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Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024; 64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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2
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Mandal SC, Chakrabarti J. In-silicon studies on hydration in EcoRI-cognate DNA complex. Biophys Chem 2023; 303:107121. [PMID: 37837721 DOI: 10.1016/j.bpc.2023.107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023]
Abstract
Restriction endonucleases (REs) cleave DNA at specific site in presence of Mg2+ ion. Experiments further emphasize the role of hydration in metal ion specificity and sequence specificity of DNA cleavage. However, the relation between hydration and specificity has not been understood till date. This leads us to study via all-atom molecular dynamics (MD) simulations how the hydration around the scissile phosphate group changes in presence of Mg2+ and Ca2+ and depend on the DNA sequence. We observe the least number of hydrogen bonds around the scissile phosphate group in presence of Mg2+ ion. We further find that the hydrogen bonds decrease at the scissile phosphate on mutating one base pair in the cleavage region of the DNA in Mg2+ loaded EcoRI-DNA complex. We also perform steered MD simulations and observe that the rate of decrease of fraction of hydrogen bonds is slower in the mutated complex than the unmutated complex.
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Affiliation(s)
- Sasthi Charan Mandal
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India..
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Neamtu A, Serban DN, Barritt GJ, Isac DL, Vasiliu T, Laaksonen A, Serban IL. Molecular dynamics simulations reveal the hidden EF-hand of EF-SAM as a possible key thermal sensor for STIM1 activation by temperature. J Biol Chem 2023; 299:104970. [PMID: 37380078 PMCID: PMC10400917 DOI: 10.1016/j.jbc.2023.104970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/07/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca2+ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca2+ depletion. STIM1 is also activated by temperature independent of ER Ca2+ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca2+ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca2+-loaded form compared to the Ca2+-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca2+ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania; Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Dragomir N Serban
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania.
| | - Greg J Barritt
- Discipline of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Dragos Lucian Isac
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Tudor Vasiliu
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden; Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, P. R. China
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4
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Kaur R, Nikkel DJ, Aboelnga MM, Wetmore SD. The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1. J Phys Chem B 2022; 126:10672-10683. [PMID: 36485014 DOI: 10.1021/acs.jpcb.2c06756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, Faculty of Science, Damietta University, New Damietta 34517, Egypt
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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5
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Aboelnga MM, Wetmore SD. Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme. J Am Chem Soc 2019; 141:8646-8656. [PMID: 31046259 DOI: 10.1021/jacs.9b03986] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohamed M. Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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6
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Krachtus D, Smith JC, Imhof P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase. Molecules 2018; 23:E3342. [PMID: 30563005 PMCID: PMC6321591 DOI: 10.3390/molecules23123342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022] Open
Abstract
Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.
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Affiliation(s)
- Dieter Krachtus
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
| | - Jeremy C Smith
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831-6255, USA.
| | - Petra Imhof
- Freie Universität Berlin, Institute for Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany.
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7
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Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Ogrizek M, Konc J, Bren U, Hodošček M, Janežič D. Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand. Chem Cent J 2016; 10:41. [PMID: 27398092 PMCID: PMC4939058 DOI: 10.1186/s13065-016-0188-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/27/2016] [Indexed: 12/24/2022] Open
Abstract
A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that Tm1631 binds with the DNA and that the Tm1631–DNA complex is an endonuclease repair system with a DNA repair function (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed that the severely bent, strained DNA binds to the protein for the entire 90 ns of classical molecular dynamics (MD) performed; we could observe no significant changes in the most distorted region of the DNA, where the cleavage of phosphodiester bond occurs. In this article, we modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond. After addition of two Mg2+ ions to the reaction center and extension of classical MD by 50 ns (totaling 140 ns), the DNA ligand stayed bolted to the protein. Results from density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the reaction is analogous to known endonuclease mechanisms: an enzyme reaction mechanism with two Mg2+ ions in the reaction center and a pentacovalent intermediate. The minimum energy pathway profile shows that the phosphodiester bond cleavage step of the reaction is kinetically controlled and not thermodynamically because of a lack of any energy barrier above the accuracy of the energy profile calculation. The role of ions is shown by comparing the results with the reaction mechanisms in the absence of the Mg2+ ions where there is a significantly higher reaction barrier than in the presence of the Mg2+ ions.A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. We modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond ![]()
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Affiliation(s)
- Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia ; Laboratory for Physical Chemistry and Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia ; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Urban Bren
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia ; Laboratory for Physical Chemistry and Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia ; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
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9
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Govindaraju A, Cortez JD, Reveal B, Christensen SM. Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease. Nucleic Acids Res 2016; 44:3276-87. [PMID: 26961309 PMCID: PMC4838377 DOI: 10.1093/nar/gkw134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/07/2023] Open
Abstract
Non-LTR retrotransposons are an important class of mobile elements that insert into host DNA by target-primed reverse transcription (TPRT). Non-LTR retrotransposons must bind to their mRNA, recognize and cleave their target DNA, and perform TPRT at the site of DNA cleavage. As DNA binding and cleavage are such central parts of the integration reaction, a better understanding of the endonuclease encoded by non-LTR retrotransposons is needed. This paper explores the R2 endonuclease domain from Bombyx mori using in vitro studies and in silico modeling. Mutations in conserved sequences located across the putative PD-(D/E)XK endonuclease domain reduced DNA cleavage, DNA binding and TPRT. A mutation at the beginning of the first α-helix of the modeled endonuclease obliterated DNA cleavage and greatly reduced DNA binding. It also reduced TPRT when tested on pre-cleaved DNA substrates. The catalytic K was located to a non-canonical position within the second α-helix. A mutation located after the fourth β-strand reduced DNA binding and cleavage. The motifs that showed impaired activity form an extensive basic region. The R2 biochemical and structural data are compared and contrasted with that of two other well characterized PD-(D/E)XK endonucleases, restriction endonucleases and archaeal Holliday junction resolvases.
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Affiliation(s)
- Aruna Govindaraju
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019-0498, USA
| | - Jeremy D. Cortez
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019-0498, USA
| | - Brad Reveal
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019-0498, USA
| | - Shawn M. Christensen
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019-0498, USA
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10
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Mones L, Tang WJ, Florián J. Empirical valence bond simulations of the chemical mechanism of ATP to cAMP conversion by anthrax edema factor. Biochemistry 2013; 52:2672-82. [PMID: 23480863 DOI: 10.1021/bi400088y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two-metal catalysis by the adenylyl cyclase domain of the anthrax edema factor toxin was simulated using the empirical valence bond (EVB) quantum mechanical/molecular mechanical approach. These calculations considered the energetics of the nucleophile deprotonation and the formation of a new P-O bond in aqueous solution and in the enzyme-substrate complex present in the crystal structure models of the reactant and product states of the reaction. Our calculations support a reaction pathway that involves metal-assisted transfer of a proton from the nucleophile to the bulk aqueous solution followed by subsequent formation of an unstable pentavalent intermediate that decomposes into cAMP and pyrophosphate (PPi). This pathway involves ligand exchange in the first solvation sphere of the catalytic metal. At 12.9 kcal/mol, the barrier for the last step of the reaction, the cleavage of the P-O bond to PPi, corresponds to the highest point on the free energy profile for this reaction pathway. However, this energy is too close to the value of 11.4 kcal/mol calculated for the barrier of the nucleophilic attack step to reach a definitive conclusion about the rate-limiting step. The calculated reaction mechanism is supported by reasonable agreement between the experimental and calculated catalytic rate constant decrease caused by the mutation of the active site lysine 346 to arginine.
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Affiliation(s)
- Letif Mones
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60660, USA
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11
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Ribeiro AJM, Ramos MJ, Fernandes PA. The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations. J Am Chem Soc 2012; 134:13436-47. [DOI: 10.1021/ja304601k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- António J. M. Ribeiro
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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12
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Density functional investigations on alkali metal (Li, Na, K) catalyzed thymidylyl (3′–5′) thymidine phosphodiester hydrolysis. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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14
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Zahran M, Berezniak T, Imhof P, Smith JC. Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease. FEBS Lett 2011; 585:2739-43. [DOI: 10.1016/j.febslet.2011.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/20/2011] [Accepted: 07/25/2011] [Indexed: 10/17/2022]
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15
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Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF. Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J Mol Biol 2010; 402:524-38. [PMID: 20691189 DOI: 10.1016/j.jmb.2010.07.050] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/22/2010] [Accepted: 07/25/2010] [Indexed: 11/19/2022]
Abstract
Cyclic diguanylate (or bis-(3'-5') cyclic dimeric guanosine monophosphate; c-di-GMP) is a ubiquitous second messenger that regulates diverse cellular functions, including motility, biofilm formation, cell cycle progression, and virulence in bacteria. In the cell, degradation of c-di-GMP is catalyzed by highly specific EAL domain phosphodiesterases whose catalytic mechanism is still unclear. Here, we purified 13 EAL domain proteins from various organisms and demonstrated that their catalytic activity is associated with the presence of 10 conserved EAL domain residues. The crystal structure of the TBD1265 EAL domain was determined in free state (1.8 Å) and in complex with c-di-GMP (2.35 A), and unveiled the role of conserved residues in substrate binding and catalysis. The structure revealed the presence of two metal ions directly coordinated by six conserved residues, two oxygens of c-di-GMP phosphate, and potential catalytic water molecule. Our results support a two-metal-ion catalytic mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
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Affiliation(s)
- Anatoli Tchigvintsev
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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16
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Xie F, Briggs JM, Dupureur CM. Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study. J Inorg Biochem 2010; 104:665-72. [PMID: 20347155 PMCID: PMC2913505 DOI: 10.1016/j.jinorgbio.2010.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 02/03/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
Abstract
Metallonucleases conduct metal-dependent nucleic acid hydrolysis. While metal ions serve in multiple mechanistic capacities in these enzymes, precisely how the attacking water is activated remains unclear for those lacking an obvious general base. All arguments hinge on appropriate pK(a)s for active site moieties very close to this species, and measurement of the pK(a) of a specific water molecule is difficult to access experimentally. Here we describe a computational approach for exploring the local electrostatic influences on the water-derived nucleophile in metallonucleases featuring the common PD...(D/E)xK motif. We utilized UHBD to predict the pK(a)s of active site groups, including that of a water molecule positioned to act as a nucleophile. The pK(a) of a Mg(II)-ligated water molecule hydrogen bonded to the conserved Lys70 in a Mg(II)-PvuII enzyme complex was calculated to be 6.5. The metal and the charge on the Lys group were removed in separate experiments; both resulted in the elevation of the pK(a) of this water molecule, consistent with contributions from both moieties to lowering this pK(a). This behavior is preserved among other PD...(D/E)xK metallonucleases. pK(a)s extracted from the pH dependence of the single turnover rate constant are compared to previous experimental data and the above predicted pK(a)s.
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17
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Prasannan CB, Xie F, Dupureur CM. Characterizing metalloendonuclease mixed metal complexes by global kinetic analysis. J Biol Inorg Chem 2010; 15:533-45. [PMID: 20084532 DOI: 10.1007/s00775-010-0621-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/21/2009] [Indexed: 11/25/2022]
Affiliation(s)
- Charulata B Prasannan
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
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18
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Dupureur CM. One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics 2010; 2:609-20. [PMID: 21072352 DOI: 10.1039/c0mt00013b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and The Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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Kirk BA, Cusack CL, Laager E, Rochlis E, Thomas T, Cassano AG. Mononuclear and dinuclear mechanisms for catalysis of phosphodiester cleavage by alkaline earth metal ions in aqueous solution. J Inorg Biochem 2009; 104:207-10. [PMID: 19932511 DOI: 10.1016/j.jinorgbio.2009.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/31/2009] [Accepted: 10/07/2009] [Indexed: 11/29/2022]
Abstract
In biological systems, enzymes often use metal ions, especially Mg(2+), to catalyze phosphodiesterolysis, and model aqueous studies represent an important avenue of examining the contributions of these ions to catalysis. We have examined Mg(2+) and Ca(2+) catalyzed hydrolysis of the model phosphodiester thymidine-5'-p-nitrophenyl phosphate (T5PNP). At 25 degrees C, we find that, despite their different Lewis acidities, these ions have similar catalytic ability with second-order rate constants for attack of T5PNP by hydroxide (k(OH)) of 4.1x10(-4)M(-1)s(-1) and 3.7x10(-4)M(-1)s(-1) in the presence of 0.30M Mg(2+) and Ca(2+), respectively, compared to 8.3x10(-7)M(-1)s(-1) in the absence of divalent metal ion. Examining the dependence of k(OH) on [M(2+)] at 50 degrees C indicates different kinetic mechanisms with Mg(2+) utilizing a single ion mechanism and Ca(2+) operating by parallel single and double ion mechanisms. Association of the metal ion(s) occurs prior to nucleophilic attack by hydroxide. Comparing the k(OH) values reveals a single Mg(2+) catalyzes the reaction by 1800-fold whereas a single Ca(2+) ion catalyzes the reaction by only 90-fold. The second Ca(2+) provides an additional 10-fold catalysis, significantly reducing the catalytic disparity between Mg(2+) and Ca(2+).
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Affiliation(s)
- Brittany A Kirk
- Department of Chemistry, Drew University, 36 Madison Ave., Madison, NJ 07940, USA
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Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol 2009; 393:140-60. [PMID: 19682999 DOI: 10.1016/j.jmb.2009.08.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 08/05/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022]
Abstract
Restriction endonucleases of the PD...D/EXK family need Mg(2+) for DNA cleavage. Whereas Mg(2+) (or Mn(2+)) promotes catalysis, Ca(2+) (without Mg(2+)) only supports DNA binding. The role of Mg(2+) in DNA cleavage by restriction endonucleases has elicited many hypotheses, differing mainly in the number of Mg(2+) involved in catalysis. To address this problem, we measured the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by BamHI, BglII, Cfr10I, EcoRI, EcoRII (catalytic domain), MboI, NgoMIV, PspGI, and SsoII, which were reported in co-crystal structure analyses to bind one (BglII and EcoRI) or two (BamHI and NgoMIV) Me(2+) per active site. DNA cleavage experiments were carried out at various Mg(2+) and Mn(2+) concentrations at constant ionic strength. All enzymes show a qualitatively similar Mg(2+) and Mn(2+) concentration dependence. In general, the Mg(2+) concentration optimum (between approximately 1 and 10 mM) is higher than the Mn(2+) concentration optimum (between approximately 0.1 and 1 mM). At still higher Mg(2+) or Mn(2+) concentrations, the activities of all enzymes tested are reduced but can be reactivated by Ca(2+). Based on these results, we propose that one Mg(2+) or Mn(2+) is critical for restriction enzyme activation, and binding of a second Me(2+) plays a role in modulating the activity. Steady-state kinetics carried out with EcoRI and BamHI suggest that binding of a second Mg(2+) or Mn(2+) mainly leads to an increase in K(m), such that the inhibitory effect of excess Mg(2+) or Mn(2+) can be overcome by increasing the substrate concentration. Our conclusions are supported by molecular dynamics simulations and are consistent with the structural observations of both one and two Me(2+) binding to these enzymes.
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Affiliation(s)
- Vera Pingoud
- Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Pinjari RV, Kaptan SS, Gejji SP. Alkali metals (Li, Na, and K) in methyl phosphodiester hydrolysis. Phys Chem Chem Phys 2009; 11:5253-62. [PMID: 19551192 DOI: 10.1039/b812000e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The phosphodiester linkage central to biological systems has been modeled by methyl phosphodiester (MPDE) in various theoretical and experimental studies. Under physiological conditions, hydrolysis of the phosphodiester is negligible, however this process can be catalyzed in the presence of metal ions. To understand the role of alkali metals in MPDE hydrolysis and, in particular, how it influences the reaction pathway and the associated energetics, density functional calculations employing the 6-31+G(d,p) basis set have been carried out. Different pathways that include the reactant, intermediates and the products have been investigated for MPDE hydrolysis catalyzed by one or two lithium ions, characterized as stationary point geometries on the potential energy surface. The pathways A and B incorporate a single lithium ion bonded to different oxygens of the diester functionality. In pathway C, a six-membered ring was noticed wherein the nucleophile bridges two lithium ions interacting with different oxygens of the phosphoryl group. Furthermore, in the pathway (D) incorporating two lithium ions, one of the lithium ions interacts with the hydroxyl group and another with the methoxy oxygen; both metal ions are coordinated by the same phosphoryl oxygen. In addition to this, yet another pathway (E), where the metal ions are bound to different oxygens of the phosphoryl group, has also been dealt with. The calculations have shown that the A and B pathways lead to a single step reaction. A three-step mechanism including the nucleophilic (hydroxyl) attack, rotation of a methyl group and, finally, departure of the methoxy group has been predicted for the D and E profiles. Both D and E pathways are favored equally (with a marginal difference of 0.3 kJ mol(-1) in their activation energies) in the gas phase and a transition state corresponding to nucleophilic attack with an energy barrier of 32.5 kJ mol(-1) was located when lithium was used. A penta-coordinated phosphorous intermediate on the potential energy surface was characterized along these pathways. MPDE hydrolysis yielded a lower energy barrier for lithium than those for the remaining alkali metal ions. This agrees well with the experimentally observed trend for the hydrolysis rates: Li > Na > K. Self consistent reaction field (SCRF) calculations reveal the lower energy barrier between the reactant and the transition state for the nucleophilic attack in nonpolar solvents. The extent of bond formation (or cleavage) in different stationary point structures along the reaction path as estimated from the electron density at the bond critical point in the molecular electron density topography, has proven useful in distinguishing the associative or dissociative reaction pathways.
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Affiliation(s)
- Rahul V Pinjari
- Department of Chemistry, University of Pune, Ganeshkhind, Pune 411007, India
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Vardi-Kilshtain A, Roca M, Warshel A. The empirical valence bond as an effective strategy for computer-aided enzyme design. Biotechnol J 2009; 4:495-500. [PMID: 19229886 DOI: 10.1002/biot.200800299] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ability of the empirical valence bond (EVB) to be used in screening active site residues in enzyme design is explored in a preliminary way. This validation is done by comparing the ability of this approach to evaluate the catalytic contributions of various residues in chorismate mutase. It is demonstrated that the EVB model can serve as an accurate tool in the final stages of computer-aided enzyme design (CAED). The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design.
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Xie F, Qureshi SH, Papadakos GA, Dupureur CM. One- and two-metal ion catalysis: global single-turnover kinetic analysis of the PvuII endonuclease mechanism. Biochemistry 2009; 47:12540-50. [PMID: 18975919 DOI: 10.1021/bi801027k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ester hydrolysis is one of the most ubiquitous reactions in biochemistry. Many of these reactions rely on metal ions for various mechanistic steps. A large number of metal-dependent nucleases have been crystallized with two metal ions in their active sites. In spite of an ongoing discussion about the roles of these metal ions in nucleic acid hydrolysis, there are very few studies which examine this issue using the native cofactor Mg(II) and global fitting of reaction progress curves. As part of a comprehensive study of the representative homodimeric PvuII endonuclease, we have collected single-turnover DNA cleavage data as a function of Mg(II) concentration and globally fit these data to a number of models which test various aspects of the metallonuclease mechanism. DNA association rate constants are approximately 100-fold higher in the presence of the catalytically nonsupportive Ca(II) versus the native cofactor Mg(II), highlighting an interesting cofactor difference. A pathway in which metal ions bind prior to DNA is kinetically favored. The data fit well to a model in which both one and two metal ions per active site (EM(2)S and EM(4)S, respectively) support cleavage. Interestingly, the cleavage rate for EM(2)S is approximately 100-fold slower than that displayed by EM(4)S. Collectively, these data indicate that for the PvuII system, catalysis involving one metal ion per active site can indeed occur, but that a more efficient two-metal ion mechanism can be operative under saturating metal ion (in vitro) conditions.
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Affiliation(s)
- Fuqian Xie
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri, St. Louis, Missouri 63121, USA
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Kinetic analysis of product release and metal ions in a metallonuclease. Arch Biochem Biophys 2009; 483:1-9. [PMID: 19161971 DOI: 10.1016/j.abb.2009.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/02/2009] [Accepted: 01/05/2009] [Indexed: 10/21/2022]
Abstract
Most nucleases rely on divalent cations as cofactors to catalyze the hydrolysis of nucleic acid phosphodiester bonds. Here both equilibrium and kinetic experiments are used to test recently proposed models regarding the metal ion dependence of product release and the degree of cooperativity between metal ions bound in the active sites of the homodimeric PvuII endonuclease. Equilibrium fluorescence anisotropy studies indicate that product binding is dramatically weakened in the presence of metal ions. Pre-steady state kinetics indicate that product release is at least partially rate limiting. Steady state and pre-steady state data fit best to models in which metals remain bound to the enzyme after the release of product. Finally, analysis of cooperative and independent binding models for metal ions indicates that single turnover kinetic data are consistent with little to no positive cooperativity between the two metal ions binding each active site.
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Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. J Mol Biol 2008; 384:489-502. [PMID: 18835275 DOI: 10.1016/j.jmb.2008.09.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/10/2008] [Accepted: 09/16/2008] [Indexed: 11/20/2022]
Abstract
The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.
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Dupureur CM. Roles of metal ions in nucleases. Curr Opin Chem Biol 2008; 12:250-5. [PMID: 18261473 DOI: 10.1016/j.cbpa.2008.01.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
Abstract
The hydrolysis of phosphodiester bonds by metallonucleases is crucial to most aspects of nucleic acid processing. In recent years, studies of the classical restriction endonucleases have given way to the characterization of metallonucleases with widely divergent active site motifs. These developments fuel debates regarding the roles of metal ions in these enzymes. It is fortuitous that the current literature also includes the increased application of a variety of computational techniques to test the roles of metal ions in nucleic acid hydrolysis by these systems. This includes recent proposals and indirect evidence that these enzymes utilize metal ion movement in these reactions.
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Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri-St. Louis, MC 27, One University Boulevard, St. Louis, MO 63121, United States.
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