9KKY
Co-crystal structure of human 8-oxoguanine glycosylase N149C mutant with DNA containing photocaged 8-oxoguanine
Summary for 9KKY
| Entry DOI | 10.2210/pdb9kky/pdb |
| Descriptor | DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3'), DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3'), N-glycosylase/DNA lyase, ... (6 entities in total) |
| Functional Keywords | dna-glycosylase, dna repair, base excision repair, hogg1, photocaged, o6-(o-nitrophenisopropyl) 8-oxoguanine, lyase |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 3 |
| Total formula weight | 47977.69 |
| Authors | Imura, T.,Yang, K.-C.,Hosokawa, Y.,Shih, H.-Y.,Ban, Y.,Yamamoto, J.,Maestre-Reyna, M. (deposition date: 2024-11-14, release date: 2025-07-23) |
| Primary citation | Imura, T.,Hosokawa, Y.,Yang, K.C.,Ban, Y.,Shih, H.Y.,Yamamoto, J.,Maestre-Reyna, M. Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target? Iucrj, 2025 Cited by PubMed Abstract: Co-crystal structures of a base-excision DNA-repair enzyme (human 8-oxoguanine DNA glycosylase; hOgg1) in complex with a photocaged 8-oxoguanine DNA lesion were determined before and after uncaging via illumination at 2.81 and 2.48 Å resolution, respectively. The structures were carefully reassessed to rapidly expand the target repertoire of light-triggered time-resolved macromolecular crystallography. Late-intermediate cryo-trapping after uncaging revealed the partial accommodation of 8-oxoguanine in the active site with 68% occupancy, which did not induce full active-site adaptation to the catalytic state. Crystal illumination led to a light-dependent loss of diffraction power, likely due to crystal-packing collapse during the very late reaction stages. This work therefore not only demonstrates that hOgg1 is well suited for time-resolved crystallography, but also that such analysis is necessary to determine further steps in its reaction. PubMed: 40658017DOI: 10.1107/S2052252525006062 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.81 Å) |
Structure validation
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