9KKY image
Deposition Date 2024-11-14
Release Date 2025-07-23
Last Version Date 2025-09-10
Entry Detail
PDB ID:
9KKY
Keywords:
Title:
Co-crystal structure of human 8-oxoguanine glycosylase N149C mutant with DNA containing photocaged 8-oxoguanine
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.81 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 65 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:N-glycosylase/DNA lyase
Gene (Uniprot):OGG1
Chain IDs:C (auth: A)
Chain Length:337
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3')
Chain IDs:A (auth: B)
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')
Chain IDs:B (auth: C)
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target?
Iucrj 12 515 522 (2025)
PMID: 40658017 DOI: 10.1107/S2052252525006062

Abstact

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.

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Primary Citation of related structures