Article
Multidisciplinary Sciences
Cameron D. Fyfe, Noelia Bernardo-Garcia, Laura Fradale, Stephane Grimaldi, Alain Guillot, Clemence Brewee, Leonard M. G. Chavas, Pierre Legrand, Alhosna Benjdia, Olivier Berteau
Summary: Methyl-coenzyme M reductase plays a central role in regulating global methane levels. The study of Methanosarcina acetivorans' Mmp10 provides insights into its unique enzyme structure and catalytic control mechanism, as well as the structural changes prior to catalysis. This research is important for understanding the catalytic mechanism of the emerging superfamily of B-12-dependent radical SAM enzymes.
Article
Biochemistry & Molecular Biology
Martin McLaughlin, Katharina Pallitsch, Gabriele Wallner, Wilfred A. van der Donk, Friedrich Hammerschmidt
Summary: The study determined the stereochemical course of the methyl group during the biosynthesis of the antibiotic fosfomycin, showing retention of configuration in the overall reaction. This outcome supports a double-inversion process and provides a method for investigating the mechanisms of other novel enzymes.
Article
Chemistry, Multidisciplinary
Jianbin Li, Amardeep Kumar, Jared C. Lewis
Summary: Despite the unique reactivity of vitamin B(12) and its derivatives, B-12-dependent enzymes remain underutilized in biocatalysis. In this study, the B-12-dependent transcription factor CarH was repurposed to enable non-native radical cyclization reactions. The engineered variant CarH* catalyzes the formation of gamma- and delta-lactams through either redox-neutral or reductive ring closure, showing marked enhancement of reactivity and selectivity compared to the free B-12 cofactor. CarH* also catalyzes an unusual spirocyclization by dearomatization of pendant arenes, producing bicyclic 1,3-diene products instead of the 1,4-dienes provided by existing methods. These results and mechanistic studies highlight the importance of protein scaffolds in controlling B-12 reactivity and expanding the synthetic utility of B-12-dependent enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Karl Gruber, Vanessa Csitkovits, Christoph Kratky, Bernhard Kraeutler, Andrzej Lyskowski
Summary: This study reveals the activation mechanism of radical enzymes dependent on coenzyme B-12, by establishing a tight caged radical reaction space in the protein to control the entire reaction pathway.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Organic
Jinyan Chen, Yunxia Yang, Chuanhua Wu, Liang Huo, Xingang Xie, Huilin Li, Xuegong She
Summary: In this study, the first de novo synthesis of 1-hydroxyl allogibberic methyl ester was achieved in a diastereoselective manner, serving as a key intermediate for the synthesis of pharbinilic acid and other bioactive molecules. This synthetic approach provides a new avenue to access diverse relevant bioactive molecules.
Article
Chemistry, Multidisciplinary
Yu-Hsuan Lee, Yu-Cheng Yeh, Po-Hsun Fan, Aoshu Zhong, Mark W. Ruszczycky, Hung-wen Liu
Summary: OxsB and AlsB are similar enzymes that can catalyze the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to form the precursor of oxetanocin A phosphate. Additionally, they can also catalyze the stereoselective C2'-methylation of 2'-deoxyadenosine mono phosphate, which proceeds with inversion of configuration. However, subsequent rounds of catalysis result in C-C dehydrogenation of the methyl group and formation of a heterodimer. These findings expand the range of reactions catalyzed by B12-dependent radical SAM enzymes and highlight the susceptibility of radical intermediates to different reaction pathways.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Yiling A. Liu, Robert Quechol, Joseph B. Solomon, Chi Chung Lee, Markus W. Ribbe, Yilin Hu, Britt Hedman, Keith O. Hodgson
Summary: This review focuses on the recent work that sheds light on the role of NifB in the formation of the [Fe8S9C] core of the nitrogenase cofactor, highlighting the structure, function, and mechanism of this unique radical SAM methyltransferase.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Feryel Soualmia, Alain Guillot, Nazarii Sabat, Clemence Brewee, Xavier Kubiak, Michael Haumann, Xavier Guinchard, Alhosna Benjdia, Olivier Berteau
Summary: B-12-dependent radical SAM enzyme TsrM has been found to catalyze both C- and N-methyl transfer reactions, and has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Kyoungmun Lee, Hyun-Ro Lee, Young Hun Kim, Jaemin Park, Suchan Cho, Sheng Li, Myungeun Seo, Siyoung Q. Choi
Summary: This study demonstrated the continuous generation of hydroxyl radicals in oil-confined aqueous microdroplets, enabling the synthesis of polymers at high reactant concentrations. The transport of hydroxyl radicals also facilitated polymerization reactions in the continuous oil phase. This interfacial phenomenon was successfully applied to the chain extension of polymers.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Physical
Xiaoming Wang, Jinlu Lian, Yonghao Wang, Xinying Zhang, Weizhen Liu, Yongjing Wang
Summary: Recently, the non-radical oxidation routes in Fenton-like systems have attracted much attention. In this study, a novel non-radical pathway is discovered in the degradation of phenol using H2O2 as the oxidant and graphene oxide-Fe3O4 composite as the catalyst. The kinetics investigation suggests the existence of different catalytic processes, and the non-radical route is confirmed by ESR spectra. This study provides insights into the adsorption-dependent catalytic Fenton-like degradation.
SURFACES AND INTERFACES
(2022)
Article
Multidisciplinary Sciences
Erica K. Sinner, Rongfeng Li, Daniel R. Marous, Craig A. Townsend
Summary: Carbapenems are important antibiotics used in the treatment of difficult infections. A new enzyme called ThnL has been discovered, which has noncanonical functions including thioether bond formation and reversible thiol/disulfide redox reaction. This expands the known activity of B-12-dependent radical SAM enzymes and allows for a better understanding of the biosynthesis of complex carbapenems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Clorice R. Reinhardt, Daniel Konstantinovsky, Alexander Soudackov, Sharon Hammes-Schiffer
Summary: This article presents a kinetic model that describes the reversible radical transfer in the enzyme ribonucleotide reductase (RNR). The model is based on experimental studies and provides insights into the time evolution and factors influencing radical transport in RNR.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Physical
Jiapian Huang, Zhiyuan Chen, Jie Wu
Summary: Methylation is a crucial process in biology, and radical-type methylation protocols have been developed for late-stage modifications of privileged scaffolds in pharmaceutical research. The chemistry involving methyl-radical-involved conversions has significantly developed in recent years. Various pathways for methyl radical generation have been explored, including photo-/electro-catalysis, transition-metal catalysis, transition-metal-free methylations, and demethylation-triggered radical cyclization/cascade reactions. Representative methyl-containing molecules produced from these reactions have been analyzed.
Article
Multidisciplinary Sciences
Olivia M. Manley, Han N. Phan, Allison K. Stewart, Dontae A. Mosley, Shan Xue, Lide Cha, Hongxia Bai, Veda C. Lightfoot, Pierson A. Rucker, Leonard Collins, Taufika Islam Williams, Wei-Chen Chang, Yisong Guo, Thomas M. Makris
Summary: Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of para-aminobenzoate (pABA) from L-tyrosine in Chlamydia trachomatis. The addition of both iron and manganese leads to the maximal formation of pABA by CADD, suggesting a heterobimetallic Fe:Mn cluster as the catalytically active form. The reaction mechanism involves O-2 activation by the Fe:Mn cluster, followed by amination and direct oxygen insertion. These findings provide insights into pABA formation in C. trachomatis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Elizabeth Parkinson, Hani G. Lakkis, Amir A. Alwali, Mary Elizabeth M. Metcalf, Ramya Modi, William W. Metcalf
Summary: The biosynthesis of dehydrofosmidomycin involves a unique transformation catalyzed by the enzyme DfmD, which rearranges, desaturates, and demethylates 2-(trimethylamino)ethylphosphonate. By characterizing the products of in vitro reactions, it is discovered that DfmD performs this transformation in two steps, yielding methyldehydrofosmidomycin.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Page N. Daniels, Hyunji Lee, Rebecca A. Splain, Chi P. Ting, Lingyang Zhu, Xiling Zhao, Bradley S. Moore, Wilfred A. van der Donk
Summary: This study identified a new biosynthetic pathway in which glycyl-tRNA is used to attach amino acids to a ribosomally synthesized peptide, generating amino acid-derived natural products. This pathway involves multiple hydroxylations and chemical modifications.
Article
Biochemistry & Molecular Biology
Martin McLaughlin, Yue Yu, Wilfred A. van der Donk
Summary: This study investigates the role of the TglA scaffold in TglHI recognition and determines the specificity of TglHI towards the C-terminal residues of its substrate TglACys using in vitro transcription-coupled translation and expressed protein ligation. The results identify a synthetically accessible TglACys fragment sufficient for modification by TglHI and reveal the L-selenocysteine analog of TglACys, TglASec, as an inhibitor of TglHI.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Page N. Daniels, Wilfred A. van der Donk
Summary: The selective chemical or enzymatic functionalization of proteins is crucial for the preparation of protein conjugates. The tailoring enzyme BhaC1 has been found to convert tryptophan into a promising moiety for bioconjugation. This enzyme exhibits high selectivity and only tolerates minor changes to the peptide sequence.
Article
Chemistry, Multidisciplinary
Maike N. Lundahl, Raymond Sarksian, Hao Yang, Richard J. Jodts, Adrien Pagnier, Donald F. Smith, Martin A. Mosquera, Wilfred A. van der Donk, Brian M. Hoffman, William E. Broderick, Joan B. Broderick
Summary: Using freeze-quench techniques and electron paramagnetic resonance (EPR) spectroscopy, the reaction pathway of an adenosylation reaction catalyzed by the radical SAM enzyme is studied. The results provide snapshots of the process, revealing the formation of organic intermediate Omega and the generation of 5'-deoxyadenosyl radical and adenosylated peptide radical. These findings help to understand the mechanism of the reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Raymond Sarksian, Julian D. Hegemann, Max A. Simon, Jeella Z. Acedo, Wilfred A. van der Donk
Summary: Lanthipeptides are a type of polycyclic peptides characterized by the presence of lanthionine and/or methyllanthionine. The stereochemical configuration of these compounds plays a crucial role in their bioactivity. In this study, the biosynthetic pathway of a lanthipeptide called SapT was reconstituted in E. coli, and for the first time, a 2S,3R stereochemistry of methyllanthionine was observed. Bioinformatic analysis suggests that this stereochemistry may also be present in other lanthipeptides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Dinh T. Nguyen, Tung T. Le, Andrew J. Rice, Graham A. Hudson, Wilfred A. van der Donk, Douglas A. Mitchell
Summary: In this study, a method for enzymatic synthesis of pyridine-based macrocyclic peptides from linear precursor peptides is reported. It is demonstrated that the pyritide-forming enzymes recognize both the leader region and a C-terminal tripeptide motif, allowing for the generation of a wide range of pyritide analogues. This approach provides a broad substrate scope for the discovery and optimization of macrocyclic peptides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Haoqian Liang, Isaiah J. Lopez, Marina Sanchez-Hidalgo, Olga Genilloud, Wilfred A. van der Donk
Summary: In this study, the in vitro biosynthesis process of class V lanthipeptide cacaoidin was reconstituted, and a novel dehydration enzyme CaoK and effector protein CaoY were discovered to play critical roles. Through mutagenesis studies and structure prediction, the importance of hydrophobic interactions in enzyme-substrate recognition was revealed.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Raymond Sarksian, Lingyang Zhu, Wilfred A. van der Donk
Summary: This report demonstrates that the biosynthesis of lanthipeptides containing the d-allo-l-MeLan macrocycle proceeds through (E)-Dhb intermediates formed by net syn-elimination of l-Thr.
CHEMICAL COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Chayanid Ongpipattanakul, Shi Liu, Youran Luo, Satish K. Nair, Wilfred A. van der Donk
Summary: The addition of Cys to dehydroalanine (Dha) and dehy-drobutyrine (Dhb) in both eukarya and bacteria plays important roles in various biological processes. In bacteria, this addition is catalyzed by lanthipeptide cyclases (LanC) proteins to produce lanthipeptides. In eukarya, the addition of Cys in glutathione to Dha/Dhb is catalyzed by eukaryotic LanC-like (LanCL) enzymes to protect cellular proteome. The crystal structures of human LanCL1 enzyme complexed with different ligands reveal the mechanism of the enzyme-catalyzed thia-Michael addition involving zinc ion activation, protonation of enolate intermediate, and stabilization of negative charge.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Luke Bown, Ryuichi Hirota, Michelle N. Goettge, Jerry Cui, David T. Krist, Lingyang Zhu, Constantin Giurgiu, Wilfred A. van der Donk, Kou-San Ju, William W. Metcalf
Summary: The study reveals the biosynthetic pathway of phosphonothrixin, which can help design strains that overproduce this potentially useful herbicide.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Chemistry, Organic
Nuria Mazo, Imran R. Rahman, Claudio D. Navo, Jesus M. Peregrina, Jesus H. Busto, Wilfred A. . van der Donk, Gonzalo Jimenez-Oses
Summary: This study reports a common strategy for the synthesis of lanthionine derivatives using nucleophilic ring opening of cyclic sulfamidates derived from amino acids. The researchers achieved regio-, chemo-, and stereoselective intramolecular S-alkylation of a cysteine residue with N-sulfonyl sulfamidates for the synthesis of cyclic lanthionine-containing peptides. Four different analogues of cytolysin S (CylLS '') were successfully synthesized and their conformational preferences and biological activities were compared with wild-type CylLS ''.
Article
Chemistry, Multidisciplinary
Richard S. Ayikpoe, Lingyang Zhu, Jeff Y. Chen, Chi P. Ting, Wilfred A. van der Donk
Summary: The domain of unknown function 692 (DUF692) is a family of enzymes involved in the biosynthesis of RiPP natural products. This study identified a new member of the DUF692 family, ChrH, and demonstrated its catalyzation of a unique chemical transformation. The characterization of ChrH expands the repertoire of reactions catalyzed by DUF692 enzymes.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Xuenan Mi, Emily K. Desormeaux, Tung T. Le, Wilfred A. van der Donk, Diwakar Shukla
Summary: This study investigated the influence of substrate sequence and solution structure on site-selectivity and order of ring formation in lanthipeptide biosynthesis. Molecular dynamic simulations revealed that the secondary structure of the core peptide played a crucial role in determining the final product's ring pattern. These findings contribute to our understanding of lanthipeptide biosynthesis and aid in bioengineering efforts for lanthipeptide-derived products.
Article
Chemistry, Multidisciplinary
Hyunji Lee, Chunyu Wu, Emily K. Desormeaux, Raymond Sarksian, Wilfred A. van der Donk
Summary: This study reports a new system for heterologous expression of class I lanthipeptides in Escherichia coli by co-expressing the producing organism's glutamyl-tRNA synthetase (GluRS) and tRNA(Glu) pair. The system allows for the production of fully-dehydrated peptides, including epilancin 15X and peptides from Bacteroidota Chryseobacterium and Runella strains. Additionally, LanCL enzymes were shown to remove glutathione adducts from C-glutathionylated peptides with dl or ll-lanthionine stereochemistry. These advancements will facilitate the discovery of new lanthipeptides through synthetic biology-driven genome mining efforts.