Structural characterization of the Fpg family of DNA glycosylases

Zharkov, Dmitry O.; Shoham, G.; Grollman, Arthur P.

doi:10.1016/s1568-7864(03)00084-3

Cited by 127 publications

(155 citation statements)

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“…Two other Fpg͞Nei glycosylases predicted to lack the characteristic zincfinger motif, A. thaliana Fpg and C. albicans Fpg, share some sequence similarity with NEIL1; in particular, they exhibit sequence features consistent with a zincless finger, including the conserved arginine. The crystal structure of unliganded EcoNei was reported to be in an open conformation, differing from that of the DNA-bound complex of the same enzyme by an angle of about 50° (12). Interestingly, the crystal structure of uncomplexed NEIL1 reported here is in the ''closed'' conformation and is superimposable onto either DNA-bound EcoNei (20) or unliganded TthFpg (21) structures (Fig.…”

Section: Resultsmentioning

confidence: 68%

“…The H2TH motif (helices C and D in NEIL1) is characteristic of the Fpg͞Nei family. In fact, a search for similar folds revealed that it is only found in members of the Fpg͞Nei family (12). In EcoNei, residues located in the loop of the H2TH motif contact the phosphate of the lesion and the two phosphates on either side (20).…”

Section: Resultsmentioning

confidence: 99%

“…Both EcoNei and EcoFpg are trifunctional enzymes containing glycosylase, ␤,␦ lyase, and 5Ј phosphodiesterase activities (16)(17)(18)(19). Fpg and Nei also share common structural motifs, including helix-two-turns-helix (H2TH) and antiparallel ␤-hairpin zinc finger motifs (6,12). A comparison of EcoNei covalently complexed to DNA (20) with the Fpg structures (21)(22)(23)(24) revealed that their overall folds are very similar; however, their substrate preferences are markedly different: EcoFpg prefers 8-oxoguanine and oxidized purines (25,26), whereas EcoNei recognizes oxidized pyrimidines (19,(27)(28)(29).…”

mentioning

confidence: 99%

“…Because NEIL1 is active on DNA-containing oxidized pyrimidines (30,32), it has been assumed that NEIL1 must possess an alternative DNAbinding motif. Interestingly, two other members of the Fpg͞Nei family, Arabidopsis thaliana Fpg and Candida albicans Fpg, also lack a zinc-finger motif (6,12).…”

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confidence: 99%

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The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity

Doublié

Bandaru

Bond

et al. 2004

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

133

189

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In prokaryotes, two DNA glycosylases recognize and excise oxidized pyrimidines: endonuclease III (Nth) and endonuclease VIII (Nei). The oxidized purine 8-oxoguanine, on the other hand, is recognized by Fpg (also known as MutM), a glycosylase that belongs to the same family as Nei. The recent availability of the human genome sequence allowed the identification of three human homologs of Escherichia coli Nei. We report here the crystal structure of a human Nei-like (NEIL) enzyme, NEIL1. The structure of NEIL1 exhibits the same overall fold as E. coli Nei, albeit with an unexpected twist. Sequence alignments had predicted that NEIL1 would lack a zinc finger, and it was therefore expected to use a different DNA-binding motif instead. Our structure revealed that, to the contrary, NEIL1 contains a structural motif composed of two antiparallel ␤-strands that mimics the antiparallel ␤-hairpin zinc finger found in other Fpg͞Nei family members but lacks the loops that harbor the zinc-binding residues and, therefore, does not coordinate zinc. This ''zincless finger'' appears to be required for NEIL1 activity, because mutating a very highly conserved arginine within this motif greatly reduces the glycosylase activity of the enzyme.

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Section: Resultsmentioning

confidence: 68%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity

Doublié

Bandaru

Bond

et al. 2004

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

133

189

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“…The Nth family utilizes an internal Lys residue as the active site for β elimination reaction, generating a 3′ phospho a,β-unsaturated aldehyde (3′ PUA), also named 3′ phosphor 4-hydroxylpentenal, at the strand break. In contrast, the members of the E. coli Fpg family including Nei (endonuclease VIII) catalyze βd elimination at the AP site by utilizing N-terminal Pro as the nucleophile and remove the deoxyribose residue to produce a 3′ phosphate terminus at the DNA strand break [41]. In both cases, the 5′ terminus retains the phosphate moiety.…”

Section: Oxidized Base-specific Dna Glycosylasesmentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged (oxidized or alkylated) or inappropriate bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS). BER involves 4-5 steps starting with base excision by a DNA glycosylase, followed by a common pathway usually involving an AP-endonuclease (APE) to generate 3′ OH terminus at the damage site, followed by repair synthesis with a DNA polymerase and nick sealing by a DNA ligase. This pathway is also responsible for repairing DNA single-strand breaks with blocked termini directly generated by ROS. Nearly all glycosylases, far fewer than their substrate lesions particularly for oxidized bases, have broad and overlapping substrate range, and could serve as back-up enzymes in vivo. In contrast, mammalian cells encode only one APE, APE1, unlike two APEs in lower organisms. In spite of overall similarity, BER with distinct subpathways in the mammals is more complex than in E. coli. The glycosylases form complexes with downstream proteins to carry out efficient repair via distinct subpathways one of which, responsible for repair of strand breaks with 3′ phosphate termini generated by the NEIL family glycosylases or by ROS, requires the phosphatase activity of polynucleotide kinase instead of APE1. Different complexes may utilize distinct DNA polymerases and ligases. Mammalian glycosylases have nonconserved extensions at one of the termini, dispensable for enzymatic activity but needed for interaction with other BER and non-BER proteins for complex formation and organelle targeting. The mammalian enzymes are sometimes covalently modified which may affect activity and complex formation. The focus of this review is on the early steps in mammalian BER for oxidized damage.

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Conformational changes of DNA repair glycosylase MutM triggered by DNA binding

Landová

Šilhán

2020

FEBS Letters

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Bacterial MutM is a DNA repair glycosylase removing DNA damage generated from oxidative stress and, therefore, preventing mutations and genomic instability. MutM belongs to the Fpg/Nei family of prokaryotic enzymes sharing structural and functional similarities with their eukaryotic counterparts, for example, NEIL1–NEIL3. Here, we present two crystal structures of MutM from pathogenic Neisseria meningitidis: a MutM holoenzyme and MutM bound to DNA. The free enzyme exists in an open conformation, while upon binding to DNA, both the enzyme and DNA undergo substantial structural changes and domain rearrangement. Our data show that not only NEI glycosylases but also the MutMs undergo dramatic conformational changes. Moreover, crystallographic data support the previously published observations that MutM enzymes are rather flexible and dynamic molecules.

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Structural characterization of the Fpg family of DNA glycosylases

Cited by 127 publications

References 124 publications

The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity

The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Conformational changes of DNA repair glycosylase MutM triggered by DNA binding

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