Article
Chemistry, Physical
Marina Lucic, Michael T. Wilson, Takehiko Tosha, Hiroshi Sugimoto, Anastasya Shilova, Danny Axford, Robin L. Owen, Michael A. . Hough, Jonathan A. R. Worrall
Summary: Controlling the reactivity of high-valent Fe(IV)-O catalytic intermediates is important for their function. Water molecules in the heme distal pocket can influence whether sequential or concerted electron transfer occurs. This study provides experimental evidence that wet and dry distal heme sites lead to different reaction pathways for Compound I, supporting the hypothesis proposed in the literature.
Article
Chemistry, Physical
Tom Coleman, Alicia M. Kirk, Joel H. Z. Lee, Daniel Z. Doherty, John B. Bruning, Elizabeth H. Krenske, James J. De Voss, Stephen G. Bell
Summary: The cytochrome P450 enzyme CYP199A4 from Rhodopseudomonas palustris strain HaA2 demonstrates efficient and selective oxidation of 4-cyclohexylbenzoic acid, but shows little to no enzyme catalyzed oxidation of the aromatic 4-phenylbenzoic acid. Molecular dynamics simulations suggest that the different geometrical requirements for efficient aromatic oxidation versus aliphatic C-H bond hydroxylation by cytochrome P450 enzymes result in chemoselectivity.
Article
Biochemistry & Molecular Biology
Federico Sebastiani, Chiara Baroni, Gaurav Patil, Andrea Dali, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich
Summary: Monoderm bacteria accumulate heme b through the coproporphyrin-dependent biosynthesis pathway. The decarboxylation of propionate groups in coproheme by coproheme decarboxylase (ChdC) is a stepwise process. H-bond interactions in the pocket of ChdCs play a crucial role in stabilizing the active site and enzyme functionality, which were evaluated through characterization of mutants complexed with coproheme and heme b via spectroscopies.
Article
Biochemistry & Molecular Biology
Andrea Dali, Thomas Gabler, Federico Sebastiani, Alina Destinger, Paul Georg Furtmueller, Vera Pfanzagl, Maurizio Becucci, Giulietta Smulevich, Stefan Hofbauer
Summary: Coproporphyrin ferrochelatases (CpfCs) are enzymes that catalyze the penultimate step in the coproporphyrin-dependent heme biosynthesis pathway. The discovery of the correct substrate for these ferrochelatases and the characterization of their binding mode provide valuable insights into the iron insertion process. This knowledge is essential for understanding the preconditions and mechanisms of iron insertion in CpfCs.
Article
Microbiology
Mahmudul Hasan, Sabrina Schulze, Leona Berndt, Gottfried J. Palm, Daniel Braga, Ingrid Richter, Daniel Last, Michael Lammers, Gerald Lackner
Summary: This study reveals the amino acid residues governing the substrate specificity of CofC in the formation of 3PG-F-420 through analysis of its crystal structure. Site-directed mutagenesis experiments further validate the role of these residues in substrate selectivity. Additionally, an unstable reaction product of CofC is discovered, and its binding mode is revealed. The role of CofD enzyme in controlling the specificity of the combined CofC/D reaction is also demonstrated. These findings provide novel insights into the biosynthesis and evolution of 3PG-F-420 and have implications for future research and biotechnological production of coenzyme F-420 derivatives.
Article
Microbiology
Mahmudul Hasan, Sabrina Schulze, Leona Berndt, Gottfried J. Palm, Daniel Braga, Ingrid Richter, Daniel Last, Michael Lammers, Gerald Lackner
Summary: Researchers analyzed the crystal structure of a CofC homolog to identify amino acid residues governing special substrate selectivity. A diagnostic residue enabled reprogramming of substrate specificity, mimicking the evolution of a novel cofactor derivative. Additionally, an unstable reaction product of CofC was revealed.
Article
Biochemistry & Molecular Biology
Federico Sebastiani, Riccardo Risorti, Chiara Niccoli, Hanna Michlits, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich
Summary: This study compares the effects of hemin reconstitution and hydrogen peroxide-mediated conversion of coproheme to heme b on the actinobacterial ChdC. The results show that the heme b ligand in the active site maintains the same conformation in both cases, with interactions with the protein. Additionally, the intermediate product rotates within the active site during decarboxylation and the strength of the proximal Fe-His bond changes.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Zejun Mo, Yuanyuan Pu, Junhao Zhou, Zonglin Tian, Jianhui Teng, Qian Chen, Lili Duan, Renxiang Liu
Summary: The study using proteomics technique found that the hybrid Va116 x Basma exhibited heterosis in nicotine content during tobacco leaf production, mainly due to over-dominant expression proteins increasing the efficiency of nicotine synthesis and transport.
SCIENTIFIC REPORTS
(2021)
Review
Chemistry, Organic
Takahiro Mori, Ikuro Abe
Summary: This review summarizes the structural analyses, mechanistic investigations, and proposed reaction mechanisms of endoperoxide-forming oxygenases, which have significant research value in the field of natural products and organic synthesis.
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Agriculture, Multidisciplinary
Samantha L. Griffin, Jonathan R. Chekan, Justin M. Lira, Andrew E. Robinson, Carla N. Yerkes, Daniel L. Siehl, Terry R. Wright, Satish K. Nair, Robert M. Cicchillo
Summary: The newly discovered EPSPS from Streptomyces sviceus represents a distinct new class (Class IV) of EPSPS enzymes that display intrinsic tolerance to high concentrations of glyphosate. By transforming dgt-28 epsps gene into stable plants, it provides robust (≥ 4x field rates) herbicide tolerance and has utility in weed-control systems comparable to commercialized events.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Luke E. Formosa, Shadi Maghool, Alice J. Sharpe, Boris Reljic, Linden Muellner-Wong, David A. Stroud, Michael T. Ryan, Megan J. Maher
Summary: COA7 is a crucial assembly factor for the biogenesis of mitochondrial complex IV. It interacts with SCO1 and SCO2 to catalyze copper relay and reduction of disulfide bonds, which are important for complex IV assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Takahiro Mori, Xin Sun, Stanislav Kadlcik, Jiri Janata, Ikuro Abe
Summary: LmbT is a glycosyltransferase enzyme that incorporates the rare amino acid L-ergothioneine (EGT) into secondary metabolites. Our analysis shows that LmbT has promiscuous substrate specificity and exhibits conformational changes upon substrate binding. The interaction between EGT and LmbT is mediated by specific salt-bridge and cation-pi interactions. This study provides structural insights into the S-glycosylation reaction catalyzed by LmbT with EGT.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Thomas L. Poulos, Jenny S. Kim, Vidhi C. Murarka
Summary: This paper examines the energetic differences in Trp radical stabilization in three different peroxidases, using thermodynamic integration and multistate Bennett acceptance ratio methods for analysis. The results show that the local solvent structure near the redox active Trp plays a significant role in stabilizing the cationic Trp radical.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jenny U. Tran, Breann L. Brown
Summary: 5-Aminolevulinic acid synthase (ALAS) is an enzyme that plays a vital role in heme biosynthesis. It is responsible for the first and rate-limiting step of heme biosynthesis in alpha-proteobacteria and several non-plant eukaryotes. Mutations in the C-terminal region of ALAS have been linked to blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C-terminal extension interacts with conserved ALAS motifs and regulates the enzyme's activity and efficiency.
Review
Chemistry, Medicinal
Takahiro Mori
Summary: Teleocidins are a type of natural products belonging to the indole alkaloid family and exhibit strong protein kinase C activation activity. They have a unique structure consisting of an indole-fused nine-membered lactam ring. Due to their distinct structures and potent biological activities, extensive studies have been conducted on the total synthesis and biosynthesis of teleocidins. The biosynthesis of teleocidins involves challenging enzymatic reactions, such as oxidative intramolecular C-N bond-forming reactions, regio- and stereo-selective reverse prenylation reactions, and methylation-triggered terpene cyclization. This review summarizes recent research on the functional and structural analyses of teleocidin biosynthetic enzymes, as well as enzyme engineering.
CHEMICAL & PHARMACEUTICAL BULLETIN
(2023)
Article
Biochemistry & Molecular Biology
Daniel Schmidt, Nikolaus Falb, Ilenia Serra, Marzia Bellei, Vera Pfanzagl, Stefan Hofbauer, Sabine Van Doorslaer, Gianantonio Battistuzzi, Paul G. Furtmuller, Christian Obinger
Article
Biochemistry & Molecular Biology
Andrea Dali, Thomas Gabler, Federico Sebastiani, Alina Destinger, Paul Georg Furtmueller, Vera Pfanzagl, Maurizio Becucci, Giulietta Smulevich, Stefan Hofbauer
Summary: Coproporphyrin ferrochelatases (CpfCs) are enzymes that catalyze the penultimate step in the coproporphyrin-dependent heme biosynthesis pathway. The discovery of the correct substrate for these ferrochelatases and the characterization of their binding mode provide valuable insights into the iron insertion process. This knowledge is essential for understanding the preconditions and mechanisms of iron insertion in CpfCs.
Article
Biochemistry & Molecular Biology
Daniel R. Ramos, Paul G. Furtmueller, Christian Obinger, Angeles Pena-Gallego, Ignacio Perez-Juste, J. Arturo Santaballa
Summary: Electronic structure calculations using DFT were conducted to examine the influence of water molecules and protonation on the heme group of peroxidases in different redox and spin states. The study discusses shared geometries, spectroscopic properties, and thermodynamics of peroxidases. Computed Gibbs free energies suggest that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) center in native ferric peroxidases with a non-bonding water molecule. Protonation of the ferryl oxygen of compound II is found to be necessary and computed Gibbs free energies reveal pK(a) values of approximately 8.5-9.0 for compound II.
Article
Chemistry, Analytical
Jürgen Beck, Matthias Biechele, Christoph Repik, Petra Gruber, Paul G. Furtmueller, Rainer Hahn
Summary: This study systematically compared the elution behavior of plasmid DNA on three common anion exchange resins. It was found that plasmid DNA consistently elutes at a characteristic salt concentration in linear gradient elution, and elutes only above this concentration in isocratic elution. Structural analysis supported this explanation.
JOURNAL OF SEPARATION SCIENCE
(2023)
Article
Agronomy
Yerko Escalona, Drazen Petrov, Edgar Galicia-Andres, Chris Oostenbrink
Summary: By using molecular dynamics simulations and creating molecular systems that resemble soil organic matter (SOM), researchers gained a better understanding of SOM. They studied standardized samples of humic substances (HSs) from various sources and analyzed the structure and dynamics to explore the relationship between properties and protonation state of carboxyl groups as well as the influence of ion interactions and pH.
Article
Biochemistry & Molecular Biology
Gaurav Patil, Hanna Michlits, Paul G. Furtmueller, Stefan Hofbauer
Summary: Coproheme decarboxylases (ChdCs) are enzymes involved in the biosynthesis of heme. This study focuses on the second part of the decarboxylation reaction catalyzed by ChdCs, which has not been previously studied. The researchers optimized the production and purification of a intermediate compound called monovinyl, monopropionate deuteroheme (MMD), and used it to study the reaction mechanism. The results indicate that the second part of the reaction is similar to the first part, with slight differences in the active site architecture and H-bonding network.
Article
Biochemistry & Molecular Biology
Federico Sebastiani, Andrea Dali, Diego Javier Alonso de Armino, Lorenzo Campagni, Gaurav Patil, Maurizio Becucci, Stefan Hofbauer, Dario A. Estrin, Giulietta Smulevich
Summary: This study focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The results show that the wild-type coproheme-CO adduct is characterized by two CO conformers, hydrogen-bonded and weak polar interaction with the distal cavity. The absence of the H118 residue leads to the formation of non-H-bonded CO species. In addition, CO binding to reversed heme b and heme d is also investigated in this work.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Thomas Gabler, Andrea Dali, Federico Sebastiani, Paul Georg Furtmueller, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich
Summary: Understanding the reaction mechanism of enzymes is challenging, but studying model substrates can provide valuable information. In this study, we investigated the mechanism of ferrous iron incorporation in a bacterial enzyme complex and discovered the role of hydrogen bond interactions in this process.
Review
Biochemistry & Molecular Biology
Nikolaus Falb, Gaurav Patil, Paul G. Furtmueller, Thomas Gabler, Stefan Hofbauer
Summary: The coproporphyrin dependent heme biosynthesis pathway is predominantly used by Gram-positive bacteria. This pathway is of interest for basic research as it relates to medical biotechnology and the development of new antibiotic targets against Gram-positive superbugs. A review of the accumulated structural data on the enzymes involved in this pathway is provided, highlighting the need for further analysis and future research to gain a comprehensive understanding of prokaryotic heme biosynthesis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)