 4YRW, 4YTZ, 4YSW, and 4YTY.
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Affiliation(s)
- Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Yuko Kawaguchi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Tomohiro Matsumura
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, ON, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, ON, Canada
- Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, ON, Canada
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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10
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Abstract
In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 Å resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.
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Affiliation(s)
- Hiroshi Ishikita
- Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Kyoto 606-8501, Japan.
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11
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Okamoto K, Kawaguchi Y, Eger BT, Pai EF, Nishino T. Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate. J Am Chem Soc 2010; 132:17080-3. [DOI: 10.1021/ja1077574] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan, Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto and The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario M5S1A8, Canada, and Department of Biochemistry, 1463 Boyce Hall, University of California, Riverside, 92521-0122, United States
| | - Yuko Kawaguchi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan, Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto and The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario M5S1A8, Canada, and Department of Biochemistry, 1463 Boyce Hall, University of California, Riverside, 92521-0122, United States
| | - Bryan T. Eger
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan, Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto and The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario M5S1A8, Canada, and Department of Biochemistry, 1463 Boyce Hall, University of California, Riverside, 92521-0122, United States
| | - Emil F. Pai
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan, Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto and The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario M5S1A8, Canada, and Department of Biochemistry, 1463 Boyce Hall, University of California, Riverside, 92521-0122, United States
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan, Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto and The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario M5S1A8, Canada, and Department of Biochemistry, 1463 Boyce Hall, University of California, Riverside, 92521-0122, United States
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12
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Okamoto K, Eger BT, Nishino T, Pai EF, Nishino T. Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol. Nucleosides Nucleotides Nucleic Acids 2008; 27:888-93. [PMID: 18600558 DOI: 10.1080/15257770802146577] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Inhibitors of xanthine oxidoreductase block conversion of xanthine to uric acid and are therefore potentially useful for treatment of hyperuricemia or gout. We determined the crystal structure of reduced bovine milk xanthine oxidoreductase complexed with oxipurinol at 2.0 A resolution. Clear electron density was observed between the N2 nitrogen of oxipurinol and the molybdenum atom of the molybdopterin cofactor, indicating that oxipurinol coordinated directly to molybdenum. Oxipurinol forms hydrogen bonds with glutamate 802, arginine 880, and glutamate 1261, which have previously been shown to be essential for the enzyme reaction. We discuss possible differences in the hypouricemic effect of inhibitors, including allopurinol and newly developed inhibitors, based on their mode of binding in the crystal structures.
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Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
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13
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Nishino T, Okamoto K, Eger BT, Pai EF, Nishino T. Mammalian xanthine oxidoreductase - mechanism of transition from xanthine dehydrogenase to xanthine oxidase. FEBS J 2008; 275:3278-89. [PMID: 18513323 DOI: 10.1111/j.1742-4658.2008.06489.x] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Reactive oxygen species are generated by various biological systems, including NADPH oxidases, xanthine oxidoreductase, and mitochondrial respiratory enzymes, and contribute to many physiological and pathological phenomena. Mammalian xanthine dehydrogenase (XDH) can be converted to xanthine oxidase (XO), which produces both superoxide anion and hydrogen peroxide. Recent X-ray crystallographic and site-directed mutagenesis studies have revealed a highly sophisticated mechanism of conversion from XDH to XO, suggesting that the conversion is not a simple artefact, but rather has a function in mammalian organisms. Furthermore, this transition seems to involve a thermodynamic equilibrium between XDH and XO; disulfide bond formation or proteolysis can then lock the enzyme in the XO form. In this review, we focus on recent advances in our understanding of the mechanism of conversion from XDH to XO.
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Affiliation(s)
- Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
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14
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Nishino T, Okamoto K, Kawaguchi Y, Hori H, Matsumura T, Eger BT, Pai EF, Nishino T. Mechanism of the conversion of xanthine dehydrogenase to xanthine oxidase: identification of the two cysteine disulfide bonds and crystal structure of a non-convertible rat liver xanthine dehydrogenase mutant. J Biol Chem 2005; 280:24888-94. [PMID: 15878860 DOI: 10.1074/jbc.m501830200] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian xanthine dehydrogenase can be converted to xanthine oxidase by modification of cysteine residues or by proteolysis of the enzyme polypeptide chain. Here we present evidence that the Cys(535) and Cys(992) residues of rat liver enzyme are indeed involved in the rapid conversion from the dehydrogenase to the oxidase. The purified mutants C535A and/or C992R were significantly resistant to conversion by incubation with 4,4'-dithiodipyridine, whereas the recombinant wild-type enzyme converted readily to the oxidase type, indicating that these residues are responsible for the rapid conversion. The C535A/C992R mutant, however, converted very slowly during prolonged incubation with 4,4'-dithiodipyridine, and this slow conversion was blocked by the addition of NADH, suggesting that another cysteine couple located near the NAD(+) binding site is responsible for the slower conversion. On the other hand, the C535A/C992R/C1316S and C535A/C992R/C1324S mutants were completely resistant to conversion, even on prolonged incubation with 4,4'-dithiodipyridine, indicating that Cys(1316) and Cys(1324) are responsible for the slow conversion. The crystal structure of the C535A/C992R/C1324S mutant was determined in its demolybdo form, confirming its dehydrogenase conformation.
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Affiliation(s)
- Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan.
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15
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Fukunari A, Okamoto K, Nishino T, Eger BT, Pai EF, Kamezawa M, Yamada I, Kato N. Y-700 [1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid]: a potent xanthine oxidoreductase inhibitor with hepatic excretion. J Pharmacol Exp Ther 2004; 311:519-28. [PMID: 15190124 DOI: 10.1124/jpet.104.070433] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Y-700 (1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid) is a newly synthesized inhibitor of xanthine oxidoreductase (XOR). Steady-state kinetics with the bovine milk enzyme indicated a mixed type inhibition with K(i) and K(i) ' values of 0.6 and 3.2 nM, respectively. Titration experiments showed that Y-700 bound tightly both to the active sulfo-form and to the inactive desulfo-form of the enzyme with K(d) values of 0.9 and 2.8 nM, respectively. X-ray crystallographic analysis of the enzyme-inhibitor complex revealed that Y-700 closely interacts with the channel leading to the molybdenum-pterin active site but does not directly coordinate to the molybdenum ion. In oxonate-treated rats, orally administered Y-700 (1-10 mg/kg) dose dependently lowered plasma urate levels. At a dose of 10 mg/kg, the hypouricemic action of Y-700 was more potent and of longer duration than that of 4-hydroxypyrazolo(3,4-d)pyrimidine, whereas its action was approximately equivalent to that of 2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid, a nonpurine inhibitor of XOR. In normal rats, orally administered Y-700 (0.3-3 mg/kg) dose dependently reduced the urinary excretion of urate and allantoin, accompanied by an increase in the excretion of hypoxanthine and xanthine. Y-700 (1 mg/kg) was absorbed rapidly by the oral route with high bioavailability (84.1%). Y-700 was hardly excreted via the kidneys but was mainly cleared via the liver. These results suggest that Y-700 will be a promising candidate for the treatment of hyperuricemia and other diseases in which XOR may be involved.
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Affiliation(s)
- Atsushi Fukunari
- Discovery Technology Laboratory, Pharmaceuticals Research Unit, Mitsubishi Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan.
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16
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Okamoto K, Matsumoto K, Hille R, Eger BT, Pai EF, Nishino T. The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition. Proc Natl Acad Sci U S A 2004; 101:7931-6. [PMID: 15148401 PMCID: PMC419534 DOI: 10.1073/pnas.0400973101] [Citation(s) in RCA: 210] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon-oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge-transfer band at approximately 640 nm. The crystal structure of the complex indicates that the catalytically labile Mo-OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the MoS group of the oxidized enzyme has become protonated to afford Mo-SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide.
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Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
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17
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Kuwabara Y, Nishino T, Okamoto K, Matsumura T, Eger BT, Pai EF, Nishino T. Unique amino acids cluster for switching from the dehydrogenase to oxidase form of xanthine oxidoreductase. Proc Natl Acad Sci U S A 2003; 100:8170-5. [PMID: 12817083 PMCID: PMC166201 DOI: 10.1073/pnas.1431485100] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Accepted: 05/19/2003] [Indexed: 11/18/2022] Open
Abstract
In mammals, xanthine oxidoreductase is synthesized as a dehydrogenase (XDH) but can be readily converted to its oxidase form (XO) either by proteolysis or modification of cysteine residues. The crystal structures of bovine milk XDH and XO demonstrated that atoms in the highly charged active-site loop (Gln-423-Lys-433) around the FAD cofactor underwent large dislocations during the conversion, blocking the approach of the NAD+ substrate to FAD in the XO form as well as changing the electrostatic environment around FAD. Here we identify a unique cluster of amino acids that plays a dual role by forming the core of a relay system for the XDH/XO transition and by gating a solvent channel leading toward the FAD ring. A more detailed structural comparison and site-directed mutagenesis analysis experiments showed that Phe-549, Arg-335, Trp-336, and Arg-427 sit at the center of a relay system that transmits modifications of the linker peptide by cysteine oxidation or proteolytic cleavage to the active-site loop (Gln-423-Lys-433). The tight interactions of these residues are crucial in the stabilization of the XDH conformation and for keeping the solvent channel closed. Both oxidative and proteolytic generation of XO effectively leads to the removal of Phe-549 from the cluster causing a reorientation of the bulky side chain of Trp-336, which then in turn forces a dislocation of Arg-427, an amino acid located in the active-site loop. The conformational change also opens the gate for the solvent channel, making it easier for oxygen to reach the reduced FAD in XO.
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Affiliation(s)
- Yoshimitsu Kuwabara
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Tomoko Nishino
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Ken Okamoto
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Tomohiro Matsumura
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Bryan T. Eger
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Emil F. Pai
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
| | - Takeshi Nishino
- Department of Biochemistry and Molecular
Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; Department of Obstetrics and
Gynecology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602,
Japan; and Departments of Biochemistry,
Medical Biophysics, and Molecular and Medical Genetics, University of Toronto
and Division of Molecular and Structural Biology, Ontario Cancer
Institute/University Health Network, 610 University Avenue, Toronto, ON,
Canada M5G 2M9
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18
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Okamoto K, Eger BT, Nishino T, Kondo S, Pai EF, Nishino T. An extremely potent inhibitor of xanthine oxidoreductase. Crystal structure of the enzyme-inhibitor complex and mechanism of inhibition. J Biol Chem 2003; 278:1848-55. [PMID: 12421831 DOI: 10.1074/jbc.m208307200] [Citation(s) in RCA: 301] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TEI-6720 (2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid) is an extremely potent inhibitor of xanthine oxidoreductase. Steady state kinetics measurements exhibit mixed type inhibition with K(i) and K(i)' values of 1.2 +/- 0.05 x 10(-10) m and 9 +/- 0.05 x 10(-10) m, respectively. Fluorescence-monitored titration experiments showed that TEI-6720 bound very tightly to both the active and the inactive desulfo-form of the enzyme. The dissociation constant determined for the desulfo-form was 2 +/- 0.03 x 10(-9) m; for the active form, the corresponding number was too low to allow accurate measurements. The crystal structure of the active sulfo-form of milk xanthine dehydrogenase complexed with TEI-6720 and determined at 2.8-A resolution revealed the inhibitor molecule bound in a long, narrow channel leading to the molybdenum-pterin active site of the enzyme. It filled up most of the channel and the immediate environment of the cofactor, very effectively inhibiting the activity of the enzyme through the prevention of substrate binding. Although the inhibitor did not directly coordinate to the molybdenum ion, numerous hydrogen bonds as well as hydrophobic interactions with the protein matrix were observed, most of which are also used in substrate recognition.
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Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-0022, Japan
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Eger BT, Okamoto K, Enroth C, Sato M, Nishino T, Pai EF, Nishino T. Purification, crystallization and preliminary X-ray diffraction studies of xanthine dehydrogenase and xanthine oxidase isolated from bovine milk. Acta Crystallogr D Biol Crystallogr 2000; 56:1656-8. [PMID: 11092937 DOI: 10.1107/s0907444900012890] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2000] [Accepted: 09/19/2000] [Indexed: 11/10/2022]
Abstract
Xanthine dehydrogenase catalyzes the oxidation of hypoxanthine to xanthine and the further oxidation of xanthine to uric acid. The enzyme is the target of the anti-gout drug allopurinol and its involvement in postischemic reperfusion injury is presently being defined. Each subunit of the homodimeric 290 kDa enzyme contains four cofactors: one Mo-pterin, two [2Fe-2S] clusters and one FAD. Both the dehydrogenase (XDH) and the proteolytically modified oxidase form (XO) of the enzyme from bovine milk have been crystallized. XO crystals belong to space group C222(1), with unit-cell parameters a = 116.3, b = 164.4, c = 153.2 A at room temperature and a = 117.8, b = 165.4, c = 154.5 A when flash-frozen. They allow data collection to 3.3 and 2.5 A, respectively. In addition, a data set was collected from frozen XDH crystals and processed to 2.1 A. These crystals belong to space group C2, with unit-cell parameters a = 169.9, b = 124.8, c = 148.6 A, beta = 90.9 degrees. The unit-cell volumes and Matthews parameters are similar for the two crystal forms. There is one monomer per asymmetric unit in the XO crystals and a complete native dimer per asymmetric unit in the XDH crystals.
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Affiliation(s)
- B T Eger
- University of Toronto, Department of Biochemistry, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
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Enroth C, Eger BT, Okamoto K, Nishino T, Nishino T, Pai EF. Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. Proc Natl Acad Sci U S A 2000; 97:10723-8. [PMID: 11005854 PMCID: PMC27090 DOI: 10.1073/pnas.97.20.10723] [Citation(s) in RCA: 495] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mammalian xanthine oxidoreductases, which catalyze the last two steps in the formation of urate, are synthesized as the dehydrogenase form xanthine dehydrogenase (XDH) but can be readily converted to the oxidase form xanthine oxidase (XO) by oxidation of sulfhydryl residues or by proteolysis. Here, we present the crystal structure of the dimeric (M(r), 290,000) bovine milk XDH at 2.1-A resolution and XO at 2.5-A resolution and describe the major changes that occur on the proteolytic transformation of XDH to the XO form. Each molecule is composed of an N-terminal 20-kDa domain containing two iron sulfur centers, a central 40-kDa flavin adenine dinucleotide domain, and a C-terminal 85-kDa molybdopterin-binding domain with the four redox centers aligned in an almost linear fashion. Cleavage of surface-exposed loops of XDH causes major structural rearrangement of another loop close to the flavin ring (Gln 423Lys 433). This movement partially blocks access of the NAD substrate to the flavin adenine dinucleotide cofactor and changes the electrostatic environment of the active site, reflecting the switch of substrate specificity observed for the two forms of this enzyme.
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Affiliation(s)
- C Enroth
- Ontario Cancer Institute/Princess Margaret Hospital, Division of Molecular and Structural Biology, 610 University Avenue, Toronto, ON, Canada M5G 2M9
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Stoll VS, Eger BT, Hynes RC, Martichonok V, Jones JB, Pai EF. Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry 1998; 37:451-62. [PMID: 9425066 DOI: 10.1021/bi971166o] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In order to probe the structural basis of stereoselectivity in the serine protease family, a series of enantiomeric boronic acids RCH2CH(NHCOCH3)B(OH)2 has been synthesized and kinetically characterized as transition-state analog inhibitors using alpha-chymotrypsin and subtilisin Carlsberg as model systems. When the R-substituent in this series was changed from a p-chlorophenyl to a 1-naphthyl group, alpha-chymotrypsin, but not subtilisin, reversed its usual preference for l-enantiomers and bound more tightly to the D-enantiomer [Martichonok, V., & Jones, J. B. (1996) J. Am. Chem. Soc. 118, 950-958]. The structural factors responsible for the differences in stereoselectivity between the two enzymes have been explored by X-ray crystallographic examination of subtilisin Carlsberg and gamma-chymotrypsin complexes of the L- and D-enantiomers of p-chlorophenyl and 1-naphthyl boronic acid derivatives. In both enzymes, the L-isomers of the inhibitors, which are more closely related to the natural L-amino acid substrates, form tetrahedral adducts, covalently linking the central boron atom and Ogamma of the catalytic serine. The d-isomers, however, differ in the way they interact with subtilisin or gamma-chymotrypsin. With subtilisin, both the D-p-chlorophenyl and D-1-naphthyl inhibitor complexes form covalent Ser Ogamma-to-boron bonds, but with gamma-chymotrypsin, the same inhibitors lead to novel tetrahedral adducts covalently linking both Ser195 Ogamma and His57 Nepsilon2 covalently via the boron atom.
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Affiliation(s)
- V S Stoll
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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Abstract
The minimal kinetic mechanism for misincorporation of a single nucleotide (dATP) into a short DNA primer/template (9/20-mer) by the Klenow fragment of DNA polymerase I [KF(exo+)] has been previously published [Kuchta, R. D., Benkovic, P., & Benkovic, S.J. (1988) Biochemistry 27, 6716-6725]. In this paper are presented refinements to this mechanism. Pre-steady-state measurements of correct nucleotide incorporation (dTTP) in the presence of a single incorrect nucleotide (dATP) with excess KF-(exo+) demonstrated that dATP binds to the KF(exo+)-9/20-mer complex in two steps preceding chemistry. Substitution of (alpha S)dATP for dATP yielded identical two-step binding kinetics, removing nucleotide binding as a cause of the elemental effect on the rate of misincorporation. Pyrophosphate release from the ternary species [KF'(exo+)-9A/20-mer-PPi] was found to occur following a rate-limiting conformational change, with this species partitioning equally to either nucleotide via internal pyrophosphorolysis or to misincorporated product. The rate of 9A/20-mer dissociation from the central ternary complex (KF'-9A/20-mer-PPi) was shown to be negligible relative to exonucleolytic editing. Pyrophosphorolysis of the misincorporated DNA product (9A/20-mer), in conjunction with measurement of the rate of dATP misincorporation, permitted determination of the overall equilibrium constant for dATP misincorporation and provided a value similar to that measured for correct incorporation. A step by step comparison of the polymerization catalyzed by the Klenow fragment for correct and incorrect nucleotide incorporation emphasizes that the major source of the enzyme's replicative fidelity arises from discrimination in the actual chemical step and from increased exonuclease activity on the ternary misincorporated product complex owing to its slower passage through the turnover sequence.
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Affiliation(s)
- B T Eger
- Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park 16802
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Eger BT, Kuchta RD, Carroll SS, Benkovic PA, Dahlberg ME, Joyce CM, Benkovic SJ. Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo-). Biochemistry 1991; 30:1441-8. [PMID: 1991125 DOI: 10.1021/bi00219a039] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inhibition of the pre-steady-state burst of nucleotide incorporation by a single incorrect nucleotide (nucleotide discrimination) was measured with the Klenow fragment of DNA polymerase I [KF(exo+)]. For the eight mispairs studied on three DNA sequences, only low levels of discrimination ranging from none to 23-fold were found. The kinetics of dNTP incorporation into the 9/20-mer at low nucleotide concentrations was also determined. A limit of greater than or equal to 250 s-1 was placed on the nucleotide off-rate from the KF(exo+)-9/20-dTTP complex in accord with nucleotide binding being at equilibrium in the overall kinetic sequence. The influence of the relatively short length of the 9/20-mer on the mechanism of DNA replication fidelity was determined by remeasuring important kinetic parameters on a 30/M13-mer with high homology to the 9/20-mer. Pre-steady-state data on the nucleotide turnover rates, the dATP(alpha S) elemental effect, and the burst of dAMP misincorporation into the 30/M13-mer demonstrated that the kinetics were not affected by the length of the DNA primer/template. The effects on fidelity of two site-specific mutations, KF(polA5) and KF(exo-), were also examined. KF(polA5) showed an increased rate of DNA dissociation and a decreased rate of polymerization resulting in less processive DNA synthesis. Nevertheless, with at least one misincorporation event, that of dAMP into the 9/20-mer, KF(polA5) displays an increased replication fidelity.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- B T Eger
- Department of Chemistry, Pennsylvania State University, University Park 16802
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