Cited by 346DNA Repair MechanismsEnzyme Structure and FunctionDNA and Nucleic Acid Chemistry

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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA

Banerjee, Anirban, Yang, Wei, Karplus, Martin, Verdine, Gregory L.·2005·Nature

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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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Background
Inhibition of DNA Glycosylases via Small Molecule Purine Analogs
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BackgroundInfluential
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“This result may arise from the fact that these site spacings are equal to or less than the DNA footprint of hOGG1 (∼10 bp) (25,26).”
Background
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Background
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Background
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Hamm, M. L., Gill, T. J., Nicolson, S. C., & Summers, M. R. (2007) · Journal of the American Chemical Society · doi:10.1021/ja0716453 · Cited by 40
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Background
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“This exo site is positioned at the entrance to the catalytic pocket and is thought to participate in the base-flipping process and to act as an initial gate keeper in screening G’s from 8-oxoG’s before full extrusion to the active site.(91) More recent studies have captured and modeled MutM in very early-encounter com…”
Background
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BackgroundMethodInfluential
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Background
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Background
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Self-citation
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“Disulfide crosslinking has been successfully used to covalently trap protein/DNA complexes (e.g., Banerjee et al., 2005, 2006).”
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“Previous structures of hOGG1 in complex with undamaged DNA (23, 24)(3) have shown that cross-linking the FIGURE 3.”
Background
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“…search, recognize, and excise oxoG from DNA has been studied quite extensively by using a combination of biochemical and structural techniques (Banerjee et al., 2005, 2006; Banerjee and Verdine, 2006; Bruner et al., 2000; Coste et al., 2004; Fromme et al., 2003, 2004; Fromme and Verdine,…”
BackgroundMethod
Disulfide bridge as a linker in nucleic acids’ bioconjugation. Part II: A summary of practical applications
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Background
Base Flipping of the Thymine Dimer in Duplex DNA
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“The crystal structure of the complex of 8-oxoguanine DNA glycosylase I with DNA has recently shown that, in the interaction between the protein and theDNA, the negative charge of 8-oxoguanine has an important role to provide the preferential binding affinity of mutagenic guanine compared with normal guanine (Banerjee…”
Background
Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V
Ahmadi, A., Rosnes, I., Blicher, P., Diekmann, R., Schüttpelz, M., Glette, K., Tørresen, J., Bjørås, M., Dalhus, B., & Rowe, A. D. (2018) · Nature Communications · doi:10.1038/s41467-018-07797-4 · Cited by 25
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DNA Damage Processing by Human 8-Oxoguanine-DNA Glycosylase Mutants with the Occluded Active Site
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“Following the results of quantum mechanics/molecular mechanics data (14) and OGG1 mechanism considerations (12), some amino acid residues were simulated in nonstandard protonation state to approximate the situation immediately preceding the nucleophilic attack.”
BackgroundInfluential
The C-terminal Lysine of Ogg2 DNA Glycosylases is a Major Molecular Determinant for Guanine/8-Oxoguanine Distinction
Faucher, F., Wallace, S. S., & Doublié, S. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.01.024 · Cited by 24
“Although a direct interaction between a protein oxygen and the N7-H of 8-oxoG has been observed in Ogg1 and Ogg2 enzymes, another hypothesis has been suggested to explain the guanine/8-oxoG distinction by Ogg glycosylases: The dipole change on the C8 and N7 atoms of 8-oxoG compared to guanine has been proposed to be i…”
Innate Immune Responses to RSV Infection Facilitated by OGG1, an Enzyme Repairing Oxidatively Modified DNA Base Lesions
Zheng, X., Wang, K., Pan, L., Hao, W., Xue, Y., Bácsi, A., Vlahopoulos, S., Radak, Z. O., Hazra, T. K., Brasier, A. R., et al. (2022) · Journal of Innate Immunity · doi:10.1159/000524186 · Cited by 24
Role of DNA repair in the protection against genotoxic stress
Camenisch, U., & Naegeli, H. (2009) · Proceedings of the Fourth International Symposium on Polarization Phenomena in Nuclear Reactions · doi:10.1007/978-3-7643-8336-7_5 · Cited by 24
Glycosidic bond cleavage in deoxynucleotides — A density functional study
Millen, A. L., & Wetmore, S. D. (2009) · Canadian Journal of Chemistry · doi:10.1139/v09-024 · Cited by 24
The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine
Šebera, J., Hattori, Y., Sato, D., Řeha, D., Nencka, R., Kohno, T., Kojima, C., Tanaka, Y., & Sychrovský, V. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx157 · Cited by 25
Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2′-deoxyguanosine and guanosine
Wu, R., Chen, Y., & Rodgers, M. T. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp05738h · Cited by 24
Comparative Effects of Ions, Molecular Crowding, and Bulk DNA on the Damage Search Mechanisms of hOGG1 and hUNG
Cravens, S. L., & Stivers, J. T. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00482 · Cited by 23
Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations
Kara, M., & Zacharias, M. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.01.032 · Cited by 23
PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes
Kuznetsov, N. A., Milov, A. D., Isaev, N. P., Vorobjev, Y. N., Koval, V. V., Dzuba, S. A., Fedorova, O. S., & Tsvetkov, Y. D. (2011) · Molecular BioSystems · doi:10.1039/c1mb05189j · Cited by 23
Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair
Jena, N. R., & Bansal, M. (2011) · Physical Biology · doi:10.1088/1478-3975/8/4/046007 · Cited by 23
A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase
Li, H., Endutkin, A. V., Bergonzo, C., Campbell, A. J., Santos, C. D. L., Grollman, A. P., Zharkov, D. O., & Simmerling, C. L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1092 · Cited by 24
“Probably the best-characterized example so far is hOGG1, which possesses an ‘exo-site,’ which traps adventitiously everted G in the lowest energy state but is only fleetingly visited by everted oxoG (60,61).”
Background
Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2
Jena, N. R., Pant, S., & Srivastava, H. K. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1883112 · Cited by 23
“After repair, these nucleotides are sent back to their original positions, mainly because of the internal dynamics of DNA and DNA–polymerase complex (Banerjee et al., 2005; Jena, 2012; Peterson, 1995; Dizdaroglu et al., 2017).”
Background
Structures and Energetics of Base Flipping of the Thymine Dimer Depend on DNA Sequence
O'Neil, L. L., & Wiest, O. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp7102935 · Cited by 23
An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine–DNA Glycosylase (hOgg1)
Kellie, J. L., Wilson, K. A., & Wetmore, S. D. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b04051 · Cited by 22
Base Excision Repair and Nucleotide Excision Repair
Izumi, T., & Mellon, I. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-803309-8.00017-3 · Cited by 22
Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA
Басов, А. А., Drobotenko, M. I., Svidlov, A. A., Gerasimenko, E. O., Malyshko, V. V., Елкина, А. А., Baryshev, M., & Dzhimak, S. S. (2020) · Molecules · doi:10.3390/molecules25163753 · Cited by 23
“So, for the catalytic activity of DNA glycosylase, 8-oxoguanine DNA glycosylase I, and alkyl adenine DNA glycosylase (which are the important DNA repair enzymes [42]), as well as DNA methyltransferase family enzymes and”
Background
Silver-coated silicon nanowire platform discriminates genomic DNA from normal and malignant human epithelial cells using label-free Raman spectroscopy
Mussi, V., Ledda, M., Polese, D., Maiolo, L., Paria, D., Barman, I., Lolli, M. G., Lisi, A., & Convertino, A. (2021) · Materials Science and Engineering C · doi:10.1016/j.msec.2021.111951 · Cited by 22
DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes
Liu, M., Zhang, J., Zhu, C., Zhang, X., Xiao, W., Yan, Y., Liu, L., Zeng, H., Gao, Y. Q., & Yi, C. (2021) · Nature Communications · doi:10.1038/s41467-021-24431-y · Cited by 23
Sequence-dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA glycosylase MutM
Sung, R.-J., Zhang, M., Qi, Y., & Verdine, G. L. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.313635 · Cited by 21
Mechanistic and Conformational Flexibility of the Covalent Linkage Formed during β-Lyase Activity on an AP-Site: Application to hOgg1
Kellie, J. L., & Wetmore, S. D. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp306344g · Cited by 22
Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes
Neely, R. K., Tamulaitis, G., Chen, K., Kubala, M. H., Šikšnys, V., & Jones, A. C. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp688 · Cited by 21
“It was first observed for the methyltransferase enzyme HhaI (1) and has since been observed in many other DNA methyltransferase systems (2–6) and several DNA-repair enzyme complexes (7,8).”
Background
Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns
Naômé, A., Schyman, P., Laaksonen, A., & Vercauteren, D. P. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp1000539 · Cited by 20
Crystal structure analysis of DNA lesion repair and tolerance mechanisms
Schneider, S., Kath‐Schorr, S., & Carell, T. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.01.005 · Cited by 20
Quantum Theoretical Study of Cleavage of the Glycosidic Bond of 2′-Deoxyadenosine: Base Excision-Repair Mechanism of DNA by MutY
Tiwari, S., Agnihotri, N. P., & Mishra, P. C. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp1109256 · Cited by 20
Computational Investigation of Glycosylase and β-Lyase Activity Facilitated by Proline: Applications to FPG and Comparisons to hOgg1
Sowlati‐Hashjin, S., & Wetmore, S. D. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp507783d · Cited by 22
Estrogen Drives Cellular Transformation and Mutagenesis in Cells Expressing the Breast Cancer–Associated R438W DNA Polymerase Lambda Protein
Nemec, A. A., Bush, K. B., Towle-Weicksel, J. B., Taylor, B. F., Schulz, V., Weidhaas, J. B., Tuck, D. P., & Sweasy, J. B. (2016) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-16-0209 · Cited by 20
“8oxoG possesses a two-atom difference compared with guanine (8), and its ability to functionally resemble thymine allows replicative polymerases to insert adenines leading to G:T transversions (9–11).”
Background
Kinetics and Thermodynamics of DNA Processing by Wild Type DNA-Glycosylase Endo III and Its Catalytically Inactive Mutant Forms
Kladova, O. A., Krasnoperov, L. N., Kuznetsov, N. A., & Fedorova, O. S. (2018) · Genes · doi:10.3390/genes9040190 · Cited by 19
Epigenetic regulation of TIMP1 expression by 8‐oxoguanine DNA glycosylase‐1 binding to DNA:RNA hybrid
Pan, L., Wang, H. Z., Luo, J., Zeng, J., Pi, J., Liu, H., Liu, C., Ba, X., Qu, X., Xiang, Y., et al. (2019) · The FASEB Journal · doi:10.1096/fj.201900993rr · Cited by 19
“As expected from previous structural and functional analysis, OGG1 showed greater affinity for dsDNA contained 8-oxoG (52, 63).”
Background
Genotoxic effects of PM10 and PM2.5 bound metals: metal bioaccessibility, free radical generation, and role of iron
Yadav, S., Kumbhar, N., Jan, R., Roy, R., & Satsangi, P. G. (2018) · Environmental Geochemistry and Health · doi:10.1007/s10653-018-0199-4 · Cited by 19
“…by hydroxyl radicals, which leads to the formation of oxidative single and clustered base damage by mutagenic lesion in cellular DNA followed by DNA strand breaking, cross linkage of DNA–protein and its basic site (Ji et al. 2005; Banerjee et al. 2005, 2006; Schyman et al. 2008; Cadet et al. 2010).”
Background
1D Radical Motion in Protein Pocket: Proton-Coupled Electron Transfer in Human Serum Albumin
Kobori, Y., & Norris, J. R. (2005) · Journal of the American Chemical Society · doi:10.1021/ja054495+ · Cited by 19
The Role of the Oxidative State and Innate Immunity Mediated by TLR7 and TLR9 in Lupus Nephritis
Miranda‐Díaz, A. G., Echavarría, R., Cardona-Muñóz, E. G., Ortiz‐Lazareno, P. C., Sierra, J. A., Gómez-Hermosillo, L. F., Casillas-Moreno, J., Campos-Bayardo, T. I., Román-Rojas, D., & García-Sánchez, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242015234 · Cited by 17
“8-OHdG can be repaired primarily by the human enzyme 8-oxo guanine DNA glycosylase 1 (hOGG1) through base excision repair mechanisms. hOGG1 performs preventive actions against inﬂammatory responses by reconﬁguring 8-OHdG levels [34,35].”
Background
Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase
Kirpota, O. O., Endutkin, A. V., Ponomarenko, M. P., Ponomarenko, P. M., Zharkov, D. O., & Nevinsky, G. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1333 · Cited by 18
“This enzyme is known to search for oxoG lesions flipping out normal bases from DNA (27), a process that overall would be more efficient in less stable duplexes.”
Background
O6-Methylguanine Repair by O6-Alkylguanine-DNA Alkyltransferase
Jena, N. R., Shukla, P. K., Jena, H. S., Mishra, P., & Suhai, S. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp907836w · Cited by 18
Pyramidalization of the Glycosidic Nitrogen Provides the Way for Efficient Cleavage of the N-Glycosidic Bond of 8-OxoG with the hOGG1 DNA Repair Protein
Šebera, J., Trantı́rek, L., Tanaka, Y., & Sychrovský, V. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp309098d · Cited by 18
Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping
Hendershot, J. M., & O’Brien, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku919 · Cited by 18
8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme
Hoppins, J. J., Gruber, D. R., Miears, H. L., Kiryutin, A. S., Kasymov, R. D., Petrova, D. V., Endutkin, A. V., Popov, A. V., Yurkovskaya, A. V., Fedechkin, S. O., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164424 · Cited by 18
Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants
Lloyd, R. S. (2022) · DNA · doi:10.3390/dna2040020 · Cited by 16
“Moreover, as revealed by various biophysical techniques and structure–function analyses, these enzymes create a flexible active site into which damaged nucleotides can be flipped and accommodated between globular and active site-forming domains (Figure 1B) [17,19,20,22,23].”
Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles
Ren, M., Gut, F., Fan, Y., Ma, J., Shan, X., Yikilmazsoy, A., Likhodeeva, M., Hopfner, K., & Zhou, C. (2024) · Nature Communications · doi:10.1038/s41467-024-53811-3 · Cited by 21
“However, when the glycosylase is covalently linked to the dsDNA, native guanine can also be ﬂ ipped out from the DNA helix, resulting in a kinked DNA strand 31 .”
Background
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics
Fadda, E., & Pomès, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq812 · Cited by 17

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.
ORCID: Banerjee, Anirban
Yang, Wei
Karplus, Martin
Verdine, Gregory L.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2005-03
Volume: 434
Issue: 7033
Pages: 612-618
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature03458
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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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA

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