101
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Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proc Natl Acad Sci U S A 2015; 112:E5228-36. [PMID: 26351676 DOI: 10.1073/pnas.1511207112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is "balanced," as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pKa of O3' of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability.
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102
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Reddy PT, Jaruga P, Nelson BC, Lowenthal MS, Jemth AS, Loseva O, Coskun E, Helleday T, Dizdaroglu M. Production, Purification, and Characterization of ¹⁵N-Labeled DNA Repair Proteins as Internal Standards for Mass Spectrometric Measurements. Methods Enzymol 2015; 566:305-32. [PMID: 26791985 DOI: 10.1016/bs.mie.2015.06.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by a variety of damaging agents, resulting in the formation of a multiplicity of lesions, which are mutagenic and cytotoxic. Unless repaired by DNA repair mechanisms before DNA replication, DNA lesions can lead to genomic instability, which is one of the hallmarks of cancer. Oxidatively induced DNA damage is mainly repaired by base excision repair pathway with the involvement of a plethora of proteins. Cancer tissues develop greater DNA repair capacity than normal tissues by overexpressing DNA repair proteins. Increased DNA repair in tumors that removes DNA lesions generated by therapeutic agents before they became toxic is a major mechanism in the development of therapy resistance. Evidence suggests that DNA repair capacity may be a predictive biomarker of patient response. Thus, knowledge of DNA-protein expressions in disease-free and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. Our laboratory has developed methodologies that use mass spectrometry with isotope dilution for the measurement of expression of DNA repair proteins in human tissues and cultured cells. For this purpose, full-length (15)N-labeled analogs of a number of human DNA repair proteins have been produced and purified to be used as internal standards for positive identification and accurate quantification. This chapter describes in detail the protocols of this work. The use of (15)N-labeled proteins as internal standards for the measurement of several DNA repair proteins in vivo is also presented.
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Affiliation(s)
- Prasad T Reddy
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA.
| | - Pawel Jaruga
- Biochemical Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Bryant C Nelson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Mark S Lowenthal
- Biochemical Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Erdem Coskun
- Biochemical Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Miral Dizdaroglu
- Biochemical Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.
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103
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Jiang Z, Xu M, Lai Y, Laverde EE, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. Bypass of a 5',8-cyclopurine-2'-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks. DNA Repair (Amst) 2015; 33:24-34. [PMID: 26123757 DOI: 10.1016/j.dnarep.2015.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/23/2015] [Accepted: 06/09/2015] [Indexed: 12/18/2022]
Abstract
5',8-Cyclopurine-2'-deoxynucleosides including 5',8-cyclo-dA (cdA) and 5',8-cyclo-dG (cdG) are induced by hydroxyl radicals resulting from oxidative stress such as ionizing radiation. 5',8-cyclopurine-2'-deoxynucleoside lesions are repaired by nucleotide excision repair with low efficiency, thereby leading to their accumulation in the human genome and lesion bypass by DNA polymerases during DNA replication and base excision repair (BER). In this study, for the first time, we discovered that DNA polymerase β (pol β) efficiently bypassed a 5'R-cdA, but inefficiently bypassed a 5'S-cdA during DNA replication and BER. We found that cell extracts from pol β wild-type mouse embryonic fibroblasts exhibited significant DNA synthesis activity in bypassing a cdA lesion located in replication and BER intermediates. However, pol β knock-out cell extracts exhibited little DNA synthesis to bypass the lesion. This indicates that pol β plays an important role in bypassing a cdA lesion during DNA replication and BER. Furthermore, we demonstrated that pol β inserted both a correct and incorrect nucleotide to bypass a cdA at a low concentration. Nucleotide misinsertion was significantly stimulated by a high concentration of pol β, indicating a mutagenic effect induced by pol β lesion bypass synthesis of a 5',8-cyclopurine-2'-deoxynucleoside. Moreover, we found that bypass of a 5'S-cdA by pol β generated an intermediate that failed to be extended by pol β, resulting in accumulation of single-strand DNA breaks. Our study provides the first evidence that pol β plays an important role in bypassing a 5',8-cyclo-dA during DNA replication and repair, as well as new insight into mutagenic effects and genome instability resulting from pol β bypassing of a cdA lesion.
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Affiliation(s)
- Zhongliang Jiang
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA
| | - Meng Xu
- Department of Chemistry and Biochemistry, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, USA
| | | | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", 15341, Agia Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, USA; Biochemistry Ph.D. Program, USA; Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA.
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104
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DNA polymerases β and λ and their roles in cell. DNA Repair (Amst) 2015; 29:112-26. [DOI: 10.1016/j.dnarep.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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105
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Freudenthal BD, Beard WA, Wilson SH. New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis. DNA Repair (Amst) 2015; 32:3-9. [PMID: 26002198 DOI: 10.1016/j.dnarep.2015.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-lapse X-ray crystallography allows visualization of intermediate structures during the DNA polymerase catalytic cycle. Employing time-lapse crystallography with human DNA polymerase β has recently allowed us to capture and solve novel intermediate structures that are not stable enough to be analyzed by traditional crystallography. The structures of these intermediates reveals exciting surprises about active site metal ions and enzyme conformational changes as the reaction proceeds from the ground state to product release. In this perspective, we provide an overview of recent advances in understanding the DNA polymerase nucleotidyl transferase reaction and highlight both the significance and mysteries of enzyme efficiency and specificity that remain to be solved.
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Affiliation(s)
- Bret D Freudenthal
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States.
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106
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Chauleau M, Das U, Shuman S. Effects of DNA3'pp5'G capping on 3' end repair reactions and of an embedded pyrophosphate-linked guanylate on ribonucleotide surveillance. Nucleic Acids Res 2015; 43:3197-207. [PMID: 25753667 PMCID: PMC4381079 DOI: 10.1093/nar/gkv179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/20/2015] [Indexed: 12/18/2022] Open
Abstract
When DNA breakage results in a 3′-PO4 terminus, the end is considered ‘dirty’ because it cannot prime repair synthesis by DNA polymerases or sealing by classic DNA ligases. The noncanonical ligase RtcB can guanylylate the DNA 3′-PO4 to form a DNA3′pp5′GOH cap. Here we show that DNA capping precludes end joining by classic ATP-dependent and NAD+-dependent DNA ligases, prevents template-independent nucleotide addition by mammalian terminal transferase, blocks exonucleolytic proofreading by Escherichia coli DNA polymerase II and inhibits proofreading by E. coli DNA polymerase III, while permitting templated DNA synthesis from the cap guanosine 3′-OH primer by E. coli DNA polymerase II (B family) and E. coli DNA polymerase III (C family). Human DNA polymerase β (X family) extends the cap primer predominantly by a single templated addition step. Cap-primed synthesis by templated polymerases embeds a pyrophosphate-linked ribonucleotide in DNA. We find that the embedded ppG is refractory to surveillance and incision by RNase H2.
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Affiliation(s)
- Mathieu Chauleau
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Ushati Das
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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107
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Baptiste BA, Jacob KD, Eckert KA. Genetic evidence that both dNTP-stabilized and strand slippage mechanisms may dictate DNA polymerase errors within mononucleotide microsatellites. DNA Repair (Amst) 2015; 29:91-100. [PMID: 25758780 DOI: 10.1016/j.dnarep.2015.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/15/2015] [Accepted: 02/16/2015] [Indexed: 12/19/2022]
Abstract
Mononucleotide microsatellites are tandem repeats of a single base pair, abundant within coding exons and frequent sites of mutation in the human genome. Because the repeated unit is one base pair, multiple mechanisms of insertion/deletion (indel) mutagenesis are possible, including strand-slippage, dNTP-stabilized, and misincorportion-misalignment. Here, we examine the effects of polymerase identity (mammalian Pols α, β, κ, and η), template sequence, dNTP pool size, and reaction temperature on indel errors during in vitro synthesis of mononucleotide microsatellites. We utilized the ratio of insertion to deletion errors as a genetic indicator of mechanism. Strikingly, we observed a statistically significant bias toward deletion errors within mononucleotide repeats for the majority of the 28 DNA template and polymerase combinations examined, with notable exceptions based on sequence and polymerase identity. Using mutator forms of Pol β did not substantially alter the error specificity, suggesting that mispairing-misalignment mechanism is not a primary mechanism. Based on our results for mammalian DNA polymerases representing three structurally distinct families, we suggest that dNTP-stabilized mutagenesis may be an alternative mechanism for mononucleotide microsatellite indel mutation. The change from a predominantly dNTP-stabilized mechanism to a strand-slippage mechanism with increasing microsatellite length may account for the differential rates of tandem repeat mutation that are observed genome-wide.
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Affiliation(s)
- Beverly A Baptiste
- The Jake Gittlen Laboratories for Cancer Research and the Department of Pathology, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Kimberly D Jacob
- The Jake Gittlen Laboratories for Cancer Research and the Department of Pathology, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Kristin A Eckert
- The Jake Gittlen Laboratories for Cancer Research and the Department of Pathology, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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108
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Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature 2015; 517:635-9. [PMID: 25409153 PMCID: PMC4312183 DOI: 10.1038/nature13886] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/23/2014] [Indexed: 12/21/2022]
Abstract
Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol β, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.
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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
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - David D. Shock
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, North Carolina 27709-2233, USA
| | - Taejin Kim
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, USA
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, 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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109
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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110
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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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111
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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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112
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Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry 2014; 53:5683-91. [PMID: 25148552 PMCID: PMC4159208 DOI: 10.1021/bi5007964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA
lesion bypass polymerases process different lesions with varying
fidelities, but the structural, dynamic, and mechanistic origins of
this phenomenon remain poorly understood. Human DNA polymerase κ
(Polκ), a member of the Y family of lesion bypass polymerases,
is specialized to bypass bulky DNA minor groove lesions in a predominantly
error-free manner, by housing them in its unique gap. We have investigated
the role of the unique Polκ gap and N-clasp structural features
in the fidelity of minor groove lesion processing with extensive molecular
modeling and molecular dynamics simulations to pinpoint their functioning
in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine,
2-acetylaminofluorene (dG-N2-AAF), that
is produced via the combustion of kerosene and diesel fuel. Our simulations
reveal how the spacious gap directionally accommodates the lesion
aromatic ring system as it transits through the stages of incorporation
of the predominant correct partner dCTP opposite the damaged guanine,
with preservation of local active site organization for nucleotidyl
transfer. Furthermore, flexibility in Polκ’s N-clasp
facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that
N-clasp flexibility depends on lesion topology, being markedly reduced
in the case of the benzo[a]pyrene-derived major adduct
to N2-dG, whose bypass by Polκ is
nearly error-free. Thus, our studies reveal how Polκ’s
unique structural and dynamic properties can regulate its bypass fidelity
of polycyclic aromatic lesions and how the fidelity is impacted by
lesion structures.
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Affiliation(s)
- Lee Lior-Hoffmann
- Department of Biology and ‡Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
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113
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Yang Y, Qin Y, Ding Q, Bakhtina M, Wang L, Tsai MD, Zhong D. Ultrafast water dynamics at the interface of the polymerase-DNA binding complex. Biochemistry 2014; 53:5405-13. [PMID: 25105470 PMCID: PMC4148141 DOI: 10.1021/bi500810a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA polymerases slide on DNA during replication, and the interface must be mobile for various conformational changes. The role of lubricant interfacial water is not understood. In this report, we systematically characterize the water dynamics at the interface and in the active site of a tight binding polymerase (pol β) in its binary complex and ternary state using tryptophan as a local optical probe. Using femtosecond spectroscopy, we observed that upon DNA recognition the surface hydration water is significantly confined and becomes bound water at the interface, but the dynamics are still ultrafast and occur on the picosecond time scale. These interfacial water molecules are not trapped but are mobile in the heterogeneous binding nanospace. Combining our findings with our previous observation of ultrafast water motions at the interface of a loose binding polymerase (Dpo4), we conclude that the binding interface is dynamic and the water molecules in various binding clefts, channels, and caves are mobile and even fluid with different levels of mobility for loose or tight binding polymerases. Such a dynamic interface should be general to all DNA polymerase complexes to ensure the biological function of DNA synthesis.
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Affiliation(s)
- Yi Yang
- Department of Physics, ‡Department of Chemistry and Biochemistry, and §Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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114
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Bebenek K, Pedersen LC, Kunkel TA. Structure-function studies of DNA polymerase λ. Biochemistry 2014; 53:2781-92. [PMID: 24716527 PMCID: PMC4018081 DOI: 10.1021/bi4017236] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
DNA polymerase λ
(pol λ) functions in DNA repair with
its main roles considered to be filling short gaps during repair of
double-strand breaks by nonhomologous end joining and during base
excision repair. As indicated by structural and biochemical studies
over the past 10 years, pol λ shares many common properties
with other family X siblings (pol β, pol μ, and terminal
deoxynucleotidyl transferase) but also has unique structural features
that determine its specific functions. In this review, we consider
how structural studies over the past decade furthered our understanding
of the behavior and biological roles of pol λ.
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Affiliation(s)
- Katarzyna Bebenek
- Laboratory of Structural Biology and ‡Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health , Research Triangle Park, North Carolina 27709, United States
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115
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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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Yang W. An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Biochemistry 2014; 53:2793-803. [PMID: 24716551 PMCID: PMC4018060 DOI: 10.1021/bi500019s] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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Y-Family
DNA polymerases specialize in translesion synthesis, bypassing
damaged bases that would otherwise block the normal progression of
replication forks. Y-Family polymerases have unique structural features
that allow them to bind damaged DNA and use a modified template base
to direct nucleotide incorporation. Each Y-Family polymerase is unique
and has different preferences for lesions to bypass and for dNTPs
to incorporate. Y-Family polymerases are also characterized by a low
catalytic efficiency, a low processivity, and a low fidelity on normal
DNA. Recruitment of these specialized polymerases to replication forks
is therefore regulated. The catalytic center of the Y-Family polymerases
is highly conserved and homologous to that of high-fidelity and high-processivity
DNA replicases. In this review, structural differences between Y-Family
and A- and B-Family polymerases are compared and correlated with their
functional differences. A time-resolved X-ray crystallographic study
of the DNA synthesis reaction catalyzed by the Y-Family DNA polymerase
human polymerase η revealed transient elements that led to the
nucleotidyl-transfer reaction.
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Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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