Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A

Journal Article · · Journal of the American Chemical Society
DOI:https://doi.org/10.1021/jacs.2c06631· OSTI ID:1994337
 [1];  [2];  [3];  [4];  [5];  [1];  [6];  [3];  [7]
  1. University of Michigan, Ann Arbor, MI (United States)
  2. University of Michigan, Ann Arbor, MI (United States); University of California, San Diego, CA (United States). Scripps Inst. of Oceanography
  3. University of Utah, Salt Lake City, UT (United States)
  4. University of Michigan, Ann Arbor, MI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute
  5. University of Michigan, Ann Arbor, MI (United States); University of Science and Technology Wuhan (China)
  6. Kumamoto University (Japan)
  7. davidhs@umich.edu

Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to > 99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Institutes of Health (NIH); Hans W. Vahlteich Professorship; Margaret J. Hunter Professorship; National Cancer Institute; National Institute of General Medical Sciences
Grant/Contract Number:
AC02-05CH11231; AC02-06CH11357
OSTI ID:
1994337
Alternate ID(s):
OSTI ID: 1901248
Journal Information:
Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Journal Issue: 42 Vol. 144; ISSN 0002-7863
Publisher:
American Chemical Society (ACS)Copyright Statement
Country of Publication:
United States
Language:
English

References (73)

A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes journal July 2002
Notoamides A–D: Prenylated Indole Alkaloids Isolated from a Marine-Derived Fungus,Aspergillus sp. journal March 2007
Biosynthesis of Complex Indole Alkaloids: Elucidation of the Concise Pathway of Okaramines journal July 2017
Three Novel, Structurally Unique Spirocyclic Alkaloids from the Halotolerant B-17 Fungal Strain ofAspergillus variecolor journal December 2007
Flavin‐Dependent Monooxygenases NotI and NotI′ Mediate Spiro‐Oxindole Formation in Biosynthesis of the Notoamides journal May 2020
Predicting the Substrate Scope of the Flavin‐Dependent Halogenase BrvH journal August 2020
Structure, Bioactivity and Synthesis of Natural Products with Hexahydropyrrolo[2,3-b]indole journal January 2011
Bioorthogonal Click Chemistry: Covalent Labeling in Living Systems journal December 2007
The ABBA family of aromatic prenyltransferases: broadening natural product diversity journal February 2008
Reinvestigation of the substrate specificity of a reverse prenyltransferase NotF from Aspergillus sp. MF297-2 journal March 2020
Applications of dimethylallyltryptophan synthases and other indole prenyltransferases for structural modification of natural products journal July 2009
Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides journal June 2012
Prenyltransferases as key enzymes in primary and secondary metabolism journal July 2015
Enzymatic studies on aromatic prenyltransferases journal March 2020
Purification and properties of dimethylallylpyrophosphate: Tryptophan dimethylallyl transferase, the first enzyme of ergot alkaloid biosynthesis in Claviceps. sp. SD 58 journal November 1976
Austamide, a new toxic metabolite from journal January 1971
Bio-mining the microbial treasures of the ocean: New natural products journal September 2011
Catalytic Mechanism of Stereospecific Formation of cis-Configured Prenylated Pyrroloindoline Diketopiperazines by Indole Prenyltransferases journal December 2013
Structure and Catalytic Mechanism of a Cyclic Dipeptide Prenyltransferase with Broad Substrate Promiscuity journal September 2012
Evolution of aromatic prenyltransferases in the biosynthesis of indole derivatives journal October 2009
Concise, biomimetic total synthesis of d,l-marcfortine C journal July 2007
Concise syntheses of the 1,7-dihydropyrano[2,3-g]indole ring system of the stephacidins, aspergamides and norgeamides journal December 2005
Pursuit of Noncovalent Interactions for Strategic Site-Selective Catalysis journal March 2017
(±)-Uncarilins A and B, Dimeric Isoechinulin-Type Alkaloids from Uncaria rhynchophylla journal February 2017
Bioinspired Indole Prenylation Reactions in Water journal August 2017
Lewis Acid Catalyzed Displacement of Trichloroacetimidates in the Synthesis of Functionalized Pyrroloindolines journal August 2016
A Mild and General Larock Indolization Protocol for the Preparation of Unnatural Tryptophans journal September 2016
Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway journal November 2020
Machine Learning in Enzyme Engineering journal December 2019
Inversion of Extender Unit Selectivity in the Erythromycin Polyketide Synthase by Acyltransferase Domain Engineering journal November 2016
Biosynthesis and Structure–Activity Relationship Studies of Okaramines That Target Insect Glutamate-Gated Chloride Channels journal January 2018
An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism journal January 2019
Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 journal February 2005
Tyrosine O -Prenyltransferase SirD Catalyzes S -, C -, and N -Prenylations on Tyrosine and Tryptophan Derivatives journal October 2013
Monoisoprenylated cyclo-L-alanyl-L-tryptophanyl. Biosynthetic precursor of echinulin journal April 1973
Genome-Based Characterization of Two Prenylation Steps in the Assembly of the Stephacidin and Notoamide Anticancer Agents in a Marine-Derived Aspergillus sp. journal September 2010
Structure−Function Analysis of an Enzymatic Prenyl Transfer Reaction Identifies a Reaction Chamber with Modifiable Specificity journal November 2010
Multisite Prenylation of 4-Substituted Tryptophans by Dimethylallyltryptophan Synthase journal January 2013
Mechanism of Dimethylallyltryptophan Synthase: Evidence for a Dimethylallyl Cation Intermediate in an Aromatic Prenyltransferase Reaction journal September 2009
Total Synthesis of Gypsetin, Deoxybrevianamide E, Brevianamide E, and Tryprostatin B:  Novel Constructions of 2,3-Disubstituted Indoles journal December 1999
Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C–C Bond Formation journal May 2020
Computational-Based Mechanistic Study and Engineering of Cytochrome P450 MycG for Selective Oxidation of 16-Membered Macrolide Antibiotics journal October 2020
Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase journal August 2020
Function and Structure of MalA/MalA′, Iterative Halogenases for Late-Stage C–H Functionalization of Indole Alkaloids journal August 2017
Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway journal January 2020
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects journal January 2006
Shornephine A: Structure, Chemical Stability, and P-Glycoprotein Inhibitory Properties of a Rare Diketomorpholine from an Australian Marine-Derived Aspergillus sp. journal September 2014
Biomimetic Total Synthesis of Malbrancheamide and Malbrancheamide B journal March 2008
Roquefortine E, a Diketopiperazine from an Australian Isolate of Gymnoascus reessii journal October 2005
Isolation of Talathermophilins from the Thermophilic Fungus Talaromyces thermophilus YM3-4 journal October 2011
New Diketopiperazine Alkaloids from Penicillium fellutanum journal March 2000
Stereoselective Synthesis of Brevianamide E journal November 2011
Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products journal June 2005
Multidimensional steric parameters in the analysis of asymmetric catalytic reactions journal March 2012
Distinct mechanisms for spiro-carbon formation reveal biosynthetic pathway crosstalk journal October 2013
Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase journal December 2016
Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels–Alderase journal September 2019
Fungal-derived brevianamide assembly by a stereoselective semipinacolase journal May 2020
Prenylated indole derivatives from fungi: structure diversity, biological activities, biosynthesis and chemoenzymatic synthesis journal January 2010
Isolation and structure (X-ray analysis) of marcfortine A, a new alkaloid from Penicillium roqueforti journal January 1980
Predictive and mechanistic multivariate linear regression models for reaction development journal January 2018
Total synthesis of (−)-penicimutanin a and related congeners journal January 2020
Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(−)-notoamide, paraherquamide and malbrancheamide pathways journal January 2012
The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria journal August 2009
Reversal of anticancer multidrug resistance by the ardeemins journal July 1998
Indole diketopiperazine alkaloids from the deep-sea-derived fungus Aspergillus sp. FS445 journal May 2021
Enzyme evolution in fungal indole alkaloid biosynthesis journal April 2020
Use of an Induced Fit Receptor Structure in Virtual Screening journal January 2006
Evolutionary Relationships of Microbial Aromatic Prenyltransferases journal November 2011
Eurotiumins A–E, Five New Alkaloids from the Marine-Derived Fungus Eurotium sp. SCSIO F452 journal April 2018
A New Prenylated Indole Diketopiperazine Alkaloid from Eurotium cristatum journal November 2014
Prenylation of Aromatic Secondary Metabolites: A New Frontier for Development of Novel Drugs journal February 2014
5-N-Acetylardeemin, a novel heterocyclic compound which reverses multiple drug resistance in tumor cells. II. Isolation and elucidation of the structure of 5-N-acetylardeemin and two congeners. journal January 1993

Similar Records

Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD
Journal Article · Fri Jun 28 00:00:00 EDT 2019 · Biochemistry · OSTI ID:1559335

Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis
Journal Article · Sun Jan 14 23:00:00 EST 2018 · Biochemical and Biophysical Research Communications · OSTI ID:23127506

Structure and specificity of a permissive bacterial C-prenyltransferase
Journal Article · Sun Feb 05 23:00:00 EST 2017 · Nature Chemical Biology · OSTI ID:1356427