Evidence map›Paper›PMID 32820047›Full record

ArticleThe Journal of biological chemistry2020

Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.

Sachiko Toma-Fukai, Ryota Hibi, Takao Naganuma, Mashito Sakai, Shinya Saijo, Nobutaka Shimizu, Michihiro Matsumoto, Toshiyuki Shimizu

Abstract read
In one paragraph

Article in The Journal of biological chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

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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

15 citing papers in PubMed.

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  15. Structural Diversity of Ubiquitin E3 Ligase.Molecules (Basel, Switzerland) · 2021
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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

8 authors.

Sachiko Toma-FukaiGraduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Ryota HibiGraduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Takao NaganumaDepartment of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjyuku-ku, Tokyo, Japan.
Mashito SakaiDepartment of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjyuku-ku, Tokyo, Japan.
Shinya SaijoPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
Nobutaka ShimizuPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
Michihiro MatsumotoDepartment of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Shinjyuku-ku, Tokyo, Japan.
Toshiyuki ShimizuGraduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. Electronic address: shimizu@mol.f.u-tokyo.ac.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

General control nonderepressible 5 (GCN5, also known as Kat2a) and p300/CBP-associated factor (PCAF, also known as Kat2b) are two homologous acetyltransferases. Both proteins share similar domain architecture consisting of a PCAF N-terminal (PCAF_N) domain, acetyltransferase domain, and a bromodomain. PCAF also acts as a ubiquitin E3 ligase whose activity is attributable to the PCAF_N domain, but its structural aspects are largely unknown. Here, we demonstrated that GCN5 exhibited ubiquitination activity in a similar manner to PCAF and its activity was supported by the ubiquitin-conjugating enzyme UbcH5. Moreover, we determined the crystal structure of the PCAF_N domain at 1.8 Å resolution and found that PCAF_N domain folds into a helical structure with a characteristic binuclear zinc region, which was not predicted from sequence analyses. The zinc region is distinct from known E3 ligase structures, suggesting this region may form a new class of E3 ligase. Our biochemical and structural study provides new insight into not only the functional significance of GCN5 but also into ubiquitin biology.

Indexed as

AnimalsCrystallography, X-RayHumansMiceModels, Molecularp300-CBP-Associated Factorp300-CBP Transcription FactorsProtein ConformationProtein DomainsUbiquitinationUbiquitin-Protein Ligasesp300-CBP-Associated Factorp300-CBP Transcription FactorsUbiquitin-Protein Ligasescrystal structureE3 ligaseE3 ubiquitin ligaseGCN5structural biologyubiquitinationubiquitin ligasezinc fingerZn ion

Identifiers

PMID32820047
PMCPMC7586209

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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.