Evidence map›Paper›PMID 31125381›Full record

ArticlePloS one2019

Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol.

Karla Frydenvang, Marlies C A Verkade-Vreeker, Floor Dohmen, Jan N M Commandeur, Maria Rafiq, Osman Mirza, Flemming Steen Jørgensen, Daan P Geerke

Abstract read
In one paragraph

Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Article
  3. Secondary Binding Site of CYP17A1 in Enhanced Sampling Simulations.Journal of chemical information and modeling · 2024
    Article
  4. Article
  5. Review
  6. 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

8 authors.

Karla FrydenvangDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
Marlies C A Verkade-VreekerAIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
Floor DohmenAIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
Jan N M CommandeurAIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
Maria RafiqDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
Osman MirzaDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
Flemming Steen JørgensenDepartment of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0001-8040-2998
Daan P GeerkeAIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, Amsterdam, the Netherlands.ORCID 0000-0002-5262-6166

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. This led e.g. to the discovery of mutant M11 that is able to metabolize a variety of drugs and drug-like compounds with relatively high activity. In order to further improve our understanding of CYP binding and reactions, we performed a co-crystallization study of mutant M11 and report here the three-dimensional structure M11 in complex with dithiothreitol (DTT) at a resolution of 2.16 Å. The structure shows that DTT can coordinate to the Fe atom in the heme group. UV/Vis spectroscopy and molecular dynamics simulation studies underline this finding and as first structure of the CYP BM3 mutant M11 in complex with a ligand, it offers a basis for structure-based design of novel mutants.

Indexed as

Amino Acid SubstitutionBacterial ProteinsCrystallography, X-RayCytochrome P-450 Enzyme SystemDithiothreitolDrug DesignHemeHumansLigandsMolecular Dynamics SimulationMutagenesis, Site-DirectedMutationNADPH-Ferrihemoprotein ReductasePharmaceutical PreparationsProtein ConformationProtein DomainsBacterial ProteinsCytochrome P-450 Enzyme SystemDithiothreitolflavocytochrome P450 BM3 monoxygenasesHemeLigandsNADPH-Ferrihemoprotein ReductasePharmaceutical PreparationsRecombinant Proteins

Identifiers

PMID31125381
PMCPMC6534296

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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.