Evidence map›Paper›PMID 39294420›Full record

ArticleNature chemistry2024

Fused radical SAM and αKG-HExxH domain proteins contain a distinct structural fold and catalyse cyclophane formation and β-hydroxylation.

Yohei Morishita, Suze Ma, Eugenio De La Mora, He Li, Heng Chen, Xinjian Ji, Anthony Usclat, Patricia Amara, Ryosuke Sugiyama, Yi Wei Tooh and 5 more

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In one paragraph

Article in Nature chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

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  5. A ribosomally synthesized and posttranslationally modified peptide with ADP-ribosylation.Proceedings of the National Academy of Sciences of the United States of America · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Yohei Morishita *Department of Pharmacy, National University of Singapore, Singapore, Singapore.ORCID 0000-0001-8442-8642
Suze Ma *Department of Chemistry, Fudan University, Shanghai, China.ORCID 0000-0001-8030-2401
Eugenio De La Mora *University Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, France.ORCID 0000-0001-6945-7357
He LiDepartment of Chemistry, Fudan University, Shanghai, China.
Heng ChenDepartment of Chemistry, Fudan University, Shanghai, China.
Xinjian JiDepartment of Chemistry, Fudan University, Shanghai, China.ORCID 0000-0003-1969-7373
Anthony UsclatUniversity Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, France.ORCID 0009-0009-0165-5336
Patricia AmaraUniversity Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, France.ORCID 0000-0001-9634-7305
Ryosuke SugiyamaDepartment of Pharmacy, National University of Singapore, Singapore, Singapore.ORCID 0000-0001-9735-1189
Yi Wei ToohDepartment of Pharmacy, National University of Singapore, Singapore, Singapore.
Gregory GunawanDepartment of Pharmacy, National University of Singapore, Singapore, Singapore.ORCID 0000-0003-2653-0280
Julien PérardUniversity Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France.
Yvain NicoletUniversity Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, France. yvain.nicolet@ibs.fr.ORCID 0000-0002-4189-7067
Qi ZhangDepartment of Chemistry, Fudan University, Shanghai, China. qizhang@sioc.ac.cn.ORCID 0000-0002-8135-2221
Brandon I MorinakaDepartment of Pharmacy, National University of Singapore, Singapore, Singapore. phambi@nus.edu.sg.ORCID 0000-0001-8239-619X

Funding

Agence Nationale de la Recherche (French National Research Agency) ANR-10-INBS-05-02Agence Nationale de la Recherche (French National Research Agency) ANR-20-CE44-0005National Natural Science Foundation of China (National Science Foundation of China) 21921003National Natural Science Foundation of China (National Science Foundation of China) 223B2701
6 · The paper itself

Abstract

Two of nature's recurring binding motifs in metalloproteins are the CxxxCxxC motif in radical SAM enzymes and the 2-His-1-carboxylate motif found both in zincins and α-ketoglutarate and non-haem iron enzymes. Here we show the confluence of these two domains in a single post-translational modifying enzyme containing an N-terminal radical S-adenosylmethionine domain fused to a C-terminal 2-His-1-carboxylate (HExxH) domain. The radical SAM domain catalyses three-residue cyclophane formation and is the signature modification of triceptides, a class of ribosomally synthesized and post-translationally modified peptides. The HExxH domain is a defining feature of zinc metalloproteases. Yet the HExxH motif-containing domain studied here catalyses β-hydroxylation and is an α-ketoglutarate non-haem iron enzyme. We determined the crystal structure for this HExxH protein at 2.8 Å, unveiling a distinct structural fold, thus expanding the family of α-ketoglutarate non-haem iron enzymes with a class that we propose to name αKG-HExxH. αKG-HExxH proteins represent a unique family of ribosomally synthesized and post-translationally modified peptide modifying enzymes that can furnish opportunities for genome mining, synthetic biology and enzymology.

Indexed as

S-AdenosylmethionineBiocatalysisCrystallography, X-RayCyclophanesHydroxylationKetoglutaric AcidsModels, MolecularProtein DomainsProtein FoldingCyclophanesKetoglutaric AcidsS-Adenosylmethionine

Identifiers

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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.