Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene

Blank, Patrick N.; Pemberton, Travis A.; Chow, Jeng-Yeong; Poulter, C. Dale; Christianson, David W.

doi:10.1021/acs.biochem.8b00899

Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene

Journal Article · Mon Oct 22 00:00:00 EDT 2018 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.8b00899· OSTI ID:1483892

Blank, Patrick N. ^[1]; Pemberton, Travis A. ^[1]; Chow, Jeng-Yeong ^[2]; ^[2]; ^[1]

Univ. of Pennsylvania, Philadelphia, PA (United States)
Univ. of Utah, Salt Lake City, UT (United States)

Linear triquinanes are sesquiterpene natural products with hydrocarbon skeletons consisting of three fused five-membered rings. Importantly, several of these compounds exhibit useful anticancer, anti-inflammatory, and antibiotic properties. However, linear triquinanes pose significant challenges to organic synthesis because of the structural and stereochemical complexity of their hydrocarbon skeletons. To illuminate nature’s solution to the generation of linear triquinanes, we now describe the crystal structure of Streptomyces clavuligerus cucumene synthase. This sesquiterpene cyclase catalyzes the stereospecific cyclization of farnesyl diphosphate to form a linear triquinane product, (5S,7S,10R,11S)-cucumene. Specifically, we report the structure of the wild-type enzyme at 3.05 Å resolution and the structure of the T181N variant at 1.96 Å resolution, both in the open active site conformations without any bound ligands. The high-resolution structure of T181N cucumene synthase enables inspection of the active site contour, which adopts a three-dimensional shape complementary to a linear triquinane. Several aromatic residues outline the active site contour and are believed to facilitate cation–π interactions that would stabilize carbocation intermediates in catalysis. Furthermore, aromatic residues in the active site not only define the template for catalysis but also play a role in reducing activation barriers in the multistep cyclization cascade.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Inst. of Health; Northeastern Collaborative Access Team; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

Grant/Contract Number:: AC02-06CH11357; SC0012704

OSTI ID:: 1483892

Alternate ID(s):: OSTI ID: 1688469

Journal Information:: Biochemistry, Journal Name: Biochemistry Journal Issue: 44 Vol. 57; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (58)

Transannular Radical Cascade as an Approach to the Diastereoselective Synthesis of Linear Triquinane Dhimane, Anne-Lise; A��ssa, Christophe; Malacria, Max Angewandte Chemie International Edition, Vol. 41, Issue 17 https://doi.org/10.1002/1521-3773(20020902)41:17<3284::AID-ANIE3284>3.0.CO;2-Z	journal	September 2002
Induced-Fit Mechanism in Class I Terpene Cyclases Baer, Philipp; Rabe, Patrick; Fischer, Katrin Angewandte Chemie International Edition, Vol. 53, Issue 29 https://doi.org/10.1002/anie.201403648	journal	May 2014
An Unusual Ring-Contraction/Rearrangement Sequence for Making Functionalized Di- and Triquinanes Nagaraju, Chinta; Prasad, Kavirayani R. Angewandte Chemie International Edition, Vol. 53, Issue 41 https://doi.org/10.1002/anie.201407680	journal	August 2014
Hedycaryol Synthase in Complex with Nerolidol Reveals Terpene Cyclase Mechanism Baer, Philipp; Rabe, Patrick; Citron, Christian A. ChemBioChem, Vol. 15, Issue 2 https://doi.org/10.1002/cbic.201300708	journal	January 2014
Aristolochene Synthase: Purification, Molecular Cloning, High-Level Expression in Escherichia coli, and Characterization of the Aspergillus terreus Cyclase Cane, David E.; Kang, Ilgu Archives of Biochemistry and Biophysics, Vol. 376, Issue 2 https://doi.org/10.1006/abbi.2000.1734	journal	April 2000
Isolation, structure and synthesis of hirsutene, a precursor hydrocarbon of coriolin biosynthesis Nozoe, Shigeo; Furukawa, Jun; Sankawa, Ushio Tetrahedron Letters, Vol. 17, Issue 3 https://doi.org/10.1016/0040-4039(76)80013-5	journal	January 1976
Elucidation of the deficiency in two yeast coenzyme Q mutants. Characterization of the structural gene encoding hexaprenyl pyrophosphate synthetase. Ashby, M. N.; Edwards, P. A. Journal of Biological Chemistry, Vol. 265, Issue 22 https://doi.org/10.1016/S0021-9258(19)38280-8	journal	August 1990
COQ2 is a candidate for the structural gene encoding para-hydroxybenzoate:polyprenyltransferase. Ashby, M. N.; Kutsunai, S. Y.; Ackerman, S. Journal of Biological Chemistry, Vol. 267, Issue 6 https://doi.org/10.1016/S0021-9258(19)50638-X	journal	February 1992
The capnellenes revisited: New structures and new biological activity Morris, Linda A.; Jaspars, Marcel; Adamson, Katy Tetrahedron, Vol. 54, Issue 42 https://doi.org/10.1016/S0040-4020(98)00784-4	journal	October 1998
Unearthing the roots of the terpenome Christianson, David W. Current Opinion in Chemical Biology, Vol. 12, Issue 2 https://doi.org/10.1016/j.cbpa.2007.12.008	journal	April 2008
Terpene synthases and the regulation, diversity and biological roles of terpene metabolism Tholl, Dorothea Current Opinion in Plant Biology, Vol. 9, Issue 3 https://doi.org/10.1016/j.pbi.2006.03.014	journal	June 2006
Multi-domain terpenoid cyclase architecture and prospects for proximity in bifunctional catalysis Chen, Mengbin; Harris, Golda G.; Pemberton, Travis A. Current Opinion in Structural Biology, Vol. 41 https://doi.org/10.1016/j.sbi.2016.05.010	journal	December 2016
Terpenoid Synthases—From Chemical Ecology and Forest Fires to Biofuels and Bioproducts Bohlmann, Joerg Structure, Vol. 19, Issue 12 https://doi.org/10.1016/j.str.2011.11.009	journal	December 2011
Substitution of Aromatic Residues with Polar Residues in the Active Site Pocket of epi -Isozizaene Synthase Leads to the Generation of New Cyclic Sesquiterpenes Blank, Patrick N.; Barrow, Golda H.; Chou, Wayne K. W. Biochemistry, Vol. 56, Issue 43 https://doi.org/10.1021/acs.biochem.7b00895	journal	October 2017
Structural and Chemical Biology of Terpenoid Cyclases Christianson, David W. Chemical Reviews, Vol. 117, Issue 17 https://doi.org/10.1021/acs.chemrev.7b00287	journal	August 2017
Delocalization of Charge and Electron Density in the Humulyl Cation—Implications for Terpene Biosynthesis Hamlin, Trevor A.; Hamann, Christian S.; Tantillo, Dean J. The Journal of Organic Chemistry, Vol. 80, Issue 8 https://doi.org/10.1021/acs.joc.5b00381	journal	April 2015
Tension between Internal and External Modes of Stabilization in Carbocations Relevant to Terpene Biosynthesis: Modulating Minima Depth via C–H···π Interactions Hong, Young J.; Tantillo, Dean J. Organic Letters, Vol. 17, Issue 21 https://doi.org/10.1021/acs.orglett.5b02740	journal	October 2015
Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase Dixit, Mudit; Weitman, Michal; Gao, Jiali ACS Catalysis, Vol. 7, Issue 1 https://doi.org/10.1021/acscatal.6b02584	journal	December 2016
Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases—Bornyl Diphosphate Synthase As a Representative Case O’Brien, Terrence E.; Bertolani, Steven J.; Zhang, Yue ACS Catalysis, Vol. 8, Issue 4 https://doi.org/10.1021/acscatal.8b00342	journal	March 2018
Exploration and Mining of the Bacterial Terpenome Cane, David E.; Ikeda, Haruo Accounts of Chemical Research, Vol. 45, Issue 3 https://doi.org/10.1021/ar200198d	journal	October 2011
Pentalenene Synthase. Purification, Molecular Cloning, Sequencing, and High-Level Expression in Escherichia coli of a Terpenoid Cyclase from Streptomyces UC5319 Cane, David E.; Sohng, Jae-Kyung; Lamberson, Carol R. Biochemistry, Vol. 33, Issue 19 https://doi.org/10.1021/bi00185a024	journal	May 1994
X-ray Crystal Structure of Aristolochene Synthase from Aspergillus terreus and Evolution of Templates for the Cyclization of Farnesyl Diphosphate ^† ^, ^‡ Shishova, Ekaterina Y.; Di Costanzo, Luigi; Cane, David E. Biochemistry, Vol. 46, Issue 7 https://doi.org/10.1021/bi0622524	journal	February 2007
Mechanistic Insights from the Binding of Substrate and Carbocation Intermediate Analogues to Aristolochene Synthase Chen, Mengbin; Al-lami, Naeemah; Janvier, Marine Biochemistry, Vol. 52, Issue 32 https://doi.org/10.1021/bi400691v	journal	July 2013
Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi -Isozizaene Synthase Li, Ruiqiong; Chou, Wayne K. W.; Himmelberger, Julie A. Biochemistry, Vol. 53, Issue 7 https://doi.org/10.1021/bi401643u	journal	February 2014
Structure of Epi-Isozizaene Synthase from Streptomyces coelicolor A3(2), a Platform for New Terpenoid Cyclization Templates ^, Aaron, Julie A.; Lin, Xin; Cane, David E. Biochemistry, Vol. 49, Issue 8 https://doi.org/10.1021/bi902088z	journal	March 2010
Enzymic formation of sesquiterpenes Cane, David E. Chemical Reviews, Vol. 90, Issue 7 https://doi.org/10.1021/cr00105a002	journal	November 1990
Structural Biology and Chemistry of the Terpenoid Cyclases Christianson, David W. Chemical Reviews, Vol. 106, Issue 8 https://doi.org/10.1021/cr050286w	journal	August 2006
Tandem radical approach to linear condensed cyclopentanoids. Total synthesis of (.+-.)-hirsutene Curran, Dennis P.; Rakiewicz, Donna M. Journal of the American Chemical Society, Vol. 107, Issue 5 https://doi.org/10.1021/ja00291a077	journal	March 1985
Theoretical Studies on Farnesyl Cation Cyclization: Pathways to Pentalenene Gutta, Pradeep; Tantillo, Dean J. Journal of the American Chemical Society, Vol. 128, Issue 18 https://doi.org/10.1021/ja058031n	journal	May 2006
Effect of Isotopically Sensitive Branching on Product Distribution for Pentalenene Synthase: Support for a Mechanism Predicted by Quantum Chemistry Zu, Liansuo; Xu, Meimei; Lodewyk, Michael W. Journal of the American Chemical Society, Vol. 134, Issue 28 https://doi.org/10.1021/ja3043245	journal	July 2012
Tandem Rh(I)-Catalyzed [(5+2)+1] Cycloaddition/Aldol Reaction for the Construction of Linear Triquinane Skeleton: Total Syntheses of (±)-Hirsutene and (±)-1-Desoxyhypnophilin Jiao, Lei; Yuan, Changxia; Yu, Zhi-Xiang Journal of the American Chemical Society, Vol. 130, Issue 13 https://doi.org/10.1021/ja7100449	journal	April 2008
Formal Homoiodo Allylsilane Annulations: Dual Total Syntheses of (±)-Hirsutene and (±)-Capnellene Shen, Shou-Jie; Li, Wei-Dong Z. The Journal of Organic Chemistry, Vol. 78, Issue 14 https://doi.org/10.1021/jo4009854	journal	July 2013
Total Synthesis of (−)-Coriolin Mizuno, Hajime; Domon, Kei; Masuya, Keiichi The Journal of Organic Chemistry, Vol. 64, Issue 8 https://doi.org/10.1021/jo981478c	journal	March 1999
Three-Component Coupling via the Squarate Ester Cascade as a Concise Route to the Bioactive Triquinane Sesquiterpene Hypnophilin Geng, Feng; Liu, Jian; Paquette, Leo A. Organic Letters, Vol. 4, Issue 1 https://doi.org/10.1021/ol0102388	journal	January 2002
Evolving biosynthetic tangos negotiate mechanistic landscapes Austin, Michael B.; O'Maille, Paul E.; Noel, Joseph P. Nature Chemical Biology, Vol. 4, Issue 4 https://doi.org/10.1038/nchembio0408-217	journal	April 2008
Sesquiterpene synthases: Passive catalysts or active players? Miller, David J.; Allemann, Rudolf K. Nat. Prod. Rep., Vol. 29, Issue 1 https://doi.org/10.1039/C1NP00060H	journal	January 2012
Pentalenene formation mechanisms redux Lodewyk, Michael W.; Willenbring, Dan; Tantillo, Dean J. Org. Biomol. Chem., Vol. 12, Issue 6 https://doi.org/10.1039/C3OB42005A	journal	January 2014
Traversing the fungal terpenome Quin, Maureen B.; Flynn, Christopher M.; Schmidt-Dannert, Claudia Nat. Prod. Rep., Vol. 31, Issue 10 https://doi.org/10.1039/C4NP00075G	journal	January 2014
Terpenoid synthase structures: a so far incomplete view of complex catalysis Gao, Yang; Honzatko, Richard B.; Peters, Reuben J. Natural Product Reports, Vol. 29, Issue 10 https://doi.org/10.1039/c2np20059g	journal	January 2012
C–H⋯π interactions as modulators of carbocation structure – implications for terpene biosynthesis Hong, Young J.; Tantillo, Dean J. Chemical Science, Vol. 4, Issue 6 https://doi.org/10.1039/c3sc50571e	journal	January 2013
Predicting pathways for terpene formation from first principles – routes to known and new sesquiterpenes Isegawa, Miho; Maeda, Satoshi; Tantillo, Dean J. Chemical Science, Vol. 5, Issue 4 https://doi.org/10.1039/c3sc53293c	journal	January 2014
Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus Chow, Jeng-Yeong; Tian, Bo-Xue; Ramamoorthy, Gurusankar Proceedings of the National Academy of Sciences, Vol. 112, Issue 18 https://doi.org/10.1073/pnas.1505127112	journal	April 2015
Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade Rynkiewicz, M. J.; Cane, D. E.; Christianson, D. W. Proceedings of the National Academy of Sciences, Vol. 98, Issue 24 https://doi.org/10.1073/pnas.231313098	journal	November 2001
Crystal Structure of Human Squalene Synthase: A KEY ENZYME IN CHOLESTEROL BIOSYNTHESIS Pandit, Jayvardhan; Danley, Dennis E.; Schulte, Gayle K. Journal of Biological Chemistry, Vol. 275, Issue 39 https://doi.org/10.1074/jbc.M004132200	journal	July 2000
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Capnellene, a natural marine compound derived from soft coral, attenuates chronic constriction injury-induced neuropathic pain in rats: The effects of capnellene on neuropathy Jean, Yen-Hsuan; Chen, Wu-Fu; Sung, Chun-Sung British Journal of Pharmacology, Vol. 158, Issue 3 https://doi.org/10.1111/j.1476-5381.2009.00323.x	journal	August 2009
Crystal Structure of Pentalenene Synthase: Mechanistic Insights on Terpenoid Cyclization Reactions in Biology Lesburg, C. A. Science, Vol. 277, Issue 5333 https://doi.org/10.1126/science.277.5333.1820	journal	September 1997
Trinuclear metal clusters in catalysis by terpenoid synthases Aaron, Julie A.; Christianson, David W. Pure and Applied Chemistry, Vol. 82, Issue 8 https://doi.org/10.1351/PAC-CON-09-09-37	journal	May 2010
Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1 Huang, Hua; Levin, Elena J.; Liu, Shian PLoS Biology, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pbio.1001911	journal	July 2014
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach Tian, Bo-Xue; Wallrapp, Frank H.; Holiday, Gemma L. PLoS Computational Biology, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pcbi.1003874	journal	October 2014
Additional New Cytotoxic Triquinane-Type Sesquiterpenoids Chondrosterins K–M from the Marine Fungus Chondrostereum sp. Huang, Lei; Lan, Wen-Jian; Deng, Rong Marine Drugs, Vol. 14, Issue 9 https://doi.org/10.3390/md14090157	journal	August 2016
Coriolin, a new Basidiomycetes Antibiotic Takeuchi, Tomio; Iinuma, Hironobu; Iwanaga, Junko The Journal of Antibiotics, Vol. 22, Issue 5 https://doi.org/10.7164/antibiotics.22.215	journal	January 1969
Antimicrobial metabolites from Lentinus crinitus. Abate, Dawit; Abraham, Wolf-Rainer The Journal of Antibiotics, Vol. 47, Issue 11 https://doi.org/10.7164/antibiotics.47.1348	journal	January 1994

Cited By (2)

Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis Zeng, Haichun; Yin, Guoping; Wei, Qian Angewandte Chemie, Vol. 131, Issue 20 https://doi.org/10.1002/ange.201813722	journal	April 2019
Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis Zeng, Haichun; Yin, Guoping; Wei, Qian Angewandte Chemie International Edition, Vol. 58, Issue 20 https://doi.org/10.1002/anie.201813722	journal	May 2019

Similar Records

Structure of Epi-Isozizaene Synthase from Streptomyces coelicolor A3(2), a Platform for New Terpenoid Cyclization Templates

Journal Article · Mon Jun 21 00:00:00 EDT 2010 · Biochemistry-US · OSTI ID:1002341

Substitution of Aromatic Residues with Polar Residues in the Active Site Pocket of epi-Isozizaene Synthase Leads to the Generation of New Cyclic Sesquiterpenes

Journal Article · Sun Oct 01 20:00:00 EDT 2017 · Biochemistry · OSTI ID:1426288

Crystal structure of F95Q epi-isozizaene synthase, an engineered sesquiterpene cyclase that generates biofuel precursors β- and γ-curcumene

Journal Article · Tue May 28 20:00:00 EDT 2019 · Journal of Structural Biology · OSTI ID:1544844

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
anions
chemical structure
conformation
hydrocarbons
monomers

Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene

Citation Formats

References (58)

Cited By (2)

Similar Records

Related Subjects