Evidence map›Paper›PMID 30054276›Full record

ArticleThe Journal of biological chemistry2018

Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.

Pavel Grinkevich, Dhiraj Sinha, Iuliia Iermak, Alena Guzanova, Marie Weiserova, Jost Ludwig, Jeroen R Mesters, Rüdiger H Ettrich

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.6field-weighted citation impact, top 37% 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

5 citing papers in PubMed, 10 citations in OpenAlex.

  1. Journal of bacteriology · 2024
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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 at 4 institutions in 3 countries.

Pavel GrinkevichFrom the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.
Dhiraj SinhaFrom the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.
Iuliia IermakFrom the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.
Alena Guzanovathe Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic.
Marie Weiserovathe Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic.
Jost LudwigFrom the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic.
Jeroen R Mestersthe Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck, Germany, and.
Rüdiger H EttrichFrom the Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic, ettrich@nh.cas.cz.ORCID 0000-0001-8624-7706
Czech Academy of Sciences · CZCzech Academy of Sciences, Institute of Microbiology · CZUniversity of Lübeck · DEUniversity of South Bohemia in České Budějovice · CZ

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 Å, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique α-helical fold. The full-length HsdR model, based on the WT structure and the C-terminal domain determined here, disclosed a proposed DNA-binding groove lined by positively charged residues.

Indexed as

Amino Acid SequenceBiophysical PhenomenaCrystallography, X-RayDeoxyribonucleases, Type I Site-SpecificDNA-Binding ProteinsEscherichia coliEscherichia coli ProteinsMultiprotein ComplexesProtein ConformationProtein DomainsProtein SubunitsDeoxyribonucleases, Type I Site-SpecificDNA-Binding Proteinsendodeoxyribonuclease EcoR124IEscherichia coli ProteinsHsdR protein, E coliMultiprotein ComplexesProtein Subunitscrystal structureC-terminal domainDNA binding proteinDNA endonucleaseEcoR124Escherichia coli (E. coli)GFP fusionHsdRrestriction-modificationX-ray crystallography

Identifiers

PMID30054276
PMCPMC6166736
OpenAlexW2884421468

What OpenQuestion holds

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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.