1
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Alnajjar K, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β. Biochemistry 2024; 63:1412-1422. [PMID: 38780930 PMCID: PMC11155676 DOI: 10.1021/acs.biochem.4c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The catalytic function of DNA polymerase β (pol β) fulfills the gap-filling requirement of the base excision DNA repair pathway by incorporating a single nucleotide into a gapped DNA substrate resulting from the removal of damaged DNA bases. Most importantly, pol β can select the correct nucleotide from a pool of similarly structured nucleotides to incorporate into DNA in order to prevent the accumulation of mutations in the genome. Pol β is likely to employ various mechanisms for substrate selection. Here, we use dCTP analogues that have been modified at the β,γ-bridging group of the triphosphate moiety to monitor the effect of leaving group basicity of the incoming nucleotide on precatalytic conformational changes, which are important for catalysis and selectivity. It has been previously shown that there is a linear free energy relationship between leaving group pKa and the chemical transition state. Our results indicate that there is a similar relationship with the rate of a precatalytic conformational change, specifically, the closing of the fingers subdomain of pol β. In addition, by utilizing analogue β,γ-CHX stereoisomers, we identified that the orientation of the β,γ-bridging group relative to R183 is important for the rate of fingers closing, which directly influences chemistry.
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Affiliation(s)
- Khadijeh
S. Alnajjar
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Katarina Wang
- Therapeutic
Radiology Department, Yale University, New Haven, Connecticut 06520, United States
| | - Isabel Alvarado-Cruz
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Cristian Chavira
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
- Department
of Cellular and Molecular Medicine, University
of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
| | - Amirsoheil Negahbani
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Beatriz Garcia-Barboza
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Myron F. Goodman
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department
of Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Joann B. Sweasy
- Fred
and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, Nebraska 68198, United States
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2
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Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity. J Biol Chem 2023; 299:102938. [PMID: 36702254 PMCID: PMC9976465 DOI: 10.1016/j.jbc.2023.102938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.
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3
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Park J, Youn HS, An JY, Lee Y, Eom SH, Wang J. Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69. Front Mol Biosci 2021; 8:704813. [PMID: 34869578 PMCID: PMC8639217 DOI: 10.3389/fmolb.2021.704813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022] Open
Abstract
DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.
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Affiliation(s)
- Jongseo Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Steitz Center for Structural Biology, GIST, Gwangju, South Korea
| | - Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Steitz Center for Structural Biology, GIST, Gwangju, South Korea.,BIO R&D Center, Ingredient Business Unit, Daesang Corporation, Gyeonggi-do, Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Steitz Center for Structural Biology, GIST, Gwangju, South Korea.,Virocure Inc., Seoul, Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Steitz Center for Structural Biology, GIST, Gwangju, South Korea.,Metabolic Regulation Research Center, Korea Research Institute of BIoscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Steitz Center for Structural Biology, GIST, Gwangju, South Korea.,Department of Chemistry, GIST, Gwangju, Korea
| | - Jimin Wang
- Steitz Center for Structural Biology, GIST, Gwangju, South Korea.,Department of Molecular Biophysics and Biochemistry, New Haven, CT, United States
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4
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Geronimo I, Vidossich P, De Vivo M. Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
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5
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Geronimo I, Vidossich P, Donati E, Vivo M. Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Elisa Donati
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Marco Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
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Abstract
DNA polymerase (dpol) β has served as a model for structural, kinetic, and computational characterization of the DNA synthesis reaction. The laboratory directed by Samuel H. Wilson has utilized a multifunctional approach to analyze the function of this enzyme at the biological, chemical, and molecular levels for nearly 50 years. Over this time, it has become evident that correlating static crystallographic structures of dpol β with solution kinetic measurements is a daunting task. However, aided by computational and spectroscopic approaches, novel and unexpected insights have emerged. While dpols generally insert wrong nucleotides with similar poor efficiencies, their capacity to insert the right nucleotide depends on the identity of the dpol. Accordingly, the ability to choose right from wrong depends on the efficiency of right, rather than wrong, nucleotide insertion. Structures of dpol β in various liganded forms published by the Wilson laboratory, and others, have provided molecular insights into the molecular attributes that hasten correct nucleotide insertion and deter incorrect nucleotide insertion. Computational approaches have bridged the gap between structures of intermediate complexes and provided insights into this basic and essential chemical reaction.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA.
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7
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Gong S, Kirmizialtin S, Chang A, Mayfield JE, Zhang YJ, Johnson KA. Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis. J Biol Chem 2020; 296:100184. [PMID: 33310704 PMCID: PMC7948414 DOI: 10.1074/jbc.ra120.016489] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 11/06/2022] Open
Abstract
Magnesium ions play a critical role in catalysis by many enzymes and contribute to the fidelity of DNA polymerases through a two-metal ion mechanism. However, specificity is a kinetic phenomenon and the roles of Mg2+ ions in each step in the catalysis have not been resolved. We first examined the roles of Mg2+ by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase. We show that Mg.dNTP binding induces an enzyme conformational change at a rate that is independent of free Mg2+ concentration. Subsequently, the second Mg2+ binds to the closed state of the enzyme-DNA-Mg.dNTP complex (Kd = 3.7 mM) to facilitate catalysis. Weak binding of the catalytic Mg2+ contributes to fidelity by sampling the correctly aligned substrate without perturbing the equilibrium for nucleotide binding at physiological Mg2+ concentrations. An increase of the Mg2+ concentration from 0.25 to 10 mM increases nucleotide specificity (kcat/Km) 12-fold largely by increasing the rate of the chemistry relative to the rate of nucleotide release. Mg2+ binds very weakly (Kd ≤ 37 mM) to the open state of the enzyme. Analysis of published crystal structures showed that HIV reverse transcriptase binds only two metal ions prior to incorporation of a correct base pair. Molecular dynamics simulations support the two-metal ion mechanism and the kinetic data indicating weak binding of the catalytic Mg2+. Molecular dynamics simulations also revealed the importance of the divalent cation cloud surrounding exposed phosphates on the DNA. These results enlighten the roles of the two metal ions in the specificity of DNA polymerases.
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Affiliation(s)
- Shanzhong Gong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrienne Chang
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Joshua E Mayfield
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.
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8
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Abstract
The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications.
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9
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Kriznik A, Libiad M, Le Cordier H, Boukhenouna S, Toledano MB, Rahuel-Clermont S. Dynamics of a Key Conformational Transition in the Mechanism of Peroxiredoxin Sulfinylation. ACS Catal 2020; 10:3326-3339. [PMID: 32363077 PMCID: PMC7189429 DOI: 10.1021/acscatal.9b04471] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/14/2020] [Indexed: 12/11/2022]
Abstract
![]()
Peroxiredoxins from
the Prx1 subfamily (Prx) are moonlighting peroxidases
that operate in peroxide signaling and are regulated by sulfinylation.
Prxs offer a major model of protein–thiol oxidative modification.
They react with H2O2 to form a sulfenic acid
intermediate that either engages into a disulfide bond, committing
the enzyme into its peroxidase cycle, or again reacts with peroxide
to produce a sulfinic acid that inactivates the enzyme. Sensitivity
to sulfinylation depends on the kinetics of these two competing reactions
and is critically influenced by a structural transition from a fully
folded (FF) to locally unfolded (LU) conformation. Analysis of the
reaction of the Tsa1 Saccharomyces cerevisiae Prx with H2O2 by Trp fluorescence-based rapid
kinetics revealed a process linked to the FF/LU transition that is
kinetically distinct from disulfide formation and suggested that sulfenate
formation facilitates local unfolding. Use of mutants of distinctive
sensitivities and of different peroxide substrates showed that sulfinylation
sensitivity is not coupled to the resolving step kinetics but depends
only on the sulfenic acid oxidation and FF-to-LU transition rate constants.
In addition, stabilization of the active site FF conformation, the
determinant of sulfinylation kinetics, is only moderately influenced
by the Prx C-terminal tail dynamics that determine the FF →
LU kinetics. From these two parameters, the relative sensitivities
of Prxs toward hyperoxidation with different substrates can be predicted,
as confirmed by in vitro and in vivo patterns of sulfinylation.
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Affiliation(s)
- Alexandre Kriznik
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
- UMS2008 IBSLor, Biophysics and Structural Biology Core Facility, Université de Lorraine, CNRS, INSERM, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Marouane Libiad
- Laboratoire Stress oxydant et Cancer, Institute for Integrative Biology of the Cell (I2BC), UMR9198, CNRS, CEA-Saclay, Université Paris-Saclay, iBiTecS/SBIGEM, Bat 142, F-91198 Gif-sur-Yvette Cedex, France
| | - Hélène Le Cordier
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Samia Boukhenouna
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
| | - Michel B. Toledano
- Laboratoire Stress oxydant et Cancer, Institute for Integrative Biology of the Cell (I2BC), UMR9198, CNRS, CEA-Saclay, Université Paris-Saclay, iBiTecS/SBIGEM, Bat 142, F-91198 Gif-sur-Yvette Cedex, France
| | - Sophie Rahuel-Clermont
- IMoPA, Université de Lorraine, CNRS, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
- UMS2008 IBSLor, Biophysics and Structural Biology Core Facility, Université de Lorraine, CNRS, INSERM, Biopole, Campus Biologie Sante′, F-54000 Nancy, France
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10
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Tsai M. Catalytic mechanism of DNA polymerases-Two metal ions or three? Protein Sci 2019; 28:288-291. [PMID: 30368961 PMCID: PMC6319748 DOI: 10.1002/pro.3542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Ming‐Daw Tsai
- Institute of Biological Chemistry, Academia SinicaTaipei115Taiwan
- Institute of Biochemical Sciences, National Taiwan UniversityTaipei106Taiwan
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11
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Beard WA, Wilson SH. DNA polymerase beta and other gap-filling enzymes in mammalian base excision repair. Enzymes 2019; 45:1-26. [PMID: 31627875 DOI: 10.1016/bs.enz.2019.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA polymerase β plays a central role in the base excision DNA repair pathway that cleanses the genome of apurinic/apyrimidinic (AP) sites. AP sites arise in DNA from spontaneous base loss and DNA damage-specific glycosylases that hydrolyze the N-glycosidic bond between the deoxyribose and damaged base. AP sites are deleterious lesions because they can be mutagenic and/or cytotoxic. DNA polymerase β contributes two enzymatic activities, DNA synthesis and lyase, during the repair of AP sites; these activities reside on carboxyl- and amino-terminal domains, respectively. Accordingly, its cellular, structural, and kinetic attributes have been extensively characterized and it serves as model enzyme for the nucleotidyl transferase reaction utilized by other replicative, repair, and trans-lesion DNA polymerases.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Durham, NC, United States.
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12
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Wang J, Smithline ZB. Crystallographic evidence for two-metal-ion catalysis in human pol η. Protein Sci 2018; 28:439-447. [PMID: 30368948 DOI: 10.1002/pro.3541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 02/06/2023]
Abstract
Extensive evidence exists that DNA polymerases use two metal ions to catalyze the phosphoryl transfer reaction. Recently, competing evidence emerged, suggesting that a third metal ion, known as MnC, may be involved in catalysis. The binding of MnC was observed in crystal structures of the replication complexes of human polymerase (pol) η, pol β, and pol μ. Its occupancy (qMnC ) in the pol η replication complexes exhibited a strong correlation with the occupancy of the formed product pyrophosphate (qPPi ), i.e., qMnC ∝ qPPi . However, a key piece of information was missing that is needed to distinguish between two possible sequences of events: (i) the chemical reaction occurs first with only two meal ions, followed by the binding of MnC in a "catch-the-product" mode; and (ii) MnC binds first, followed by the chemical reaction with all three metal ions in a "push-the-reaction-forward" mode. Both mechanisms can lead to a strong correlation between qMnC and qPPi . However, qMnC ≤ qPPi in the first scenario, whereas qMnC ≥ qPPi in the second. In this study, an analysis of crystallographic data published recently for pol η complexes shows that the formation of the product pyrophosphate definitely precedes the binding of MnC. Therefore, just like all other DNA polymerases, human pol η employs a two-metal-ion catalytic mechanism. Rather than help to catalyze the reaction, MnC stabilizes the formed product, which remains trapped inside the crystals, before it slowly diffuses out.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
| | - Zachary B Smithline
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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13
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Stevens DR, Hammes-Schiffer S. Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations. J Am Chem Soc 2018; 140:8965-8969. [PMID: 29932331 DOI: 10.1021/jacs.8b05177] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The enzyme human DNA polymerase η (Pol η) is critical for bypassing lesions during DNA replication. In addition to the two Mg2+ ions aligning the active site, experiments suggest that a third Mg2+ ion could play an essential catalytic role. Herein the role of this third metal ion is investigated with quantum mechanical/molecular mechanical (QM/MM) free energy simulations of the phosphoryl transfer reaction and a proposed self-activating proton transfer from the incoming nucleotide to the pyrophosphate leaving group. The simulations with only two metal ions in the active site support a sequential mechanism, with phosphoryl transfer followed by relatively fast proton transfer. The simulations with three metal ions in the active site suggest that the third metal ion may play a catalytic role through electrostatic interactions with the leaving group. These electrostatic interactions stabilize the product, making the phosphoryl transfer reaction more thermodynamically favorable with a lower free energy barrier relative to the activated state corresponding to the deprotonated 3'OH nucleophile, and also inhibit the subsequent proton transfer. The possibility that Mg2+-bound hydroxide acts as the base deprotonating the 3'OH nucleophile is also explored.
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Affiliation(s)
- David R Stevens
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
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14
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Raper AT, Reed AJ, Suo Z. Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion. Chem Rev 2018; 118:6000-6025. [DOI: 10.1021/acs.chemrev.7b00685] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Austin T. Raper
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Kumar Vashishtha A, H. Konigsberg W. Effect of Different Divalent Cations on the Kinetics and Fidelity of DNA Polymerases. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.4.272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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16
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The thumb domain is not essential for the catalytic action of HoLaMa DNA polymerase. Protein J 2017; 36:453-460. [DOI: 10.1007/s10930-017-9740-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Wu WJ, Yang W, Tsai MD. How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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19
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Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase. Sci Rep 2017; 7:5797. [PMID: 28724886 PMCID: PMC5517523 DOI: 10.1038/s41598-017-05534-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II). A machine-learning algorithm called linear discriminant analysis (LDA) was trained by using the large collection of Mn(II) and Mg(II) binding sites available in the protein data bank (PDB). Application of the model to DNA primase revealed a preference in the enzyme's second metal binding site for Mn(II) over Mg(II), suggesting that T7 DNA primase activity modulation when bound to Mn(II) is based on structural changes in the enzyme.
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20
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Samara NL, Gao Y, Wu J, Yang W. Detection of Reaction Intermediates in Mg 2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography. Methods Enzymol 2017; 592:283-327. [PMID: 28668125 DOI: 10.1016/bs.mie.2017.03.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates. Here we present protocols used for successful studies of Mg2+-dependent DNA polymerases and ribonucleases that are applicable to analyses of a variety of metal ion-dependent reactions.
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Affiliation(s)
- Nadine L Samara
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States; Section on Biological Chemistry, NIDCR, National Institutes of Health, Bethesda, MD, United States
| | - Yang Gao
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States
| | - Jinjun Wu
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States.
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21
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Yang W, Weng PJ, Gao Y. A new paradigm of DNA synthesis: three-metal-ion catalysis. Cell Biosci 2016; 6:51. [PMID: 27602203 PMCID: PMC5012070 DOI: 10.1186/s13578-016-0118-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 01/11/2023] Open
Abstract
Enzyme catalysis has been studied for over a century. How it actually occurs has not been visualized until recently. By combining in crystallo reaction and X-ray diffraction analysis of reaction intermediates, we have obtained unprecedented atomic details of the DNA synthesis process. Contrary to the established theory that enzyme-substrate complexes and transition states have identical atomic composition and catalysis occurs by the two-metal-ion mechanism, we have discovered that an additional divalent cation has to be captured en route to product formation. Unlike the canonical two metal ions, which are coordinated by DNA polymerases, this third metal ion is free of enzyme coordination. Its location between the α- and β-phosphates of dNTP suggests that the third metal ion may drive the phosphoryltransfer from the leaving group opposite to the 3'-OH nucleophile. Experimental data indicate that binding of the third metal ion may be the rate-limiting step in DNA synthesis and the free energy associated with the metal-ion binding can overcome the activation barrier to the DNA synthesis reaction.
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Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Peter J Weng
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Yang Gao
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
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22
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Vashishtha AK, Wang J, Konigsberg WH. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. J Biol Chem 2016; 291:20869-20875. [PMID: 27462081 DOI: 10.1074/jbc.r116.742494] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Divalent metal ions are essential components of DNA polymerases both for catalysis of the nucleotidyl transfer reaction and for base excision. They occupy two sites, A and B, for DNA synthesis. Recently, a third metal ion was shown to be essential for phosphoryl transfer reaction. The metal ion in the A site is coordinated by the carboxylate of two highly conserved acidic residues, water molecules, and the 3'-hydroxyl group of the primer so that the A metal is in an octahedral complex. Its catalytic function is to lower the pKa of the hydroxyl group, making it a highly effective nucleophile that can attack the α phosphorous atom of the incoming dNTP. The metal ion in the B site is coordinated by the same two carboxylates that are affixed to the A metal ion as well as the non-bridging oxygen atoms of the incoming dNTP. The carboxyl oxygen of an adjacent peptide bond serves as the sixth ligand that completes the octahedral coordination geometry of the B metal ion. Similarly, two metal ions are required for proofreading; one helps to lower the pKa of the attacking water molecule, and the other helps to stabilize the transition state for nucleotide excision. The role of different divalent cations are discussed in relation to these two activities as well as their influence on base selectivity and misincorporation by DNA polymerases. Some, but not all, of the effects of these different metal ions can be rationalized based on their intrinsic properties, which are tabulated in this review.
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Affiliation(s)
- Ashwani Kumar Vashishtha
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8024 and
| | - Jimin Wang
- the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114
| | - William H Konigsberg
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8024 and
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23
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Gao Y, Yang W. Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Science 2016; 352:1334-7. [PMID: 27284197 DOI: 10.1126/science.aad9633] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/10/2016] [Indexed: 12/23/2022]
Abstract
It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.
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Affiliation(s)
- Yang Gao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Abstract
It is now common knowledge that enzymes are mobile entities relying on complex atomic-scale dynamics and coordinated conformational events for proper ligand recognition and catalysis. However, the exact role of protein dynamics in enzyme function remains either poorly understood or difficult to interpret. This mini-review intends to reconcile biophysical observations and biological significance by first describing a number of common experimental and computational methodologies employed to characterize atomic-scale residue motions on various timescales in enzymes, and second by illustrating how the knowledge of these motions can be used to describe the functional behavior of enzymes and even act upon it. Two biologically relevant examples will be highlighted, namely the HIV-1 protease and DNA polymerase β enzyme systems.
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25
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Dahl JM, Lieberman KR, Wang H. Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations. J Biol Chem 2016; 291:6456-70. [PMID: 26797125 PMCID: PMC4813572 DOI: 10.1074/jbc.m115.701797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/02/2016] [Indexed: 11/06/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) require divalent metal cations for phosphodiester bond formation in the polymerase site and for hydrolytic editing in the exonuclease site. Me(2+) ions are intimate architectural components of each active site, where they are coordinated by a conserved set of amino acids and functional groups of the reaction substrates. Therefore Me(2+) ions can influence the noncovalent transitions that occur during each nucleotide addition cycle. Using a nanopore, transitions in individual Φ29 DNAP complexes are resolved with single-nucleotide spatial precision and sub-millisecond temporal resolution. We studied Mg(2+) and Mn(2+), which support catalysis, and Ca(2+), which supports deoxynucleoside triphosphate (dNTP) binding but not catalysis. We examined their effects on translocation, dNTP binding, and primer strand transfer between the polymerase and exonuclease sites. All three metals cause a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Me(2+) also promotes an increase in the backward translocation rate that is dependent upon the primer terminal 3'-OH group. Me(2+) modulates the translocation rates but not their response to force, suggesting that Me(2+) does not affect the distance to the transition state of translocation. Absent Me(2+), the primer strand transfer pathway between the polymerase and exonuclease sites displays additional kinetic states not observed at >1 mm Me(2+). Complementary dNTP binding is affected by Me(2+) identity, with Ca(2+) affording the highest affinity, followed by Mn(2+), and then Mg(2+). Both Ca(2+) and Mn(2+) substantially decrease the dNTP dissociation rate relative to Mg(2+), while Ca(2+) also increases the dNTP association rate.
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Affiliation(s)
- Joseph M Dahl
- From the Departments of Biomolecular Engineering and
| | | | - Hongyun Wang
- Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064
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26
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Moscato B, Swain M, Loria JP. Induced Fit in the Selection of Correct versus Incorrect Nucleotides by DNA Polymerase β. Biochemistry 2015; 55:382-95. [PMID: 26678253 DOI: 10.1021/acs.biochem.5b01213] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA polymerase β (Pol β) repairs single-nucleotide gapped DNA (sngDNA) by enzymatic incorporation of the Watson-Crick partner nucleotide at the gapped position opposite the templating nucleotide. The process by which the matching nucleotide is incorporated into a sngDNA sequence has been relatively well-characterized, but the process of discrimination from nucleotide misincorporation remains unclear. We report here NMR spectroscopic characterization of full-length, uniformly labeled Pol β in apo, sngDNA-bound binary, and ternary complexes containing matching and mismatching nucleotide. Our data indicate that, while binding of the correct nucleotide to the binary complex induces chemical shift changes consistent with the process of enzyme closure, the ternary Pol β complex containing a mismatching nucleotide exhibits no such changes and appears to remain in an open, unstable, binary-like conformation. Our findings support an induced-fit mechanism for polymerases in which a closed ternary complex can only be achieved in the presence of matching nucleotide.
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Affiliation(s)
- Beth Moscato
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Monalisa Swain
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - J Patrick Loria
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06520, United States.,Department of Molecular Biophysics and Biochemistry, Yale University , 260 Whitney Avenue, New Haven, Connecticut 06520, United States
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27
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Miller BR, Beese LS, Parish CA, Wu EY. The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure 2015. [PMID: 26211612 DOI: 10.1016/j.str.2015.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3'-hydroxyl.
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Affiliation(s)
- Bill R Miller
- Department of Biology, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA; Department of Chemistry, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, 255 Nanaline H. Duke Building, Durham, NC 27710, USA
| | - Carol A Parish
- Department of Chemistry, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA.
| | - Eugene Y Wu
- Department of Biology, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, USA; Department of Biochemistry, Duke University Medical Center, 255 Nanaline H. Duke Building, Durham, NC 27710, USA.
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28
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Perera L, Beard WA, Pedersen LG, Wilson SH. Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 97:83-113. [PMID: 25458356 PMCID: PMC5573153 DOI: 10.1016/bs.apcsb.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We review theoretical attempts to model the chemical insertion reactions of nucleoside triphosphates catalyzed by the nucleic acid polymerases using combined quantum mechanical/molecular mechanical methodology. Due to an existing excellent database of high-resolution X-ray crystal structures, the DNA polymerase β system serves as a useful template for discussion and comparison. The convergence of structures of high-quality complexes and continued developments of theoretical techniques suggest a bright future for understanding the global features of nucleic acid polymerization.
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Affiliation(s)
- Lalith Perera
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.
| | - William A Beard
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Lee G Pedersen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel H Wilson
- Laboratory of Structural Biology, National Institution of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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29
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Moustafa IM, Korboukh VK, Arnold JJ, Smidansky ED, Marcotte LL, Gohara DW, Yang X, Sánchez-Farrán MA, Filman D, Maranas JK, Boehr DD, Hogle JM, Colina CM, Cameron CE. Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase. J Biol Chem 2014; 289:36229-48. [PMID: 25378410 DOI: 10.1074/jbc.m114.616193] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity.
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Affiliation(s)
| | | | - Jamie J Arnold
- From the Department of Biochemistry and Molecular Biology
| | | | - Laura L Marcotte
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - David W Gohara
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | | | | | - David Filman
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | | | | | - James M Hogle
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Coray M Colina
- the Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 and
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30
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Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH. Substrate-induced DNA polymerase β activation. J Biol Chem 2014; 289:31411-22. [PMID: 25261471 DOI: 10.1074/jbc.m114.607432] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerases and substrates undergo conformational changes upon forming protein-ligand complexes. These conformational adjustments can hasten or deter DNA synthesis and influence substrate discrimination. From structural comparison of binary DNA and ternary DNA-dNTP complexes of DNA polymerase β, several side chains have been implicated in facilitating formation of an active ternary complex poised for chemistry. Site-directed mutagenesis of these highly conserved residues (Asp-192, Arg-258, Phe-272, Glu-295, and Tyr-296) and kinetic characterization provides insight into the role these residues play during correct and incorrect insertion as well as their role in conformational activation. The catalytic efficiencies for correct nucleotide insertion for alanine mutants were wild type ∼ R258A > F272A ∼ Y296A > E295A > D192A. Because the efficiencies for incorrect insertion were affected to about the same extent for each mutant, the effects on fidelity were modest (<5-fold). The R258A mutant exhibited an increase in the single-turnover rate of correct nucleotide insertion. This suggests that the wild-type Arg-258 side chain generates a population of non-productive ternary complexes. Structures of binary and ternary substrate complexes of the R258A mutant and a mutant associated with gastric carcinomas, E295K, provide molecular insight into intermediate structural conformations not appreciated previously. Although the R258A mutant crystal structures were similar to wild-type enzyme, the open ternary complex structure of E295K indicates that Arg-258 stabilizes a non-productive conformation of the primer terminus that would decrease catalysis. Significantly, the open E295K ternary complex binds two metal ions indicating that metal binding cannot overcome the modified interactions that have interrupted the closure of the N-subdomain.
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Affiliation(s)
- William A Beard
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - David D Shock
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Vinod K Batra
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Rajendra Prasad
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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31
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Towle-Weicksel JB, Dalal S, Sohl CD, Doublié S, Anderson KS, Sweasy JB. Fluorescence resonance energy transfer studies of DNA polymerase β: the critical role of fingers domain movements and a novel non-covalent step during nucleotide selection. J Biol Chem 2014; 289:16541-50. [PMID: 24764311 DOI: 10.1074/jbc.m114.561878] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During DNA repair, DNA polymerase β (Pol β) is a highly dynamic enzyme that is able to select the correct nucleotide opposite a templating base from a pool of four different deoxynucleoside triphosphates (dNTPs). To gain insight into nucleotide selection, we use a fluorescence resonance energy transfer (FRET)-based system to monitor movement of the Pol β fingers domain during catalysis in the presence of either correct or incorrect dNTPs. By labeling the fingers domain with ((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (IAEDANS) and the DNA substrate with Dabcyl, we are able to observe rapid fingers closing in the presence of correct dNTPs as the IAEDANS comes into contact with a Dabcyl-labeled, one-base gapped DNA. Our findings show that not only do the fingers close after binding to the correct dNTP, but that there is a second conformational change associated with a non-covalent step not previously reported for Pol β. Further analyses suggest that this conformational change corresponds to the binding of the catalytic metal into the polymerase active site. FRET studies with incorrect dNTP result in no changes in fluorescence, indicating that the fingers do not close in the presence of incorrect dNTP. Together, our results show that nucleotide selection initially occurs in an open fingers conformation and that the catalytic pathways of correct and incorrect dNTPs differ from each other. Overall, this study provides new insight into the mechanism of substrate choice by a polymerase that plays a critical role in maintaining genome stability.
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Affiliation(s)
| | | | - Christal D Sohl
- Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Sylvie Doublié
- the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405
| | - Karen S Anderson
- Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520 and
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32
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Abstract
![]()
DNA
polymerase (pol) β is a small eukaryotic DNA polymerase
composed of two domains. Each domain contributes an enzymatic activity
(DNA synthesis and deoxyribose phosphate lyase) during the repair
of simple base lesions. These domains are termed the polymerase and
lyase domains, respectively. Pol β has been an excellent model
enzyme for studying the nucleotidyl transferase reaction and substrate
discrimination at a molecular level. In this review, recent crystallographic
studies of pol β in various liganded and conformational states
during the insertion of right and wrong nucleotides as well as during
the bypass of damaged DNA (apurinic sites and 8-oxoguanine) are described.
Structures of these catalytic intermediates provide unexpected insights
into mechanisms by which DNA polymerases enhance genome stability.
These structures also provide an improved framework that permits computational
studies to facilitate the interpretation of detailed kinetic analyses
of this model enzyme.
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Affiliation(s)
- William A Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive, P.O. Box 12233, MD F3-01, Research Triangle Park, North Carolina 27709, United States
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33
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Abstract
![]()
This review will summarize our structural
and kinetic studies of
RB69 DNA polymerase (RB69pol) as well as selected variants of the
wild-type enzyme that were undertaken to obtain a deeper understanding
of the exquisitely high fidelity of B family replicative DNA polymerases.
We discuss how the structures of the various RB69pol ternary complexes
can be used to rationalize the results obtained from pre-steady-state
kinetic assays. Our main findings can be summarized as follows. (i)
Interbase hydrogen bond interactions can increase catalytic efficiency
by 5000-fold; meanwhile, base selectivity is not solely determined
by the number of hydrogen bonds between the incoming dNTP and the
templating base. (ii) Minor-groove hydrogen bond interactions at positions n – 1 and n – 2 of the primer
strand and position n – 1 of the template
strand in RB69pol ternary complexes are essential for efficient primer
extension and base selectivity. (iii) Partial charge interactions
among the incoming dNTP, the penultimate base pair, and the hydration
shell surrounding the incoming dNTP modulate nucleotide insertion
efficiency and base selectivity. (iv) Steric clashes between mismatched
incoming dNTPs and templating bases with amino acid side chains in
the nascent base pair binding pocket (NBP) as well as weak interactions
and large gaps between the incoming dNTPs and the templating base
are some of the reasons that incorrect dNTPs are incorporated so inefficiently
by wild-type RB69pol. In addition, we developed a tC°–tCnitro Förster resonance energy transfer assay to monitor
partitioning of the primer terminus between the polymerase and exonuclease
subdomains.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8024, United States
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34
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Gouge J, Rosario S, Romain F, Beguin P, Delarue M. Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. J Mol Biol 2013; 425:4334-52. [PMID: 23856622 DOI: 10.1016/j.jmb.2013.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022]
Abstract
Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a series of high-resolution X-ray structures that mimic the pre-catalytic state, the post-catalytic state and a competent state that can be transformed into the two other ones in crystallo via the addition of dAMPcPP and Zn(2+), respectively. We examined the effect of Mn(2+), Co(2+) and Zn(2+) because they all have a marked influence on the kinetics of the reaction. We demonstrate a dynamic role of divalent transition metal ions bound to site A: (i) Zn(2+) (or Co(2+)) in Metal A site changes coordination from octahedral to tetrahedral after the chemical step, which explains the known higher affinity of Tdt for the primer strand when these ions are present, and (ii) metal A has to leave to allow the translocation of the primer strand and to clear the active site, a typical feature for a ratchet-like mechanism. Except for Zn(2+), the sugar puckering of the primer strand 3' terminus changes from C2'-endo to C3'-endo during catalysis. In addition, our data are compatible with a scheme where metal A is the last component that binds to the active site to complete its productive assembly, as already inferred in human pol beta. The new structures have potential implications for modeling pol mu, a closely related polX implicated in the repair of DNA double-strand breaks, in a complex with a DNA synapsis.
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Affiliation(s)
- Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 rue du Dr Roux, 75015 Paris, France
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35
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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36
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Freudenthal BD, Beard WA, Wilson SH. Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure 2012; 20:1829-37. [PMID: 22959623 PMCID: PMC3496073 DOI: 10.1016/j.str.2012.08.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 11/23/2022]
Abstract
DNA polymerase and substrate conformational changes are essential for high-fidelity DNA synthesis. Structures of DNA polymerase (pol) β in complex with DNA show the enzyme in an "open" conformation. Subsequent to binding the nucleotide, the polymerase "closes" around the nascent base pair with two metals positioned for chemistry. However, structures of substrate/active site intermediates prior to closure are lacking. By destabilizing the closed complex, we determined unique ternary complex structures of pol β with correct and incorrect incoming nucleotides bound to the open conformation. These structures reveal that Watson-Crick hydrogen bonding is assessed upon initial complex formation. Importantly, nucleotide-bound states representing intermediate metal coordination states occur with active site assembly. The correct, but not incorrect, nucleotide maintains Watson-Crick hydrogen bonds during interconversion of these states. These structures indicate that the triphosphate of the incoming nucleotide undergoes rearrangement prior to closure, providing an opportunity to deter misinsertion and increase fidelity.
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Affiliation(s)
- Bret D. Freudenthal
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
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37
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Balbo PB, Wang ECW, Tsai MD. Kinetic mechanism of active site assembly and chemical catalysis of DNA polymerase β. Biochemistry 2011; 50:9865-75. [PMID: 22010960 DOI: 10.1021/bi200954r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been inferred from structural and computational studies that the mechanism of DNA polymerases involves subtle but important discrete steps that occur between binding and recognition of the correct dNTP and chemical catalysis. These steps potentially include local conformational changes involving active site residues, reorganization of Mg(2+)-coordinating ligands, and proton transfer. Here we address this broad issue by conducting extensive transient state kinetic analyses of DNA polymerase β (Pol β). We also performed kinetic simulations to evaluate alternative kinetic models. These studies provide some support for two-step subdomain closing and define constraints under which a kinetically significant prechemistry step can occur. To experimentally identify additional microscopic steps, we developed a stopped flow absorbance assay to measure proton formation that occurs during catalysis. These studies provide direct evidence that formation of the enzyme-bound 3'-O(-) nucleophile is rate determining for chemistry. We additionally show that at low pH the chemical step is rate limiting for catalysis, but at high pH, a postchemistry conformational step is rate limiting due to a pH-dependent increase in the rate of nucleotidyl transfer. Finally, we performed exhaustive analyses of [Mg(2+)] and pH effects. In contrast to published studies, the results suggest an irregular pH dependence of k(pol), which is consistent with general base catalysis involving cooperativity between two or more protonic residues. Overall, the results represent significant advancement in the kinetic mechanism of Pol β and also reconcile some computational and experimental findings.
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Affiliation(s)
- Paul B Balbo
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei 115, Taiwan
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38
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Ram Prasad B, Warshel A. Prechemistry versus preorganization in DNA replication fidelity. Proteins 2011; 79:2900-19. [PMID: 21905114 DOI: 10.1002/prot.23128] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/30/2011] [Accepted: 07/05/2011] [Indexed: 01/30/2023]
Abstract
The molecular origin of nucleotide insertion catalysis and fidelity of DNA polymerases is explored by means of computational simulations. Special attention is paid to the examination of the validity of proposals that invoke prechemistry effects, checkpoints concepts, and dynamical effects. The simulations reproduce the observed fidelity in Pol β, starting with the relevant observed X-ray structures of the complex with the right (R) and wrong (W) nucleotides. The generation of free energy surfaces for the R and W systems also allowed us to analyze different proposals about the origin of the fidelity and to reach several important conclusions. It is found that the potential of mean force (PMF) obtained by proper sampling does not support QM/MM-based proposals of a large barrier before the prechemistry state. Furthermore, examination of dynamical proposals by the renormalization approach indicates that the motions from open to close configurations do not contribute to catalysis or fidelity. Finally we discuss and analyze the induced fit concept and show that, despite its importance, it does not explain fidelity. That is, the fidelity is apparently due to the change in the preorganization of the chemical site, as a result of the relaxation of the binding site upon binding of the incorrect nucleotide. Finally and importantly, since the issue is the barrier associated with the enzyme-substrate (ES)/DNA complex at the chemical transition state and not the path to this complex formation (unless this path involves rate determining steps), it is also not useful to invoke checkpoints while discussing fidelity.
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Affiliation(s)
- B Ram Prasad
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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39
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Klvaňa M, Jeřábek P, Goodman MF, Florián J. An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity. Biochemistry 2011; 50:7023-32. [PMID: 21739967 DOI: 10.1021/bi200790s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show how a restricted reaction surface can be used to facilitate the calculation of biologically important contributions of active site geometries and dynamics to DNA polymerase fidelity. Our analysis, using human DNA polymerase beta (pol β), is performed within the framework of an electrostatic linear free energy response (EFER) model. The structure, dynamics, and energetics of pol β-DNA-dNTP interactions are computed between two points on the multidimensional reaction free energy surface. "Point 1" represents a ground state activation intermediate (GSA), which is obtained by deprotonating the terminal 3'OH group of the primer DNA strand. "Point 2" is the transition state (PTS) for the attack of the 3'O(-) (O(nuc)) on the P(α) atom of dNTP substrate, having the electron density of a dianionic phosphorane intermediate. Classical molecular dynamics simulations are used to compute the geometric and dynamic contributions to the formation of right and wrong O(nuc)-P chemical bonds. Matched dCTP·G and mismatched dATP·G base pairs are used to illustrate the analysis. Compared to the dCTP·G base pair, the dATP·G mismatch has fewer GSA configurations with short distances between O(nuc) and P(α) atoms and between the oxygen in the scissile P-O bond (O(lg)) and the nearest structural water. The thumb subdomain conformation of the GSA complex is more open for the mismatch, and the H-bonds in the mispair become more extended during the nucleophilic attack than in the correct pair. The electrostatic contributions of pol β and DNA residues to catalysis of the right and wrong P-O(nuc) bond formation are 5.3 and 3.1 kcal/mol, respectively, resulting in an 80-fold contribution to fidelity. The EFER calculations illustrate the considerable importance of Arg183 and an O(lg)-proximal water molecule to pol β fidelity.
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Affiliation(s)
- Martin Klvaňa
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, United States
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40
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Bermek O, Grindley NDF, Joyce CM. Distinct roles of the active-site Mg2+ ligands, Asp882 and Asp705, of DNA polymerase I (Klenow fragment) during the prechemistry conformational transitions. J Biol Chem 2010; 286:3755-66. [PMID: 21084297 DOI: 10.1074/jbc.m110.167593] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerases catalyze the incorporation of deoxynucleoside triphosphates into a growing DNA chain using a pair of Mg(2+) ions, coordinated at the active site by two invariant aspartates, whose removal by mutation typically reduces the polymerase activity to barely detectable levels. Using two stopped-flow fluorescence assays that we developed previously, we have investigated the role of the carboxylate ligands, Asp(705) and Asp(882), of DNA polymerase I (Klenow fragment) in the early prechemistry steps that prepare the active site for catalysis. We find that neither carboxylate is required for an early conformational transition, reported by a 2-aminopurine probe, that takes place in the open ternary complex after binding of the complementary dNTP. However, the subsequent fingers-closing step requires Asp(882); this step converts the open ternary complex into the closed conformation, creating the active-site geometry required for catalysis. Crystal structures indicate that the Asp(882) position changes very little during fingers-closing; this side chain may therefore serve as an anchor point to receive the dNTP-associated metal ion as the nucleotide is delivered into the active site. The Asp(705) carboxylate is not required until after the fingers-closing step, and we suggest that its role is to facilitate the entry of the second Mg(2+) into the active site. The two early prechemistry steps that we have studied take place normally at very low Mg(2+) concentrations, although higher concentrations are needed for covalent nucleotide addition, consistent with the second metal ion entering the ternary complex after fingers-closing.
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Affiliation(s)
- Oya Bermek
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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41
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Wang M, Lee HR, Konigsberg W. Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex. Biochemistry 2009; 48:2075-86. [PMID: 19228037 DOI: 10.1021/bi801627h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rapid chemical quench assays, as well as equilibrium and stopped-flow fluorescence experiments, were performed with an RB69 DNA polymerase (RB69 pol)-primer-template (P/T) complex containing 2-aminopurine (dAP) and a metal exchange-inert Rh(III) derivative of a deoxynucleoside triphosphate (Rh.dTTP). The objective was to determine the effect of catalytic metal ion (A site) occupancy on the affinity of an incoming Rh.dTTP for the RB69 pol-P/T binary complex and on the rate of the conformational change induced by Rh.dTTP binding. With Ca(2+) in the A site, the affinity of the incoming Rh.dTTP for the RB69 pol-P/T binary complex and the conformational change rate can be determined in the absence of chemistry. When Mg(2+) was added to a ternary complex containing Rh.dTTP opposite dAP, the templating base, nucleotidyl transfer occurred, but the rate of product formation was only one-tenth of that found with Mg.dTTP, as determined by rapid chemical quench assays. Rates of conformational change subsequent to formation of a ternary complex, in the absence of chemistry, were estimated from the rate of change in dAP fluorescence with an increase in the Rh.dTTP concentration. We have shown that there is an initial rapid quenching of dAP fluorescence followed by a second phase of dAP quenching, which has nearly the same rate as that of dTMP incorporation, as estimated from rapid chemical quench experiments. We have also demonstrated that the affinity of Rh.dTTP for occupancy of the B metal ion site is dependent on the presence of Ca(2+). However, a saturating Rh.dTTP concentration in the absence of Ca(2+) results in full quenching of dAP fluorescence, whereas a saturating Ca(2+) concentration in the absence of Rh.dTTP gives only partial quenching of dAP fluorescence. The implications of these results for the mechanism of Fingers closing, metal ion binding, and base selectivity are discussed.
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Affiliation(s)
- Mina Wang
- Molecular Biophysics and Biochemistry Department, Yale University, 333 Cedar Street, New Haven, Connecticut 06520, USA
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42
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Lee HR, Wang M, Konigsberg W. The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase. Biochemistry 2009; 48:2087-98. [PMID: 19228036 DOI: 10.1021/bi8016284] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two divalent metal ions are required for nucleotide incorporation by DNA polymerases. Here we use the bacteriophage RB69 DNA polymerase (RB69 pol) and the metal ion exchange-inert nucleotide analogue rhodium(III) deoxythymidine triphosphate (Rh.dTTP) to investigate the requirements of metal binding to the "A" site and to the "B" site, independently. We show that while binding of a metal ion to the A site is required for the nucleotidyl transfer reaction to occur, this metal binding is insufficient to initiate the prechemistry enzyme isomerization that has been observed with this polymerase. Moreover, we show that binding of a deoxynucleoside triphosphate (dNTP), in the absence of a catalytic metal ion, is sufficient to induce this conformational change. In this report, we also present several lines of evidence (from pulse-chase, rapid chemical quench-flow, and stopped-flow fluorescence experiments) for the reverse rate of the enzyme isomerization, closed to open, of a DNA polymerase complex. The implications of these data for the fidelity of DNA polymerization by RB69 pol are discussed.
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Affiliation(s)
- Harold R Lee
- Molecular Biophysics and Biochemistry Department, Yale University, 333 Cedar Street, New Haven, Connecticut 06520, USA
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43
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Kim S, Liu C, Halkidis K, Gamper HB, Hou YM. Distinct kinetic determinants for the stepwise CCA addition to tRNA. RNA (NEW YORK, N.Y.) 2009; 15:1827-1836. [PMID: 19696158 PMCID: PMC2743048 DOI: 10.1261/rna.1669109] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 07/15/2009] [Indexed: 05/28/2023]
Abstract
The universally conserved CCA sequence is present at the 3' terminal 74-76 positions of all active tRNA molecules as a functional tag to participate in ribosome protein synthesis. The CCA enzyme catalyzes CCA synthesis in three sequential steps of nucleotide addition at rapid and identical rates. However, the kinetic determinant of each addition is unknown, thus limiting the insights into the kinetic basis of CCA addition. Using our recently developed single turnover kinetics of Escherichia coli CCA enzyme as a model, we show here that the identical rate of the stepwise CCA addition is determined by distinct kinetic parameters. Specifically, the kinetics of C74 and C75 addition is controlled by the chemistry of nucleotidyl transfer, whereas the kinetics of A76 addition is controlled by a prechemistry conformational transition of the active site. In multiple turnover condition, all three steps are controlled by slow product release, indicating enzyme processivity from one addition to the next. However, the processivity decreases as the enzyme progresses to complete the CCA synthesis. Together, these results suggest the existence of a network of diverse kinetic parameters that determines the overall rate of CCA addition for tRNA maturation.
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Affiliation(s)
- Sangbumn Kim
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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44
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Bakhtina M, Roettger MP, Tsai MD. Contribution of the reverse rate of the conformational step to polymerase beta fidelity. Biochemistry 2009; 48:3197-208. [PMID: 19231836 DOI: 10.1021/bi802119f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A complete understanding of the kinetic mechanism of fidelity requires comparison of correct and incorrect dNTP incorporation pathways in both the forward and reverse directions. The studies presented here focus on the dNTP-induced conformational step, which has historically been proposed by many to be the major determinant of fidelity. As it was recently highlighted [Tsai, Y. C., and Johnson, K. A. (2006) Biochemistry 45, 9675-9687], chemistry can be the slowest step in the forward direction of the correct dNTP incorporation pathway, yet the corresponding microscopic rate constant would not contribute toward fidelity in the case when the reverse rate of the conformational step is slower than chemistry. Here we use a stopped-flow technique to directly measure the reverse rate of the conformational step in the DNA polymerase beta (Pol beta) kinetic pathway. Extensive pre-steady-state kinetic studies presented include the utilization of 2-aminopurine-labeled DNA substrates, 2-aminopurine nucleotide triphosphate, a nonhydrolyzable nucleotide analogue dAMPCPP, and a rapid sequential mixing reaction scheme. Additionally, the effect of mismatched dNTPs, various metal ions, and the presence of the 3'-terminal hydroxyl group of the primer on the rate of the reverse "opening" conformational step were analyzed. Our analyses indicate that reverse "opening" is drastically facilitated in the presence of mismatched ternary complexes, which is in agreement with the hypothesis that the ternary complex is destabilized by the presence of incorrect dNTP. By analysis of the relative magnitudes of chemistry and reverse "opening" in the presence of both matched and mismatched matched ternary complexes, this work further validates that, for Pol beta, fidelity is dictated by the differences in free energy required to reach the highest energy transition state of the chemical step.
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Affiliation(s)
- Marina Bakhtina
- Department of Chemistry and The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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45
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Roettger MP, Bakhtina M, Tsai MD. Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways. Biochemistry 2008; 47:9718-27. [PMID: 18717589 PMCID: PMC2646765 DOI: 10.1021/bi800689d] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While matched nucleotide incorporation by DNA polymerase beta (Pol beta) has been well-studied, a true understanding of polymerase fidelity requires comparison of both matched and mismatched dNTP incorporation pathways. Here we examine the mechanism of misincorporation for wild-type (WT) Pol beta and an error-prone I260Q variant using stopped-flow fluorescence assays and steady-state fluorescence spectroscopy. In stopped-flow, a biphasic fluorescence trace is observed for both enzymes during mismatched dNTP incorporation. The fluorescence transitions are in the same direction as that observed for matched dNTP, albeit with lower amplitude. Assignments of the fast and slow fluorescence phases are designated to the same mechanistic steps previously determined for matched dNTP incorporation. For both WT and I260Q mismatched dNTP incorporation, the rate of the fast phase, reflecting subdomain closing, is comparable to that induced by correct dNTP. Pre-steady-state kinetic evaluation reveals that both enzymes display similar correct dNTP insertion profiles, and the lower fidelity intrinsic to the I260Q mutant results from enhanced efficiency of mismatched incorporation. Notably, in comparison to WT, I260Q demonstrates enhanced intensity of fluorescence emission upon mismatched ternary complex formation. Both kinetic and steady-state fluorescence data suggest that relaxed discrimination against incorrect dNTP by I260Q is a consequence of a loss in ability to destabilize the mismatched ternary complex. Overall, our results provide first direct evidence that mismatched and matched dNTP incorporations proceed via analogous kinetic pathways, and support our standing hypothesis that the fidelity of Pol beta originates from destabilization of the mismatched closed ternary complex and chemical transition state.
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Affiliation(s)
- Michelle P Roettger
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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46
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Murphy DL, Kosa J, Jaeger J, Sweasy JB. The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding. Biochemistry 2008; 47:8048-57. [PMID: 18616290 DOI: 10.1021/bi702104y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endogenous DNA damage occurs at a rate of at least 20,000 lesions per cell per day. Base excision repair (BER) is a key pathway for maintaining genome stability. Several pol beta variants were identified as conferring resistance to 3'-azido-3'-deoxythymidine (AZT) in Escherichia coli (Kosa et al. (1999) J. Biol. Chem. 274, 3851-3858). Detailed biochemical studies on one of these AZT-resistant variants, His285 to Asp, have shown that the H285D variant of pol beta possesses pre-steady-state kinetics that are similar to the wild-type polymerase. In gap filling assays with 5-bp gapped DNA, H285D showed a slight mutator phenotype. In depth single turnover kinetic analysis revealed that H285D is much more efficient than wild-type pol beta at extending mispaired primer termini. This mispair extension property of H285D is attributed to a greatly increased binding to the next correct nucleotide in the presence of a mispair. This change in K d(dNTP),app is not accompanied by a change in k pol; values for k pol are the same for both H285D and wild-type. Close examination of available structural data, as well as molecular modeling, has shown that residue 285 is able to make several stabilizing contacts in the fingers domain of the polymerase, and the introduction of a negatively charged side chain could have important effects on the enzyme. It is postulated that the loss of the contact between His285, Lys289, and Ile323 is responsible for the ability of H285D to extend mispairs through disruption of contacts near the C-terminal end of pol beta and propagation into the nucleotide binding pocket.
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Affiliation(s)
- Drew L Murphy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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47
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Tang KH, Tsai MD. Structure and function of 2:1 DNA polymerase.DNA complexes. J Cell Physiol 2008; 216:315-20. [PMID: 18393274 DOI: 10.1002/jcp.21458] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
DNA polymerases are required for DNA replication and DNA repair in all of the living organisms. Different DNA polymerases are responsible different stages of DNA metabolism, and many of them are multifunctional enzymes. It was generally assumed that the different reactions are catalyzed by the same enzyme molecule. In addition to 1:1 DNA polymerase.DNA complex reported by crystallization studies, 2:1 and higher order DNA polymerase.DNA complexes have been identified in solution studies by various biochemical and biophysical approaches. Further, abundant evidences for the DNA polymerase-DNA interactions in several DNA polymerases suggested that the 2:1 complex represents the more active form. This review describes the current status of this emerging subject and explores their potential in vitro and in vivo functional significance, particularly for the 2:1 complexes of mammalian DNA polymerase beta (Pol beta), the Klenow fragment of E. coli DNA polymerase I (KF), and T4 DNA polymerase.
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Affiliation(s)
- Kuo-Hsiang Tang
- Department of Chemistry, The Ohio State University, Columbus, Ohio, USA
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48
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Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH. Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol Cell 2008; 30:315-24. [PMID: 18471977 DOI: 10.1016/j.molcel.2008.02.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/31/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
Abstract
We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substituting Mn(2+) for Mg(2+) significantly decreases the fidelity of DNA synthesis. The structures reveal that the enzyme is in a closed conformation like that observed with a matched Watson-Crick base pair. The incorrect dAMPCPP binds in a conformation identical to that observed with the correct nucleotide. To accommodate the incorrect nucleotide and closed protein conformation, the template strand in the vicinity of the active site has shifted upstream over 3 A, removing the coding base from the active site and generating an abasic templating pocket. The primer terminus rotates as its complementary template base is repositioned. This rotation moves O3' of the primer terminus away from the alpha-phosphate of the incoming nucleotide, thereby deterring misincorporation.
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Affiliation(s)
- Vinod K Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
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49
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Joyce CM, Potapova O, Delucia AM, Huang X, Basu VP, Grindley NDF. Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 2008; 47:6103-16. [PMID: 18473481 DOI: 10.1021/bi7021848] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have developed a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP and have used this and other fluorescence assays to place the fingers-closing step within the reaction pathway. Because the rate of fingers-closing was substantially faster than the rate of nucleotide incorporation measured in chemical quench experiments, fingers-closing cannot be the rate-limiting prechemistry step defined by earlier kinetic studies. Experiments using Ca (2+) instead of Mg (2+) as the metal cofactor suggest instead that the prechemistry step may involve a change in metal ion occupancy at the polymerase active site. The use of ribonucleotide substrates shows there is a base discriminating step that precedes fingers-closing. This earlier step, detected by 2-AP fluorescence, is promoted by complementary nucleotides (ribo- as well as deoxyribo-) but is blocked by mismatches. The complementary rNTP blocks the subsequent fingers-closing step. Thus, discrimination against rNTPs occurs during the transition from open to closed conformations, whereas selection against mismatched bases is initiated earlier in the pathway, in the open complex. Mismatched dNTPs accelerate DNA release from the polymerase, suggesting the existence of an early intermediate in which DNA binding is destabilized relative to the binary complex; this could correspond to a conformation that allows an incoming dNTP to preview the template base. The early kinetic checkpoints identified by this study provide an efficient mechanism for the rejection of mismatched bases and ribose sugars and thus enhance polymerase throughput.
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Affiliation(s)
- Catherine M Joyce
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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50
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Mendieta J, Cases-González CE, Matamoros T, Ramírez G, Menéndez-Arias L. A Mg2+-induced conformational switch rendering a competent DNA polymerase catalytic complex. Proteins 2008; 71:565-74. [PMID: 17963236 DOI: 10.1002/prot.21711] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The structural and dynamical changes occurring before nucleotide addition were studied using molecular dynamics (MD) simulations of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexes containing one or two Mg2+ ions in the presence of dNTP. Our models revealed that the formation of a catalytically competent DNA polymerase complex required subtle rearrangements at the catalytic site A, which occurred only when an Mg2+ ion was bound. This model has been validated using pre-steady-state kinetics to show that free Mg2+ is necessary to obtain a catalytically competent polymerase. Kinetic studies carried out with Be2+ as a cofactor permitted the functional discrimination between metal sites A and B. At low concentrations, Be2+ increased the catalytic efficiency of the polymerase, while at higher concentrations, it competed with Mg2+ for binding to site A, and inhibited DNA polymerization. In agreement with experimental data, MD simulations revealed that the catalytic attack distance between the 3-OH of the primer and the phosphorus in complexes containing Be2+ instead of Mg2+ at site A was above 4.5 A. Our findings provide a detailed description of the mechanism of DNA polymerization and should be helpful to understand the molecular basis of DNA replication fidelity.
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Affiliation(s)
- Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
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