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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].”
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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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