Evidence map›Paper›PMID 29795342›Full record

ArticleNature2018

Structural basis of ubiquitin modification by the Legionella effector SdeA.

Yanan Dong, Yajuan Mu, Yongchao Xie, Yupeng Zhang, Youyou Han, Yu Zhou, Wenhe Wang, Zihe Liu, Mei Wu, Hao Wang and 13 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.

0numbers the graph read from it
0cells of the map it votes in
49citing papers in PubMed
8.8field-weighted citation impact, top 1% of its field
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

49 citing papers in PubMed, 91 citations in OpenAlex.

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  16. CapturingFrontiers in molecular biosciences · 2024
    Article
  17. Review
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  19. The Sde phosphoribosyl-linked ubiquitin transferases protect theProceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors at 5 institutions in 1 country.

Yanan DongBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Yajuan MuBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Yongchao XieBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Yupeng ZhangBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Youyou HanBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Yu ZhouNational Institute of Biological Sciences, Beijing, China.
Wenhe WangBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Zihe LiuBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Mei WuInstitute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Hao WangBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Man PanTsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing, China.
Ning XuBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Cong-Qiao XuDepartment of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing, China.
Maojun YangBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Shilong FanBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Haiteng DengBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Tianwei TanBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Xiaoyun LiuInstitute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Lei LiuTsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing, China.
Jun LiDepartment of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing, China.
Jiawei WangBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Xianyang FangBeijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Yue FengBeijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. fengyue@mail.buct.edu.cn.
Tsinghua University · CNBeijing University of Chemical Technology · CNPeking University · CNCenter for Life Sciences · CNNational Institute of Biological Sciences, Beijing · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.

Indexed as

UbiquitinationADP Ribose TransferasesArginineBacterial ProteinsCatalytic DomainCrystallography, X-RayLegionella pneumophilaMembrane ProteinsModels, MolecularMolecular ChaperonesNADPhosphoric Diester HydrolasesProtein Processing, Post-TranslationalSubstrate SpecificityUbiquitinADP Ribose TransferasesArginineBacterial ProteinsIcmS protein, Legionella pneumophilaMembrane ProteinsMolecular ChaperonesNADPhosphoric Diester HydrolasesSdeA protein, Legionella pneumophilaUbiquitin

Identifiers

PMID29795342
OpenAlexW2803636593

What OpenQuestion holds

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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.