Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments

Eckenroth, B.E.; Cao, Vy Bao; Averill, April M.; Dragon, Julie; Doublié, Sylvie

doi:10.1016/j.str.2020.08.001

Cited by 22 publications

(52 citation statements)

References 55 publications

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“…In the apo-EcoNei structure, the C-terminal domain requires a reported ∼50° rotation to form the closed ligand complex ( 62 ) ( Supplementary Figure S4 ). Another glycosylase of the Fpg/Nei family, Nei-like 2 (NEIL2), is also predicted to undergo a similar conformational change between the unliganded and bound forms ( 68 ).…”

Section: Resultsmentioning

confidence: 99%

“…In the same H2TH family as EcoNei Neisseria meningitidis formamidopyrimidine DNA glycosylase (Fpg) was shown to undergo a 22° conformational change upon binding DNA ( 69 ). Additionally, the unliganded mammalian NEIL2 crystalized in an open conformation with a large conformational change upon binding DNA shown using small angle X-ray scattering( 68 ). NTHL1, is the first reported member of the HhH family of DNA glycosylases to show structural evidence of a large conformational change and joins the UDG and H2TH glycosylase families in this respect ( 62 , 70 ).…”

Section: Discussionmentioning

confidence: 99%

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Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Carroll

Zahn

Hanley

et al. 2021

Nucleic Acids Research

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Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Carroll

Zahn

Hanley

et al. 2021

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Bahat et al (2020),Eckenroth et al (2021), Filipc ˇı ´k et al (2020), Gandini et al (2020), Garcia-Doval et al (2020), He et al (2020), Ja ¨ger et al (2020), Jensen et al (2020), Micevski et al (2020), Nie et al (2021), Sakurai et al (2020), Zhu et al (2020) and Zimanyi et al (2020).…”

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confidence: 99%

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

McCoy

Sammito

Read

2022

Acta Crystallogr D Struct Biol

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The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.

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“…In the apo-EcoNei structure, the C-terminal domain requires a reported ~50 o rotation to form the closed ligand complex (63)(Figure S1). Another glycosylase of the Fpg/Nei family, Nei-like 2 (NEIL2) is also predicted to undergo a similar conformational change between the unliganded and bound forms (69).…”

Section: The Flexible Linker Is Necessary For the Open Statementioning

confidence: 99%

Caught in Motion: Human NTHL1 Undergoes Interdomain Rearrangement Necessary for Catalysis

Carroll

Zahn

Hanley

et al. 2021

Preprint

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Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTLH1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a lower binding affinity for lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

show abstract

Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments

Cited by 22 publications

References 55 publications

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

Caught in Motion: Human NTHL1 Undergoes Interdomain Rearrangement Necessary for Catalysis

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