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Song Y, Zhang C, Omenn GS, O’Meara MJ, Welch JD. Predicting the Structural Impact of Human Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572928. [PMID: 38187531 PMCID: PMC10769328 DOI: 10.1101/2023.12.21.572928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
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Affiliation(s)
- Yuxuan Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D. Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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2
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Yu M, Wu M, Secundo F, Liu Z. Detection, production, modification, and application of arylsulfatases. Biotechnol Adv 2023; 67:108207. [PMID: 37406746 DOI: 10.1016/j.biotechadv.2023.108207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Arylsulfatase is a subset of sulfatase which catalyzes the hydrolysis of aryl sulfate ester. Arylsulfatase is widely distributed among microorganisms, mammals and green algae, but the arylsulfatase-encoding gene has not yet been found in the genomes of higher plants so far. Arylsulfatase plays an important role in the sulfur flows between nature and organisms. In this review, we present the maturation and catalytic mechanism of arylsulfatase, and the recent literature on the expression and production of arylsulfatase in wild-type and engineered microorganisms, as well as the modification of arylsulfatase by genetic engineering are summarized. We focus on arylsulfatases from microbial origin and give an overview of different assays and substrates used to determine the arylsulfatase activity. Furthermore, the researches about arylsulfatase application on the field of agar desulfation, soil sulfur cycle and soil evaluation are also discussed. Finally, the perspectives concerning the future research on arylsulfatase are prospected.
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Affiliation(s)
- Mengjiao Yu
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Meixian Wu
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, via Mario Bianco 9, Milan 20131, Italy
| | - Zhen Liu
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China.
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3
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Zhi N, Zhu H, Qiao J, Dong M. Recent progress in radical SAM enzymes: New reactions and mechanisms. CHINESE SCIENCE BULLETIN-CHINESE 2021. [DOI: 10.1360/tb-2021-1067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Galván AE, Paul NP, Chen J, Yoshinaga-Sakurai K, Utturkar SM, Rosen BP, Yoshinaga M. Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin. Microbiol Spectr 2021; 9:e0050221. [PMID: 34378964 PMCID: PMC8552651 DOI: 10.1128/spectrum.00502-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/15/2021] [Indexed: 01/11/2023] Open
Abstract
The soil bacterium Burkholderia gladioli GSRB05 produces the natural compound arsinothricin [2-amino-4-(hydroxymethylarsinoyl) butanoate] (AST), which has been demonstrated to be a broad-spectrum antibiotic. To identify the genes responsible for AST biosynthesis, a draft genome sequence of B. gladioli GSRB05 was constructed. Three genes, arsQML, in an arsenic resistance operon were found to be a biosynthetic gene cluster responsible for synthesis of AST and its precursor, hydroxyarsinothricin [2-amino-4-(dihydroxyarsinoyl) butanoate] (AST-OH). The arsL gene product is a noncanonical radical S-adenosylmethionine (SAM) enzyme that is predicted to transfer the 3-amino-3-carboxypropyl (ACP) group from SAM to the arsenic atom in inorganic arsenite, forming AST-OH, which is methylated by the arsM gene product, a SAM methyltransferase, to produce AST. Finally, the arsQ gene product is an efflux permease that extrudes AST from the cells, a common final step in antibiotic-producing bacteria. Elucidation of the biosynthetic gene cluster for this novel arsenic-containing antibiotic adds an important new tool for continuation of the antibiotic era. IMPORTANCE Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. Here, we report identification of the biosynthetic gene cluster for arsinothricin and demonstrate that only three genes, two of which are novel, are required for the biosynthesis and transport of arsinothricin, in contrast to the phosphonate counterpart, phosphinothricin, which requires over 20 genes. Our discoveries will provide insight for the development of more effective organoarsenical antibiotics and illustrate the previously unknown complexity of the arsenic biogeochemical cycle, as well as bring new perspective to environmental arsenic biochemistry.
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Affiliation(s)
- Adriana E. Galván
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Ngozi P. Paul
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Kunie Yoshinaga-Sakurai
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Sagar M. Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, Florida, USA
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5
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Chen Y, Wang J, Li G, Yang Y, Ding W. Current Advancements in Sactipeptide Natural Products. Front Chem 2021; 9:595991. [PMID: 34095082 PMCID: PMC8172795 DOI: 10.3389/fchem.2021.595991] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products that benefited from genome sequencing technology in the past two decades. RiPPs are widely distributed in nature and show diverse chemical structures and rich biological activities. Despite the various structural characteristic of RiPPs, they follow a common biosynthetic logic: a precursor peptide containing an N-terminal leader peptide and a C-terminal core peptide; in some cases,a follower peptide is after the core peptide. The precursor peptide undergoes a series of modification, transport, and cleavage steps to form a mature natural product with specific activities. Sactipeptides (Sulfur-to-alpha carbon thioether cross-linked peptides) belong to RiPPs that show various biological activities such as antibacterial, spermicidal and hemolytic properties. Their common hallmark is an intramolecular thioether bond that crosslinks the sulfur atom of a cysteine residue to the α-carbon of an acceptor amino acid, which is catalyzed by a rSAM enzyme. This review summarizes recent achievements concerning the discovery, distribution, structural elucidation, biosynthesis and application prospects of sactipeptides.
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Affiliation(s)
- Yunliang Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Jinxiu Wang
- Northwest Institute of Eco-Environmental and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guoquan Li
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Yunpeng Yang
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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6
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Dong G, Cao L, Ryde U. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. J Biol Inorg Chem 2018; 23:221-229. [PMID: 29204715 PMCID: PMC5816104 DOI: 10.1007/s00775-017-1522-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022]
Abstract
Lipoyl synthase (LipA) catalyses the final step of the biosynthesis of the lipoyl cofactor by insertion of two sulfur atoms at the C6 and C8 atoms of the protein-bound octanoyl substrate. In this reaction, two [4Fe4S] clusters and two molecules of S-adenosyl-L-methionine are used. One of the two FeS clusters is responsible for the generation of a powerful oxidant, the 5'-deoxyadenosyl radical (5'-dA•). The other (the auxiliary cluster) is the source of both sulfur atoms that are inserted into the substrate. In this paper, the spin state of the FeS clusters and the reaction mechanism is investigated by the combined quantum mechanical and molecular mechanics approach. The calculations show that the ground state of the two FeS clusters, both in the [4Fe4S]2+ oxidation state, is a singlet state with antiferromagnetically coupled high-spin Fe ions and that there is quite a large variation of the energies of the various broken-symmetry states, up to 40 kJ/mol. For the two S-insertion reactions, the highest energy barrier is found for the hydrogen-atom abstraction from the octanoyl substrate by 5'-dA•. The formation of 5'-dA• is very facile for LipA, with an energy barrier of 6 kJ/mol for the first S-insertion reaction and without any barrier for the second S-insertion reaction. In addition, the first S ion attack on the C6 radical of octanoyl was found to take place directly by the transfer of the H6 from the substrate to 5'-dA•, whereas for the second S-insertion reaction, a C8 radical intermediate was formed with a rate-limiting barrier of 71 kJ/mol.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
| | - Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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7
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Schramma KR, Forneris CC, Caruso A, Seyedsayamdost MR. Mechanistic Investigations of Lysine-Tryptophan Cross-Link Formation Catalyzed by Streptococcal Radical S-Adenosylmethionine Enzymes. Biochemistry 2018; 57:461-468. [PMID: 29320164 DOI: 10.1021/acs.biochem.7b01147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptide is a ribosomally synthesized and post-translationally modified peptide with a unique cyclization motif consisting of an intramolecular lysine-tryptophan cross-link. Three radical S-adenosylmethionine enzymes, StrB, AgaB, and SuiB from different species of Streptococcus, have been shown to install this modification onto their respective precursor peptides in a leader-dependent fashion. Herein, we conduct detailed investigations to differentiate among several plausible mechanistic proposals, specifically addressing radical versus electrophilic addition to the indole during cross-link formation, the role of substrate side chains in binding in the enzyme active site, and the identity of the catalytic base in the reaction cycle. Our results are consistent with a radical electrophilic aromatic substitution mechanism for the key carbon-carbon bond-forming step. They also elaborate on other mechanistic features that underpin this unique and synthetically challenging post-translational modification.
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Affiliation(s)
- Kelsey R Schramma
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Clarissa C Forneris
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Alessio Caruso
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University , Princeton, New Jersey 08544, United States
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8
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Saichana N, Tanizawa K, Ueno H, Pechoušek J, Novák P, Frébortová J. Characterization of auxiliary iron-sulfur clusters in a radical S-adenosylmethionine enzyme PqqE from Methylobacterium extorquens AM1. FEBS Open Bio 2017; 7:1864-1879. [PMID: 29226074 PMCID: PMC5715301 DOI: 10.1002/2211-5463.12314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 11/10/2022] Open
Abstract
PqqE is a radical S‐adenosyl‐l‐methionine (SAM) enzyme that catalyzes the initial reaction of pyrroloquinoline quinone (PQQ) biosynthesis. PqqE belongs to the SPASM (subtilosin/PQQ/anaerobic sulfatase/mycofactocin maturating enzymes) subfamily of the radical SAM superfamily and contains multiple Fe–S clusters. To characterize the Fe–S clusters in PqqE from Methylobacterium extorquens AM1, Cys residues conserved in the N‐terminal signature motif (CX3CX2C) and the C‐terminal seven‐cysteine motif (CX9–15GX4CXnCX2CX5CX3CXnC; n = an unspecified number) were individually or simultaneously mutated into Ser. Biochemical and Mössbauer spectral analyses of as‐purified and reconstituted mutant enzymes confirmed the presence of three Fe–S clusters in PqqE: one [4Fe–4S]2+ cluster at the N‐terminal region that is essential for the reductive homolytic cleavage of SAM into methionine and 5′‐deoxyadenosyl radical, and one each [4Fe–4S]2+ and [2Fe–2S]2+ auxiliary clusters in the C‐terminal SPASM domain, which are assumed to serve for electron transfer between the buried active site and the protein surface. The presence of [2Fe–2S]2+ cluster is a novel finding for radical SAM enzyme belonging to the SPASM subfamily. Moreover, we found uncommon ligation of the auxiliary [4Fe–4S]2+ cluster with sulfur atoms of three Cys residues and a carboxyl oxygen atom of a conserved Asp residue.
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Affiliation(s)
- Natsaran Saichana
- Centre of the Region Haná for Biotechnological and Agricultural Research Faculty of Science Palacký University Olomouc Czech Republic.,Present address: School of Science Mae Fah Luang University Chiang Rai Thailand
| | - Katsuyuki Tanizawa
- Centre of the Region Haná for Biotechnological and Agricultural Research Faculty of Science Palacký University Olomouc Czech Republic.,Comprehensive Research Institute for Food and Agriculture Faculty of Agriculture Ryukoku University Otsu Japan
| | - Hiroshi Ueno
- Comprehensive Research Institute for Food and Agriculture Faculty of Agriculture Ryukoku University Otsu Japan
| | - Jiří Pechoušek
- Regional Centre of Advanced Technologies and Materials Department of Experimental Physics Faculty of Science Palacký University Olomouc Czech Republic
| | - Petr Novák
- Regional Centre of Advanced Technologies and Materials Department of Experimental Physics Faculty of Science Palacký University Olomouc Czech Republic
| | - Jitka Frébortová
- Centre of the Region Haná for Biotechnological and Agricultural Research Faculty of Science Palacký University Olomouc Czech Republic
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9
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Krishnamoorthy E, Hassan S, Hanna LE, Padmalayam I, Rajaram R, Viswanathan V. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode. J Theor Biol 2017; 420:259-266. [DOI: 10.1016/j.jtbi.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/22/2016] [Accepted: 09/05/2016] [Indexed: 10/20/2022]
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10
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Makins C, Ghosh S, Román-Meléndez GD, Malec PA, Kennedy RT, Marsh ENG. Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity? J Biol Chem 2016; 291:26806-26815. [PMID: 27834682 DOI: 10.1074/jbc.m116.751040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/31/2016] [Indexed: 01/09/2023] Open
Abstract
Viperin is an endoplasmic reticulum-associated antiviral responsive protein that is highly up-regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-l-methionine (SAM) enzyme, but it is unknown whether viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS). Numerous enveloped viruses utilize cholesterol-rich lipid rafts to bud from the host cell membrane, and it is thought that by inhibiting FPPS activity (and therefore cholesterol synthesis), viperin retards viral budding from infected cells. We demonstrate that, consistent with this hypothesis, overexpression of viperin in human embryonic kidney cells reduces the intracellular rate of accumulation of FPPS but does not inhibit or inactivate FPPS. The endoplasmic reticulum-localizing, N-terminal amphipathic helix of viperin is specifically required for viperin to reduce cellular FPPS levels. However, although viperin reductively cleaves SAM to form 5'-deoxyadenosine in a slow, uncoupled reaction characteristic of radical SAM enzymes, this cleavage reaction is independent of FPPS. Furthermore, mutation of key cysteinyl residues ligating the catalytic [Fe4S4] cluster in the radical SAM domain, surprisingly, does not abolish the inhibitory activity of viperin against FPPS; indeed, some mutations potentiate viperin activity. These observations imply that viperin does not act as a radical SAM enzyme in regulating FPPS.
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Affiliation(s)
- Caitlyn Makins
- From the Departments of Chemistry and.,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | | | | | | | | | - E Neil G Marsh
- From the Departments of Chemistry and .,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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11
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Lanz ND, Lee KH, Horstmann AK, Pandelia ME, Cicchillo RM, Krebs C, Booker SJ. Characterization of Lipoyl Synthase from Mycobacterium tuberculosis. Biochemistry 2016; 55:1372-83. [PMID: 26841001 DOI: 10.1021/acs.biochem.5b01216] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The prevalence of multiple and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is on the rise, necessitating the identification of new targets to combat an organism that has infected one-third of the world's population, according to the World Health Organization. The biosynthesis of the lipoyl cofactor is one possible target, given its critical importance in cellular metabolism and the apparent lack of functional salvage pathways in Mtb that are found in humans and many other organisms. The lipoyl cofactor is synthesized de novo in two committed steps, involving the LipB-catalyzed transfer of an octanoyl chain derived from fatty acid biosynthesis to a lipoyl carrier protein and the LipA-catalyzed insertion of sulfur atoms at C6 and C8 of the octanoyl chain. A number of in vitro studies of lipoyl synthases from Escherichia coli, Sulfolobus solfataricus, and Thermosynechococcus elongatus have been conducted, but the enzyme from Mtb has not been characterized. Herein, we show that LipA from Mtb contains two [4Fe-4S] clusters and converts an octanoyl peptide substrate to the corresponding lipoyl peptide product via the same C6-monothiolated intermediate as that observed in the E. coli LipA reaction. In addition, we show that LipA from Mtb forms a complex with the H protein of the glycine cleavage system and that the strength of association is dependent on the presence of S-adenosyl-l-methionine. We also show that LipA from Mtb can complement a lipA mutant of E. coli, demonstrating the commonalities of the two enzymes. Lastly, we show that the substrate for LipA, which normally acts on a post-translationally modified protein, can be reduced to carboxybenzyl-octanoyllysine.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Kyung-Hoon Lee
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Abigail K Horstmann
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Robert M Cicchillo
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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12
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Suess DLM, Kuchenreuther JM, De La Paz L, Swartz JR, Britt RD. Biosynthesis of the [FeFe] Hydrogenase H Cluster: A Central Role for the Radical SAM Enzyme HydG. Inorg Chem 2016; 55:478-87. [PMID: 26703931 PMCID: PMC4780679 DOI: 10.1021/acs.inorgchem.5b02274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hydrogenase enzymes catalyze the rapid and reversible interconversion of H2 with protons and electrons. The active site of the [FeFe] hydrogenase is the H cluster, which consists of a [4Fe-4S]H subcluster linked to an organometallic [2Fe]H subcluster. Understanding the biosynthesis and catalytic mechanism of this structurally unusual active site will aid in the development of synthetic and biological hydrogenase catalysts for applications in solar fuel generation. The [2Fe]H subcluster is synthesized and inserted by three maturase enzymes-HydE, HydF, and HydG-in a complex process that involves inorganic, organometallic, and organic radical chemistry. HydG is a member of the radical S-adenosyl-l-methionine (SAM) family of enzymes and is thought to play a prominent role in [2Fe]H subcluster biosynthesis by converting inorganic Fe(2+), l-cysteine (Cys), and l-tyrosine (Tyr) into an organometallic [(Cys)Fe(CO)2(CN)](-) intermediate that is eventually incorporated into the [2Fe]H subcluster. In this Forum Article, the mechanism of [2Fe]H subcluster biosynthesis is discussed with a focus on how this key [(Cys)Fe(CO)2(CN)](-) species is formed. Particular attention is given to the initial metallocluster composition of HydG, the modes of substrate binding (Fe(2+), Cys, Tyr, and SAM), the mechanism of SAM-mediated Tyr cleavage to CO and CN(-), and the identification of the final organometallic products of the reaction.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jon M. Kuchenreuther
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Liliana De La Paz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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13
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Saichana N, Tanizawa K, Pechoušek J, Novák P, Yakushi T, Toyama H, Frébortová J. PqqE from Methylobacterium extorquens AM1: a radical S-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen. J Biochem 2016; 159:87-99. [PMID: 26188050 PMCID: PMC4882640 DOI: 10.1093/jb/mvv073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/01/2015] [Indexed: 11/12/2022] Open
Abstract
Methylobacterium extorquens AM1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (PQQ), a cofactor of a number of bacterial dehydrogenases, into the culture medium. To elucidate the molecular mechanism of PQQ biosynthesis, we are focusing on PqqE which is believed to be the enzyme catalysing the first reaction of the pathway. PqqE belongs to the radical S-adenosyl-l-methionine (SAM) superfamily, in which most, if not all, enzymes are very sensitive to dissolved oxygen and rapidly inactivated under aerobic conditions. We here report that PqqE from M. extorquens AM1 is markedly oxygen-tolerant; it was efficiently expressed in Escherichia coli cells grown aerobically and affinity-purified to near homogeneity. The purified and reconstituted PqqE contained multiple (likely three) iron-sulphur clusters and showed the reductive SAM cleavage activity that was ascribed to the consensus [4Fe-4S](2+) cluster bound at the N-terminus region. Mössbauer spectrometric analyses of the as-purified and reconstituted enzymes revealed the presence of [4Fe-4S](2+) and [2Fe-2S](2+) clusters as the major forms with the former being predominant in the reconstituted enzyme. PqqE from M.extorquens AM1 may serve as a convenient tool for studying the molecular mechanism of PQQ biosynthesis, avoiding the necessity of establishing strictly anaerobic conditions.
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Affiliation(s)
- Natsaran Saichana
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research
| | - Katsuyuki Tanizawa
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research
| | - Jiří Pechoušek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Petr Novák
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Toshiharu Yakushi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515; and
| | - Hirohide Toyama
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Jitka Frébortová
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research;
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14
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Abstract
Proton reduction and H2 oxidation are key elementary reactions for solar fuel production. Hydrogenases interconvert H+ and H2 with remarkable efficiency and have therefore received much attention in this context. For [FeFe]-hydrogenases, catalysis occurs at a unique cofactor called the H-cluster. In this article, we discuss ways in which EPR spectroscopy has elucidated aspects of the bioassembly of the H-cluster, with a focus on four case studies: EPR spectroscopic identification of a radical en route to the CO and CN- ligands of the H-cluster, tracing 57Fe from the maturase HydG into the H-cluster, characterization of the auxiliary Fe-S cluster in HydG, and isotopic labeling of the CN- ligands of HydA for electronic structure studies of its Hox state. Advances in cell-free maturation protocols have enabled several of these mechanistic studies, and understanding H-cluster maturation may in turn provide insights leading to improvements in hydrogenase production for biotechnological applications.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - R. David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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15
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Ji X, Li Y, Ding W, Zhang Q. Substrate-Tuned Catalysis of the RadicalS-Adenosyl-L-Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis. Angew Chem Int Ed Engl 2015; 54:9021-4. [DOI: 10.1002/anie.201503976] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/23/2022]
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16
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Ji X, Li Y, Ding W, Zhang Q. Substrate-Tuned Catalysis of the RadicalS-Adenosyl-L-Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Nakai T, Ito H, Kobayashi K, Takahashi Y, Hori H, Tsubaki M, Tanizawa K, Okajima T. The Radical S-Adenosyl-L-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds. J Biol Chem 2015; 290:11144-66. [PMID: 25778402 DOI: 10.1074/jbc.m115.638320] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Indexed: 11/06/2022] Open
Abstract
The bacterial enzyme designated QhpD belongs to the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes and participates in the post-translational processing of quinohemoprotein amine dehydrogenase. QhpD is essential for the formation of intra-protein thioether bonds within the small subunit (maturated QhpC) of quinohemoprotein amine dehydrogenase. We overproduced QhpD from Paracoccus denitrificans as a stable complex with its substrate QhpC, carrying the 28-residue leader peptide that is essential for the complex formation. Absorption and electron paramagnetic resonance spectra together with the analyses of iron and sulfur contents suggested the presence of multiple (likely three) [4Fe-4S] clusters in the purified and reconstituted QhpD. In the presence of a reducing agent (sodium dithionite), QhpD catalyzed the multiple-turnover reaction of reductive cleavage of SAM into methionine and 5'-deoxyadenosine and also the single-turnover reaction of intra-protein sulfur-to-methylene carbon thioether bond formation in QhpC bound to QhpD, producing a multiknotted structure of the polypeptide chain. Homology modeling and mutagenic analysis revealed several conserved residues indispensable for both in vivo and in vitro activities of QhpD. Our findings uncover another challenging reaction catalyzed by a radical SAM enzyme acting on a ribosomally translated protein substrate.
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Affiliation(s)
- Tadashi Nakai
- From the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Hiroto Ito
- From the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kazuo Kobayashi
- From the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Yasuhiro Takahashi
- the Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Hiroshi Hori
- the Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan, and
| | - Motonari Tsubaki
- the Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan, and
| | - Katsuyuki Tanizawa
- From the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan, the Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Toshihide Okajima
- From the Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan,
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18
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19
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Mehta AP, Abdelwahed SH, Mahanta N, Fedoseyenko D, Philmus B, Cooper LE, Liu Y, Jhulki I, Ealick SE, Begley TP. Radical S-adenosylmethionine (SAM) enzymes in cofactor biosynthesis: a treasure trove of complex organic radical rearrangement reactions. J Biol Chem 2014; 290:3980-6. [PMID: 25477515 DOI: 10.1074/jbc.r114.623793] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F420, and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry.
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Affiliation(s)
- Angad P Mehta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Sameh H Abdelwahed
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Nilkamal Mahanta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Dmytro Fedoseyenko
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Benjamin Philmus
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Lisa E Cooper
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Yiquan Liu
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Isita Jhulki
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Steven E Ealick
- the Department of Chemistry, Cornell University, Ithaca, New York 14850
| | - Tadhg P Begley
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
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20
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Lanz ND, Pandelia ME, Kakar ES, Lee KH, Krebs C, Booker SJ. Evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase. Biochemistry 2014; 53:4557-72. [PMID: 24901788 PMCID: PMC4216189 DOI: 10.1021/bi500432r] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N(6)-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe-4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5'-deoxyadenosyl 5'-radical (5'-dA(•)). In the LS reaction, two equivalents of 5'-dA(•) are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe-4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N(6)-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe-4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe-4S](0) clusters.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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21
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Frey PA. Travels with carbon-centered radicals. 5'-deoxyadenosine and 5'-deoxyadenosine-5'-yl in radical enzymology. Acc Chem Res 2014; 47:540-9. [PMID: 24308628 DOI: 10.1021/ar400194k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As a graduate student under Professor R. H. Abeles, I began my journey with 5'-deoxyadenosine, studying the coenzyme B12 (adenosylcobalamin)-dependent dioldehydrase (DDH). I proved that suicide inactivation of dioldehydrase by glycolaldehyde proceeded with irreversible cleavage of adenosylcobalamin to 5'-deoxyadenosine. I further showed that suicide inactivation by [2-(3)H]glycolaldehyde produced 5'-deoxy[(3)H]adenosine, the first demonstration of hydrogen transfer to adenosyl-C5' of adenosylcobalamin. The tritium kinetic isotope effect (T)k was 15, which correlated well with the measurement (D)k = 12 for transformation of [1-(2)H]propane-1,2-diol to [2-(2)H]propionaldehyde by DDH. After establishing my own research program, I returned to the glycolaldehyde inactivation of DDH, showing by EPR that suicide inactivation produced glycolaldehyde-2-yl. In retrospect, suicide inactivation involved scission of adenosylcobalamin to 5'-deoxyadenosine-5'-yl, which abstracted a hydrogen from glycolaldehyde. Captodative-stabilized glycolaldehyde-2-yl could not react further, leading to suicide inactivation. In 1986, my colleagues and I took up the problem of the mechanism by which lysine 2,3-aminomutase (LAM) catalyzes S-adenosylmethionine (SAM) and pyridoxal-5'-phosphate (PLP)-dependent interconversion of l-lysine and l-β-lysine. Because the reaction followed the pattern of adenosylcobalamin-dependent rearrangements, I postulated that SAM might be an evolutionary predecessor to adenosylcobalamin. Testing this hypothesis, we traced hydrogen transfer from lysine through the adenosyl-C5' of SAM to β-lysine. Thus, the 5'-deoxyadenosyl of SAM mediated hydrogen transfer by LAM exactly as in adenosylcobalamin mediated hydrogen transfer in B12-dependent isomerizations. The mechanism postulated that SAM cleaves to form 5'-deoxyadenosine-5'-yl followed by abstraction of C3(H) from PLP-α-lysine aldimine to form PLP-α-lysine-3-yl. PLP-α-lysine-3-yl isomerizes to pyridoxal-β-lysine-2-yl, and a hydrogen abstraction from 5'-deoxyadenosine regenerates 5'-deoxyadenosine-5'-yl and releases β-lysine. Of four radicals in the postulated mechanism, three have been characterized by EPR spectroscopy as kinetically competent intermediates. The analysis of the role of iron allowed researchers to elucidate the mechanism by which SAM is cleaved to 5'-deoxyadenosine-5'-yl. LAM contains one [4Fe-4S] cluster ligated by three cysteine residues. As shown by ENDOR spectroscopy and X-ray crystallography, the fourth ligand to the cluster is SAM, through the methionyl carboxylate and amino groups. Inner sphere electron transfer within the [4Fe-4S](1+)-SAM complex leads to [4Fe-4S](2+)-Met and 5'-deoxyadenosine-5'-yl. The iron-binding motif in LAM, CxxxCxxC, found by other groups in four other SAM-dependent enzymes, is the founding motif for the radical SAM superfamily. These enzymes number in the tens of thousands and are responsible for highly diverse and chemically difficult transformations in the biosphere. Available information supports the hypothesis that this superfamily provides the chemical context from which the much more structurally complex adenosylcobalamin evolved.
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Affiliation(s)
- Perry A. Frey
- University of Wisconsin—Madison, 1710 University Avenue, Madison, Wisconsin 53726, United States
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22
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Della Sala G, Hochmuth T, Costantino V, Teta R, Gerwick W, Gerwick L, Piel J, Mangoni A. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:809-818. [PMID: 24249289 PMCID: PMC3908369 DOI: 10.1111/1758-2229.12081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 06/22/2013] [Indexed: 05/31/2023]
Abstract
Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two different examples of the swf cluster were present in the metagenome of P. simplex. A third example of the cluster is present in the previously sequenced genome of a poribacterium from the sponge Aplysina aerophoba but was formerly considered orthologous to the wcb/rkp cluster. The swf cluster was also found in six additional species of sponges. Therefore, the swf cluster represents the second group of mono-modular PKS, after the supA family, to be widespread in marine sponges. The putative swf operon consists of swfA (type I PKS/FAS), swfB (reductase and sulphotransferase domains) and swfC (radical S-adenosylmethionine, or radical SAM). Activation of the acyl carrier protein (ACP) domain of the SwfA protein to its holo-form by co-expression with Svp is the first functional proof of swf type genes in marine sponges. However, the precise biosynthetic role of the swf clusters remains unknown.
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Affiliation(s)
- Gerardo Della Sala
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Thomas Hochmuth
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - William Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenoessische Technische Hochschule (ETH) ZurichWolfgang-Pauli-Str. 10, 8093, Zurich, Switzerland
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
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23
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Mahanta N, Fedoseyenko D, Dairi T, Begley TP. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J Am Chem Soc 2013; 135:15318-21. [PMID: 24083939 PMCID: PMC3855536 DOI: 10.1021/ja408594p] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Menaquinone (MK, vitamin K2) is a lipid-soluble molecule that participates in the bacterial electron transport chain. In mammalian cells, MK functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. Recently, a new pathway for the biosynthesis of this cofactor was discovered in Streptomyces coelicolor A3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by MqnA and an unidentified enzyme. Here, we reconstitute the biosynthesis of aminofutalosine and demonstrate that the missing enzyme (aminofutalosine synthase, MqnE) is a radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl)oxy]benzoic acid. This is a new reaction type in the radical SAM superfamily.
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Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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24
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Palmer LD, Downs DM. The thiamine biosynthetic enzyme ThiC catalyzes multiple turnovers and is inhibited by S-adenosylmethionine (AdoMet) metabolites. J Biol Chem 2013; 288:30693-30699. [PMID: 24014032 DOI: 10.1074/jbc.m113.500280] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ThiC (4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase; EC 4.1.99.17) is a radical S-adenosylmethionine (AdoMet) enzyme that uses a [4Fe-4S](+) cluster to reductively cleave AdoMet to methionine and a 5'-deoxyadenosyl radical that initiates catalysis. In plants and bacteria, ThiC converts the purine intermediate 5-aminoimidazole ribotide to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate, an intermediate of thiamine pyrophosphate (coenzyme B1) biosynthesis. In this study, assay conditions were implemented that consistently generated 5-fold molar excess of HMP, demonstrating that ThiC undergoes multiple turnovers. ThiC activity was improved by in situ removal of product 5'-deoxyadenosine. The activity was inhibited by AdoMet metabolites S-adenosylhomocysteine, adenosine, 5'-deoxyadenosine, S-methyl-5'-thioadenosine, methionine, and homocysteine. Neither adenosine nor S-methyl-5'-thioadenosine had been shown to inhibit radical AdoMet enzymes, suggesting that ThiC is distinct from other family members. The parameters for improved ThiC activity and turnover described here will facilitate kinetic and mechanistic analyses of ThiC.
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Affiliation(s)
- Lauren D Palmer
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Diana M Downs
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602.
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25
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Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Curr Opin Chem Biol 2013; 17:613-8. [PMID: 23856057 DOI: 10.1016/j.cbpa.2013.05.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/28/2013] [Indexed: 01/24/2023]
Abstract
Wyosine and its derivatives are highly modified, acid labile tricyclic bases found at position 37 of tRNA(Phe) in archaea and eukarya. The formation of the common 4-demethylwyosine structural feature entails condensation of pyruvate and N-methylguanosine catalyzed by TYW1. This review will focus on the mechanism of this complex radical mediated transformation.
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26
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Challand MR, Salvadori E, Driesener RC, Kay CWM, Roach PL, Spencer J. Cysteine methylation controls radical generation in the Cfr radical AdoMet rRNA methyltransferase. PLoS One 2013; 8:e67979. [PMID: 23861844 PMCID: PMC3702613 DOI: 10.1371/journal.pone.0067979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
The 'radical S-adenosyl-L-methionine (AdoMet)' enzyme Cfr methylates adenosine 2503 of the 23S rRNA in the peptidyltransferase centre (P-site) of the bacterial ribosome. This modification protects host bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), from numerous antibiotics, including agents (e.g. linezolid, retapamulin) that were developed to treat such organisms. Cfr contains a single [4Fe-4S] cluster that binds two separate molecules of AdoMet during the reaction cycle. These are used sequentially to first methylate a cysteine residue, Cys338; and subsequently generate an oxidative radical intermediate that facilitates methyl transfer to the unreactive C8 (and/or C2) carbon centres of adenosine 2503. How the Cfr active site, with its single [4Fe-4S] cluster, catalyses these two distinct activities that each utilise AdoMet as a substrate remains to be established. Here, we use absorbance and electron paramagnetic resonance (EPR) spectroscopy to investigate the interactions of AdoMet with the [4Fe-4S] clusters of wild-type Cfr and a Cys338 Ala mutant, which is unable to accept a methyl group. Cfr binds AdoMet with high (∼ 10 µM) affinity notwithstanding the absence of the RNA cosubstrate. In wild-type Cfr, where Cys338 is methylated, AdoMet binding leads to rapid oxidation of the [4Fe-4S] cluster and production of 5'-deoxyadenosine (DOA). In contrast, while Cys338 Ala Cfr binds AdoMet with equivalent affinity, oxidation of the [4Fe-4S] cluster is not observed. Our results indicate that the presence of a methyl group on Cfr Cys338 is a key determinant of the activity of the enzyme towards AdoMet, thus enabling a single active site to support two distinct modes of AdoMet cleavage.
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Affiliation(s)
- Martin R. Challand
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | | | - Christopher W. M. Kay
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - Peter L. Roach
- Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
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27
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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28
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Analysis of ThiC variants in the context of the metabolic network of Salmonella enterica. J Bacteriol 2012; 194:6088-95. [PMID: 22961850 DOI: 10.1128/jb.01361-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In bacteria, the 4-amino-hydroxymethyl-2-methylpyrimidine (HMP) moiety of thiamine is synthesized from 5-aminoimidazole ribotide (AIR), a branch point metabolite of purine and thiamine biosynthesis. ThiC is a member of the radical S-adenosylmethionine (AdoMet) superfamily and catalyzes the complex chemical rearrangement of AIR to HMP-P. As reconstituted in vitro, the ThiC reaction requires AdoMet, AIR, and reductant. This study analyzed variants of ThiC in vivo and in vitro to probe the metabolic network surrounding AIR in Salmonella enterica. Several variants of ThiC that required metabolic perturbations to function in vivo were biochemically characterized in vitro. Results presented herein indicate that the subtleties of the metabolic network have not been captured in the current reconstitution of the ThiC reaction.
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29
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Abstract
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Methylation is an essential and ubiquitous reaction that plays an important role in a wide range of biological processes. Most biological methylations use S-adenosylmethionine (SAM) as the methyl donor and proceed via an SN2 displacement mechanism. However, researchers have discovered an increasing number of methylations that involve radical chemistry. The enzymes known to catalyze these reactions all belong to the radical SAM superfamily. This family of enzymes utilizes a specialized [4Fe-4S] cluster for reductive cleavage of SAM to yield a highly reactive 5'-deoxyadenosyl (dAdo) radical. Radical chemistry is then imposed on a variety of organic substrates, leading to a diverse array of transformations. Until recently, researchers had not fully understood how these enzymes employ radical chemistry to mediate a methyl transfer reaction. Sequence analyses reveal that the currently identified radical SAM methyltransferases (RSMTs) can be grouped into three classes, which appear distinct in protein architecture and mechanism. Class A RSMTs mainly include the rRNA methyltransferases RlmN and Cfr from various origins. As exemplified by Escherichia coli RlmN, these proteins have a single canonical radical SAM core domain that includes an (βα)6 partial barrel most similar to that of pyruvate formate lyase-activase. The exciting recent studies on RlmN and Cfr are beginning to provide insights into the intriguing chemistry of class A RSMTs. These enzymes utilize a methylene radical generated on a unique methylated cysteine residue. However, based on the variety of substrates used by the other classes of RSMTs, alternative mechanisms are likely to be discovered. Class B RSMTs contain a proposed N-terminal cobalamin binding domain in addition to a radical SAM domain at the C-terminus. This class of proteins methylates diverse substrates at inert sp3 carbons, aromatic heterocycles, and phosphinates, possibly involving a cobalamin-mediated methyl transfer process. Class C RSMTs share significant sequence similarity with coproporphyrinogen III oxidase HemN. Despite methylating similar substrates (aromatic heterocycles), class C RSMTs likely employ a mechanism distinct from that of class A because two conserved cysteines that are required for class A are typically not found in class C RSMTs. Class A and class B enzymes probably share the use of two molecules of SAM: one to generate a dAdo radical and one to provide the methyl group to the substrate. In class A, a cysteine would act as a conduit of the methyl group whereas in class B cobalamin may serve this purpose. Currently no clues are available regarding the mechanism of class C RSMTs, but the sequence similarities between its members and HemN and the observation that HemN binds two SAM molecules suggest that class C enzymes could use two SAM molecules for catalysis. The diverse strategies for using two SAM molecules reflect the rich chemistry of radical-mediated methylation reactions and the remarkable versatility of the radical SAM superfamily.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | | | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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Duffus BR, Hamilton TL, Shepard EM, Boyd ES, Peters JW, Broderick JB. Radical AdoMet enzymes in complex metal cluster biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1254-63. [PMID: 22269887 DOI: 10.1016/j.bbapap.2012.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/01/2012] [Indexed: 10/14/2022]
Abstract
Radical S-adenosylmethionine (AdoMet) enzymes comprise a large superfamily of proteins that engage in a diverse series of biochemical transformations through generation of the highly reactive 5'-deoxyadenosyl radical intermediate. Recent advances into the biosynthesis of unique iron-sulfur (FeS)-containing cofactors such as the H-cluster in [FeFe]-hydrogenase, the FeMo-co in nitrogenase, as well as the iron-guanylylpyridinol (FeGP) cofactor in [Fe]-hydrogenase have implicated new roles for radical AdoMet enzymes in the biosynthesis of complex inorganic cofactors. Radical AdoMet enzymes in conjunction with scaffold proteins engage in modifying ubiquitous FeS precursors into unique clusters, through novel amino acid decomposition and sulfur insertion reactions. The ability of radical AdoMet enzymes to modify common metal centers to unusual metal cofactors may provide important clues into the stepwise evolution of these and other complex bioinorganic catalysts. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Benjamin R Duffus
- The Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA
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31
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Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 2011; 19:1038-52. [PMID: 21827941 DOI: 10.1016/j.str.2011.06.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/01/2011] [Accepted: 06/09/2011] [Indexed: 01/06/2023]
Abstract
Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.
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Challand MR, Driesener RC, Roach PL. Radical S-adenosylmethionine enzymes: mechanism, control and function. Nat Prod Rep 2011; 28:1696-721. [PMID: 21779595 DOI: 10.1039/c1np00036e] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Martin R Challand
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS81TD, USA
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Zhang Q, Liu W. Complex biotransformations catalyzed by radical S-adenosylmethionine enzymes. J Biol Chem 2011; 286:30245-30252. [PMID: 21771780 DOI: 10.1074/jbc.r111.272690] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The radical S-adenosylmethionine (AdoMet) superfamily currently comprises thousands of proteins that participate in numerous biochemical processes across all kingdoms of life. These proteins share a common mechanism to generate a powerful 5'-deoxyadenosyl radical, which initiates a highly diverse array of biotransformations. Recent studies are beginning to reveal the role of radical AdoMet proteins in the catalysis of highly complex and chemically unusual transformations, e.g. the ThiC-catalyzed complex rearrangement reaction. The unique features and intriguing chemistries of these proteins thus demonstrate the remarkable versatility and sophistication of radical enzymology.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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