1
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Nguyen N, Forstater JH, McIntosh JA. Decarboxylation in Natural Products Biosynthesis. JACS AU 2024; 4:2715-2745. [PMID: 39211618 PMCID: PMC11350588 DOI: 10.1021/jacsau.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms and act on a large variety of substrates, making them appealing in terms of biotechnological applications. This Perspective focuses on the occurrence of decarboxylation reactions in natural product biosynthesis and provides a perspective on their applications in biocatalysis for fine chemicals and pharmaceuticals.
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2
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Peng F, Ke Z, Jin H, Wang W, Zhang H, Li Y. Structural insights into the regulation mechanism of Mycobacterium tuberculosis MftR. FASEB J 2024; 38:e23724. [PMID: 38837712 DOI: 10.1096/fj.202302409rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024]
Abstract
Mycobacterium tuberculosis, the pathogen of the deadly disease tuberculosis, depends on the redox cofactor mycofactocin (MFT) to adapt to and survive under hypoxic conditions. MftR is a TetR family transcription regulator that binds upstream of the MFT gene cluster and controls MFT synthesis. To elucidate the structural basis underlying MftR regulation, we determined the crystal structure of Mycobacterium tuberculosis MftR (TB-MftR). The structure revealed an interconnected hydrogen bond network in the α1-α2-α3 helices of helix-turn-helix (HTH) DNA-binding domain that is essential for nucleic acid interactions. The ligand-binding domain contains a hydrophobic cavity enclosing long-chain fatty acyl-CoAs like the key regulatory ligand oleoyl-CoA. Despite variations in ligand-binding modes, comparative analyses suggest regulatory mechanisms are largely conserved across TetR family acyl-CoA sensors. By elucidating the intricate structural mechanisms governing DNA and ligand binding by TB-MftR, our study enhances understanding of the regulatory roles of this transcription factor under hypoxic conditions, providing insights that could inform future research into Mycobacterium tuberculosis pathogenesis.
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Affiliation(s)
- Fei Peng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Zunhui Ke
- Department of Blood Transfusion, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoruo Jin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wang
- Medical Subcenter of HUST Analytical & Testing Center, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haoran Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Wuhan, China
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3
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Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A. Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol 2024; 20:382-391. [PMID: 38158457 DOI: 10.1038/s41589-023-01493-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
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Affiliation(s)
- Xavier Kubiak
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Ivan Polsinelli
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | - Cameron D Fyfe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Laura Fradale
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Clémence Brewee
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | | | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
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4
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Lien Y, Lachowicz JC, Mendauletova A, Zizola C, Ngendahimana T, Kostenko A, Eaton SS, Latham JA, Grove TL. Structural, Biochemical, and Bioinformatic Basis for Identifying Radical SAM Cyclopropyl Synthases. ACS Chem Biol 2024; 19:370-379. [PMID: 38295270 PMCID: PMC10878394 DOI: 10.1021/acschembio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
The importance of radical S-adenosyl-l-methionine (RS) enzymes in the maturation of ribosomally synthesized and post-translationally modified peptides (RiPPs) continues to expand, specifically for the RS-SPASM subfamily. We recently discovered an RS-SPASM enzyme that installs a carbon-carbon bond between the geminal methyls of valine residues, resulting in the formation of cyclopropylglycine (CPG). Here, we sought to define the family of cyclopropyl (CP) synthases because of the importance of cyclopropane scaffolds in pharmaceutical development. Using RadicalSAM.org, we bioinformatically expanded the family of CP synthases and assigned unique peptide sequences to each subclade. We identified a unique RiPP biosynthetic pathway that encodes a precursor peptide, TigB, with a repeating TIGSVS motif. Using LCMS and NMR techniques, we show that the RS enzyme associated with the pathway, TigE, catalyzes the formation of a methyl-CPG from the conserved isoleucine residing in the repeating motif of TigB. Furthermore, we obtained a crystal structure of TigE, which reveals an unusual tyrosyl ligation to the auxiliary I [4Fe-4S] cluster, provided by a glycine-tyrosine-tryptophan motif unique to all CP synthases. Further, we show that this unique tyrosyl ligation is absolutely required for TigE activity. Together, our results provide insight into how CP synthases perform this unique reaction.
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Affiliation(s)
- Yi Lien
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Jake C. Lachowicz
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Aigera Mendauletova
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Cynthia Zizola
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Thacien Ngendahimana
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Anastasiia Kostenko
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Sandra S. Eaton
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - John A. Latham
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
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5
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Johnson BA, Clark KA, Bushin LB, Spolar CN, Seyedsayamdost MR. Expanding the Landscape of Noncanonical Amino Acids in RiPP Biosynthesis. J Am Chem Soc 2024; 146:3805-3815. [PMID: 38316431 DOI: 10.1021/jacs.3c10824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Advancements in DNA sequencing technologies and bioinformatics have enabled the discovery of new metabolic reactions from overlooked microbial species and metagenomic sequences. Using a bioinformatic co-occurrence strategy, we previously generated a network of ∼600 uncharacterized quorum-sensing-regulated biosynthetic gene clusters that code for ribosomally synthesized and post-translationally modified peptide (RiPP) natural products and are tailored by radical S-adenosylmethionine (RaS) enzymes in streptococci. The most complex of these is the GRC subfamily, named after a conserved motif in the precursor peptide and found exclusively in Streptococcus pneumoniae, the causative agent of bacterial pneumonia. In this study, using both in vivo and in vitro approaches, we have elucidated the modifications installed by the grc biosynthetic enzymes, including a ThiF-like adenylyltransferase/cyclase that generates a C-terminal Glu-to-Cys thiolactone macrocycle, and two RaS enzymes, which selectively epimerize the β-carbon of threonine and desaturate histidine to generate the first instances of l-allo-Thr and didehydrohistidine in RiPP biosynthesis. RaS-RiPPs that have been discovered thus far have stood out for their exotic macrocycles. The product of the grc cluster breaks this trend by generating two noncanonical residues rather than an unusual macrocycle in the peptide substrate. These modifications expand the landscape of nonproteinogenic amino acids in RiPP natural product biosynthesis and motivate downstream biocatalytic applications of the corresponding enzymes.
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Affiliation(s)
- Brooke A Johnson
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Calvin N Spolar
- 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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6
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Fix I, Heidinger L, Friedrich T, Layer G. The Radical SAM Heme Synthase AhbD from Methanosarcina barkeri Contains Two Auxiliary [4Fe-4S] Clusters. Biomolecules 2023; 13:1268. [PMID: 37627333 PMCID: PMC10452713 DOI: 10.3390/biom13081268] [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: 07/11/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
In archaea and sulfate-reducing bacteria, heme is synthesized via the siroheme-dependent pathway. The last step of this route is catalyzed by the Radical SAM enzyme AhbD and consists of the conversion of iron-coproporphyrin III into heme. AhbD belongs to the subfamily of Radical SAM enzymes containing a SPASM/Twitch domain carrying either one or two auxiliary iron-sulfur clusters in addition to the characteristic Radical SAM cluster. In previous studies, AhbD was reported to contain one auxiliary [4Fe-4S] cluster. In this study, the amino acid sequence motifs containing conserved cysteine residues in AhbD proteins from different archaea and sulfate-reducing bacteria were reanalyzed. Amino acid sequence alignments and computational structural models of AhbD suggested that a subset of AhbD proteins possesses the full SPASM motif and might contain two auxiliary iron-sulfur clusters (AuxI and AuxII). Therefore, the cluster content of AhbD from Methanosarcina barkeri was studied using enzyme variants lacking individual clusters. The purified enzymes were analyzed using UV/Visible absorption and EPR spectroscopy as well as iron/sulfide determinations showing that AhbD from M. barkeri contains two auxiliary [4Fe-4S] clusters. Heme synthase activity assays suggested that the AuxI cluster might be involved in binding the reaction intermediate and both clusters potentially participate in electron transfer.
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Affiliation(s)
- Isabelle Fix
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
| | - Lorenz Heidinger
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (L.H.); (T.F.)
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (L.H.); (T.F.)
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
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7
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Van V, Brown JB, O'Shea CR, Rosenbach H, Mohamed I, Ejimogu NE, Bui TS, Szalai VA, Chacón KN, Span I, Zhang F, Smith AT. Iron-sulfur clusters are involved in post-translational arginylation. Nat Commun 2023; 14:458. [PMID: 36709327 PMCID: PMC9884297 DOI: 10.1038/s41467-023-36158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Eukaryotic arginylation is an essential post-translational modification that modulates protein stability and regulates protein half-life. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA transferases (ATE1s), which are conserved across the eukaryotic domain. Despite their conservation and importance, little is known regarding the structure, mechanism, and regulation of ATE1s. In this work, we show that ATE1s bind a previously undiscovered [Fe-S] cluster that is conserved across evolution. We characterize the nature of this [Fe-S] cluster and find that the presence of the [Fe-S] cluster in ATE1 is linked to its arginylation activity, both in vitro and in vivo, and the initiation of the yeast stress response. Importantly, the ATE1 [Fe-S] cluster is oxygen-sensitive, which could be a molecular mechanism of the N-degron pathway to sense oxidative stress. Taken together, our data provide the framework of a cluster-based paradigm of ATE1 regulatory control.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Corin R O'Shea
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ijaz Mohamed
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Nna-Emeka Ejimogu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Toan S Bui
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Veronika A Szalai
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kelly N Chacón
- Department of Chemistry, Reed College, Portland, OR, 97202, USA
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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8
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Li X, Yu F, Wang F, Wang S, Han R, Cheng Y, Zhao M, Sun J, Xue Z. Point mutation of V252 in neomycin C epimerase enlarges substrate-binding pocket and improves neomycin B accumulation in Streptomyces fradiae. BIORESOUR BIOPROCESS 2022; 9:123. [PMID: 38647873 PMCID: PMC10991966 DOI: 10.1186/s40643-022-00613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/19/2022] [Indexed: 12/09/2022] Open
Abstract
Neomycin, an aminoglycoside antibiotic with broad-spectrum antibacterial resistance, is widely used in pharmaceutical and agricultural fields. However, separation and purification of neomycin B as an active substance from Streptomyces fradiae are complicated. Although NeoN can catalyze conversion of neomycin C to neomycin B, the underlying catalytic mechanism is still unclear. In this study, the genomic information of high-yielding mutant S. fradiae SF-2 was elucidated using whole-genome sequencing. Subsequently, the mechanism of NeoN in catalyzing conversion of neomycin C to neomycin B was resolved based on NeoN-SAM-neomycin C ternary complex. Mutant NeoNV252A showed improved NeoN activity, and the recombinant strain SF-2-NeoNV252A accumulated 16,766.6 U/mL neomycin B, with a decrease in neomycin C ratio from 16.1% to 6.28%, when compared with the parental strain SF-2. In summary, this study analyzed the catalytic mechanism of NeoN, providing significant reference for rational design of NeoN to improve neomycin B production and weaken the proportion of neomycin C.
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Affiliation(s)
- Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Fei Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Fang Wang
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Sang Wang
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Rumeng Han
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Yihan Cheng
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Ming Zhao
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Junfeng Sun
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China
| | - Zhenglian Xue
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu, 241000, China.
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9
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Kostenko A, Lien Y, Mendauletova A, Ngendahimana T, Novitskiy IM, Eaton SS, Latham JA. Identification of a poly-cyclopropylglycine-containing peptide via bioinformatic mapping of radical S-adenosylmethionine enzymes. J Biol Chem 2022; 298:101881. [PMID: 35367210 PMCID: PMC9062424 DOI: 10.1016/j.jbc.2022.101881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/28/2023] Open
Abstract
Peptide-derived natural products are a large class of bioactive molecules that often contain chemically challenging modifications. In the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs), radical-SAM (rSAM) enzymes have been shown to catalyze the formation of ether, thioether, and carbon-carbon bonds on the precursor peptide. The installation of these bonds typically establishes the skeleton of the mature RiPP. To facilitate the search for unexplored rSAM-dependent RiPPs for the community, we employed a bioinformatic strategy to screen a subfamily of peptide-modifying rSAM enzymes which are known to bind up to three [4Fe-4S] clusters. A sequence similarity network was used to partition related families of rSAM enzymes into >250 clusters. Using representative sequences, genome neighborhood diagrams were generated using the Genome Neighborhood Tool. Manual inspection of bacterial genomes yielded numerous putative rSAM-dependent RiPP pathways with unique features. From this analysis, we identified and experimentally characterized the rSAM enzyme, TvgB, from the tvg gene cluster from Halomonas anticariensis. In the tvg gene cluster, the precursor peptide, TvgA, is comprised of a repeating TVGG motif. Structural characterization of the TvgB product revealed the repeated formation of cyclopropylglycine, where a new bond is formed between the γ-carbons on the precursor valine. This novel RiPP modification broadens the functional potential of rSAM enzymes and validates the proposed bioinformatic approach as a practical broad search tool for the discovery of new RiPP topologies.
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Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Yi Lien
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Aigera Mendauletova
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - John A Latham
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA.
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10
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Richardson KH, Seif-Eddine M, Sills A, Roessler MM. Controlling and exploiting intrinsic unpaired electrons in metalloproteins. Methods Enzymol 2022; 666:233-296. [PMID: 35465921 DOI: 10.1016/bs.mie.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
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Affiliation(s)
| | - Maryam Seif-Eddine
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Adam Sills
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Maxie M Roessler
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom.
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11
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Yokoyama K, Li D, Pang H. Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. ACS BIO & MED CHEM AU 2022; 2:94-108. [PMID: 35480226 PMCID: PMC9026282 DOI: 10.1021/acsbiomedchemau.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023]
Abstract
![]()
MoaA is one of the
most conserved radical S-adenosyl-l-methionine
(SAM) enzymes, and is found in most organisms in
all three kingdoms of life. MoaA contributes to the biosynthesis of
molybdenum cofactor (Moco), a redox enzyme cofactor used in various
enzymes such as purine and sulfur catabolism in humans and anaerobic
respiration in bacteria. Unlike many other cofactors, in most organisms,
Moco cannot be taken up as a nutrient and requires de novo biosynthesis.
Consequently, Moco biosynthesis has been linked to several human health
problems, such as human Moco deficiency disease and bacterial infections.
Despite
the medical and biological significance, the biosynthetic mechanism
of Moco’s characteristic pyranopterin structure remained elusive
for more than two decades. This transformation requires the actions
of the MoaA radical SAM enzyme and another protein, MoaC. Recently,
MoaA and MoaC functions were elucidated as a radical SAM GTP 3′,8-cyclase
and cyclic pyranopterin monophosphate (cPMP) synthase, respectively.
This finding resolved the key mystery in the field and revealed new
opportunities in studying the enzymology and chemical biology of MoaA
and MoaC to elucidate novel mechanisms in enzyme catalysis or to address
unsolved questions in Moco-related human health problems. Here, we
summarize the recent progress in the functional and mechanistic studies
of MoaA and MoaC and discuss the field’s future directions.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Di Li
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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12
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Lee YH, Hou X, Chen R, Feng J, Liu X, Ruszczycky MW, Gao JM, Wang B, Zhou J, Liu HW. Radical S-Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S. J Am Chem Soc 2022; 144:4478-4486. [PMID: 35238201 DOI: 10.1021/jacs.1c12010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The biosynthesis of blasticidin S has drawn attention due to the participation of the radical S-adenosyl methionine (SAM) enzyme BlsE. The original assignment of BlsE as a radical-mediated, redox-neutral decarboxylase is unusual because this reaction appears to serve no biosynthetic purpose and would need to be reversed by a subsequent carboxylation step. Furthermore, with the exception of BlsE, all other radical SAM decarboxylases reported to date are oxidative in nature. Careful analysis of the BlsE reaction, however, demonstrates that BlsE is not a decarboxylase but instead a lyase that catalyzes the dehydration of cytosylglucuronic acid (CGA) to form cytosyl-4'-keto-3'-deoxy-d-glucuronic acid, which can rapidly decarboxylate nonenzymatically in vitro. Analysis of substrate isotopologs, fluorinated analogues, as well as computational models based on X-ray crystal structures of the BlsE·SAM (2.09 Å) and BlsE·SAM·CGA (2.62 Å) complexes suggests that BlsE catalysis likely proceeds via direct elimination of water from the CGA C4' α-hydroxyalkyl radical as opposed to 1,2-migration of the C3'-hydroxyl prior to dehydration. Biosynthetic and mechanistic implications of the revised assignment of BlsE are discussed.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Xueli Hou
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ridao Chen
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiao Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States.,School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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13
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Mendauletova A, Kostenko A, Lien Y, Latham J. How a Subfamily of Radical S-Adenosylmethionine Enzymes Became a Mainstay of Ribosomally Synthesized and Post-translationally Modified Peptide Discovery. ACS BIO & MED CHEM AU 2022; 2:53-59. [PMID: 37102180 PMCID: PMC10114670 DOI: 10.1021/acsbiomedchemau.1c00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Radical S-adenosylmethionine (rSAM) enzymes are a large and diverse superfamily of enzymes, some of which are known to participate in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Specifically, a subfamily of rSAM proteins with an elongated C-terminus known as a SPASM domain have become a fixation in the discovery of new RiPP natural products. Arguably, a structural study, a bioinformatic study, and a functional study built the foundation of the research for rSAM-SPASM-protein-modified RiPPs. In this Review, we focus on these three studies and how they initiated what has become an increasingly productive field. In addition, we discuss the current state of RiPPs that depends on rSAM-SPASM proteins and provide guidelines to consider in future research. Lastly, we discuss how genome mining tools have become a powerful means to identify and predict new RiPP natural products. Despite the state of our current knowledge, we do not completely understand the relationship of rSAM-SPASM chemistry, substrate recognition, and the structure-function relationship as it pertains to RiPP biosynthesis, and as such, there remain many interesting findings waiting to be discovered in the future.
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Affiliation(s)
- Aigera Mendauletova
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Anastasiia Kostenko
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Yi Lien
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - John Latham
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
- ; Tel.: +1 303 871 2533; Fax: +1 303 871 2254
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14
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Besandre RA, Chen Z, Davis I, Zhang J, Ruszczycky MW, Liu A, Liu HW. HygY Is a Twitch Radical SAM Epimerase with Latent Dehydrogenase Activity Revealed upon Mutation of a Single Cysteine Residue. J Am Chem Soc 2021; 143:15152-15158. [PMID: 34491039 DOI: 10.1021/jacs.1c05727] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HygY is a SPASM/twitch radical SAM enzyme hypothesized to catalyze the C2'-epimerization of galacamine during the biosynthesis of hygromycin B. This activity is confirmed via biochemical and structural analysis of the derivatized reaction products using chemically synthesized deuterated substrate, high-resolution mass spectrometry and 1H NMR. Electron paramagnetic resonance spectroscopy of the reduced enzyme is consistent with ligation of two [Fe4S4] clusters characteristic of the twitch radical SAM subgroup. HygY catalyzed epimerization proceeds with incorporation of a single solvent Hydron into the talamine product facilitated by the catalytic cysteine-183 residue. Mutation of this cysteine to alanine converts HygY from a C2'-epimerase to an C2'-dehydrogenase with comparable activity. The SPASM/twitch radical SAM enzymes often serve as anaerobic oxidases making the redox-neutral epimerases in this class rather interesting. The discovery of latent dehydrogenase activity in a twitch epimerase may therefore offer new insights into the mechanistic features that distinguish oxidative versus redox-neutral SPASM/twitch enzymes and lead to the evolution of new enzyme activities.
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Affiliation(s)
- Ronald A Besandre
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Zhang Chen
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States
| | - Jiawei Zhang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
| | - Mark Walter Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, United States
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15
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Pang H, Walker LM, Silakov A, Zhang P, Yang W, Elliott SJ, Yokoyama K. Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3',8-Cyclase MoaA. J Am Chem Soc 2021; 143:13835-13844. [PMID: 34423974 DOI: 10.1021/jacs.1c06268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity of the reactions catalyzed by radical S-adenosyl-l-methionine (SAM) enzymes is achieved at least in part through the variety of mechanisms to quench their radical intermediates. In the SPASM-twitch family, the largest family of radical SAM enzymes, the radical quenching step is thought to involve an electron transfer to or from an auxiliary 4Fe-4S cluster in or adjacent to the active site. However, experimental demonstration of such functions remains limited. As a representative member of this family, MoaA has one radical SAM cluster ([4Fe-4S]RS) and one auxiliary cluster ([4Fe-4S]AUX), and catalyzes a unique 3',8-cyclization of GTP into 3',8-cyclo-7,8-dihydro-GTP (3',8-cH2GTP) in the molybdenum cofactor (Moco) biosynthesis. Here, we report a mechanistic investigation of the radical quenching step in MoaA, a chemically challenging reduction of 3',8-cyclo-GTP-N7 aminyl radical. We first determined the reduction potentials of [4Fe-4S]RS and [4Fe-4S]AUX as -510 mV and -455 mV, respectively, using a combination of protein film voltammogram (PFV) and electron paramagnetic resonance (EPR) spectroscopy. Subsequent Q-band EPR characterization of 5'-deoxyadenosine C4' radical (5'-dA-C4'•) trapped in the active site revealed isotropic exchange interaction (∼260 MHz) between 5'-dA-C4'• and [4Fe-4S]AUX1+, suggesting that [4Fe-4S]AUX is in the reduced (1+) state during the catalysis. Together with density functional theory (DFT) calculation, we propose that the aminyl radical reduction proceeds through a proton-coupled electron transfer (PCET), where [4Fe-4S]AUX serves as an electron donor and R17 residue acts as a proton donor. These results provide detailed mechanistic insights into the radical quenching step of radical SAM enzyme catalysis.
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Affiliation(s)
- Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Lindsey M Walker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
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16
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Balo AR, Tao L, Britt RD. Characterizing SPASM/twitch Domain-Containing Radical SAM Enzymes by EPR Spectroscopy. APPLIED MAGNETIC RESONANCE 2021; 53:809-820. [PMID: 35509369 PMCID: PMC9012708 DOI: 10.1007/s00723-021-01406-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
Owing to their importance, diversity and abundance of generated paramagnetic species, radical S-adenosylmethionine (rSAM) enzymes have become popular targets for electron paramagnetic resonance (EPR) spectroscopic studies. In contrast to prototypic single-domain and thus single-[4Fe-4S]-containing rSAM enzymes, there is a large subfamily of rSAM enzymes with multiple domains and one or two additional iron-sulfur cluster(s) called the SPASM/twitch domain-containing rSAM enzymes. EPR spectroscopy is a powerful tool that allows for the observation of the iron-sulfur clusters as well as potentially trappable paramagnetic reaction intermediates. Here, we review continuous-wave and pulse EPR spectroscopic studies of SPASM/twitch domain-containing rSAM enzymes. Among these enzymes, we will review in greater depth four well-studied enzymes, BtrN, MoaA, PqqE, and SuiB. Towards establishing a functional consensus of the additional architecture in these enzymes, we describe the commonalities between these enzymes as observed by EPR spectroscopy.
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Affiliation(s)
- Aidin R. Balo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - R. David Britt
- Department of Chemistry, University of California, Davis, CA 95616 USA
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17
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Abstract
57Fe Mӧssbauer spectroscopy is unparalleled in the study of Fe-S cluster-containing proteins because of its unique ability to detect all forms of iron. Enrichment of biological samples with the 57Fe isotope and manipulation of experimental parameters such as temperature and magnetic field allow for elucidation of the number of Fe-S clusters present in a given protein, their nuclearity, oxidation state, geometry, and ligation environment, as well as any transient states relevant to enzyme chemistry. This chapter is arranged in five sections to help navigate an experimentalist to utilize 57Fe Mӧssbauer spectroscopy for delineating the role and structure of biological Fe-S clusters. The first section lays out the tools and technical considerations for the preparation of 57Fe-labeled samples. The choice of experimental parameters and their effects on the Mӧssbauer spectra are presented in the following two sections. The last two sections provide a theoretical and practical guide on spectral acquisition and analysis relevant to Fe-S centers.
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18
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Zhu W, Walker LM, Tao L, Iavarone AT, Wei X, Britt RD, Elliott SJ, Klinman JP. Structural Properties and Catalytic Implications of the SPASM Domain Iron-Sulfur Clusters in Methylorubrum extorquens PqqE. J Am Chem Soc 2020; 142:12620-12634. [PMID: 32643933 DOI: 10.1021/jacs.0c02044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the relationship between the metallocofactor and its protein environment is the key to uncovering the mechanism of metalloenzymes. PqqE, a radical S-adenosylmethionine enzyme in pyrroloquinoline quinone (PQQ) biosynthesis, contains three iron-sulfur cluster binding sites. Two auxiliary iron-sulfur cluster binding sites, designated as AuxI and AuxII, use distinctive ligands compared to other proteins in the family while their functions remain unclear. Here, we investigate the electronic properties of these iron-sulfur clusters and compare the catalytic efficiency of wild-type (WT) Methylorubrum extorquens AM1 PqqE to a range of mutated constructs. Using native mass spectrometry, protein film electrochemistry, and electron paramagnetic resonance spectroscopy, we confirm the previously proposed incorporation of a mixture of [2Fe-2S] and [4Fe-4S] clusters at the AuxI site and are able to assign redox potentials to each of the three iron-sulfur clusters. Significantly, a conservative mutation at AuxI, C268H, shown to selectively incorporate a [4Fe-4S] cluster, catalyzes an enhancement of uncoupled S-adenosylmethionine cleavage relative to WT, together with the elimination of detectable peptide cross-linked product. While a [4Fe-4S] cluster can be tolerated at the AuxI site, the aggregate findings suggest a functional [2Fe-2S] configuration within the AuxI site. PqqE variants with nondestructive ligand replacements at AuxII also show that the reduction potential at this site can be manipulated by changing the electronegativity of the unique aspartate ligand. A number of novel mechanistic features are proposed based on the kinetic and spectroscopic data. Additionally, bioinformatic analyses suggest that the unique ligand environment of PqqE may be relevant to its role in PQQ biosynthesis within an oxygen-dependent biosynthetic pathway.
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Affiliation(s)
- Wen Zhu
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States
| | - Lindsey M Walker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lizhi Tao
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States
| | - Xuetong Wei
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, United States
| | - R David Britt
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Judith P Klinman
- California Institute for Quantitative Biosciences, University of California-Berkeley, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, United States.,Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
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19
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20
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Ngendahimana T, Ayikpoe R, Latham JA, Eaton GR, Eaton SS. Structural insights for vanadium catecholates and iron‑sulfur clusters obtained from multiple data analysis methods applied to electron spin relaxation data. J Inorg Biochem 2019; 201:110806. [PMID: 31505439 PMCID: PMC6859209 DOI: 10.1016/j.jinorgbio.2019.110806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/06/2019] [Accepted: 08/21/2019] [Indexed: 01/22/2023]
Abstract
Electron paramagnetic resonance (EPR) inversion recovery curves for vanadium catecholates and iron‑sulfur clusters were analyzed with three models: the sum of two exponentials, a stretched exponential, and a model-free distribution of exponentials (UPEN). For all data sets studied fits with a stretched exponential were statistically indistinguishable from the sum of two exponentials, and were significantly better than for single exponentials. UPEN provides insights into the structures of the distributions. For a vanadium(IV) tris catecholate the distribution of relaxation rates calculated with UPEN shows the contribution from spectral diffusion at low temperatures. The energy of the local mode for this complex, found from the temperature dependence of the spin lattice relaxation, is consistent with values expected for a metal-ligand vibration. For the [2Fe-2S]+ cluster in pyruvate formate lyase activating enzyme (PFL-AE) the small stretched exponential β values (0.3) at low temperature and the distributions calculated with UPEN reflect the contribution from a second rapidly relaxing species that could be difficult to detect by continuous wave EPR. The distributions in 1/T1 for the [4Fe-4S]+ clusters in Mycofactocin maturase were about a factor of four wider than for the three other systems studied. The very broad distribution of relaxation rates may be due to protein mobility and distributions in electronic energies and local environments for the clusters. UPEN provides insight into several situations that can result in low values of stretch parameter β including contributions from spectral diffusion, overlapping signals from distinguishable clusters, or very wide distributions.
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Affiliation(s)
- Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States of America
| | - Richard Ayikpoe
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States of America
| | - John A Latham
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States of America
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States of America
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States of America..
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21
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Walker LM, Li B, Niks D, Hille R, Elliott SJ. Deconvolution of reduction potentials of formate dehydrogenase from Cupriavidus necator. J Biol Inorg Chem 2019; 24:889-898. [PMID: 31463592 DOI: 10.1007/s00775-019-01701-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022]
Abstract
The formate dehydrogenase enzyme from Cupriavidus necator (FdsABG) carries out the two-electron oxidation of formate to CO2, but is also capable of reducing CO2 back to formate, a potential biofuel. FdsABG is a heterotrimeric enzyme that performs this transformation using nine redox-active cofactors: a bis(molybdopterin guanine dinucleotide) (bis-MGD) at the active site coupled to seven iron-sulfur clusters, and one equivalent of flavin mononucleotide (FMN). To better understand the pathway of electron flow in FdsABG, the reduction potentials of the various cofactors were examined through direct electrochemistry. Given the redundancy of cofactors, a truncated form of the FdsA subunit was developed that possesses only the bis-MGD active site and a singular [4Fe-4S] cluster. Electrochemical characterization of FdsABG compared to truncated FdsA shows that the measured reduction potentials are remarkably similar despite the truncation with two observable features at - 265 mV and - 455 mV vs SHE, indicating that the voltammetry of the truncated enzyme is representative of the reduction potentials of the intact heterotrimer. By producing truncated FdsA without the necessary maturation factors required for bis-MGD insertion, a form of the truncated FdsA that possesses only the [4Fe-4S] was produced, which gives a single voltammetric feature at - 525 mV, allowing the contributions of the molybdenum cofactor to be associated with the observed feature at - 265 mV. This method allowed for the deconvolution of reduction potentials for an enzyme with highly complex cofactor content to know more about the thermodynamic landscape of catalysis.
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Affiliation(s)
- Lindsey M Walker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Bin Li
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA.
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22
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Ayikpoe RS, Latham JA. MftD Catalyzes the Formation of a Biologically Active Redox Center in the Biosynthesis of the Ribosomally Synthesized and Post-translationally Modified Redox Cofactor Mycofactocin. J Am Chem Soc 2019; 141:13582-13591. [PMID: 31381312 DOI: 10.1021/jacs.9b06102] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mycofactocin (MFT) is a putative ribosomally synthesized and post-translationally modified (RiPP) redox cofactor. The biosynthesis of MFT is encoded by the gene cluster mftABCDEF. While processing of the precursor peptide by MftB, MftC, and MftE has been shown to result in the formation of the small molecule 3-amino-5-[(p-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidinone (AHDP), no activity has been shown for the putative dehydrogenase MftD and the putative glycosyltransferase MftF. In addition, evidence demonstrating that MFT is a redox cofactor has only been limited to the requirement of mft genes for ethanol assimilation in Mycobacterium smegmatis mc2155. Here, we demonstrate that MftD catalyzes the oxidative deamination of AHDP, forming an α-keto moiety on the resulting molecule, which we call pre-mycofactocin (PMFT). We characterize PMFT by 1D and 2D NMR spectroscopy techniques and by high-resolution mass spectrometry data to solve its structure. We further characterized PMFT by cyclic voltammetry and found its midpoint potential to be ∼255 mV. Lastly, we demonstrate that PMFT is a biologically active redox cofactor that oxidizes NADH bound by M. smegmatis carveol dehydrogenase (MsCDH) and can be used by MsCDH in the oxidation of carveol. These data demonstrate for the first time that PMFT functions as a biologically active redox mediator and provides the most direct evidence to date that MFT is a RiPP-derived redox cofactor.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80210 , United States
| | - John A Latham
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80210 , United States
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23
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Hegemann JD, Bobeica SC, Walker MC, Bothwell IR, van der Donk WA. Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications. ACS Synth Biol 2019; 8:1204-1214. [PMID: 31042373 PMCID: PMC6525029 DOI: 10.1021/acssynbio.9b00080] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclization is a common strategy to confer proteolytic resistance to peptide scaffolds. Thus, cyclic peptides have been the focus of extensive bioengineering efforts. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a superfamily of peptidic natural products that often contain macrocycles. In the RiPP family of lanthipeptides, macrocyclization is accomplished through formation of thioether cross-links between cysteines and dehydrated serines/threonines. The recent production of lanthipeptide libraries and development of methods to display lanthipeptides on yeast or phage highlights their potential for bioengineering and synthetic biology. In this regard, the prochlorosins are especially promising as the corresponding class II lanthipeptide synthetase ProcM matures numerous precursor peptides with diverse core peptide sequences. To facilitate future bioengineering projects, one of its native substrates, ProcA2.8, was subjected in this study to in-depth mutational analysis to test the limitations of ProcM-mediated cyclization. Alanine scan mutagenesis was performed on all residues within the two rings, and multiple prolines were introduced at various positions. Moreover, mutation, deletion, and insertion of residues in the region linking the two lanthionine rings was tested. Additional residues were also introduced or deleted from either ring, and inversion of ring forming residues was attempted to generate diastereomers. The findings were used for epitope grafting of the RGD integrin binding epitope within prochlorosin 2.8, resulting in a low nanomolar affinity binder of the αvβ3 integrin that was more stable toward proteolysis and displayed higher affinity than the linear counterpart.
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Affiliation(s)
- Julian D. Hegemann
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Silvia C. Bobeica
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Mark C. Walker
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Ian R. Bothwell
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
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24
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Occurrence, function, and biosynthesis of mycofactocin. Appl Microbiol Biotechnol 2019; 103:2903-2912. [PMID: 30778644 DOI: 10.1007/s00253-019-09684-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 10/27/2022]
Abstract
Mycofactocin is a member of the rapidly growing class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Although the mycofactocin biosynthetic pathway is widely distributed among Mycobacterial species, the structure, function, and biosynthesis of the pathway product remain unknown. This mini-review will discuss the current state of knowledge regarding the mycofactocin biosynthetic pathway. In particular, we focus on the architecture and distribution of the mycofactocin biosynthetic cluster, mftABCDEF, among the Actinobacteria phylum. We discuss the potential molecular and physiological role of mycofactocin. We review known biosynthetic steps involving MftA, MftB, MftC, and MftE and relate them to pyrroloquinoline quinone biosynthesis. Lastly, we propose the function of the remaining putative biosynthetic enzymes, MftD and MftF.
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