Structural Characterization of Viral Ortholog of Human DNA Glycosylase NEIL1 Bound to Thymine Glycol or 5-Hydroxyuracil-containing DNA

Imamura, Kiichi; Averill, April M.; Wallace, Susan S.; Doublié, Sylvie

doi:10.1074/jbc.m111.315309

Cited by 49 publications

(83 citation statements)

References 61 publications

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“…For oxoG-recognizing Fpg proteins, the similar lesion recognition loop is much longer, although the lesion recognition loops of Bacillus stearothermophilus Fpg (BstFpg) and Lactococcus lactis Fpg were either visible or disordered in different structures (36,38,39); for Arabidopsis thaliana Fpg which does not excise oxoG, its corresponding loop was found to be in one uniform conformation in the apo and THF-bound structures (40). For the Tg-recognizing MvNei1, only one conformation was observed for the corresponding loop in the apo, THF-and Tg-bound structures of MvNei1, which mostly resembles the THF-bound NEIL1 structure (33,34). Nevertheless, our structures revealed that the lesion recognition loop of NEIL1 can adopt multiple conformations, and this flexibility is important for optimal substrate binding.…”

Section: Discussionmentioning

confidence: 99%

“…Although the crystal structure of NEIL1 protein is determined (32), a complex structure of NEIL1 bound to duplex DNA has not been reported. Recent studies have determined several complex structures of MvNei1 (mimivirus Nei1), a viral ortholog of human NEIL1 (33,34). However, MvNei1 and NEIL1 have apparent differences in their 3D structures and enzymatic properties (5).…”

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confidence: 99%

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Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

Zhu

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

119

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NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we present crystal structures of human NEIL1 bound to a range of duplex DNA. Together with computational and biochemical analyses, our results suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)-a preferred substrate-for optimal binding in its active site. Moreover, this tautomerization event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the present example represents the first documented case of enzymepromoted tautomerization for efficient substrate recognition and catalysis in an enzyme-catalyzed reaction.base-excision repair | substrate recognition | enzyme catalysis | glycosylase | QM/MM D NA oxidation damage can be induced by both endogenous and environmental reactive oxygen species. Such oxidized DNA bases are primarily recognized and removed by the baseexcision repair (BER) pathway, which is initiated by a lesionspecific DNA glycosylase (1-4). Based on sequence homology and structural motifs, glycosylases that cleave oxidation damage are grouped into two families: the helix-hairpin-helix (HhH) family and the Fpg/Nei family (5, 6); the latter is named after the prototypical bacterial members formamidopyrimidine DNA glycosylase (Fpg) and endonuclease eight (Nei).NEIL1 (Nei-like 1) is one such Fpg/Nei family glycosylase that guards the mammalian genome against oxidation damage (7-10). NEIL1 is bifunctional in that it catalyzes both the hydrolysis of the N-glycosylic bond linking a base to a deoxyribose (glycosylase activity) and the subsequent cleavage of the DNA 3′ to the newly created apurinic/apyrimidinic site (lyase activity) (7-10). The N terminus contains the glycosylase domain of NEIL1, and the C terminus is intrinsically disordered (8,11). Whereas the C terminus is dispensable for both glycosylase and lyase activities in vitro, it interacts with many proteins in vivo and is required for efficient DNA repair activity inside the cells (12, 13). NEIL1 is also unique among the three human NEIL proteins in that it is increased in an S-phase-specific manner and carries out prereplicative repair of oxidized bases in the human genome (8,12). Moreover, increasing literature has further emphasized the importance of NEIL1's cellular repair activity, as NEIL1 deficiency has led to multiple abnormalities and is associated with severe human diseases, including cancer (14-19). Additionally, emerging evidence has also implicated a role of NEIL1 in active DNA demethylation (20)(21)(22).NEIL1 is capable of removing a wide array of oxidized pyrimidines and purines; representative substrates of extensive investigations include thymine glycol (Tg), 5-hydroxyuracil (5-OHU), 5-hydroxycytosine (5-OHC), dihydrothymine (DHT), and dihydrouracil (DHU), as well as the formamidopyridines (FapyA and FapyG), spiroiminodihydantoin (Sp), and guanidinohydanto...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

Zhu

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

119

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“…However, FapyG is recognized even when this loop is deleted (42). There are currently no structures of bacterial Nei or Nth with lesions in the substrate binding pocket, but the structure of a viral ortholog of human NEIL1, MvNei, has been solved with Tg or 5-hydroxyuracil in the binding site pocket (43). Fig.…”

Section: Discussionmentioning

confidence: 99%

Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases

Nelson

Dunn

Kathe

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

113

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DNA glycosylases are enzymes that perform the initial steps of base excision repair, the principal repair mechanism that identifies and removes endogenous damages that occur in an organism's DNA. We characterized the motion of single molecules of three bacterial glycosylases that recognize oxidized bases, Fpg, Nei, and Nth, as they scan for damages on tightropes of λ DNA. We find that all three enzymes use a key "wedge residue" to scan for damage because mutation of this residue to an alanine results in faster diffusion. Moreover, all three enzymes bind longer and diffuse more slowly on DNA that contains the damages they recognize and remove. Using a sliding window approach to measure diffusion constants and a simple chemomechanical simulation, we demonstrate that these enzymes diffuse along DNA, pausing momentarily to interrogate random bases, and when a damaged base is recognized, they stop to evert and excise it.DNA repair | search mechanisms O xidative DNA damage is produced endogenously during normal cellular metabolism or exogenously by chemical agents and ionizing radiation (1, 2). Oxidatively induced DNA damage resulting from attack by reactive oxygen species accounts for approximately one-half of all DNA base damages (3). Some oxidative base damages, such as thymine glycol, are blocks to DNA polymerases and thus potentially lethal; however, the majority of oxidative base lesions mispair with noncognate bases and are potentially mutagenic (4). Therefore, damaged bases must be repaired to maintain the cell's genomic integrity. With substantial in vivo steady-state levels of oxidative damages, alkylation damages, and apurinic/apyrimidinic (AP) sites among the nearly six billion normal bases, how DNA repair enzymes locate these damages in the sea of undamaged bases has been the subject of much speculation.The DNA repair mechanism responsible for the removal of the majority of endogenous DNA damages is the base excision repair (BER) pathway (4-6). The critical first step in BER is carried out by a DNA glycosylase that, fueled only by thermal energy, locates a damaged base and cleaves the N-glycosyl bond, thus removing the base lesion from the sugar phosphate backbone. Glycosylases are small monomeric proteins that are found in all living organisms and can be separated into different families based on substrate specificity and structural motifs. In Escherichia coli, there are three glycosylases, Nth, Fpg, and Nei, that directly remove oxidized DNA bases, and all three have an associated lyase activity that cleaves the DNA backbone. These glycosylases are members of two structural families, the helixhairpin-helix (HhH) or Nth superfamily and the helix-two turnshelix (H2TH) or Fpg/Nei family (7-9) (Fig. 1A). Interestingly, the HhH superfamily member, endonuclease III (Nth), and Fpg/ Nei family member, endonuclease VIII (Nei), primarily catalyze the removal of oxidized pyrimidines, such as 5,6-dihydroxy-5, 6-dihydrothymine (Tg), whereas formamidopyrimidine DNA glycosylase (Fpg) primarily removes oxidized purines...

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“…As yet there are no structures of the mammalian glycosylases that recognize oxidized pyrimidines (NTH1 and the three NEIL proteins) with DNA lesions in the substrate binding pocket. However, the structures of two viral orthologs of the NEIL proteins, mimivirus Nei1 and Nei2, have been solved in complex with DNA, and in the case of mimivirus Nei1, with lesions in the active site [23,24]. The latter structures together with site-specific mutagenesis clearly show that there are no specific interactions between amino acid residues in the glycosylase and the lesion, supporting prior hypotheses that the lesion search must occur before extrusion of the DNA base.…”

Section: Base Excision Repair Enzyme Structures Inform Functionmentioning

confidence: 99%

Base excision repair: A critical player in many games

2014

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This perspective reviews the many dimensions of base excision repair from a 10,000 foot vantage point and provides one person’s view on where the field is headed. Enzyme function is considered under the lens of X-ray diffraction and single molecule studies. Base excision repair in chromatin and telomeres, regulation of expression and the role of posttranslational modifications are also discussed in the context of enzyme activities, cellular localization and interacting partners. The specialized roles that base excision repair play in transcriptional activation by active demethylation and targeted oxidation as well as how base excision repair functions in the immune processes of somatic hypermutation and class switch recombination and its possible involvement in retroviral infection are also discussed. Finally the complexities of oxidative damage and its repair and its link to neurodegenerative disorders, as well as the role of base excision repair as a tumor suppressor are examined in the context of damage, repair and aging. By outlining the many base excision repair-related mysteries that have yet to be unraveled, hopefully this perspective will stimulate further interest in the field.

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Structural Characterization of Viral Ortholog of Human DNA Glycosylase NEIL1 Bound to Thymine Glycol or 5-Hydroxyuracil-containing DNA

Cited by 49 publications

References 61 publications

Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases

Base excision repair: A critical player in many games

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