Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene
Abstract
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.
- Authors:
-
- Univ. of Pennsylvania, Philadelphia, PA (United States)
- Univ. of Utah, Salt Lake City, UT (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); Northeastern Collaborative Access Team; National Inst. of Health
- OSTI Identifier:
- 1483892
- Grant/Contract Number:
- AC02-06CH11357; SC0012704; P1 GM103403; S10 RR02905
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Biochemistry
- Additional Journal Information:
- Journal Volume: 57; Journal Issue: 44; Journal ID: ISSN 0006-2960
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; hydrocarbons; anions; monomers; chemical structure; conformation
Citation Formats
Blank, Patrick N., Pemberton, Travis A., Chow, Jeng-Yeong, Poulter, C. Dale, and Christianson, David W. Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene. United States: N. p., 2018.
Web. doi:10.1021/acs.biochem.8b00899.
Blank, Patrick N., Pemberton, Travis A., Chow, Jeng-Yeong, Poulter, C. Dale, & Christianson, David W. Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene. United States. https://doi.org/10.1021/acs.biochem.8b00899
Blank, Patrick N., Pemberton, Travis A., Chow, Jeng-Yeong, Poulter, C. Dale, and Christianson, David W. 2018.
"Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene". United States. https://doi.org/10.1021/acs.biochem.8b00899. https://www.osti.gov/servlets/purl/1483892.
@article{osti_1483892,
title = {Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene},
author = {Blank, Patrick N. and Pemberton, Travis A. and Chow, Jeng-Yeong and Poulter, C. Dale and Christianson, David W.},
abstractNote = {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.},
doi = {10.1021/acs.biochem.8b00899},
url = {https://www.osti.gov/biblio/1483892},
journal = {Biochemistry},
issn = {0006-2960},
number = 44,
volume = 57,
place = {United States},
year = {Mon Oct 22 00:00:00 EDT 2018},
month = {Mon Oct 22 00:00:00 EDT 2018}
}
Web of Science
Works referenced in this record:
Crystal Structure of Pentalenene Synthase: Mechanistic Insights on Terpenoid Cyclization Reactions in Biology
journal, September 1997
- Lesburg, C. A.
- Science, Vol. 277, Issue 5333
Tension between Internal and External Modes of Stabilization in Carbocations Relevant to Terpene Biosynthesis: Modulating Minima Depth via C–H···π Interactions
journal, October 2015
- Hong, Young J.; Tantillo, Dean J.
- Organic Letters, Vol. 17, Issue 21
X-ray Crystal Structure of Aristolochene Synthase from Aspergillus terreus and Evolution of Templates for the Cyclization of Farnesyl Diphosphate † , ‡
journal, February 2007
- Shishova, Ekaterina Y.; Di Costanzo, Luigi; Cane, David E.
- Biochemistry, Vol. 46, Issue 7
Crystal Structure of Human Squalene Synthase: A KEY ENZYME IN CHOLESTEROL BIOSYNTHESIS
journal, July 2000
- Pandit, Jayvardhan; Danley, Dennis E.; Schulte, Gayle K.
- Journal of Biological Chemistry, Vol. 275, Issue 39
Antimicrobial metabolites from Lentinus crinitus.
journal, January 1994
- Abate, Dawit; Abraham, Wolf-Rainer
- The Journal of Antibiotics, Vol. 47, Issue 11
Isolation, structure and synthesis of hirsutene, a precursor hydrocarbon of coriolin biosynthesis
journal, January 1976
- Nozoe, Shigeo; Furukawa, Jun; Sankawa, Ushio
- Tetrahedron Letters, Vol. 17, Issue 3
Pentalenene Synthase. Purification, Molecular Cloning, Sequencing, and High-Level Expression in Escherichia coli of a Terpenoid Cyclase from Streptomyces UC5319
journal, May 1994
- Cane, David E.; Sohng, Jae-Kyung; Lamberson, Carol R.
- Biochemistry, Vol. 33, Issue 19
Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi -Isozizaene Synthase
journal, February 2014
- Li, Ruiqiong; Chou, Wayne K. W.; Himmelberger, Julie A.
- Biochemistry, Vol. 53, Issue 7
Capnellene, a natural marine compound derived from soft coral, attenuates chronic constriction injury-induced neuropathic pain in rats: The effects of capnellene on neuropathy
journal, August 2009
- Jean, Yen-Hsuan; Chen, Wu-Fu; Sung, Chun-Sung
- British Journal of Pharmacology, Vol. 158, Issue 3
Terpene synthases and the regulation, diversity and biological roles of terpene metabolism
journal, June 2006
- Tholl, Dorothea
- Current Opinion in Plant Biology, Vol. 9, Issue 3
Formal Homoiodo Allylsilane Annulations: Dual Total Syntheses of (±)-Hirsutene and (±)-Capnellene
journal, July 2013
- Shen, Shou-Jie; Li, Wei-Dong Z.
- The Journal of Organic Chemistry, Vol. 78, Issue 14
Trinuclear metal clusters in catalysis by terpenoid synthases
journal, May 2010
- Aaron, Julie A.; Christianson, David W.
- Pure and Applied Chemistry, Vol. 82, Issue 8
Structural Biology and Chemistry of the Terpenoid Cyclases
journal, August 2006
- Christianson, David W.
- Chemical Reviews, Vol. 106, Issue 8
Coriolin, a new Basidiomycetes Antibiotic
journal, January 1969
- Takeuchi, Tomio; Iinuma, Hironobu; Iwanaga, Junko
- The Journal of Antibiotics, Vol. 22, Issue 5
How good are my data and what is the resolution?
journal, June 2013
- Evans, Philip R.; Murshudov, Garib N.
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
Transannular Radical Cascade as an Approach to the Diastereoselective Synthesis of Linear Triquinane
journal, September 2002
- Dhimane, Anne-Lise; A��ssa, Christophe; Malacria, Max
- Angewandte Chemie International Edition, Vol. 41, Issue 17
Sesquiterpene synthases: Passive catalysts or active players?
journal, January 2012
- Miller, David J.; Allemann, Rudolf K.
- Nat. Prod. Rep., Vol. 29, Issue 1
Terpenoid synthase structures: a so far incomplete view of complex catalysis
journal, January 2012
- Gao, Yang; Honzatko, Richard B.; Peters, Reuben J.
- Natural Product Reports, Vol. 29, Issue 10
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Additional New Cytotoxic Triquinane-Type Sesquiterpenoids Chondrosterins K–M from the Marine Fungus Chondrostereum sp.
journal, August 2016
- Huang, Lei; Lan, Wen-Jian; Deng, Rong
- Marine Drugs, Vol. 14, Issue 9
Evolving biosynthetic tangos negotiate mechanistic landscapes
journal, April 2008
- Austin, Michael B.; O'Maille, Paul E.; Noel, Joseph P.
- Nature Chemical Biology, Vol. 4, Issue 4
Hedycaryol Synthase in Complex with Nerolidol Reveals Terpene Cyclase Mechanism
journal, January 2014
- Baer, Philipp; Rabe, Patrick; Citron, Christian A.
- ChemBioChem, Vol. 15, Issue 2
Theoretical Studies on Farnesyl Cation Cyclization: Pathways to Pentalenene
journal, May 2006
- Gutta, Pradeep; Tantillo, Dean J.
- Journal of the American Chemical Society, Vol. 128, Issue 18
Unearthing the roots of the terpenome
journal, April 2008
- Christianson, David W.
- Current Opinion in Chemical Biology, Vol. 12, Issue 2
Tandem Rh(I)-Catalyzed [(5+2)+1] Cycloaddition/Aldol Reaction for the Construction of Linear Triquinane Skeleton: Total Syntheses of (±)-Hirsutene and (±)-1-Desoxyhypnophilin
journal, April 2008
- Jiao, Lei; Yuan, Changxia; Yu, Zhi-Xiang
- Journal of the American Chemical Society, Vol. 130, Issue 13
An Unusual Ring-Contraction/Rearrangement Sequence for Making Functionalized Di- and Triquinanes
journal, August 2014
- Nagaraju, Chinta; Prasad, Kavirayani R.
- Angewandte Chemie International Edition, Vol. 53, Issue 41
Pentalenene formation mechanisms redux
journal, January 2014
- Lodewyk, Michael W.; Willenbring, Dan; Tantillo, Dean J.
- Org. Biomol. Chem., Vol. 12, Issue 6
Structural and Chemical Biology of Terpenoid Cyclases
journal, August 2017
- Christianson, David W.
- Chemical Reviews, Vol. 117, Issue 17
Tandem radical approach to linear condensed cyclopentanoids. Total synthesis of (.+-.)-hirsutene
journal, March 1985
- Curran, Dennis P.; Rakiewicz, Donna M.
- Journal of the American Chemical Society, Vol. 107, Issue 5
Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus
journal, April 2015
- Chow, Jeng-Yeong; Tian, Bo-Xue; Ramamoorthy, Gurusankar
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 18
Aristolochene Synthase: Purification, Molecular Cloning, High-Level Expression in Escherichia coli, and Characterization of the Aspergillus terreus Cyclase
journal, April 2000
- Cane, David E.; Kang, Ilgu
- Archives of Biochemistry and Biophysics, Vol. 376, Issue 2
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1
journal, July 2014
- Huang, Hua; Levin, Elena J.; Liu, Shian
- PLoS Biology, Vol. 12, Issue 7
The capnellenes revisited: New structures and new biological activity
journal, October 1998
- Morris, Linda A.; Jaspars, Marcel; Adamson, Katy
- Tetrahedron, Vol. 54, Issue 42
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Effect of Isotopically Sensitive Branching on Product Distribution for Pentalenene Synthase: Support for a Mechanism Predicted by Quantum Chemistry
journal, July 2012
- Zu, Liansuo; Xu, Meimei; Lodewyk, Michael W.
- Journal of the American Chemical Society, Vol. 134, Issue 28
Enzymic formation of sesquiterpenes
journal, November 1990
- Cane, David E.
- Chemical Reviews, Vol. 90, Issue 7
Multi-domain terpenoid cyclase architecture and prospects for proximity in bifunctional catalysis
journal, December 2016
- Chen, Mengbin; Harris, Golda G.; Pemberton, Travis A.
- Current Opinion in Structural Biology, Vol. 41
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Structure of Epi-Isozizaene Synthase from Streptomyces coelicolor A3(2), a Platform for New Terpenoid Cyclization Templates ,
journal, March 2010
- Aaron, Julie A.; Lin, Xin; Cane, David E.
- Biochemistry, Vol. 49, Issue 8
Mechanistic Insights from the Binding of Substrate and Carbocation Intermediate Analogues to Aristolochene Synthase
journal, July 2013
- Chen, Mengbin; Al-lami, Naeemah; Janvier, Marine
- Biochemistry, Vol. 52, Issue 32
Predicting pathways for terpene formation from first principles – routes to known and new sesquiterpenes
journal, January 2014
- Isegawa, Miho; Maeda, Satoshi; Tantillo, Dean J.
- Chemical Science, Vol. 5, Issue 4
Terpenoid Synthases—From Chemical Ecology and Forest Fires to Biofuels and Bioproducts
journal, December 2011
- Bohlmann, Joerg
- Structure, Vol. 19, Issue 12
C–H⋯π interactions as modulators of carbocation structure – implications for terpene biosynthesis
journal, January 2013
- Hong, Young J.; Tantillo, Dean J.
- Chemical Science, Vol. 4, Issue 6
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
journal, October 2014
- Tian, Bo-Xue; Wallrapp, Frank H.; Holiday, Gemma L.
- PLoS Computational Biology, Vol. 10, Issue 10
Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases—Bornyl Diphosphate Synthase As a Representative Case
journal, March 2018
- O’Brien, Terrence E.; Bertolani, Steven J.; Zhang, Yue
- ACS Catalysis, Vol. 8, Issue 4
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, October 2017
- Blank, Patrick N.; Barrow, Golda H.; Chou, Wayne K. W.
- Biochemistry, Vol. 56, Issue 43
Delocalization of Charge and Electron Density in the Humulyl Cation—Implications for Terpene Biosynthesis
journal, April 2015
- Hamlin, Trevor A.; Hamann, Christian S.; Tantillo, Dean J.
- The Journal of Organic Chemistry, Vol. 80, Issue 8
Induced-Fit Mechanism in Class I Terpene Cyclases
journal, May 2014
- Baer, Philipp; Rabe, Patrick; Fischer, Katrin
- Angewandte Chemie International Edition, Vol. 53, Issue 29
Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade
journal, November 2001
- Rynkiewicz, M. J.; Cane, D. E.; Christianson, D. W.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 24
Three-Component Coupling via the Squarate Ester Cascade as a Concise Route to the Bioactive Triquinane Sesquiterpene Hypnophilin
journal, January 2002
- Geng, Feng; Liu, Jian; Paquette, Leo A.
- Organic Letters, Vol. 4, Issue 1
Exploration and Mining of the Bacterial Terpenome
journal, October 2011
- Cane, David E.; Ikeda, Haruo
- Accounts of Chemical Research, Vol. 45, Issue 3
Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase
journal, December 2016
- Dixit, Mudit; Weitman, Michal; Gao, Jiali
- ACS Catalysis, Vol. 7, Issue 1
Total Synthesis of (−)-Coriolin
journal, March 1999
- Mizuno, Hajime; Domon, Kei; Masuya, Keiichi
- The Journal of Organic Chemistry, Vol. 64, Issue 8
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Traversing the fungal terpenome
journal, January 2014
- Quin, Maureen B.; Flynn, Christopher M.; Schmidt-Dannert, Claudia
- Nat. Prod. Rep., Vol. 31, Issue 10
Elucidation of the deficiency in two yeast coenzyme Q mutants. Characterization of the structural gene encoding hexaprenyl pyrophosphate synthetase.
journal, August 1990
- Ashby, M. N.; Edwards, P. A.
- Journal of Biological Chemistry, Vol. 265, Issue 22
COQ2 is a candidate for the structural gene encoding para-hydroxybenzoate:polyprenyltransferase.
journal, February 1992
- Ashby, M. N.; Kutsunai, S. Y.; Ackerman, S.
- Journal of Biological Chemistry, Vol. 267, Issue 6
Works referencing / citing this record:
Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis
journal, May 2019
- Zeng, Haichun; Yin, Guoping; Wei, Qian
- Angewandte Chemie International Edition, Vol. 58, Issue 20
Unprecedented [5.5.5.6]Dioxafenestrane Ring Construction in Fungal Insecticidal Sesquiterpene Biosynthesis
journal, April 2019
- Zeng, Haichun; Yin, Guoping; Wei, Qian
- Angewandte Chemie, Vol. 131, Issue 20