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Bhandari S, Bisht KS, Merkler DJ. The Biosynthesis and Metabolism of the N-Acylated Aromatic Amino Acids: N-Acylphenylalanine, N-Acyltyrosine, N-Acyltryptophan, and N-Acylhistidine. Front Mol Biosci 2022; 8:801749. [PMID: 35047560 PMCID: PMC8762209 DOI: 10.3389/fmolb.2021.801749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
The fatty acid amides are a family of lipids composed of two chemical moieties, a fatty acid and a biogenic amine linked together in an amide bond. This lipid family is structurally related to the endocannabinoid anandamide (N-arachidonoylethanolamine) and, thus, is frequently referred to as a family of endocannabinoid-related lipids. The fatty acid amide family is divided into different classes based on the conjugate amine; anandamide being a member of the N-acylethanolamine class (NAE). Another class within the fatty acid amide family is the N-acyl amino acids (NA-AAs). The focus of this review is a sub-class of the NA-AAs, the N-acyl aromatic amino acids (NA-ArAAs). The NA-ArAAs are not broadly recognized, even by those interested in the endocannabinoids and endocannabinoid-related lipids. Herein, the NA-ArAAs that have been identified from a biological source will be highlighted and pathways for their biosynthesis, degradation, enzymatic modification, and transport will be presented. Also, information about the cellular functions of the NA-ArAAs will be placed in context with the data regarding the identification and metabolism of these N-acylated amino acids. A review of the current state-of-knowledge about the NA-ArAAs is to stimulate future research about this underappreciated sub-class of the fatty acid amide family.
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Affiliation(s)
- Suzeeta Bhandari
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Kirpal S Bisht
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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Abstract
This review presents a historical outline of the research on vanillyl alcohol oxidase (VAO) from Penicillium simplicissimum, one of the canonical members of the VAO/PCMH flavoprotein family. After describing its discovery and initial biochemical characterization, we discuss the physiological role, substrate scope, and catalytic mechanism of VAO, and review its three-dimensional structure and mechanism of covalent flavinylation. We also explain how protein engineering provided a deeper insight into the role of certain amino acid residues in determining the substrate specificity and enantioselectivity of the enzyme. Finally, we summarize recent computational studies about the migration of substrates and products through the enzyme's structure and the phylogenetic distribution of VAO and related enzymes.
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Affiliation(s)
- Tom A Ewing
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Gudrun Gygli
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands.
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Fan J, Liao G, Ludwig-Radtke L, Yin WB, Li SM. Formation of Terrestric Acid in Penicillium crustosum Requires Redox-Assisted Decarboxylation and Stereoisomerization. Org Lett 2019; 22:88-92. [DOI: 10.1021/acs.orglett.9b04002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jie Fan
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Ge Liao
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Lena Ludwig-Radtke
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg 35037, Germany
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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Ewing TA, Fraaije MW, Mattevi A, van Berkel WJ. The VAO/PCMH flavoprotein family. Arch Biochem Biophys 2017; 632:104-117. [DOI: 10.1016/j.abb.2017.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/26/2017] [Accepted: 06/29/2017] [Indexed: 01/15/2023]
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Ewing TA, Nguyen QT, Allan RC, Gygli G, Romero E, Binda C, Fraaije MW, Mattevi A, van Berkel WJH. Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. J Biol Chem 2017; 292:14668-14679. [PMID: 28717004 DOI: 10.1074/jbc.m117.778449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
A number of oxidoreductases from the VAO/para-cresol methylhydroxylase flavoprotein family catalyze the oxidation of para-substituted phenols. One of the best-studied is vanillyl-alcohol oxidase (VAO) from the fungus Penicillium simplicissimum For oxidation of phenols by VAO to occur, they must first be bound in the active site of the enzyme in their phenolate anion form. The crystal structure of VAO reveals that two tyrosine residues, Tyr-108 and Tyr-503, are positioned to facilitate this deprotonation. To investigate their role in catalysis, we created three VAO variants, Y108F, Y503F, and Y108F/Y503F, and studied their biochemical properties. Steady-state kinetics indicated that the presence of at least one of the tyrosine residues is essential for efficient catalysis by VAO. Stopped-flow kinetics revealed that the reduction of VAO by chavicol or vanillyl alcohol occurs at two different rates: kobs1, which corresponds to its reaction with the deprotonated form of the substrate, and kobs2, which corresponds to its reaction with the protonated form of the substrate. In Y108F, Y503F, and Y108F/Y503F, the relative contribution of kobs2 to the reduction is larger than in wild-type VAO, suggesting deprotonation is impaired in these variants. Binding studies disclosed that the competitive inhibitor isoeugenol is predominantly in its deprotonated form when bound to wild-type VAO, but predominantly in its protonated form when bound to the variants. These results indicate that Tyr-108 and Tyr-503 are responsible for the activation of substrates in VAO, providing new insights into the catalytic mechanism of VAO and related enzymes that oxidize para-substituted phenols.
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Affiliation(s)
- Tom A Ewing
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Quoc-Thai Nguyen
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.,the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and.,the Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Robert C Allan
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Gudrun Gygli
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Elvira Romero
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Claudia Binda
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Marco W Fraaije
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Andrea Mattevi
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands,
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Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis. Appl Environ Microbiol 2016; 82:1945-1957. [PMID: 26773087 DOI: 10.1128/aem.03011-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/10/2016] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequence of the type strain of the myxobacterial genus Chondromyces, Chondromyces crocatus Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr-) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family, Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.
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Abstract
Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.
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Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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Abstract
A new route to Cbz-(S)-dolaphenine, a recurring element in bioactive peptidic natural products, has been implemented, which closely parallels the biogenetic pathway. Cyclodehydration of 11 to yield thiazoline 2 allows for a Ni(0)-promoted decarbonylative aromatization to provide the thiazole framework with retention of stereochemistry.
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Affiliation(s)
- Pablo García-Reynaga
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
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Structure, biosynthesis and possible function of tunichromes and related compounds. Comp Biochem Physiol B Biochem Mol Biol 2012; 163:1-25. [PMID: 22580032 DOI: 10.1016/j.cbpb.2012.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 01/26/2023]
Abstract
Several species of ascidians (phylum Chordata, subphylum Urochordata) contain a group of oligopeptides called "tunichromes" in their blood cells. These peptides have been implicated in (a) metal chelation and accumulation/sequestration of vanadium or iron; (b) crosslinking of structural fibers in tunic formation, (c) wound healing and (d) defense reactions. However, their biosynthesis, metabolism, and biological function remain largely un-elucidated due to their extreme instability and high reactivity. Tunichromes and related compounds uniquely possess dehydrodopamine moieties, all originating from post-translational modification of peptidyl tyrosine. It is conceivable that the presence of such novel post-translationally modified groups provide attributes that are crucial for their biological roles. Therefore, we examined the chemistry and reactivity of tunichromes in light of the available knowledge of the biochemistry of simple monomeric dehydro-N-acyldopamine units. Based on the reactivity of such simple compounds, the potential biological activities of tunichromes are predicted. Their possible biosynthetic route from peptidyl tyrosine is critically evaluated to provide a better basis for unraveling their biological functions. Prevalence of dehydro-N-acyldopamine units in different tunichromes, some marine antibiotic compounds, insect cuticular sclerotizing precursors and some bioadhesive marine proteins may aid in the de novo design of unique biomaterials with potential antibiotic/adhesive properties.
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Sugumaran M, Robinson WE. Bioactive dehydrotyrosyl and dehydrodopyl compounds of marine origin. Mar Drugs 2010; 8:2906-35. [PMID: 21339956 PMCID: PMC3039461 DOI: 10.3390/md8122906] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 11/26/2010] [Accepted: 12/01/2010] [Indexed: 02/02/2023] Open
Abstract
The amino acid, tyrosine, and its hydroxylated product, 3,4-dihydroxyphenylalanine (dopa), plays an important role in the biogenesis of a number of potentially important bioactive molecules in marine organisms. Interestingly, several of these tyrosyl and dopa-containing compounds possess dehydro groups in their side chains. Examples span the range from simple dehydrotyrosine and dehydrodopamines to complex metabolic products, including peptides and polycyclic alkaloids. Based on structural information, these compounds can be subdivided into five categories: (a) Simple dehydrotyrosine and dehydrotyramine containing molecules; (b) simple dehydrodopa derivatives; (c) peptidyl dehydrotyrosine and dehydrodopa derivatives; (d) multiple dehydrodopa containing compounds; and (e) polycyclic condensed dehydrodopa derivatives. These molecules possess a wide range of biological activities that include (but are not limited to) antitumor activity, antibiotic activity, cytotoxicity, antioxidant activity, multidrug resistance reversal, cell division inhibition, immunomodulatory activity, HIV-integrase inhibition, anti-viral, and anti-feeding (or feeding deterrent) activity. This review summarizes the structure, distribution, possible biosynthetic origin, and biological activity, of the five categories of dehydrotyrosine and dehydrodopa containing compounds.
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Affiliation(s)
- Manickam Sugumaran
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - William E. Robinson
- Environmental, Earth and Ocean Sciences Department, University of Massachusetts Boston, Boston, MA 02125, USA; E-Mail:
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