Evidence map›Paper›PMID 39487094›Full record

ArticleChemistry (Weinheim an der Bergstrasse, Germany)2025

Origins of Catalysis in Non-Heme Fe(II)/2-Oxoglutarate-Dependent Histone Lysine Demethylase KDM4A with Differently Methylated Histone H3 Peptides.

Sudheesh Devadas, Midhun George Thomas, Simahudeen Bathir Jaber Sathik Rifayee, Bhargav Varada, Walter White, Ethan Sommer, Kylin Campbell, Christopher J Schofield, Christo Z Christov

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2025. 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
–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

2 citing papers in PubMed.

  1. Article
  2. Oriented Electric Fields─Universal Catalysts.Accounts of chemical research · 2025
    Article
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

9 authors.

Sudheesh DevadasDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.ORCID https://orcid.org/0000-0002-1161-9760
Midhun George ThomasDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.ORCID https://orcid.org/0000-0002-6298-7061
Simahudeen Bathir Jaber Sathik RifayeeDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.ORCID https://orcid.org/0000-0001-8557-078X
Bhargav VaradaDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.ORCID https://orcid.org/0000-0001-7046-4140
Walter WhiteDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.
Ethan SommerDepartment of Biomedical Engineering, Michigan Technological University, Houghton, MI-49931, United States.
Kylin CampbellDepartment of Biological Sciences, Michigan Technological University, Houghton, MI-49931, United States.
Christopher J SchofieldChemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
Christo Z ChristovDepartment of Chemistry, Michigan Technological University, Houghton, MI-49931, United States.ORCID https://orcid.org/0000-0002-4481-0246

Funding

Understanding the Ligand Binding by Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Histone DemethylasesR15GM139118 · NIGMS · MICHIGAN TECHNOLOGICAL UNIVERSITY · PI CHRISTOV, CHRISTO ZHIVKOV · 2021 to 2024
$786k
NIGMS NIH HHS 2R15GM139118-02NIGMS NIH HHS R15 GM139118
6 · The paper itself

Abstract

Histone lysine demethylase 4 A (KDM4A), a non-heme Fe(II)/2-oxoglutarate (2OG) dependent oxygenase that catalyzes the demethylation of tri-methylated lysine residues at the 9, 27, and 36 positions of histone H3 (H3 K9me3, H3 K27me3, and H3 K36me3). These methylated residues show contrasting transcriptional roles; therefore, understanding KDM4A's catalytic mechanisms with these substrates is essential to explain the factors that control the different sequence-dependent demethylations. In this study, we use molecular dynamics (MD)-based combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate determinants of KDM4A catalysis with H3 K9me3, H3 K27me3 and H3 K36me3 substrates. In KDM4A-H3

Indexed as

Ferrous CompoundsHistonesJumonji Domain-Containing Histone DemethylasesKetoglutaric AcidsPeptidesBiocatalysisCatalysisHumansLysineMethylationMolecular Dynamics SimulationQuantum TheoryFerrous CompoundsHistonesJumonji Domain-Containing Histone DemethylasesKDM4A protein, humanKetoglutaric AcidsLysinePeptidesElectric FieldEnzyme CatalysisKDM4AMolecular DynamicsNon-Heme Fe(II)/2-Oxoglutarate-dependent oxygenasesQM/MM

Identifiers

PMID39487094
PMCPMC12400301

What OpenQuestion holds

Textmetadata
LicenceTDM
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.