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ORIGINAL RESEARCH article

Front. Chem.
Sec. Theoretical and Computational Chemistry
Volume 12 - 2024 | doi: 10.3389/fchem.2024.1430796
This article is part of the Research Topic Exploration of the Role of Heme Proteins in Biology with Experimental and Computational Methods View all articles

Trapping the substrate radical of heme synthase AhbD

Provisionally accepted
Lorenz Heidinger Lorenz Heidinger *Isabelle Fix Isabelle Fix *Thorsten Friedrich Thorsten Friedrich *Gunhild Layer Gunhild Layer *
  • University of Freiburg, Freiburg, Germany

The final, formatted version of the article will be published soon.

    The heme synthase AhbD catalyzes the last step of the siroheme-dependent heme biosynthesis pathway, which is operative in archaea and sulfate-reducing bacteria. The AhbD-catalyzed reaction consists of the oxidative decarboxylation of two propionate side chains of iron-coproporphyrin III to the corresponding vinyl groups of heme b. AhbD is a Radical SAM enzyme employing radical chemistry to achieve the decarboxylation reaction. Previously, it was proposed that the central iron ion of the substrate iron-coproporphyrin III participates in the reaction by enabling electron transfer from the initially formed substrate radical to an iron-sulfur cluster in AhbD. In this study, we investigated the substrate radical that is formed during AhbD catalysis. While the iron-coproporphyrinyl radical was not detected by electron paramagnetic resonance (EPR) spectroscopy, trapping and visualization of the substrate radical was successful by employing substrate analogs such as coproporphyrin III and zinc-coproporphyrin III. The radical signals detected by EPR were analyzed by simulations based on density functional theory (DFT) calculations. The observed radical species on the substrate analogs indicate that hydrogen atom abstraction takes place at the -position of the propionate side chain and that an electron donating ligand is located in proximity to the central metal ion of the porphyrin.

    Keywords: siroheme-dependent heme biosynthesis, Radical SAM enzymes, iron-coproporphyrin III, EPR spectroscopy, Electron Transfer

    Received: 10 May 2024; Accepted: 28 Jun 2024.

    Copyright: © 2024 Heidinger, Fix, Friedrich and Layer. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Lorenz Heidinger, University of Freiburg, Freiburg, Germany
    Isabelle Fix, University of Freiburg, Freiburg, Germany
    Thorsten Friedrich, University of Freiburg, Freiburg, Germany
    Gunhild Layer, University of Freiburg, Freiburg, Germany

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