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Wei W, Siegbahn PEM, Liao R. Mechanism of the Dinuclear Iron Enzymep‐Aminobenzoate N‐oxygenase from Density Functional Calculations. ChemCatChem 2018. [DOI: 10.1002/cctc.201801072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen‐Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm University Stockholm SE-10691 Sweden
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
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52
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Kretsch AM, Morgan GL, Tyrrell J, Mevers E, Vallet-Gély I, Li B. Discovery of (Dihydro)pyrazine N-Oxides via Genome Mining in Pseudomonas. Org Lett 2018; 20:4791-4795. [PMID: 30073838 DOI: 10.1021/acs.orglett.8b01944] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Overexpression of the Pseudomonas virulence factor ( pvf) biosynthetic operon led to the identification of a family of pyrazine N-oxides (PNOs), including a novel dihydropyrazine N,N'-dioxide (dPNO) metabolite. The nonribosomal peptide synthetase responsible for production of (d)PNOs was characterized, and a biosynthetic pathway for (d)PNOs was proposed. This work highlights the unique chemistry catalyzed by pvf-encoded enzymes and sets the stage for bioactivity studies of the metabolites produced by the virulence pathway.
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Affiliation(s)
- Ashley M Kretsch
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Gina L Morgan
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Jillian Tyrrell
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Isabelle Vallet-Gély
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Univ. Paris-Sud, Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France
| | - Bo Li
- Department of Chemistry , The University of North Carolina at Chapel Hill , 250 Bell Tower Road , Chapel Hill , North Carolina 27599 , United States
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53
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Komor AJ, Jasniewski AJ, Que L, Lipscomb JD. Diiron monooxygenases in natural product biosynthesis. Nat Prod Rep 2018; 35:646-659. [PMID: 29552683 PMCID: PMC6051903 DOI: 10.1039/c7np00061h] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2017 The participation of non-heme dinuclear iron cluster-containing monooxygenases in natural product biosynthetic pathways has been recognized only recently. At present, two families have been discovered. The archetypal member of the first family, CmlA, catalyzes β-hydroxylation of l-p-aminophenylalanine (l-PAPA) covalently linked to the nonribosomal peptide synthetase (NRPS) CmlP, thereby effecting the first step in the biosynthesis of chloramphenicol by Streptomyces venezuelae. CmlA houses the diiron cluster in a metallo-β-lactamase protein fold instead of the 4-helix bundle fold of nearly every other diiron monooxygenase. CmlA couples O2 activation and substrate hydroxylation via a structural change caused by formation of the l-PAPA-loaded CmlP:CmlA complex. The other new diiron family is typified by two enzymes, AurF and CmlI, which catalyze conversion of aryl-amine substrates to aryl-nitro products with incorporation of oxygen from O2. AurF from Streptomyces thioluteus catalyzes the formation of p-nitrobenzoate from p-aminobenzoate as a precursor to the biostatic compound aureothin, whereas CmlI from S. venezuelae catalyzes the ultimate aryl-amine to aryl-nitro step in chloramphenicol biosynthesis. Both enzymes stabilize a novel type of peroxo-intermediate as the reactive species. The rare 6-electron N-oxygenation reactions of CmlI and AurF involve two progressively oxidized pathway intermediates. The enzymes optimize efficiency by utilizing one of the reaction pathway intermediates as an in situ reductant for the diiron cluster, while simultaneously generating the next pathway intermediate. For CmlI, this reduction allows mid-pathway regeneration of the peroxo intermediate required to complete the biosynthesis. CmlI ensures specificity by carrying out the multistep aryl-amine oxygenation without dissociating intermediate products.
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Affiliation(s)
- Anna J Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Andrew J Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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55
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Tsutsumi H, Katsuyama Y, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis. J Am Chem Soc 2018; 140:6631-6639. [DOI: 10.1021/jacs.8b02769] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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56
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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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57
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Zhang L, Xu Y, Makris TM, Wang Q. Enhanced Arylamine N-Oxygenase Activity of Polymer–Enzyme Assemblies by Facilitating Electron-Transferring Efficiency. Biomacromolecules 2018; 19:918-925. [DOI: 10.1021/acs.biomac.7b01706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Yanmei Xu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
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58
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Wang C, Chen H. Convergent Theoretical Prediction of Reactive Oxidant Structures in Diiron Arylamine Oxygenases AurF and CmlI: Peroxo or Hydroperoxo? J Am Chem Soc 2017; 139:13038-13046. [DOI: 10.1021/jacs.7b06343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chao Wang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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59
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Tomita H, Katsuyama Y, Minami H, Ohnishi Y. Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem 2017; 292:15859-15869. [PMID: 28774961 DOI: 10.1074/jbc.m117.791269] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Rufomycin is a circular heptapeptide with anti-mycobacterial activity and is produced by Streptomyces atratus ATCC 14046. Its structure contains three non-proteinogenic amino acids, N-dimethylallyltryptophan, trans-2-crotylglycine, and 3-nitrotyrosine (3NTyr). Although the rufomycin structure was already reported in the 1960s, its biosynthesis, including 3NTyr generation, remains unclear. To elucidate the rufomycin biosynthetic pathway, we assembled a draft genome sequence of S. atratus and identified the rufomycin biosynthetic gene cluster (ruf cluster), consisting of 20 ORFs (rufA-rufT). We found a putative heptamodular nonribosomal peptide synthetase encoded by rufT, a putative tryptophan N-dimethylallyltransferase encoded by rufP, and a putative trimodular type I polyketide synthase encoded by rufEF Moreover, the ruf cluster contains an apparent operon harboring putative cytochrome P450 (rufO) and nitric oxide synthase (rufN) genes. A similar operon, txtDE, is responsible for the formation of 4-nitrotryptophan in thaxtomin biosynthesis; the cytochrome P450 TxtE catalyzes the 4-nitration of Trp. Therefore, we hypothesized that RufO should catalyze the Tyr 3-nitration. Disruption of rufO abolished rufomycin production by S. atratus, which was restored when 3NTyr was added to the culture medium of the disruptant. Recombinant RufO protein exhibited Tyr 3-nitration activity both in vitro and in vivo Spectroscopic analysis further revealed that RufO recognizes Tyr as the substrate with a dissociation constant of ∼0.1 μm These results indicate that RufO is an unprecedented cytochrome P450 that catalyzes Tyr nitration. Taken together with the results of an in silico analysis of the ruf cluster, we propose a rufomycin biosynthetic pathway in S. atratus.
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Affiliation(s)
- Hiroya Tomita
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657.,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Yohei Katsuyama
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Hiromichi Minami
- the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasuo Ohnishi
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
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60
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Jasniewski AJ, Komor AJ, Lipscomb JD, Que L. Unprecedented (μ-1,1-Peroxo)diferric Structure for the Ambiphilic Orange Peroxo Intermediate of the Nonheme N-Oxygenase CmlI. J Am Chem Soc 2017; 139:10472-10485. [PMID: 28673082 PMCID: PMC5568637 DOI: 10.1021/jacs.7b05389] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The final step in the biosynthesis of the antibiotic chloramphenicol is the oxidation of an aryl-amine substrate to an aryl-nitro product catalyzed by the N-oxygenase CmlI in three two-electron steps. The CmlI active site contains a diiron cluster ligated by three histidine and four glutamate residues and activates dioxygen to perform its role in the biosynthetic pathway. It was previously shown that the active oxidant used by CmlI to facilitate this chemistry is a peroxo-diferric intermediate (CmlIP). Spectroscopic characterization demonstrated that the peroxo binding geometry of CmlIP is not consistent with the μ-1,2 mode commonly observed in nonheme diiron systems. Its geometry was tentatively assigned as μ-η2:η1 based on comparison with resonance Raman (rR) features of mixed-metal model complexes in the absence of appropriate diiron models. Here, X-ray absorption spectroscopy (XAS) and rR studies have been used to establish a refined structure for the diferric cluster of CmlIP. The rR experiments carried out with isotopically labeled water identified the symmetric and asymmetric vibrations of an Fe-O-Fe unit in the active site at 485 and 780 cm-1, respectively, which was confirmed by the 1.83 Å Fe-O bond observed by XAS. In addition, a unique Fe···O scatterer at 2.82 Å observed from XAS analysis is assigned as arising from the distal O atom of a μ-1,1-peroxo ligand that is bound symmetrically between the irons. The (μ-oxo)(μ-1,1-peroxo)diferric core structure associated with CmlIP is unprecedented among diiron cluster-containing enzymes and corresponding biomimetic complexes. Importantly, it allows the peroxo-diferric intermediate to be ambiphilic, acting as an electrophilic oxidant in the initial N-hydroxylation of an arylamine and then becoming a nucleophilic oxidant in the final oxidation of an aryl-nitroso intermediate to the aryl-nitro product.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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61
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A new strategy for aromatic ring alkylation in cylindrocyclophane biosynthesis. Nat Chem Biol 2017; 13:916-921. [DOI: 10.1038/nchembio.2421] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/12/2017] [Indexed: 12/25/2022]
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62
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Scott TA, Heine D, Qin Z, Wilkinson B. An L-threonine transaldolase is required for L-threo-β-hydroxy-α-amino acid assembly during obafluorin biosynthesis. Nat Commun 2017; 8:15935. [PMID: 28649989 PMCID: PMC5490192 DOI: 10.1038/ncomms15935] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/15/2017] [Indexed: 12/15/2022] Open
Abstract
β-Lactone natural products occur infrequently in nature but possess a variety of potent and valuable biological activities. They are commonly derived from β-hydroxy-α-amino acids, which are themselves valuable chiral building blocks for chemical synthesis and precursors to numerous important medicines. However, despite a number of excellent synthetic methods for their asymmetric synthesis, few effective enzymatic tools exist for their preparation. Here we report cloning of the biosynthetic gene cluster for the β-lactone antibiotic obafluorin and delineate its biosynthetic pathway. We identify a nonribosomal peptide synthetase with an unusual domain architecture and an L-threonine:4-nitrophenylacetaldehyde transaldolase responsible for (2S,3R)-2-amino-3-hydroxy-4-(4-nitrophenyl)butanoate biosynthesis. Phylogenetic analysis sheds light on the evolutionary origin of this rare enzyme family and identifies further gene clusters encoding L-threonine transaldolases. We also present preliminary data suggesting that L-threonine transaldolases might be useful for the preparation of L-threo-β-hydroxy-α-amino acids.
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Affiliation(s)
- Thomas A. Scott
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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63
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β-Lactone formation during product release from a nonribosomal peptide synthetase. Nat Chem Biol 2017; 13:737-744. [PMID: 28504677 DOI: 10.1038/nchembio.2374] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/07/2017] [Indexed: 11/09/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are multidomain modular biosynthetic assembly lines that polymerize amino acids into a myriad of biologically active nonribosomal peptides (NRPs). NRPS thioesterase (TE) domains employ diverse release strategies for off-loading thioester-tethered polymeric peptides from termination modules typically via hydrolysis, aminolysis, or cyclization to provide mature antibiotics as carboxylic acids/esters, amides, and lactams/lactones, respectively. Here we report the enzyme-catalyzed formation of a highly strained β-lactone ring during TE-mediated cyclization of a β-hydroxythioester to release the antibiotic obafluorin (Obi) from an NRPS assembly line. The Obi NRPS (ObiF) contains a type I TE domain with a rare catalytic cysteine residue that plays a direct role in β-lactone ring formation. We present a detailed genetic and biochemical characterization of the entire Obi biosynthetic gene cluster in plant-associated Pseudomonas fluorescens ATCC 39502 that establishes a general strategy for β-lactone biogenesis.
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64
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Kudo K, Ozaki T, Shin-ya K, Nishiyama M, Kuzuyama T. Biosynthetic Origin of the Hydroxamic Acid Moiety of Trichostatin A: Identification of Unprecedented Enzymatic Machinery Involved in Hydroxylamine Transfer. J Am Chem Soc 2017; 139:6799-6802. [DOI: 10.1021/jacs.7b02071] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kei Kudo
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taro Ozaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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65
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Park K, Li N, Kwak Y, Srnec M, Bell CB, Liu LV, Wong SD, Yoda Y, Kitao S, Seto M, Hu M, Zhao J, Krebs C, Bollinger JM, Solomon EI. Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF. J Am Chem Soc 2017; 139:7062-7070. [PMID: 28457126 DOI: 10.1021/jacs.7b02997] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reaction shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. This activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.,Department of Chemistry, KAIST , Daejeon 34141, Republic of Korea
| | - Ning Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yeonju Kwak
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Martin Srnec
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Caleb B Bell
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Lei V Liu
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | - Shaun D Wong
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States
| | | | - Shinji Kitao
- Research Reactor Institute, Kyoto University , Kumatori-cho, Osaka 590-0494, Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University , Kumatori-cho, Osaka 590-0494, Japan
| | - Michael Hu
- Advanced Photon Source, Argonne National Laboratory , Lemont, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Lemont, Illinois 60439, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305-5080, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Stanford, California 94309, United States
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66
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Zhang Q, Li H, Yu L, Sun Y, Zhu Y, Zhu H, Zhang L, Li SM, Shen Y, Tian C, Li A, Liu HW, Zhang C. Characterization of the flavoenzyme XiaK as an N-hydroxylase and implications in indolosesquiterpene diversification. Chem Sci 2017; 8:5067-5077. [PMID: 28970893 PMCID: PMC5613243 DOI: 10.1039/c7sc01182b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/27/2017] [Indexed: 01/10/2023] Open
Abstract
Flavoenzymes are ubiquitous in biological systems and catalyze a diverse range of chemical transformations.
Flavoenzymes are ubiquitous in biological systems and catalyze a diverse range of chemical transformations. The flavoenzyme XiaK from the biosynthetic pathway of the indolosesquiterpene xiamycin A is demonstrated to mediate the in vivo biotransformation of xiamycin A into multiple products, including a chlorinated adduct as well as dimers characterized by C–N and N–N linkages that are hypothesized to form via radical-based mechanisms. Isolation and characterization of XiaK in vitro shows that it acts as a flavin-dependent N-hydroxylase that catalyzes the hydroxylation of xiamycin A at the carbazole nitrogen to form N-hydroxyxiamycin, a product which was overlooked in earlier in vivo experiments because its chemical and chromatographic properties are similar to those of oxiamycin. N-Hydroxyxiamycin is shown to be unstable under aerobic conditions, and characterization by electron paramagnetic resonance spectroscopy demonstrates formation of an N-hydroxycarbazole radical adduct. This radical species is proposed to serve as a key intermediate leading to the formation of the multiple xiamycin A adducts. This study suggests that non-enzyme catalyzed reactions may play a greater role in the biosynthesis of natural products than has been previously recognized.
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Affiliation(s)
- Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Huixian Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ; .,Institute of Marine Natural Products , School of Marine Sciences , South China Sea Resource Exploitation and Protection Collaborative Innovation Center , Sun Yat-sen University , 135 West Xingang Road , Guangzhou 510006 , China
| | - Lu Yu
- Hefei National Laboratory of Microscale Physical Sciences , School of Life Science , University of Science and Technology of China , Hefei , 230027 , China.,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei , 230031 , P. R. China
| | - Yu Sun
- State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Hanning Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie , Philipps-Universität Marburg , Deutschhausstrasse 17a , 35037 Marburg , Germany
| | - Yuemao Shen
- State Key Laboratory of Microbial Technology , School of Life Science , Shandong University , Jinan 250100 , China
| | - Changlin Tian
- Hefei National Laboratory of Microscale Physical Sciences , School of Life Science , University of Science and Technology of China , Hefei , 230027 , China.,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei , 230031 , P. R. China
| | - Ang Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy , Department of Chemistry , University of Texas at Austin , Austin , TX 78712 , USA .
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
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67
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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68
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Haq IU, Dini-Andreote F, van Elsas JD. Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions. MICROBIAL ECOLOGY 2017; 73:236-252. [PMID: 27844108 PMCID: PMC5209427 DOI: 10.1007/s00248-016-0885-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/24/2016] [Indexed: 05/05/2023]
Abstract
In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime. In the system, B. terrae BS001 apparently perceived the presence of the fungal hyphae already at the early experimental stages (T1, T2), by strongly upregulating a suite of chemotaxis and flagellar motility genes. With respect to specific metabolism and energy generation, a picture of differential involvement in different metabolic routes was obtained. Initial (T1, T2) up- or downregulation of ethanolamine and mandelate uptake and utilization pathways was substituted by a strong investment, in the presence of the fungus, in the expression of putative metabolic gene clusters (T3). Specifically at T3, five clustered genes that are potentially involved in energy generation coupled to an oxidative stress response, and two genes encoding short-chain dehydrogenases/oxidoreductases (SDR), were highly upregulated. In contrast, the dnaE2 gene (related to general stress response; encoding error-prone DNA polymerase) was transcriptionally downregulated at this stage. This study revealed that B. terrae BS001, from a stress-induced state, resulting from the soil extract agar milieu, responds positively to fungal hyphae that encroach upon it, in a temporally dynamic manner. The response is characterized by phases in which the modulation of (1) chemotaxis, (2) metabolic activity, and (3) oxidative stress responses are key mechanisms.
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Affiliation(s)
- Irshad Ul Haq
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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69
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Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. J Biol Inorg Chem 2016; 22:221-235. [DOI: 10.1007/s00775-016-1425-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
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70
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Sohn YS, Lee SG, Lee KH, Ku B, Shin HC, Cha SS, Kim YG, Lee HS, Kang SG, Oh BH. Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase. PLoS One 2016; 11:e0167549. [PMID: 27907125 PMCID: PMC5132392 DOI: 10.1371/journal.pone.0167549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/16/2016] [Indexed: 11/19/2022] Open
Abstract
A hypothetical protein TON_0340 of a Thermococcus species is a protein conserved in a variety of organisms including human. Herein, we present four different crystal structures of TON_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. Biochemical and mutational analyses involving many phosphorous compounds show that TON_0340 is a Mn2+-dependent phosphatase. Mg2+ binds to TON_0340 less tightly and activates the phosphatase activity less efficiently than Mn2+. Whereas Ca2+ and Zn2+ are able to bind to the protein, they are unable to activate its enzymatic activity. Since the active-site cavity is small and largely composed of nearly invariant stretches of 11 or 13 amino acids, the physiological substrates of TON_0340 and its homologues are likely to be a small and the same molecule. The Mn2+-bound TON_0340 structure provides a canonical model for the ubiquitously present TON_0340 homologues and lays a strong foundation for the elucidation of their substrate and biological function.
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Affiliation(s)
- Young-Sik Sohn
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Seong-Gyu Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Kwang-Hoon Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Sung-Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea
- * E-mail:
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71
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Jasniewski AJ, Knoot CJ, Lipscomb JD, Que L. A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme β-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase. Biochemistry 2016; 55:5818-5831. [PMID: 27668828 PMCID: PMC5258830 DOI: 10.1021/acs.biochem.6b00834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinuclear iron cluster that is reduced to the diferrous state (WTR) to initiate O2 activation. However, rapid O2 activation occurs only when WTR is bound to CmlP, the NRPS to which l-PAPA is covalently attached. Here the X-ray crystal structure of WTR is reported, which is very similar to that of the as-isolated diferric enzyme in which the irons are coordinately saturated. X-ray absorption spectroscopy is used to investigate the WTR cluster ligand structure as well as the structures of WTR in complex with a functional CmlP variant (CmlPAT) with and without l-PAPA attached. It is found that formation of the active WTR:CmlPAT-l-PAPA complex converts at least one iron of the cluster from six- to five-coordinate by changing a bidentately bound amino acid carboxylate to monodentate on Fe1. The only bidentate carboxylate in the structure of WTR is E377. The crystal structure of the CmlA variant E377D shows only monodentate carboxylate coordination. Reduced E377D reacts rapidly with O2 in the presence or absence of CmlPAT-l-PAPA, showing loss of regulation. However, this variant fails to catalyze hydroxylation, suggesting that E377 has the dual role of coupling regulation of O2 reactivity with juxtaposition of the substrate and the reactive oxygen species. The carboxylate shift in response to substrate binding represents a novel regulatory strategy for oxygen activation in diiron oxygenases.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Cory J. Knoot
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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72
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Kositzki R, Mebs S, Marx J, Griese JJ, Schuth N, Högbom M, Schünemann V, Haumann M. Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations. Inorg Chem 2016; 55:9869-9885. [PMID: 27610479 DOI: 10.1021/acs.inorgchem.6b01752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O2) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O2 reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal-ligand bond lengths, metal-metal distances, metal oxidation states, spin configurations, valence-level degeneracy, molecular orbital composition, nuclear quadrupole splitting energies, and vibrational normal modes for both cofactors. A protonation state with an axial water (H2O) ligand at Mn or Fe in binding site 1 and a metal-bridging hydroxo group (μOH) in a hydrogen-bonded network is assigned. Our comprehensive picture of the molecular, electronic, and dynamic properties of the cofactors highlights reorientation of the unique axis along the Mn-OH2 bond for the Mn1(III) Jahn-Teller ion but along the Fe-μOH bond for the octahedral Fe1(III). This likely corresponds to a more positive redox potential of the Mn(III)Fe(III) cofactor and higher proton affinity of its μOH group. Refined model structures for the Mn(III)Fe(III) and Fe(III)Fe(III) cofactors are presented. Implications of our findings for the site-specific metalation of R2lox and performance of the O2 reduction and cross-link formation reactions are discussed.
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Affiliation(s)
- Ramona Kositzki
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Jennifer Marx
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden
| | - Nils Schuth
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University , 10691 Stockholm, Sweden.,Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin , 14195 Berlin, Germany
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73
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A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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74
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Jasniewski AJ, Engstrom LM, Vu VV, Park MH, Que L. X-ray absorption spectroscopic characterization of the diferric-peroxo intermediate of human deoxyhypusine hydroxylase in the presence of its substrate eIF5a. J Biol Inorg Chem 2016; 21:605-18. [PMID: 27380180 PMCID: PMC4990465 DOI: 10.1007/s00775-016-1373-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Human deoxyhypusine hydroxylase (hDOHH) is an enzyme that is involved in the critical post-translational modification of the eukaryotic translation initiation factor 5A (eIF5A). Following the conversion of a lysine residue on eIF5A to deoxyhypusine (Dhp) by deoxyhypusine synthase, hDOHH hydroxylates Dhp to yield the unusual amino acid residue hypusine (Hpu), a modification that is essential for eIF5A to promote peptide synthesis at the ribosome, among other functions. Purification of hDOHH overexpressed in E. coli affords enzyme that is blue in color, a feature that has been associated with the presence of a peroxo-bridged diiron(III) active site. To gain further insight into the nature of the diiron site and how it may change as hDOHH goes through the catalytic cycle, we have conducted X-ray absorption spectroscopic studies of hDOHH on five samples that represent different species along its reaction pathway. Structural analysis of each species has been carried out, starting with the reduced diferrous state, proceeding through its O2 adduct, and ending with a diferric decay product. Our results show that the Fe⋯Fe distances found for the five samples fall within a narrow range of 3.4-3.5 Å, suggesting that hDOHH has a fairly constrained active site. This pattern differs significantly from what has been associated with canonical dioxygen activating nonheme diiron enzymes, such as soluble methane monooxygenase and Class 1A ribonucleotide reductases, for which the Fe⋯Fe distance can change by as much as 1 Å during the redox cycle. These results suggest that the O2 activation mechanism for hDOHH deviates somewhat from that associated with the canonical nonheme diiron enzymes, opening the door to new mechanistic possibilities for this intriguing family of enzymes.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Lisa M Engstrom
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Van V Vu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City, Vietnam
| | - Myung Hee Park
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA.
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75
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Solomon EI, Park K. Structure/function correlations over binuclear non-heme iron active sites. J Biol Inorg Chem 2016; 21:575-88. [PMID: 27369780 PMCID: PMC5010389 DOI: 10.1007/s00775-016-1372-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea
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76
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Knoot CJ, Kovaleva EG, Lipscomb JD. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway. J Biol Inorg Chem 2016; 21:589-603. [PMID: 27229511 PMCID: PMC4994471 DOI: 10.1007/s00775-016-1363-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/16/2016] [Indexed: 11/28/2022]
Abstract
The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form.
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Affiliation(s)
- Cory J Knoot
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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77
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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78
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Komor AJ, Rivard BS, Fan R, Guo Y, Que L, Lipscomb JD. Mechanism for Six-Electron Aryl-N-Oxygenation by the Non-Heme Diiron Enzyme CmlI. J Am Chem Soc 2016; 138:7411-21. [PMID: 27203126 PMCID: PMC4914076 DOI: 10.1021/jacs.6b03341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ultimate step in chloramphenicol (CAM) biosynthesis is a six-electron oxidation of an aryl-amine precursor (NH2-CAM) to the aryl-nitro group of CAM catalyzed by the non-heme diiron cluster-containing oxygenase CmlI. Upon exposure of the diferrous cluster to O2, CmlI forms a long-lived peroxo intermediate, P, which reacts with NH2-CAM to form CAM. Since P is capable of at most a two-electron oxidation, the overall reaction must occur in several steps. It is unknown whether P is the oxidant in each step or whether another oxidizing species participates in the reaction. Mass spectrometry product analysis of reactions under (18)O2 show that both oxygen atoms in the nitro function of CAM derive from O2. However, when the single-turnover reaction between (18)O2-P and NH2-CAM is carried out in an (16)O2 atmosphere, CAM nitro groups contain both (18)O and (16)O, suggesting that P can be reformed during the reaction sequence. Such reformation would require reduction by a pathway intermediate, shown here to be NH(OH)-CAM. Accordingly, the aerobic reaction of NH(OH)-CAM with diferric CmlI yields P and then CAM without an external reductant. A catalytic cycle is proposed in which NH2-CAM reacts with P to form NH(OH)-CAM and diferric CmlI. Then the NH(OH)-CAM rereduces the enzyme diiron cluster, allowing P to reform upon O2 binding, while itself being oxidized to NO-CAM. Finally, the reformed P oxidizes NO-CAM to CAM with incorporation of a second O2-derived oxygen atom. The complete six-electron oxidation requires only two exogenous electrons and could occur in one active site.
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Affiliation(s)
- Anna J. Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Brent S. Rivard
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - John D. Lipscomb
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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79
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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80
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Jayapal P, Ansari A, Rajaraman G. Computational Examination on the Active Site Structure of a (Peroxo)diiron(III) Intermediate in the Amine Oxygenase AurF. Inorg Chem 2015; 54:11077-82. [PMID: 26588098 DOI: 10.1021/acs.inorgchem.5b00872] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we report the first computational investigation on the structure and properties of the (peroxo)diiron(III) intermediate of the AurF enzyme. Our calculations predict that, in the oxidized state of the AurF enzyme, the peroxo ligand is depicted in a μ-1,1-coordination mode with a protonated bridging ligand and is not in a μ-η(2):η(2) or μ-1,2 mode. Computed spectral data for the μ-1,1-coordination mode correlate well with experimental observations and unravel the potential of the energetics-spectroscopic approach adapted here.
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Affiliation(s)
- Prabha Jayapal
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
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81
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Snyder RA, Betzu J, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins. Biochemistry 2015; 54:4637-51. [PMID: 26154739 DOI: 10.1021/acs.biochem.5b00324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DFsc (single-chain due ferri) proteins allow for modeling binuclear non-heme iron enzymes with a similar fold. Three 4A → 4G variants of DFsc were studied to investigate the effects of (1) increasing the size of the substrate/solvent access channel (G4DFsc), (2) including an additional His residue in the first coordination sphere along with three additional helix-stabilizing mutations [3His-G4DFsc(Mut3)], and (3) the three helix-stabilizing mutations alone [G4DFsc(Mut3)] on the biferrous structures and their O2 reactivities. Near-infrared circular dichroism and magnetic circular dichroism (MCD) spectroscopy show that the 4A → 4G mutations increase coordination of the diiron site from 4-coordinate/5-coordinate to 5-coordinate/5-coordinate, likely reflecting increased solvent accessibility. While the three helix-stabilizing mutations [G4DFsc(Mut3)] do not affect the coordination number, addition of the third active site His residue [3His-G4DFsc(Mut3)] results in a 5-coordinate/6-coordinate site. Although all 4A→ 4G variants have significantly slower pseudo-first-order rates when reacting with excess O2 than DFsc (∼2 s(-1)), G4DFsc and 3His-G4DFsc(Mut3) have rates (∼0.02 and ∼0.04 s(-1)) faster than that of G4DFsc(Mut3) (∼0.002 s(-1)). These trends in the rate of O2 reactivity correlate with exchange coupling between the Fe(II) sites and suggest that the two-electron reduction of O2 occurs through end-on binding at one Fe(II) rather than through a peroxy-bridged intermediate. UV-vis absorption and MCD spectroscopies indicate that an Fe(III)Fe(III)-OH species first forms in all three variants but converts into an Fe(III)-μ-OH-Fe(III) species only in the 2-His forms, a process inhibited by the additional active site His ligand that coordinatively saturates one of the iron centers in 3His-G4DFsc(Mut3).
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Affiliation(s)
- Rae Ana Snyder
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Justine Betzu
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Susan E Butch
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Amanda J Reig
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - William F DeGrado
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | - Edward I Solomon
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States.,∥Stanford Synchrotron Radiation Laboratory, Stanford University, SLAC, Menlo Park, California 94025, United States
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82
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Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC, Gerwick L, Gerwick WH. Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. JOURNAL OF NATURAL PRODUCTS 2015; 78:1671-82. [PMID: 26149623 PMCID: PMC4681511 DOI: 10.1021/acs.jnatprod.5b00301] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An innovative approach was developed for the discovery of new natural products by combining mass spectrometric metabolic profiling with genomic analysis and resulted in the discovery of the columbamides, a new class of di- and trichlorinated acyl amides with cannabinomimetic activity. Three species of cultured marine cyanobacteria, Moorea producens 3L, Moorea producens JHB, and Moorea bouillonii PNG, were subjected to genome sequencing and analysis for their recognizable biosynthetic pathways, and this information was then compared with their respective metabolomes as detected by MS profiling. By genome analysis, a presumed regulatory domain was identified upstream of several previously described biosynthetic gene clusters in two of these cyanobacteria, M. producens 3L and M. producens JHB. A similar regulatory domain was identified in the M. bouillonii PNG genome, and a corresponding downstream biosynthetic gene cluster was located and carefully analyzed. Subsequently, MS-based molecular networking identified a series of candidate products, and these were isolated and their structures rigorously established. On the basis of their distinctive acyl amide structure, the most prevalent metabolite was evaluated for cannabinomimetic properties and found to be moderate affinity ligands for CB1.
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Affiliation(s)
- Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - Isaac Yuheng Tian
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- University of California Berkeley, USA
| | | | - Anton Korobeynikov
- Faculty of Mathematics and Mechanics, Saint Petersburg State University, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Russia
- Algorithmic Biology Laboratory, Saint Petersburg Academic University, Russia
| | - Emily A. Monroe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- Department of Biology, William Paterson University of New Jersey, USA
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
| | - Vincenzo Di Marzo
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
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83
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Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc 2015; 137:9302-14. [PMID: 26090726 DOI: 10.1021/jacs.5b03524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the single-chain due ferri (DFsc) peptide scaffold, the differential oxidase and oxygenase reactivities of two 4A→4G variants, one with two histidines at the diiron center (G4DFsc) and the other with three histidines (3His-G4DFsc(Mut3)), are explored. By controlling the reaction conditions, the active form responsible for 4-aminophenol (4-AP) oxidase activity in both G4DFsc and 3His-G4DFsc(Mut3) is determined to be the substrate-bound biferrous site. Using circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies, 4-AP is found to bind directly to the biferrous sites of the DF proteins. In G4DFsc, 4-AP increases the coordination of the biferrous site, while in 3His-G4DFsc(Mut3), the coordination number remains the same and the substrate likely replaces the additional bound histidine. This substrate binding enables a two-electron process where 4-AP is oxidized to benzoquinone imine and O2 is reduced to H2O2. In contrast, only the biferrous 3His variant is found to be active in the oxygenation of p-anisidine to 4-nitroso-methoxybenzene. From CD, MCD, and VTVH MCD, p-anisidine addition is found to minimally perturb the biferrous centers of both G4DFsc and 3His-G4DFsc(Mut3), indicating that this substrate binds near the biferrous site. In 3His-G4DFsc(Mut3), the coordinative saturation of one iron leads to the two-electron reduction of O2 at the second iron to generate an end-on hydroperoxo-Fe(III) active oxygenating species.
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Affiliation(s)
- Rae Ana Snyder
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Susan E Butch
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Amanda J Reig
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - William F DeGrado
- ⊥Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Edward I Solomon
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States.,§Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, California 94025, United States
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84
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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85
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Liao RZ, Siegbahn PEM. Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB. Chem Sci 2015; 6:2754-2764. [PMID: 28706665 PMCID: PMC5489048 DOI: 10.1039/c5sc00313j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/02/2015] [Indexed: 12/22/2022] Open
Abstract
DFT calculations are used to elucidate the reaction mechanism and selectivity of BoxB catalyzed benzoyl-CoA epoxidation.
Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron enzymes. We report a density functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O2 molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O–O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal mol–1, respectively. The barrier difference is 2.8 kcal mol–1, corresponding to a diastereomeric excess of about 99 : 1. Further isomerization from epoxide to phenol is found to have quite a high barrier, which cannot compete with the product release step. After product release into solution, fast epoxide–oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide to regenerate benzoyl-CoA by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2–O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3–O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal mol–1. Further experimental studies are encouraged to verify our results.
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Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory for Large-Format Battery Materials and System , Ministry of Education , School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , Wuhan 430074 , China .
| | - Per E M Siegbahn
- Department of Organic Chemistry , Arrhenius Laboratory , Stockholm University , SE-10691 Stockholm , Sweden .
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86
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Makris TM, Vu VV, Meier KK, Komor AJ, Rivard BS, Münck E, Que L, Lipscomb JD. An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway. J Am Chem Soc 2015; 137:1608-17. [PMID: 25564306 PMCID: PMC4318726 DOI: 10.1021/ja511649n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces venezuelae CmlI catalyzes the six-electron oxygenation of the arylamine precursor of chloramphenicol in a nonribosomal peptide synthetase (NRPS)-based pathway to yield the nitroaryl group of the antibiotic. Optical, EPR, and Mössbauer studies show that the enzyme contains a nonheme dinuclear iron cluster. Addition of O(2) to the diferrous state of the cluster results in an exceptionally long-lived intermediate (t(1/2) = 3 h at 4 °C) that is assigned as a peroxodiferric species (CmlI-peroxo) based upon the observation of an (18)O(2)-sensitive resonance Raman (rR) vibration. CmlI-peroxo is spectroscopically distinct from the well characterized and commonly observed cis-μ-1,2-peroxo (μ-η(1):η(1)) intermediates of nonheme diiron enzymes. Specifically, it exhibits a blue-shifted broad absorption band around 500 nm and a rR spectrum with a ν(O-O) that is at least 60 cm(-1) lower in energy. Mössbauer studies of the peroxo state reveal a diferric cluster having iron sites with small quadrupole splittings and distinct isomer shifts (0.54 and 0.62 mm/s). Taken together, the spectroscopic comparisons clearly indicate that CmlI-peroxo does not have a μ-η(1):η(1)-peroxo ligand; we propose that a μ-η(1):η(2)-peroxo ligand accounts for its distinct spectroscopic properties. CmlI-peroxo reacts with a range of arylamine substrates by an apparent second-order process, indicating that CmlI-peroxo is the reactive species of the catalytic cycle. Efficient production of chloramphenicol from the free arylamine precursor suggests that CmlI catalyzes the ultimate step in the biosynthetic pathway and that the precursor is not bound to the NRPS during this step.
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Affiliation(s)
- Thomas M. Makris
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Van V. Vu
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Anna J. Komor
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - Brent S. Rivard
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University,
Pittsburgh, PA 15213, United States
| | - Lawrence Que
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis,
Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of
Minnesota, Minneapolis, MN 55455
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87
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Indest KJ, Eberly JO, Hancock DE. Expression and characterization of an N-oxygenase from Rhodococcus jostii RHAI. J GEN APPL MICROBIOL 2015; 61:217-23. [DOI: 10.2323/jgam.61.217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karl J. Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Jed O. Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Dawn E. Hancock
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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88
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Shafaat HS, Griese JJ, Pantazis DA, Roos K, Andersson CS, Popović-Bijelić A, Gräslund A, Siegbahn PEM, Neese F, Lubitz W, Högbom M, Cox N. Electronic structural flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins. J Am Chem Soc 2014; 136:13399-409. [PMID: 25153930 DOI: 10.1021/ja507435t] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The electronic structure of the Mn/Fe cofactor identified in a new class of oxidases (R2lox) described by Andersson and Högbom [Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5633] is reported. The R2lox protein is homologous to the small subunit of class Ic ribonucleotide reductase (R2c) but has a completely different in vivo function. Using multifrequency EPR and related pulse techniques, it is shown that the cofactor of R2lox represents an antiferromagnetically coupled Mn(III)/Fe(III) dimer linked by a μ-hydroxo/bis-μ-carboxylato bridging network. The Mn(III) ion is coordinated by a single water ligand. The R2lox cofactor is photoactive, converting into a second form (R2loxPhoto) upon visible illumination at cryogenic temperatures (77 K) that completely decays upon warming. This second, unstable form of the cofactor more closely resembles the Mn(III)/Fe(III) cofactor seen in R2c. It is shown that the two forms of the R2lox cofactor differ primarily in terms of the local site geometry and electronic state of the Mn(III) ion, as best evidenced by a reorientation of its unique (55)Mn hyperfine axis. Analysis of the metal hyperfine tensors in combination with density functional theory (DFT) calculations suggests that this change is triggered by deprotonation of the μ-hydroxo bridge. These results have important consequences for the mixed-metal R2c cofactor and the divergent chemistry R2lox and R2c perform.
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Affiliation(s)
- Hannah S Shafaat
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, Mülheim an der Ruhr D-45470, Germany
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89
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Characterization of the N-oxygenase AurF from Streptomyces thioletus. Bioorg Med Chem 2014; 22:5569-77. [PMID: 24973817 DOI: 10.1016/j.bmc.2014.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 11/21/2022]
Abstract
AurF catalyzes the N-oxidation of p-aminobenzoic acid to p-nitrobenzoic acid in the biosynthesis of the antibiotic aureothin. Here we report the characterization of AurF under optimized conditions to explore its potential use in biocatalysis. The pH optimum of the enzyme was established to be 5.5 using phenazine methosulfate (PMS)/NADH as the enzyme mediator system, showing ~10-fold higher activity than previous reports in literature. Kinetic characterization at optimized conditions give a Km of 14.7 ± 1.1 μM, a kcat of 47.5 ± 5.4 min(-1) and a kcat/Km of 3.2 ± 0.4 μM(-1)min(-1). PMS/NADH and the native electron transfer proteins showed significant formation of the p-hydroxylaminobenzoic acid intermediate, however H2O2 produced mostly p-nitrobenzoic acid. Alanine scanning identified the role of important active site residues. The substrate specificity of AurF was examined and rationalized based on the protein crystal structure. Kinetic studies indicate that the Km is the main determinant of AurF activity toward alternative substrates.
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90
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Abstract
Important biomimetic steps in natural product synthesis have been promoted by transition metals, as exemplified by this beautiful ruthenium-catalyzed rearrangement of an endoperoxide into elysiapyrone A. Such reactions are supposed to occur during the biosynthesis, yet under different catalysis conditions.
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Affiliation(s)
- Xu-Wen Li
- Muséum National d'Histoire Naturelle and Centre National de la Recherche Scientifique
- Unité “Molécules de Communication et Adaptation des Micro-organismes” (UMR 7245 CNRS-MNHN)
- 75005 Paris, France
| | - Bastien Nay
- Muséum National d'Histoire Naturelle and Centre National de la Recherche Scientifique
- Unité “Molécules de Communication et Adaptation des Micro-organismes” (UMR 7245 CNRS-MNHN)
- 75005 Paris, France
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91
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Zhu Y, Zhang Q, Li S, Lin Q, Fu P, Zhang G, Zhang H, Shi R, Zhu W, Zhang C. Insights into Caerulomycin A Biosynthesis: A Two-Component Monooxygenase CrmH-Catalyzed Oxime Formation. J Am Chem Soc 2013; 135:18750-3. [PMID: 24295370 DOI: 10.1021/ja410513g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yiguang Zhu
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Qingbo Zhang
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Sumei Li
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Qinheng Lin
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Fu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School
of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guangtao Zhang
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Haibo Zhang
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Rong Shi
- Département
de Biochimie, de Microbiologie et de Bio-informatique, PROTEO et IBIS, Université Laval, Québec, G1V 0A6, Canada
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School
of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Changsheng Zhang
- CAS Key
Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center
for Marine Microbiology, Guangdong Key Laboratory of Marine Materia
Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
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92
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Pandelia ME, Li N, Nørgaard H, Warui DM, Rajakovich LJ, Chang WC, Booker SJ, Krebs C, Bollinger JM. Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate. J Am Chem Soc 2013; 135:15801-12. [PMID: 23987523 PMCID: PMC3869994 DOI: 10.1021/ja405047b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or monounsaturated C(n) fatty aldehydes to formate and the corresponding C(n-1) alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 cosubstrate to the oxidation state of water and incorporates one O-atom from O2 into the formate coproduct. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2(III/III) complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2(III/III) center with resolved subsites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t(1/2) ~ 400 s at 5 °C) to produce a very modest yield of formate (<0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazinium methylsulfate ((MeO)PMS) to yield product, albeit at only ~50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or heterodinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2(III/III)-peroxyhemiacetal complex, which undergoes reductive O-O-bond cleavage, leading to C1-C2 radical fragmentation and formation of the alk(a/e)ne and formate products.
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Affiliation(s)
- Maria E. Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ning Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hanne Nørgaard
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Douglas M. Warui
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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93
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Barry SM, Challis GL. Mechanism and Catalytic Diversity of Rieske Non-Heme Iron-Dependent Oxygenases. ACS Catal 2013; 3. [PMID: 24244885 DOI: 10.1021/cs400087p] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rieske non-heme iron-dependent oxygenases are important enzymes that catalyze a wide variety of reactions in the biodegradation of xenobiotics and the biosynthesis of bioactive natural products. In this perspective article, we summarize recent efforts to elucidate the catalytic mechanisms of Rieske oxygenases and highlight the diverse range of reactions now known to be catalyzed by such enzymes.
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Affiliation(s)
- Sarah M. Barry
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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94
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Zhang J, Lu X, Li JJ. Conversion of fatty aldehydes into alk (a/e)nes by in vitro reconstituted cyanobacterial aldehyde-deformylating oxygenase with the cognate electron transfer system. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:86. [PMID: 23759169 PMCID: PMC3691600 DOI: 10.1186/1754-6834-6-86] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 06/03/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biosynthesis of fatty alk(a/e)ne in cyanobacteria has been considered as a potential basis for the sunlight-driven and carbon-neutral bioprocess producing advanced solar biofuels. Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in that pathway. The heterologous or chemical reducing systems were generally used in in vitro ADO activity assay. The cognate electron transfer system from cyanobacteria to support ADO activity is still unknown. RESULTS We identified the potential endogenous reducing system including ferredoxin (Fd) and ferredoxin-NADP+ reductase (FNR) to support ADO activity in Synechococcus elongatus PCC7942. ADO (Synpcc7942_1593), FNR (SynPcc7942_0978), and Fd (SynPcc7942_1499) from PCC7942 were cloned, overexpressed, purified, and characterized. ADO activity was successfully supported with the endogenous electron transfer system, which worked more effectively than the heterologous and chemical ones. The results of the hybrid Fd/FNR reducing systems demonstrated that ADO was selective against Fd. And it was observed that the cognate reducing system produced less H2O2 than the heterologous one by 33% during ADO-catalyzed reactions. Importantly, kcat value of ADO 1593 using the homologous Fd/FNR electron transfer system is 3.7-fold higher than the chemical one. CONCLUSIONS The cognate electron transfer system from cyanobacteria to support ADO activity was identified and characterized. For the first time, ADO was functionally in vitro reconstituted with the endogenous reducing system from cyanobacteria, which supported greater activity than the surrogate and chemical ones, and produced less H2O2 than the heterologous one. The identified Fd/FNR electron transfer system will be potentially useful for improving ADO activity and further enhancing the biosynthetic efficiency of hydrocarbon biofuels in cyanobacteria.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| | - Jian-Jun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
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95
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Krebs C, Dassama LMK, Matthews ML, Jiang W, Price JC, Korboukh V, Li N, Bollinger JM. Novel Approaches for the Accumulation of Oxygenated Intermediates to Multi-Millimolar Concentrations. Coord Chem Rev 2013; 257:10.1016/j.ccr.2012.06.020. [PMID: 24368870 PMCID: PMC3870000 DOI: 10.1016/j.ccr.2012.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metalloenzymes that utilize molecular oxygen as a co-substrate catalyze a wide variety of chemically difficult oxidation reactions. Significant insight into the reaction mechanisms of these enzymes can be obtained by the application of a combination of rapid kinetic and spectroscopic methods to the direct structural characterization of intermediate states. A key limitation of this approach is the low aqueous solubility (< 2 mM) of the co-substrate, O2, which undergoes further dilution (typically by one-third or one-half) upon initiation of reactions by rapid-mixing. This situation imposes a practical upper limit on [O2] (and therefore on the concentration of reactive intermediate(s) that can be rapidly accumulated) of ∼1-1.3 mM in such experiments as they are routinely carried out. However, many spectroscopic methods benefit from or require significantly greater concentrations of the species to be studied. To overcome this problem, we have recently developed two new approaches for the preparation of samples of oxygenated intermediates: (1) direct oxygenation of reduced metalloenzymes using gaseous O2 and (2) the in situ generation of O2 from chlorite catalyzed by the enzyme chlorite dismutase (Cld). Whereas the former method is applicable only to intermediates with half lives of several minutes, owing to the sluggishness of transport of O2 across the gas-liquid interface, the latter approach has been successfully applied to trap several intermediates at high concentration and purity by the freeze-quench method. The in situ approach permits generation of a pulse of at least 5 mM O2 within ∼ 1 ms and accumulation of O2 to effective concentrations of up to ∼ 11 mM (i.e. ∼ 10-fold greater than by the conventional approach). The use of these new techniques for studies of oxygenases and oxidases is discussed.
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Affiliation(s)
- Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Laura M. K. Dassama
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Megan L. Matthews
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wei Jiang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - John C. Price
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Victoria Korboukh
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ning Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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96
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Cooper HLR, Mishra G, Huang X, Pender-Cudlip M, Austin RN, Shanklin J, Groves JT. Parallel and competitive pathways for substrate desaturation, hydroxylation, and radical rearrangement by the non-heme diiron hydroxylase AlkB. J Am Chem Soc 2012; 134:20365-75. [PMID: 23157204 PMCID: PMC3531984 DOI: 10.1021/ja3059149] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A purified and highly active form of the non-heme diiron hydroxylase AlkB was investigated using the diagnostic probe substrate norcarane. The reaction afforded C2 (26%) and C3 (43%) hydroxylation and desaturation products (31%). Initial C-H cleavage at C2 led to 7% C2 hydroxylation and 19% 3-hydroxymethylcyclohexene, a rearrangement product characteristic of a radical rearrangement pathway. A deuterated substrate analogue, 3,3,4,4-norcarane-d(4), afforded drastically reduced amounts of C3 alcohol (8%) and desaturation products (5%), while the radical rearranged alcohol was now the major product (65%). This change in product ratios indicates a large kinetic hydrogen isotope effect of ∼20 for both the C-H hydroxylation at C3 and the desaturation pathway, with all of the desaturation originating via hydrogen abstraction at C3 and not C2. The data indicate that AlkB reacts with norcarane via initial C-H hydrogen abstraction from C2 or C3 and that the three pathways, C3 hydroxylation, C3 desaturation, and C2 hydroxylation/radical rearrangement, are parallel and competitive. Thus, the incipient radical at C3 either reacts with the iron-oxo center to form an alcohol or proceeds along the desaturation pathway via a second H-abstraction to afford both 2-norcarene and 3-norcarene. Subsequent reactions of these norcarenes lead to detectable amounts of hydroxylation products and toluene. By contrast, the 2-norcaranyl radical intermediate leads to C2 hydroxylation and the diagnostic radical rearrangement, but this radical apparently does not afford desaturation products. The results indicate that C-H hydroxylation and desaturation follow analogous stepwise reaction channels via carbon radicals that diverge at the product-forming step.
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Affiliation(s)
| | - Girish Mishra
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973
| | - Xiongyi Huang
- Department of Chemistry, Princeton University, Princeton NJ 08544
| | | | | | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton NJ 08544
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97
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Cotruvo JA, Stubbe J. Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study. Metallomics 2012; 4:1020-36. [PMID: 22991063 PMCID: PMC3488304 DOI: 10.1039/c2mt20142a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.
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Affiliation(s)
- Joseph A. Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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98
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Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem 2012; 4:900-6. [PMID: 23089864 PMCID: PMC3568993 DOI: 10.1038/nchem.1454] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 08/09/2012] [Indexed: 12/18/2022]
Abstract
De novo proteins provide a unique opportunity for investigating the structure-function relationships of metalloproteins in a minimal, well-defined, and controlled scaffold. Herein, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the due ferri family. Originally created to catalyze O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyze the selective N-hydroxylation of arylamines by remodeling the substrate access cavity and introducing a critical third His ligand to the metal binding cavity. Additional second-and third-shell modifications were required to stabilize the His ligand in the core of the protein. These changes resulted in at least a 106 –fold increase in the relative rates of the two reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
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Affiliation(s)
- Amanda J Reig
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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99
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Abstract
The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC-MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.
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Affiliation(s)
- Haige Lu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Emmanuel Chanco
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA ; Department of Chemistry, University of Illinois at Urbana-Champaign, USA
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100
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Jayapal P, Rajaraman G. On the controversy of metal ion composition on amine oxygenase (AurF): a computational investigation. Phys Chem Chem Phys 2012; 14:9050-3. [DOI: 10.1039/c2cp40874k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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