Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

[1]  C. Costello,et al.  Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues , 2022, JACS Au.

[2]  C. Willis,et al.  Synthetic and biosynthetic methods for selective cyclisations of 4,5-epoxy alcohols to tetrahydropyrans , 2022, Organic & biomolecular chemistry.

[3]  Gourab Mukherjee,et al.  Local Charge Distributions, Electric Dipole Moments, and Local Electric Fields Influence Reactivity Patterns and Guide Regioselectivities in α-Ketoglutarate-Dependent Non-heme Iron Dioxygenases. , 2021, Accounts of chemical research.

[4]  K. Houk,et al.  Enzymatic control of endo- and exo-stereoselective Diels–Alder reactions with broad substrate scope , 2021, Nature Catalysis.

[5]  Binju Wang,et al.  Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. , 2021, Angewandte Chemie.

[6]  Yu Chen,et al.  Origin of Site Selectivity in Toluene Hydroxylation by Cytochrome P450 Enzymes. , 2021, The Journal of organic chemistry.

[7]  K. Houk,et al.  Computational Exploration of How Enzyme XimE Converts Natural S-Epoxide to Pyran and R-Epoxide to Furan , 2021 .

[8]  Richard H. Henchman,et al.  Mechanism of Oxidative Ring‐Closure as Part of the Hygromycin Biosynthesis Step by a Nonheme Iron Dioxygenase , 2021 .

[9]  K. Houk,et al.  Catalytic mechanism and endo-to-exo selectivity reversion of an octalin-forming natural Diels–Alderase , 2021, Nature Catalysis.

[10]  P. Xu,et al.  Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX , 2021, Nature Communications.

[11]  K. Houk,et al.  An enzymatic Alder-ene reaction , 2020, Nature.

[12]  T. J. Simpson,et al.  Mixing and matching genes of marine and terrestrial origin in the biosynthesis of the mupirocin antibiotics† , 2020, Chemical science.

[13]  N. Lehnert,et al.  Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair , 2020, ACS central science.

[14]  Ya-Jian Hu,et al.  Recent Advances in the Total Synthesis of Natural Products Containing Eight-Membered Carbocycles (2009-2019). , 2020, Chemical reviews.

[15]  M. Kurnikova,et al.  Epoxidation Catalyzed by the Non-heme Iron- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate. , 2020, Journal of the American Chemical Society.

[16]  S. Matile,et al.  Primary Anion-π Catalysis of Epoxide-Opening Ether Cyclization into Rings of Different Sizes: Access to New Reactivity. , 2020, Angewandte Chemie.

[17]  P. Anastas,et al.  Designing for a green chemistry future , 2020, Science.

[18]  N. Lehnert,et al.  Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation , 2019, ACS catalysis.

[19]  Matthieu Coupet,et al.  Study of bicyclomycin biosynthesis in Streptomyces cinnamoneus by genetic and biochemical approaches , 2019, Scientific Reports.

[20]  A. Mansha,et al.  Selective hydrogen atom abstraction from dihydroflavonol is the key step in the flavonol synthesis enzyme and avoids by-products. , 2019, Journal of the American Chemical Society.

[21]  T. Borowski,et al.  On the reaction mechanism of an endoperoxide ring formation by fumitremorgin B endoperoxidase. The right arrangement makes a difference. , 2019, Dalton transactions.

[22]  Meilan Huang,et al.  Reaction Mechanism of Histone Demethylation in αKG-Dependent Non-Heme Iron Enzymes. , 2019, The journal of physical chemistry. B.

[23]  Benjamin D. Allen,et al.  Hydrogen Donation but not Abstraction by a Tyrosine (Y68) during Endoperoxide Installation by Verruculogen Synthase (FtmOx1). , 2019, Journal of the American Chemical Society.

[24]  Yi-Lei Zhao,et al.  Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis , 2019, ACS Catalysis.

[25]  M. W. van der Kamp,et al.  A Rieske oxygenase/epoxide hydrolase-catalysed reaction cascade creates oxygen heterocycles in mupirocin biosynthesis , 2018, Nature Catalysis.

[26]  Hai-Xue Pan,et al.  Enzymatic Formation of Oxygen‐Containing Heterocycles in Natural Product Biosynthesis , 2018, Chembiochem : a European journal of chemical biology.

[27]  S. Jacobsen,et al.  Resistance-Gene Directed Discovery of a Natural Product Herbicide with a New Mode of Action , 2018, Nature.

[28]  C. Krebs,et al.  Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance. , 2018, Journal of the American Chemical Society.

[29]  Ville R. I. Kaila,et al.  Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ , 2018, Nature Communications.

[30]  Hai-Xue Pan,et al.  A Six-Oxidase Cascade for Tandem C-H Bond Activation Revealed by Reconstitution of Bicyclomycin Biosynthesis. , 2018, Angewandte Chemie.

[31]  C. Walsh,et al.  Recent Advances in Enzymatic Complexity Generation: Cyclization Reactions. , 2017, Biochemistry.

[32]  Wenzhen Lai,et al.  Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. , 2017, Physical chemistry chemical physics : PCCP.

[33]  Wenyou Zhu,et al.  Mechanistic Insights into the Decoupled Desaturation and Epoxidation Catalyzed by Dioxygenase AsqJ Involved in the Biosynthesis of Quinolone Alkaloids , 2017 .

[34]  S. D. de Visser,et al.  Understanding How Prolyl-4-hydroxylase Structure Steers a Ferryl Oxidant toward Scission of a Strong C-H Bond. , 2017, Journal of the American Chemical Society.

[35]  J. Kästner,et al.  Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations. , 2017, The journal of physical chemistry. B.

[36]  Christopher T. Walsh,et al.  Oxidative Cyclization in Natural Product Biosynthesis. , 2017, Chemical reviews.

[37]  Yongjun Liu,et al.  Insights into the unprecedented epoxidation mechanism of fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus by QM/MM calculations. , 2017, Physical chemistry chemical physics : PCCP.

[38]  Kevin N Dyer,et al.  Ligand-induced and small-molecule control of substrate loading in a hexameric helicase , 2016, Proceedings of the National Academy of Sciences.

[39]  Pengfei Li,et al.  MCPB.py: A Python Based Metal Center Parameter Builder , 2016, J. Chem. Inf. Model..

[40]  T. Borowski,et al.  Mechanism of O2 Activation by α-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study. , 2016, The journal of physical chemistry. A.

[41]  R. Pohl,et al.  Synthesis of bridged diketopiperazines by using the persistent radical effect and a formal synthesis of bicyclomycin. , 2015, Angewandte Chemie.

[42]  Matthew N. Grayson,et al.  Efficient Biosynthesis of Fungal Polyketides Containing the Dioxabicyclo-octane Ring System. , 2015, Journal of the American Chemical Society.

[43]  J. Frisvad,et al.  Reconstitution of biosynthetic machinery for the synthesis of the highly elaborated indole diterpene penitrem. , 2015, Angewandte Chemie.

[44]  Wei‐Lie Xiao,et al.  Triterpenoids from the Schisandraceae family: an update. , 2015, Natural product reports.

[45]  Bernhard Rupp,et al.  Models of protein–ligand crystal structures: trust, but verify , 2015, Journal of Computer-Aided Molecular Design.

[46]  Kenji Watanabe,et al.  Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis. , 2015, Journal of the American Chemical Society.

[47]  J. Hohmann,et al.  Euphorbia diterpenes: isolation, structure, biological activity, and synthesis (2008-2012). , 2014, Chemical reviews.

[48]  David Baker,et al.  Computational enzyme design. , 2013, Angewandte Chemie.

[49]  Michael A McDonough,et al.  Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases. , 2012, Current opinion in structural biology.

[50]  F. Neese,et al.  Electronic structure analysis of the oxygen-activation mechanism by Fe(II)- and α-ketoglutarate (αKG)-dependent dioxygenases. , 2012, Chemistry.

[51]  A. Minami,et al.  Sequential enzymatic epoxidation involved in polyether lasalocid biosynthesis. , 2012, Journal of the American Chemical Society.

[52]  X. Chen,et al.  Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis , 2012, Nature.

[53]  Hui Chen,et al.  The directive of the protein: how does cytochrome P450 select the mechanism of dopamine formation? , 2011, Journal of the American Chemical Society.

[54]  Eric N. Jacobsen,et al.  Attractive noncovalent interactions in asymmetric catalysis: Links between enzymes and small molecule catalysts , 2010, Proceedings of the National Academy of Sciences.

[55]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[56]  George M. Sheldrick,et al.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[57]  S. Afiyatullov,et al.  FtmOx1, a non-heme Fe(II) and alpha-ketoglutarate-dependent dioxygenase, catalyses the endoperoxide formation of verruculogen in Aspergillus fumigatus. , 2009, Organic & biomolecular chemistry.

[58]  P. Schreiner,et al.  (Thio)urea organocatalysis--what can be learnt from anion recognition? , 2009, Chemical Society reviews.

[59]  Abigail G Doyle,et al.  Small-molecule H-bond donors in asymmetric catalysis. , 2007, Chemical reviews.

[60]  Wladek Minor,et al.  HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. , 2006, Acta crystallographica. Section D, Biological crystallography.

[61]  H. Kohn,et al.  The molecular basis for the mode of action of bicyclomycin. , 2005, Current drug targets. Infectious disorders.

[62]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[63]  P. Schreiner Metal-free organocatalysis through explicit hydrogen bonding interactions. , 2003, Chemical Society reviews.

[64]  Giovanni Scalmani,et al.  Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model , 2003, J. Comput. Chem..

[65]  Christopher I. Bayly,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..

[66]  L. Yet Metal-mediated synthesis of medium-sized rings. , 2000, Chemical reviews.

[67]  A. Thorpe,et al.  Theozymes for Intramolecular Ring Cyclization Reactions , 1999 .

[68]  R. Lerner,et al.  Structural basis for antibody catalysis of a disfavored ring closure reaction. , 1999, Biochemistry.

[69]  V. Barone,et al.  Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .

[70]  Robin Taylor,et al.  Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii , 1996 .

[71]  R. Lerner,et al.  Oxepane Synthesis Along a Disfavored Pathway: The Rerouting of a Chemical Reaction Using a Catalytic Antibody , 1995 .

[72]  N. Kanoh,et al.  ENZYMATIC REACTION OF (3E,6S,7S)-LAUREDIOL AND THE MOLECULAR MODELING STUDIES ON THE CYCLIZATION OF LAUREDIOLS , 1995 .

[73]  R. Lerner,et al.  The energetic advantage of 5-exo versus 6-endo epoxide openings: a preference overwhelmed by antibody catalysis , 1993 .

[74]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[75]  R. Lerner,et al.  Antibody catalysis of a disfavored chemical transformation. , 1993, Science.

[76]  Robert M. Williams,et al.  Bicyclomycin: synthetic, mechanistic, and biological studies , 1988 .

[77]  Michael Dolg,et al.  Energy‐adjusted ab initio pseudopotentials for the first row transition elements , 1987 .

[78]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[79]  L. Mandolini,et al.  Ring closure reactions of bifunctional chain molecules , 1981 .

[80]  H. Aoki,et al.  Bicyclomycin, a new antibiotic. I. Taxonomy, isolation and characterization. , 1972, The Journal of antibiotics.

[81]  B. Hauer,et al.  Supporting Information Stereoselective Directed Cationic Cascades Enabled by Molecular Anchoring in Terpene Cyclases , 2021 .

[82]  J. Berger,et al.  Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. , 2005, Structure.

[83]  K N Houk,et al.  Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules. , 2005, Journal of chemical theory and computation.

[84]  P. Afonine,et al.  research papers Acta Crystallographica Section D Biological , 2003 .

[85]  Vincent B. Chen,et al.  Acta Crystallographica Section D Biological , 2001 .

[86]  C. Bayly,et al.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method , 2000, J. Comput. Chem..

[87]  K. Houk,et al.  Predicting Antibody Catalyst Selectivity from Optimum Binding of Catalytic Groups to a Hapten , 1996 .

[88]  T. Huynh-Dinh,et al.  The logic of chemical synthesis , 1996 .

[89]  Jorge M. Seminario,et al.  Calculation of intramolecular force fields from second‐derivative tensors , 1996 .

[90]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals , 1985 .