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Structure paper

TitleStructural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Journal, issue, pagesNucleic Acids Res., Vol. 50, Page 11072-11092, Year 2022
Publish dateMay 19, 2021 (structure data deposition date)
AuthorsFranck, C. / Stephane, G. / Julien, C. / Virginie, G. / Martine, G. / Norbert, G. / Fabrice, C. / Didier, F. / Josef, S.M. / Bertrand, C.
External linksNucleic Acids Res. / PubMed:36300625
MethodsX-ray diffraction
Resolution1.1 - 2.04 Å
Structure data

PDB-7olb:
Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-7oli:
Crystal structure of Pab-AGOG in complex with 8-oxoguanosine
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7ou3:
Crystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase from Thermococcus gammatolerans
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-7oue:
Crystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7oy7:
Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing cytosine opposite to lesion)
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7p0w:
Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing thymine opposite to lesion)
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-7p8l:
Crystal structure of Pyrococcus abyssi 8-oxoguanine DNA glycosylase (PabAGOG) in complex with dsDNA containing cytosine opposite to 8-oxoG
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-7p9z:
Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

Chemicals

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-CIT:
CITRIC ACID

ChemComp-CL:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-8HG:
2'-DEOXY-8-OXOGUANOSINE

ChemComp-GOL:
GLYCEROL

ChemComp-PO4:
PHOSPHATE ION

ChemComp-K:
Unknown entry

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

Source
  • pyrococcus abyssi (strain ge5 / orsay) (archaea)
  • thermococcus gammatolerans (strain dsm 15229 / jcm 11827 / ej3) (archaea)
  • synthetic construct (others)
  • pyrococcus abyssi (archaea)
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / Archaea / Pyrococcus abyssi / Thermococcus gammatolerans / trapped double-stranded DNA intermediate / AGOG / protein-DNA complex

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