8FTJ

Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea

Summary for 8FTJ

• Entry DOI: 10.2210/pdb8ftj/pdb
• Descriptor: Endonuclease 8-like 1, DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3'), DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3'), ... (6 entities in total)
• Functional Keywords: base-excision repair enzyme, dna glycosylase, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 41994.96

Authors

Tomar, R.,Sharma, P.,Harp, J.M.,Egli, M.,Stone, M.P. (deposition date: 2023-01-12, release date: 2023-04-26, Last modification date: 2024-11-20)

Primary citation

Tomar, R.,Minko, I.G.,Sharma, P.,Kellum, A.H.,Lei, L.,Harp, J.M.,Iverson, T.M.,Lloyd, R.S.,Egli, M.,Stone, M.P.
Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase.
Nucleic Acids Res., 51:3754-3769, 2023

PubMed 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.

PubMed: 37014002
DOI: 10.1093/nar/gkad164

Experimental method

X-RAY DIFFRACTION (2.3 Å)