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Structure paper

TitleA unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.
Journal, issue, pagesNat Commun, Year 2026
Publish dateJan 27, 2026 (structure data deposition date)
AuthorsSyed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. ...Syed, A. / Serafim, L.F. / Arvai, A.S. / Minko, I.G. / Tang, H.Y.H. / Huffman, J.L. / Mol, C.D. / Hitomi, K. / Sarker, A.H. / Parikh, S. / Tsai, C.L. / Bacolla, A. / Shin, D.S. / Cunningham, R.P. / Iwai, S. / Chowdhury, D. / Lloyd, R.S. / Ivanov, I. / Tainer, J.A.
External linksNat Commun / PubMed:42457729
MethodsX-ray diffraction
Resolution1.85 - 3.5 Å
Structure data

PDB-10mn:
Crystal structure of human OGG1 (WT) in a product bound state in the presence of the agonist F51
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-9nz8:
Crystal structure of human OGG1 in a DNA-free state
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-9nz9:
Crystal structure of product-bound human OGG1(WT)
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-9nza:
Crystal structure of human OGG1 (WT) in a product bound state in the presence of the agonist F01
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-9nzc:
Crystal structure of AfNth1:Tg-DNA duplex complex in a pre-intermediate state
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

PDB-9nzd:
Crystal structure of AfNth1-K122A mutant bound to Tg-DNA duplex complex in an intermediate state
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9o00:
Crystal structure of AfOgg1 in a DNA-free state
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-9o01:
Crystal structure of AfOgg1-D140N mutant bound to 8-OG DNA duplex in an intermediate state
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-9o02:
Crystal structure of AfOgg1-K122S mutant bound to 8-OG DNA duplex in an intermediate state
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-9o03:
Crystal structure of AfOgg1:8OG-DNA duplex in a product-bound state
Method: X-RAY DIFFRACTION / Resolution: 2 Å

Chemicals

PDB-1c6r:
CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS

PDB-1c6s:
THE SOLUTION STRUCTURE OF CYTOCHROME C6 FROM THE THERMOPHILIC CYANOBACTERIUM SYNECHOCOCCUS ELONGATUS, NMR, 20 STRUCTURES

ChemComp-HOH:
WATER

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-OXG:
8-OXOGUANINE

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-MG:
Unknown entry

ChemComp-MOO:
MOLYBDATE ION

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • archaeoglobus fulgidus (archaea)
KeywordsHYDROLASE / LYASE/DNA / DNA-glycosylase / AP-lyase / LYASE-DNA complex / LYASE

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