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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
Abstract
How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.
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“In fact, the structures of DNA in complex with N-glycosylase/DNA lyase (OGG1), which is a base-excision repair enzyme for 8oxoG, exist in a catalytically active form for 8oxoG that is adjacent to guanine only in the 5’-position in -AGGT- sequences (S12 Fig) [40,48–51].”
Citations
Cites
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,429
Crystal structure of the nucleosome core particle at 2.8 Å resolution
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. (1997) · Nature · doi:10.1038/38444 · Cited by 9,466
Huang, H., Chopra, R., Verdine, G. L., & Harrison, S. C. (1998) · Science · doi:10.1126/science.282.5394.1669 · Cited by 1,420
Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
Bruner, S. D., Norman, D. P. G., & Verdine, G. L. (2000) · Nature · doi:10.1038/35002510 · Cited by 972
Carson, M. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891007240 · Cited by 809
Mutagenesis by 8-oxoguanine: an enemy within
Grollman, A. P., & Moriya, M. (1993) · Trends in Genetics · doi:10.1016/0168-9525(93)90089-z · Cited by 807
Michaels, M. L., & Miller, J. H. (1992) · Journal of Bacteriology · doi:10.1128/jb.174.20.6321-6325.1992 · Cited by 697
Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., & Karplus, M. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp0029109 · Cited by 515
Brooks, C. L., Karplus, M., & Pettitt, B. M. 1. (1988) · Advances in chemical physics · doi:10.1002/9780470141205 · Cited by 502
Free Energy Simulations Come of Age: Protein−Ligand Recognition
Simonson, T., Archontis, G., & Karplus, M. (2002) · Accounts of Chemical Research · doi:10.1021/ar010030m · Cited by 379
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CHARMM: The biomolecular simulation program
Brooks, B. R., Brooks, C. L., MacKerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21287 · Cited by 9,115
Base-excision repair of oxidative DNA damage
David, S. S., O'Shea, V. L., & Kundu, S. (2007) · Nature · doi:10.1038/nature05978 · Cited by 1,238
“For this reason, Verdine and co-workers used an innovative covalent trapping method to secure OGG1 in proximity to a G·C base pai”
MethodBlainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L., & Xie, X. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509723103 · Cited by 467
Self-citationQM/MM Methods for Biological Systems
Senn, H. M., & Thiel, W. (2006) · Springer eBooks · doi:10.1007/128_2006_084 · Cited by 435
DNA glycosylases: In DNA repair and beyond
Jacobs, A. L., & Schär, P. (2012) · Chromosoma · doi:10.1007/s00412-011-0347-4 · Cited by 407
Senn, H. M., & Thiel, W. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2007.01.684 · Cited by 386
Structure of the Human MutSα DNA Lesion Recognition Complex
Warren, J. J., Pohlhaus, T. J., Changela, A., Iyer, R. R., Modrich, P. L., & Beese, L. S. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.04.018 · Cited by 361
DNA damage by reactive species: Mechanisms, mutation and repair
Jena, N. R. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9218-2 · Cited by 358
Nonspecifically bound proteins spin while diffusing along DNA
Blainey, P. C., Luo, G., Kou, S. C., Mangel, W. F., Verdine, G. L., Bagchi, B., & Xie, X. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1716 · Cited by 329
Zharkov, D. O. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-7543-2 · Cited by 314
Berti, P. J., & McCann, J. A. B. (2006) · Chemical Reviews · doi:10.1021/cr040461t · Cited by 258
8-Oxoguanine DNA glycosylase 1: Beyond repair of the oxidatively modified base lesions
Ba, X., & Boldogh, I. R. (2017) · Redox Biology · doi:10.1016/j.redox.2017.11.008 · Cited by 255
Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation
Visnes, T., Cázares‐Körner, A., Hao, W., Wallner, O. A., Masuyer, G., Loseva, O., Mortusewicz, O., Wiita, E., Sarno, A., Manoilov, A., et al. (2018) · Science · doi:10.1126/science.aar8048 · Cited by 235
Hitomi, K., Iwai, S., & Tainer, J. A. (2007) · DNA Repair · doi:10.1016/j.dnarep.2006.10.004 · Cited by 220
Frontiers in Molecular Dynamics Simulations of DNA
Pérez, A., Luque, F. J., & Orozco, M. (2011) · Accounts of Chemical Research · doi:10.1021/ar2001217 · Cited by 215
Direct Reversal of DNA Alkylation Damage
Mishina, Y., Duguid, E. M., & He, C. (2006) · Chemical Reviews · doi:10.1021/cr0404702 · Cited by 215
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA
Parker, J. B., Bianchet, M. A., Krosky, D. J., Friedman, J. I., Amzel, L. M., & Stivers, J. T. (2007) · Nature · doi:10.1038/nature06131 · Cited by 200
DNA–Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes
Tretyakova, N. Y., Groehler, A. S., & Ji, S. (2015) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5b00056 · Cited by 205
Pan, L., Zhu, B., Hao, W., Zeng, X., Vlahopoulos, S., Hazra, T. K., Hegde, M. L., Radak, Z. O., Bácsi, A., Brasier, A. R., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.751453 · Cited by 203
“Importantly, when 8-oxoG was placed in the synthetic probes outside of OGG1’s “footprint” (39, 40) at 8 –11 bp from the NF- B-binding motif, OGG1 increased its DNA occupancy.”
BackgroundInfluentialStructure of a DNA Glycosylase Searching for Lesions
Banerjee, A., Santos, W. L., & Verdine, G. L. (2006) · Science · doi:10.1126/science.1120288 · Cited by 194
Self-citationStructural basis of histone demethylation by LSD1 revealed by suicide inactivation
Yang, M., Culhane, J. C., Szewczuk, L. M., Gocke, C. B., Brautigam, C. A., Tomchick, D. R., Machius, M., Cole, P. A., & Yu, H. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1255 · Cited by 181
“Covalent tethering of substrates to enzymes or cofactors has proven to be an effective strategy for capturing transient enzyme–substrate complexes and enabling their structural characterizatio”
BackgroundThe Role of Oxidative Stress, Mitochondrial Function, and Autophagy in Diabetic Polyneuropathy
Sifuentes-Franco, S., Pacheco-Moisés, F. P., Rodríguez-Carrizález, A. D., & Miranda‐Díaz, A. G. (2017) · Journal of Diabetes Research · doi:10.1155/2017/1673081 · Cited by 186
“In normal conditions, the 8-OHdG can be repaired by the endonuclease 8-oxoguanine DNA glycosylase (hOGG1) enzyme through mechanisms of base excision [40].”
BackgroundRecent advances in the structural mechanisms of DNA glycosylases
Brooks, S. C., Adhikary, S., Rubinson, E. H., & Eichman, B. F. (2012) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2012.10.005 · Cited by 183
Detection of Damaged DNA Bases by DNA Glycosylase Enzymes
Friedman, J. I., & Stivers, J. T. (2010) · Biochemistry · doi:10.1021/bi100593a · Cited by 181
“method developed in the Verdine lab (20-22, 26-28).”
BackgroundMethodSpecificity of Human Thymine DNA Glycosylase Depends on N -Glycosidic Bond Stability
Bennett, M. T., Rodgers, M. T., Hebert, A. S., Ruslander, L. E., Eisele, L. E., & Drohat, A. C. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0634829 · Cited by 172
Sequence-Dependent Basepair Opening in DNA Double Helix
Krueger, A., Protozanova, E., & Frank-Kamenetskii, M. D. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.078774 · Cited by 166
“DNA damage repair enzymes, such as uracil DNA glycosylase (9,10), 8-oxoguanine DNA glycosylase I (11, 12 ), and alkyl adenine DNA glycosylase (13) also utilize the baseflipping mechanism.”
BackgroundMolecular dynamics simulations of nucleic acid–protein complexes
MacKerell, A. D., & Nilsson, L. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.012 · Cited by 165
Zou, X., Koh, G. C. C., Nanda, A. S., Degasperi, A., Urgo, K., Roumeliotis, T. I., Agu, C. A., Badja, C., Momen, S., Young, J., et al. (2021) · Nature Cancer · doi:10.1038/s43018-021-00200-0 · Cited by 164
DNA base repair – recognition and initiation of catalysis
Dalhus, B., Laerdahl, J. K., Backe, P. H., & Bjørås, M. (2009) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2009.00188.x · Cited by 176
Structure and Substrate Recognition of the Escherichia coli DNA Adenine Methyltransferase
Horton, J. R., Liebert, K., Békés, M., Jeltsch, A., & Cheng, X. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.028 · Cited by 141
Structure and mechanism for DNA lesion recognition
Yang, W. (2007) · Cell Research · doi:10.1038/cr.2007.116 · Cited by 137
Amouroux, R., Campalans, A., Epe, B., & Radicella, J. P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1247 · Cited by 140
“explain DNA-glycosylase damage recognition (11,12).”
The Role of 8-Oxoguanine DNA Glycosylase-1 in Inflammation
Ba, X., Aguilera-Aguirre, L., Rashid, Q. T. A., Bácsi, A., Radak, Z. O., Sur, S., Hosoki, K., Hegde, M. L., & Boldogh, I. R. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms150916975 · Cited by 128
“The flipped out 8-oxoG base is excised via cleavage of its N-glycosidic bond, and 8-oxoG is released from DNA as a free base [21,22].”
BackgroundDNA apurinic-apyrimidinic site binding and excision by endonuclease IV
Garcin, E. D., Hosfield, D. J., Desai, S. A., Haas, B. J., Bjørås, M., Cunningham, R. P., & Tainer, J. A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1414 · Cited by 114
“Thus, binding of these damaged bases might involve a solvent-exposed 'preincision' pocket outside the active site, as seen for human oxoguanine DNA glycosylase 1 (ref”
BackgroundPierre, V. C., Kaiser, J. T., & Barton, J. K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610170104 · Cited by 113
Zharkov, D. O., Mechetin, G. V., & Nevinsky, G. A. (2009) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2009.10.017 · Cited by 113
“A technique of disulfide crosslinking, which have proved tremendously useful with some other DNA glycosylases [52,96] may be applied to obtain such complexes.”
BackgroundMethodTanner, L., Single, A., Bhongir, R. K. V., Heusel, M., Mohanty, T., Karlsson, C. A. Q., Pan, L., Clausson, C.-M., Bergwik, J., Wang, K., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36314-5 · Cited by 111
Breakdown of oligosaccharides by the process of elimination
Yip, V. L. Y., & Withers, S. G. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.02.005 · Cited by 108
Poor base stacking at DNA lesions may initiate recognition by many repair proteins
Yang, W. (2006) · DNA repair · doi:10.1016/j.dnarep.2006.02.004 · Cited by 105
Biological Properties of Single Chemical−DNA Adducts: A Twenty Year Perspective
Delaney, J. C., & Essigmann, J. M. (2007) · Chemical Research in Toxicology · doi:10.1021/tx700292a · Cited by 102
Lee, S., & Verdine, G. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902908106 · Cited by 102
Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA
Bagchi, B., Blainey, P. C., & Xie, X. S. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp077568f · Cited by 100
The Structure of the Human AGT Protein Bound to DNA and its Implications for Damage Detection
Duguid, E. M., Rice, P. A., & He, C. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.028 · Cited by 96
“As demonstrated recently for hOGG1, the base-flipping DNA repair proteins may possess a mechanism that prefers the specific lesion to be inserted fully into the active site, while undamaged bases are more likely to be at a second binding conformation.(47) In the absence of an alkyl lesion, a normal base such as thymin…”
BackgroundFree-energy calculations in structure-based drug design
Shirts, M. R., Mobley, D. L., & Brown, S. P. (2010) · Cambridge University Press eBooks · doi:10.1017/cbo9780511730412.007 · Cited by 100
Computational Approaches for Investigating Base Flipping in Oligonucleotides
Priyakumar, U. D., & MacKerell, A. D. (2005) · Chemical Reviews · doi:10.1021/cr040475z · Cited by 94
Kinetic gating mechanism of DNA damage recognition by Rad4/XPC
Chen, X., Velmurugu, Y., Zheng, G., Park, B., Shim, Y., Kim, Y., Liu, L., Houten, B. V., He, C., Ansari, A., et al. (2015) · Nature Communications · doi:10.1038/ncomms6849 · Cited by 94
Separation-of-function mutants unravel the dual-reaction mode of human 8-oxoguanine DNA glycosylase
Dalhus, B., Forsbring, M., Helle, I. H., Vik, E. S., Forstrøm, R. J., Backe, P. H., Alseth, I., & Bjørås, M. (2011) · Structure · doi:10.1016/j.str.2010.09.023 · Cited by 89
“, 1997), it has been proposed that Lys249 is important for specific recognition of 8oxoG versus normal guanine partly through formation of an electrostatic dipole between the Lys249 and Cys253 side chains (Banerjee et al., 2005).”
BackgroundMethodInfluentialCrystal structure of a p53 core tetramer bound to DNA
Malecka, K. A., Ho, W. C., & Marmorstein, R. (2008) · Oncogene · doi:10.1038/onc.2008.400 · Cited by 87
“This particular strategy, which requires some knowledge of the protein/DNA interface, has previously lead to high-resolution structures and a deeper understanding of HIV-1 reverse transcriptase(Huang et al., 1998) and MutM DNA glycosylase(Banerjee et al., 2006; Banerjee et al., 2005).”
BackgroundTime-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
Neely, R. K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki995 · Cited by 87
“TaqI (3)] and various DNA repair enzymes (4), including recently the human proteins AGT (5) and oxoG interacting with undamaged DNA (6).”
Pantsar, T., Rissanen, S., Dauch, D., Laitinen, T., Vattulainen, I., & Poso, A. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006458 · Cited by 85
İleritürk, M., Benzer, F., Aksu, E. H., Yıldırım, S., Kandemır, F. M., Doğan, T., Dörtbudak, M. Y., & Genç, A. (2020) · Journal of Food Biochemistry · doi:10.1111/jfbc.13593 · Cited by 81
An unprecedented nucleic acid capture mechanism for excision of DNA damage
Rubinson, E. H., Gowda, A. S. P., Spratt, T. E., Gold, B. I., & Eichman, B. F. (2010) · Nature · doi:10.1038/nature09428 · Cited by 81
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT
Hu, J., Ma, A., & Dinner, A. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708058105 · Cited by 79
“In contrast to the ‘‘push–pull’’ mechanism once proposed for nucleotide flipping (2, 5), we observe a two-step process that promotes a kinetic, rather than a thermodynamic (3, 7, 8), gate-keeping strategy for lesion discrimination.”
BackgroundLead (Pb) induced Oxidative Stress as a Mechanism to Cause Neurotoxicity in Drosophila melanogaster
Olakkaran, S., Anupama, K. P., Antony, A., & Gurushankara, H. P. (2021) · Toxicology · doi:10.1016/j.tox.2021.152959 · Cited by 77
Radom, C. T., Banerjee, A., & Verdine, G. L. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m608989200 · Cited by 75
Duplex interrogation by a direct DNA repair protein in search of base damage
Yi, C., Chen, B., Qi, B., Zhang, W., Jia, G., Zhang, L., Li, C. J., Dinner, A. R., Yang, C., & He, C. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2320 · Cited by 76
Reading the chromatinized genome
Michael, A. K., & Thomä, N. H. (2021) · Cell · doi:10.1016/j.cell.2021.05.029 · Cited by 79
OGG1-DNA interactions facilitate NF-κB binding to DNA targets
Pan, L., Hao, W., Zheng, X., Zeng, X., Abbasi, A. A., Boldogh, I. R., & Ba, X. (2017) · Scientific Reports · doi:10.1038/srep43297 · Cited by 77
8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutS
Macpherson, P. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki813 · Cited by 76
“OGG1 scans the helix and, possible alerted to the presence of its substrate by an altered torsional rigidity in the DNA (48,49), extrudes the oxidized base from the helix and accommodates it deep within the active site (50,51).”
BackgroundhOGG1 Ser326Cys polymorphism and susceptibility to gallbladder cancer in a Chinese population
Jiao, X., Huang, J., Wu, S., MingdeLv, Hu, Y., Jianfu, Su, X., Luo, C., & Broelsch, C. (2007) · International Journal of Cancer · doi:10.1002/ijc.22748 · Cited by 72
“Thus, organisms have developed a highly efficient DNA repair machinery consisting of several genes and pathways responsible for removing and repairing damaged DNA; interindividual variation in the repair capacity have been implicated as a cancer susceptibility factor.(21)”
BackgroundIsolation, Characterization, and Independent Synthesis of Guanine Oxidation Products
Gimisis, T., & Cismaş, C. (2006) · European Journal of Organic Chemistry · doi:10.1002/ejoc.200500581 · Cited by 72
Breiner, B., Kaya, K., Roy, S., Yang, W., & Alabugin, I. V. (2012) · Organic & Biomolecular Chemistry · doi:10.1039/c2ob00052k · Cited by 70
Kinetic Conformational Analysis of Human 8-Oxoguanine-DNA Glycosylase
Kuznetsov, N. A., Koval, V. V., Nevinsky, G. A., Douglas, K. T., Zharkov, D. O., & Fedorova, O. S. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m605788200 · Cited by 70
Extrahelical Damaged Base Recognition by DNA Glycosylase Enzymes
Stivers, J. T. (2007) · Chemistry - A European Journal · doi:10.1002/chem.200701501 · Cited by 70
Lee, H.-T., Lin, C.-S., Lee, C.-S., Tsai, C.-Y., & Wei, Y.-H. (2013) · Clinical & Experimental Immunology · doi:10.1111/cei.12256 · Cited by 71
UVA irradiation induces relocalisation of the DNA repair protein hOGG1 to nuclear speckles
Campalans, A., Amouroux, R., Bravard, A., Epe, B., & Radicella, J. P. (2006) · Journal of Cell Science · doi:10.1242/jcs.03312 · Cited by 67
“One open question is how hOGG1 and other proteins initiating DNA repair manage to find and repair the damaged DNA, especially considering the high degree of DNA condensation in the cell nucleus (Halford and Marko, 2004; Banerjee et al., 2005).”
BackgroundEfficient Removal of Formamidopyrimidines by 8-Oxoguanine Glycosylases
Krishnamurthy, N., Haraguchi, K., Greenberg, M. M., & David, S. S. (2007) · Biochemistry · doi:10.1021/bi701619u · Cited by 66
“Calculations have also indicated the importance of favorable dipole–dipole interactions in hOGG1 recognition of OG (51).”
BackgroundJiang, Y. L., Krosky, D. J., Seiple, L. A., & Stivers, J. T. (2005) · Journal of the American Chemical Society · doi:10.1021/ja055846n · Cited by 67
Surviving the Sun: Repair and bypass of DNA UV lesions
Yang, W. (2011) · Protein Science · doi:10.1002/pro.723 · Cited by 62
“Forced binding of normal DNA or noncognate substrate to repair enzymes can bypass the first step of the DNA rigidity test, but usually cannot pass the second step of the base specificity test.(53,54)”
BackgroundTautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair
Zhu, C., Lu, L., Zhang, J., Yue, Z., Song, J., Zong, S., Liu, M., Stovicek, O., Gao, Y. Q., & Yi, C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604591113 · Cited by 64
“The use of different binding pockets to discriminate a flipped base has precedence in the case of hOGG1, which uses two distinct pockets for recognizing oxoG and G (43).”
BackgroundStudying protein-DNA interactions using atomic force microscopy
Beckwitt, E. C., Kong, M., & Houten, B. V. (2017) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2017.06.028 · Cited by 64
“sapiens Nonspecific 0, 33, 70 1 9, 9, 9 [55] Nonspecific 80 1YQK [116] 2”
Roles of DNA repair enzyme OGG1 in innate immunity and its significance for lung cancer
Vlahopoulos, S., Adamaki, M., Khoury, N., Zoumpourlis, V. C., & Boldogh, I. R. (2018) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2018.09.004 · Cited by 68
Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation
Esadze, A., & Stivers, J. T. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00513 · Cited by 63
Interactions between low energy electrons and DNA: a perspective from first-principles simulations
Kohanoff, J. J., McAllister, M., Tribello, G. A., & Gu, B. (2017) · Journal of Physics Condensed Matter · doi:10.1088/1361-648x/aa79e3 · Cited by 62
Synthesis and Structure of Duplex DNA Containing the Genotoxic Nucleobase Lesion N7-Methylguanine
Lee, S., Bowman, B. R., Ueno, Y., Wang, S., & Verdine, G. L. (2008) · Journal of the American Chemical Society · doi:10.1021/ja8025328 · Cited by 62
Maiti, A., Noon, M. S., MacKerell, A. D., Pozharski, E. V., & Drohat, A. C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201010109 · Cited by 61
Synthesis of Site-Specific DNA–Protein Conjugates and Their Effects on DNA Replication
Yeo, J. E., Wickramaratne, S., Khatwani, S. L., Wang, Y.-C., Vervacke, J. S., Distefano, M. D., & Tretyakova, N. Y. (2014) · ACS Chemical Biology · doi:10.1021/cb5001795 · Cited by 63
Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex
Velmurugu, Y., Chen, X., Slogoff-Sevilla, P., Min, J., & Ansari, A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514666113 · Cited by 60
Jacob, K. D., Hooten, N. N., Tadokoro, T., Lohani, A., Barnes, J., & Evans, M. K. (2013) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2013.05.010 · Cited by 59
Shen, J., Gai, D., Patrick, A. N., Greenleaf, W. B., & Chen, X. S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409646102 · Cited by 58
Damage Detection and Base Flipping in Direct DNA Alkylation Repair
Yang, C., Garcia, K., & He, C. (2009) · ChemBioChem · doi:10.1002/cbic.200800580 · Cited by 57
CUX2 Protein Functions as an Accessory Factor in the Repair of Oxidative DNA Damage
Pal, R., Ramdzan, Z. M., Kaur, S. J., Duquette, P. M., Marcotte, R., Leduy, L., Davoudi, S., Lamarche‐Vane, N., Iulianella, A., & Nepveu, A. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.651042 · Cited by 58
8-Oxoguanine DNA Glycosylases: One Lesion, Three Subfamilies
Faucher, F., Doublié, S., & Jia, Z. (2012) · International Journal of Molecular Sciences · doi:10.3390/ijms13066711 · Cited by 64
“the steric hindrance created by the alanine methyl group [40].”
BackgroundCorrect and incorrect nucleotide incorporation pathways in DNA polymerase β
Radhakrishnan, R., & Tamar Schlick, A. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.09.059 · Cited by 55
Chowdhury, R., Amin, M. A., & Bhattacharyya, K. (2015) · The Journal of Physical Chemistry B · doi:10.1021/jp5120042 · Cited by 55
Nartey, C. M., Nam, K., Oo, K., Kutchukian, P. S., Bowman, B. R., Karplus, M., & Verdine, G. L. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.316497 · Cited by 57
“We were quite intrigued by this seemingly perfect superposition between the dDXL G-complex and the LRC, given the significant calculated energy difference between inserting a G versus an oxoG into the active site (34).”
BackgroundMethodInfluentialActive destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition
Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V., Santos, C. D. L., Grollman, A. P., Fedorova, O. S., Zharkov, D. O., & Simmerling, C. L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1300 · Cited by 54
“Structural studies with three other DNA glycosylases, human 8-oxoguanine-DNA glycosylase OGG1 (34,35), human uracil-DNA glycosylase (36) and E. coli alkylpurine-DNA glycosylase AlkA (37) suggest that extensive sampling of normal bases ending in a catalytically improper conformation of the enzyme– substrate complex may…”
BackgroundEnzymatically inactive OGG1 binds to DNA and steers base excision repair toward gene transcription
Hao, W., Wang, J., Zhang, Y., Wang, C., Xia, L., Zhang, W., Zafar, M., Kang, J., Wang, R., Bohio, A. A., et al. (2020) · The FASEB Journal · doi:10.1096/fj.201902243r · Cited by 53
Synthesis of Sequence-Specific DNA–Protein Conjugates via a Reductive Amination Strategy
Wickramaratne, S., Mukherjee, S., Villalta, P. W., Schärer, O. D., & Tretyakova, N. Y. (2013) · Bioconjugate Chemistry · doi:10.1021/bc400018u · Cited by 53
Lenz, T., Bonnist, E. Y. M., Pljevaljčić, G., Neely, R. K., Dryden, D. T. F., Scheidig, A. J., Jones, A. C., & Weinhold, E. G. (2007) · Journal of the American Chemical Society · doi:10.1021/ja069366n · Cited by 52
Step-by-step mechanism of DNA damage recognition by human 8-oxoguanine DNA glycosylase
Кузнецова, А. А., Kuznetsov, N. A., Ishchenko, A. A., Saparbaev, M. K., & Fedorova, O. S. (2013) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2013.09.035 · Cited by 51
Regulation of DNA glycosylases and their role in limiting disease
Sampath, H., McCullough, A. K., & Lloyd, R. S. (2012) · Free Radical Research · doi:10.3109/10715762.2012.655730 · Cited by 49
“coli endonuclease III (Nth) [57], 8-oxoguanine DNA glycosylase OGG1 [15,21,35,202] and human alkyl adenine glycosylase (AAG) [93].”
A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex
Banerjee, A., & Verdine, G. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603644103 · Cited by 48
Self-citationD’Augustin, O., Huet, S., Campalans, A., & Radicella, J. P. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218360 · Cited by 52
Mechanism of DNA loading by the DNA repair helicase XPD
Constantinescu-Aruxandei, D., Petrovic‐Stojanovska, B., Penedo, J. C., White, M. F., & Naismith, J. H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw102 · Cited by 48
Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS
Saharay, M., Guo, H., & Smith, J. C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012947 · Cited by 51
“as implemented in CHARMM. The SCC-DFTB method is a fast semi-empirical density functional approach that has been extensively tested and applied to several enzymes”
MethodPaquet, N., Adams, M. N., Leong, V., Ashton, N. W., Touma, C., Gamsjaeger, R., Cubeddu, L., Beard, S., Burgess, J. T., Bolderson, E., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv790 · Cited by 49
“While the modality of binding to the 8-oxoG is well documented (8,40), the selective recognition of the damaged base versus unmodified guanine is still not well understood.”
BackgroundQi, Y., Spong, M. C., Nam, K., Karplus, M., & Verdine, G. L. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.069799 · Cited by 47
van Haren, M. J., Marechal, N., Troffer-Charlier, N., Cianciulli, A., Sbardella, G., Cavarelli, J., & Martin, N. I. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618401114 · Cited by 47
“The covalent tethering of substrates to enzymes has proven to be an effective strategy for capturing difficult to characterize enzyme–substrate complexes, leading to their structural characterization (26, 27).”
BackgroundOxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter
Bielskutė, S., Plavec, J., & Podbevšek, P. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab057 · Cited by 52
“OGG1 initiates excision by hydrogen bonding with the protonated N7 of oxoG (61,62).”
Background
Metadata
- Authors
- Banerjee, A., Yang, W., Karplus, M., & Verdine, G. L.
- Affiliations
- Harvard University (US)
- Institut de Science et d'Ingénierie Supramoléculaires (FR)
- Corresponding author
- Karplus, Martin
- Verdine, Gregory L.
- Venue
- Nature
- Published
- 2005-03
- Volume
- 434
- Issue
- 7033
- Pages
- 612-618
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2077615862
- Cited by
- 346
- References
- 31
- Citations by year
- 2026: 8 · 2025: 9 · 2024: 8 · 2023: 6 · 2022: 16 · 2021: 16 · 2020: 15 · 2019: 10 · 2018: 19 · 2017: 20 · 2016: 14 · 2015: 18 · 2014: 15 · 2013: 11 · 2012: 18
- FWCI
- 10.71
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA100742)
- National Institute of General Medical Sciences (R01GM044853)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- OGG1, 8-oxoguanine, oxidative DNA damage, DNA repair, lesion recognition, X-ray crystal structure, free energy difference
- MeSH terms
- Base Sequence, Binding Sites, Computer Simulation, Disulfides, DNA, DNA Damage, DNA Repair, Guanine, Humans, Models, Molecular, Nucleic Acid Conformation, Protein Conformation, Structure-Activity Relationship, Substrate Specificity, Thermodynamics, Reproducibility of Results, Crystallography, X-Ray, DNA Glycosylases
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