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A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc Natl Acad Sci U S A 2008; 105:4615-20. [PMID: 18353991 DOI: 10.1073/pnas.0708058105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
O(6)-alkylguanine-DNA alkyltransferase (AGT) repairs damage to the human genome by flipping guanine and thymine bases into its active site for irreversible transfer of alkyl lesions to Cys-145, but how the protein identifies its targets has remained unknown. Understanding molecular recognition in this system, which can serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all kingdoms of life, is particularly important given that inhibitors are in clinical trials as anticancer therapeutics. Computational approaches introduced recently for harvesting and statistically characterizing trajectories of molecularly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT and the forces that promote it. In contrast to previously proposed flipping mechanisms, we observe a two-step process that promotes a kinetic, rather than a thermodynamic, gate-keeping strategy for lesion discrimination. Connection is made to recent single-molecule studies of DNA-repair proteins sliding on DNA to understand how they sense subtle chemical differences between bases efficiently.
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. Ab Initio Comprehensive Conformational Analysis of 2‘-Deoxyuridine, the Biologically Significant DNA Minor Nucleoside, and Reconstruction of Its Low-Temperature Matrix Infrared Spectrum. J Phys Chem B 2007; 112:1240-50. [DOI: 10.1021/jp074747o] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yevgen P. Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Roman O. Zhurakivsky
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Mahmoud Ghomi
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Svitlana P. Samijlenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143, Kyiv, Ukraine, UMR CNRS 7033, Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Université Pierre et Marie Curie, GENOPOLE-Campus 1, 5 rue Henri Desbruères, 91030 Evry Cedex, France, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France, and Department of Quantum Radiophysics, Faculty of
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Priyakumar UD, MacKerell AD. Computational approaches for investigating base flipping in oligonucleotides. Chem Rev 2006; 106:489-505. [PMID: 16464016 DOI: 10.1021/cr040475z] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- U Deva Priyakumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 21201, USA
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Liu P, Burdzy A, Sowers LC. Substrate recognition by a family of uracil-DNA glycosylases: UNG, MUG, and TDG. Chem Res Toxicol 2002; 15:1001-9. [PMID: 12184783 DOI: 10.1021/tx020030a] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In response to continuous hydrolytic and oxidative DNA damage, cells of all organisms have a complex network of repair systems that recognize, remove, and rebuild the injured sites. Damaged pyrimidines are generally removed by glycosylases that must scan the entire genome to locate lesions with sufficient fidelity to selectively remove the damage without inadvertent removal of normal bases. We report here studies conducted with a series of base analogues designed to test mechanisms of base recognition suggested by structural studies of glycosylase complexes. The oligonucleotide series examined here includes 5-halouracils with increasing substituent size and purine analogues placed opposite the target uracil with hydrogen, amino, and keto substituents in the 2- and 6-positions. The glycosylases studied here include Escherichia coli uracil-DNA glycosylase (UNG), E. coli mismatch uracil-DNA glycosylase (MUG), and the Methanobacterium thermoautotrophicum mismatch thymine-DNA glycosylase (TDG). The results of this study suggest that these glycosylases utilize several strategies for base identification, including (1) steric limitations on the size of the 5-substituent, (2) electronic-inductive properties of the 5-substituent, (3) reduced thermal stability of mispairs, and (4) specific functional groups on the purine base in the opposing strand. Contrary to predictions based upon the crystal structure, the preference of MUG for mispaired uracil over thymine is not based upon steric exclusion. Furthermore, the preference for mispaired uracil over uracil paired with adenine is more likely due to reduced thermal stability as opposed to specific recognition of the mispaired guanine. On the other hand, TDG, which exhibits modest discrimination among various pyrimidines, shows strong interactions with functional groups present on the purine opposite the target pyrimidine. These results provide new insights into the mechanisms of base selection by DNA repair glycosylases.
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Affiliation(s)
- Pingfang Liu
- Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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Antony J, Medvedev DM, Stuchebrukhov AA. Theoretical Study of Electron Transfer between the Photolyase Catalytic Cofactor FADH- and DNA Thymine Dimer. J Am Chem Soc 2000. [DOI: 10.1021/ja993784t] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Antony
- Contribution from the Department of Chemistry, University of California, Davis, California 95616
| | - Dmitry M. Medvedev
- Contribution from the Department of Chemistry, University of California, Davis, California 95616
| | - Alexei A. Stuchebrukhov
- Contribution from the Department of Chemistry, University of California, Davis, California 95616
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Shroyer MJ, Bennett SE, Putnam CD, Tainer JA, Mosbaugh DW. Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis. Biochemistry 1999; 38:4834-45. [PMID: 10200172 DOI: 10.1021/bi982986j] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of the conserved histidine-187 located in the leucine intercalation loop of Escherichia coli uracil-DNA glycosylase (Ung) was investigated. Using site-directed mutagenesis, an Ung H187D mutant protein was created, overproduced, purified to apparent homogeneity, and characterized in comparison to wild-type Ung. The properties of Ung H187D differed from Ung with respect to specific activity, substrate specificity, DNA binding, pH optimum, and inhibition by uracil analogues. Ung H187D exhibited a 55000-fold lower specific activity and a shift in pH optimum from pH 8.0 to 7.0. Under reaction conditions optimal for wild-type Ung (pH 8.0), the substrate preference of Ung H187D on defined single- and double-stranded oligonucleotides (25-mers) containing a site-specific uracil target was U/G-25-mer > U-25-mer > U/A-25-mer. However, Ung H187D processed these same DNA substrates at comparable rates at pH 7.0 and the activity was stimulated approximately 3-fold relative to the U-25-mer substrate. Ung H187D was less susceptible than Ung to inhibition by uracil, 6-amino uracil, and 5-fluorouracil. Using UV-catalyzed protein/DNA cross-linking to measure DNA binding affinity, the efficiency of Ung H187D binding to thymine-, uracil-, and apyrimidinic-site-containing DNA was (dT20) = (dT19-U) >/= (dT19-AP). Comparative analysis of the biochemical properties and the X-ray crystallographic structures of Ung and Ung H187D [Putnam, C. D., Shroyer, M. J. N., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W., and Tainer, J. A. (1999) J. Mol. Biol. 287, 331-346] provided insight regarding the role of His-187 in the catalytic mechanism of glycosylic bond cleavage. A novel mechanism is proposed wherein the developing negative charge on the uracil ring and concomitant polarization of the N1-C1' bond is sustained by resonance effects and hydrogen bonding involving the imidazole side chain of His-187.
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Affiliation(s)
- M J Shroyer
- Departments of Microbiology, Environmental and Molecular Toxicology, Biochemistry and Biophysics, and the Environmental Health Science Center, Oregon State University, Corvallis, Oregon 97331, USA
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Affiliation(s)
- S H Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709-2233, USA.
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Affiliation(s)
- H A Nash
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA.
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Singer B, Hang B. What structural features determine repair enzyme specificity and mechanism in chemically modified DNA? Chem Res Toxicol 1997; 10:713-32. [PMID: 9250405 DOI: 10.1021/tx970011e] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A crucial question in repair is how do enzymes recognize substrates. In surveying the relevant literature, it becomes evident that there are no rules which can be clearly applied. At this time it appears that uracil glycosylase is the only repair enzyme for which all the known substrates can be rationalized on the basis of chemical structure. When surveying the multiplicity of substrates for m3A-DNA glycosylase, it is difficult, on the basis of present knowledge, to explain why 1,N6-etheno-A (epsilon A) is as good a substrate, if not better, than m3A for which the enzyme is named. There is no apparent unifying chemical structure which is required for recognition. It should also be noted that many studies of the mechanism of m3A-DNA glycosylase only utilized-N-3- and N-7-alkylpurines. On this basis, an electron-deficient purine, and later pyrimidine, was considered to be the recognition signal. Since epsilon A and Hx do not fall in this class, this is one illustration of why exploring new substrates becomes important in elucidating enzyme mechanisms. Ubiquitous enzymes, such as 5'-AP endonucleases, are present in both prokaryotes and eukaryotes. The primary function is the same, i.e., repair of an AP site which occurs through natural processes or from the action of DNA glycosylases. There are, however, completely unrelated substrates such as the exocyclic adducts pBQ-dC and pBQ-dG. pBQ-dC is repaired by both the human HAP1 and E. coli Exo III and Endo IV, while pBQ-dG is only repaired by the E. coli enzymes. Yet, when repair of these adducts occurs, it is by the same unusual pathway which differs from the usual base excision repair mechanism. This finding may ultimately not be as unusual as it now seems. The understanding of substrate recognition by repair enzymes, which can have different repair pathways, is complex. For example, three exocyclic derivatives which each have either the same modification (1,N4-epsilon dA and 3,N4-epsilon dC) or the same base with different modifying groups (3,N4-epsilon dC and 3,N4-pBQ-dC) are repaired by three separate enzymes and two mechanism (Figure 9). Investigators have also reported that two separate enzymes and pathways can be found for simple adducts such as m6G and O4T. It is not clear why, for these adducts, both MGMT and excision repair can be utilized. This could be visualized as a "backup" system and may be more common than now known. We cannot think like an enzyme or vice versa. In the absence of enough necessary information, we can only be descriptive. What information is necessary for further understanding? (1) More detailed structural studies of adducts in defined oligonucleotides would be useful. (2) New substrates should be explored. For example, is the mechanism for PBQ-dC (and pBQ-dG) repair unique? This involves guesswork and intuition. (3) For the adducts mentioned in this Perspective and others, understanding enzyme/substrate recognition will be facilitated by cocrystallography and site-directed mutagenesis. (4) Genetic approaches, such as knockouts or targeted mutations in repair genes, should be expanded in order to focus on the physiological role of a specific enzyme. Above all: structure, structure, structure! Enzymologists, organic chemists, physical chemiste, X-ray crystallographers, and others must combine forces if the fundamental problems addressed here are to be understood.
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Affiliation(s)
- B Singer
- Donner Laboratory, Lawrence Berkeley National Laboratory, University of California, 94720, USA
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Kumar NV, Varshney U. Contrasting effects of single stranded DNA binding protein on the activity of uracil DNA glycosylase from Escherichia coli towards different DNA substrates. Nucleic Acids Res 1997; 25:2336-43. [PMID: 9171083 PMCID: PMC146742 DOI: 10.1093/nar/25.12.2336] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Excision of uracil from tetraloop hairpins and single stranded ('unstructured') oligodeoxyribonucleotides by Escherichia coli uracil DNA glycosylase has been investigated. We show that, compared with a single stranded reference substrate, uracil from the first, second, third and the fourth positions of the loops is excised with highly variable efficiencies of 3.21, 0.37, 5.9 and 66.8%, respectively. More importantly, inclusion of E.coli single stranded DNA binding protein (SSB) in the reactions resulted in approximately 7-140-fold increase in the efficiency of uracil excision from the first, second or the third position in the loop but showed no significant effect on its excision from the fourth position. In contrast, the presence of SSB decreased uracil excision from the single stranded ('unstructured') substrates approximately 2-3-fold. The kinetic studies show that the increased efficiency of uracil release from the first, second and the third positions of the tetraloops is due to a combination of both the improved substrate binding and a large increase in the catalytic rates. On the other hand, the decreased efficiency of uracil release from the single stranded substrates ('unstructured') is mostly due to the lowering of the catalytic rates. Chemical probing with KMnO4showed that the presence of SSB resulted in the reduction of cleavage of the nucleotides in the vicinity of dUMP residue in single stranded substrates but their increased susceptibility in the hairpin substrates. We discuss these results to propose that excision of uracil from DNA-SSB complexes by uracil DNA glycosylase involves base flipping. The use of SSB in the various applications of uracil DNA glycosylase is also discussed.
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Affiliation(s)
- N V Kumar
- Centre for Genetic Engineering, Indian Institute of Science, Bangalore 560 012, India
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