Base excision repair of the N -(2-deoxy- d - erythro -pentofuranosyl)-urea lesion by the hNEIL1 glycosylase

Tomar, Rachana; Minko, Irina G.; Sharma, Pankaj; Kellum, Jr., Andrew H.; Lei, Li; Harp, Joel M.; Iverson, T. M.; Lloyd, R. Stephen; Egli, Martin; Stone, Michael P.

doi:10.1093/nar/gkad164

Title: Base excision repair of the N -(2-deoxy- d - erythro -pentofuranosyl)-urea lesion by the hNEIL1 glycosylase

Journal Article · 03 April 2023 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad164 · OSTI ID:1968354

Tomar, Rachana; Minko, Irina G.; Sharma, Pankaj;

; Lei, Li; Harp, Joel M.; Iverson, T. M.; Lloyd, R. Stephen;

;

Abstract The N-(2-deoxy-d-erythro-pentofuranosyl)-urea DNA lesion forms following hydrolytic fragmentation of cis-5R,6S- and trans-5R,6R-dihydroxy-5,6-dihydrothymidine (thymine glycol, Tg) or from oxidation of 7,8-dihydro-8-oxo-deoxyguanosine (8-oxodG) and subsequent hydrolysis. It interconverts between α and β deoxyribose anomers. Synthetic oligodeoxynucleotides containing this adduct are efficiently incised by unedited (K242) and edited (R242) forms of the hNEIL1 glycosylase. The structure of a complex between the active site unedited mutant CΔ100 P2G hNEIL1 (K242) glycosylase and double-stranded (ds) DNA containing a urea lesion reveals a pre-cleavage intermediate, in which the Gly2 N-terminal amine forms a conjugate with the deoxyribose C1′ of the lesion, with the urea moiety remaining intact. This structure supports a proposed catalytic mechanism in which Glu3-mediated protonation of O4′ facilitates attack at deoxyribose C1′. The deoxyribose is in the ring-opened configuration with the O4′ oxygen protonated. The electron density of Lys242 suggests the ‘residue 242-in conformation’ associated with catalysis. This complex likely arises because the proton transfer steps involving Glu6 and Lys242 are hindered due to Glu6-mediated H-bonding with the Gly2 and the urea lesion. Consistent with crystallographic data, biochemical analyses show that the CΔ100 P2G hNEIL1 (K242) glycosylase exhibits a residual activity against urea-containing dsDNA.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: AHA fellowship; National Institute of Environmental Health Sciences; National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-06CH11357; W-31109-ENG-38

OSTI ID:: 1968354

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 8 Vol. 51; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Pre-Replicative Repair of Oxidized Bases Maintains Fidelity in Mammalian Genomes: The Cowcatcher Role of NEIL1 DNA Glycosylase Rangaswamy, Suganya; Pandey, Arvind; Mitra, Sankar Genes, Vol. 8, Issue 7 https://doi.org/10.3390/genes8070175	journal	June 2017
Excision of Oxidatively Generated Guanine Lesions by Competitive DNA Repair Pathways Shafirovich, Vladimir; Geacintov, Nicholas E. International Journal of Molecular Sciences, Vol. 22, Issue 5 https://doi.org/10.3390/ijms22052698	journal	March 2021

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