Evidence map›Paper›PMID 38842936›Full record

ArticleNucleic acids research2024

Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function.

Markéta Šoltysová, Jana Škerlová, Petr Pachl, Karel Škubník, Milan Fábry, Irena Sieglová, Martina Farolfi, Irina Grishkovskaya, Michal Babiak, Jiří Nováček and 2 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 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 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Markéta ŠoltysováStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.ORCID 0000-0002-6194-2339
Jana ŠkerlováStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.ORCID 0000-0002-9579-4047
Petr PachlStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.ORCID 0000-0001-9215-9817
Karel ŠkubníkCryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia.
Milan FábryStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.
Irena SieglováStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.
Martina FarolfiLaboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 20, Czechia.
Irina GrishkovskayaResearch Institute of Molecular Pathology, Campus-ViennaBiocenter 1, 1030 Vienna, Austria.
Michal BabiakCryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia.
Jiří NováčekCryoElectron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, 601 77, Czechia.ORCID 0000-0003-4013-3898
Libor KrásnýLaboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague 142 20, Czechia.ORCID 0000-0002-4120-4347
Pavlína ŘezáčováStructural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, 166 10, Czechia.ORCID 0000-0001-9626-346X

Funding

Czech Science Foundation 23-06295SEuropean UnionEuropean Union - Next Generation EUInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesMinistry of EducationNational Institute of virology and bacteriology LX22NPO5103
6 · The paper itself

Abstract

The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.

Indexed as

Bacillus subtilisBacterial ProteinsCryoelectron MicroscopyModels, MolecularRepressor ProteinsBinding SitesCrystallography, X-RayDNADNA, BacterialDNA-Binding ProteinsFructosediphosphatesGene Expression Regulation, BacterialOperonProtein BindingProtein MultimerizationBacterial ProteinsDNADNA, BacterialDNA-Binding Proteinsfructose-1,6-diphosphateFructosediphosphatesRepressor Proteins

Identifiers

PMID38842936
PMCPMC11229326

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.