Evidence map›Paper›PMID 28724886›Full record

ArticleScientific reports2017

Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase.

Stefan Ilic, Sabine R Akabayov, Roy Froimovici, Ron Meiry, Dan Vilenchik, Alfredo Hernandez, Haribabu Arthanari, Barak Akabayov

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.1field-weighted citation impact, top 50% 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

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. NMR-Fragment Based Virtual Screening: A Brief Overview.Molecules (Basel, Switzerland) · 2018
    Review
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 2 institutions in 2 countries.

Stefan IlicDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Sabine R AkabayovDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Roy FroimoviciDepartment of Communication Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Ron MeiryDepartment of Communication Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Dan VilenchikDepartment of Communication Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Alfredo HernandezDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts, 02115, USA.
Haribabu ArthanariDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts, 02115, USA.
Barak AkabayovDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. akabayov@bgu.ac.il.
Ben-Gurion University of the Negev · ILHarvard University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II). A machine-learning algorithm called linear discriminant analysis (LDA) was trained by using the large collection of Mn(II) and Mg(II) binding sites available in the protein data bank (PDB). Application of the model to DNA primase revealed a preference in the enzyme's second metal binding site for Mn(II) over Mg(II), suggesting that T7 DNA primase activity modulation when bound to Mn(II) is based on structural changes in the enzyme.

Indexed as

Cations, DivalentCoenzymesDNA PrimaseMagnetic Resonance SpectroscopyManganeseProtein ConformationRNACations, DivalentCoenzymesDNA PrimaseManganeseRNARNA primers

Identifiers

PMID28724886
PMCPMC5517523
OpenAlexW2735571628

What OpenQuestion holds

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LicenceCC BY
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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.