Evidence map›Paper›PMID 40658017›Full record

ArticleIUCrJ2025

Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target?

Tomoki Imura, Yuhei Hosokawa, Kai Chun Yang, Yuki Ban, Hsuan Yu Shih, Junpei Yamamoto, Manuel Maestre-Reyna

Abstract read
In one paragraph

Article in IUCrJ, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Tomoki ImuraDivision of Chemistry, Graduate School of Engineering Science, University of Osaka, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
Yuhei HosokawaDepartment of Chemistry, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan.ORCID 0000-0001-9559-8567
Kai Chun YangDepartment of Chemistry, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan.ORCID 0009-0006-9790-1244
Yuki BanDivision of Chemistry, Graduate School of Engineering Science, University of Osaka, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
Hsuan Yu ShihDepartment of Chemistry, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan.ORCID 0009-0009-7273-7830
Junpei YamamotoDivision of Chemistry, Graduate School of Engineering Science, University of Osaka, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.ORCID 0000-0002-5036-991X
Manuel Maestre-ReynaDepartment of Chemistry, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan.

Funding

Japan Science and Technology Agency, Fusion Oriented REsearch for disruptive Science and Technology JPMJFR2057National Science and Technology Council 111-2113-M-002-029-MY3National Taiwan University 112L8943
6 · The paper itself

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.

Indexed as

DNA GlycosylasesGuanineCatalytic DomainCrystallography, X-RayDNA RepairHumansModels, MolecularProtein Conformation8-hydroxyguanineDNA GlycosylasesGuanineoxoguanine glycosylase 1, humanDNA repairhOgg1intermediate trappingphotocaged substrate analogs

Identifiers

PMID40658017
PMCPMC12403168

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.