Structural insight on assembly-line catalysis in terpene biosynthesis

Faylo, Jacque L.; van Eeuwen, Trevor; Kim, Hee Jong; Gorbea Colón, Jose J.; Garcia, Benjamin A.; Murakami, Kenji; Christianson, David W.

doi:10.1038/s41467-021-23589-9

Title: Structural insight on assembly-line catalysis in terpene biosynthesis

Journal Article · Wed Jun 09 00:00:00 EDT 2021 · Nature Communications

DOI:https://doi.org/10.1038/s41467-021-23589-9· OSTI ID:1816540

Faylo, Jacque L. ^[1];

^[2]; Kim, Hee Jong ^[2];

^[2]; Garcia, Benjamin A. ^[3];

^[3];

^[1]

Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Chemistry. Roy and Diana Vagelos Labs.
Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine. Dept. of Biochemistry and Biophysics; Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine. Biochemistry and Molecular Biophysics Graduate Group
Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine. Dept. of Biochemistry and Biophysics

Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene.

View Accepted Manuscript (DOE)

Cite

Export

Save

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF); National Cancer Institute (NCI)

Grant/Contract Number:: AC05-76RL01830; GM56838; GM123233; AI118891; CA196539; T32-GM008275; T32-GM071339; DGE-1845298; U24GM129547; HSSN261200800001E; S10OD023592; R01-GM129325

OSTI ID:: 1816540

Journal Information:: Nature Communications, Vol. 12, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (53)

Channeling of Substrates and Intermediates in Enzyme-Catalyzed Reactions Huang, Xinyi; Holden, Hazel M.; Raushel, Frank M. Annual Review of Biochemistry, Vol. 70, Issue 1 https://doi.org/10.1146/annurev.biochem.70.1.149	journal	June 2001
GraFix: sample preparation for single-particle electron cryomicroscopy Kastner, Berthold; Fischer, Niels; Golas, Monika Mariola Nature Methods, Vol. 5, Issue 1 https://doi.org/10.1038/nmeth1139	journal	December 2007
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues Das, R. K.; Pappu, R. V. Proceedings of the National Academy of Sciences, Vol. 110, Issue 33 https://doi.org/10.1073/pnas.1304749110	journal	July 2013
Simplified Protocol for Cross-linking Mass Spectrometry Using the MS-Cleavable Cross-linker DSBU with Efficient Cross-link Identification Pan, Dongqing; Brockmeyer, Andreas; Mueller, Franziska Analytical Chemistry, Vol. 90, Issue 18 https://doi.org/10.1021/acs.analchem.8b02593	journal	August 2018
Higher-order oligomerization of a chimeric αβγ bifunctional diterpene synthase with prenyltransferase and class II cyclase activities is concentration-dependent Ronnebaum, Trey A.; Gupta, Kushol; Christianson, David W. Journal of Structural Biology, Vol. 210, Issue 1 https://doi.org/10.1016/j.jsb.2020.107463	journal	April 2020
The PRIDE database and related tools and resources in 2019: improving support for quantification data Perez-Riverol, Yasset; Csordas, Attila; Bai, Jingwen Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1106	journal	November 2018
Structure of and kinetic channelling in bifunctional dihydrofolate reductase–thymidylate synthase Knighton, Daniel R.; Kan, Chen-Chen; Howland, Eleanor Nature Structural Biology, Vol. 1, Issue 3 https://doi.org/10.1038/nsb0394-186	journal	March 1994
Dynamic Metabolons Moller, B. L. Science, Vol. 330, Issue 6009 https://doi.org/10.1126/science.1194971	journal	December 2010
Fusion of farnesyldiphosphate synthase and epi -aristolochene synthase, a sesquiterpene cyclase involved in capsidiol biosynthesis in Nicotiana tabacum : Fusions of FPPS and Brodelius, Maria; Lundgren, Anneli; Mercke, Per European Journal of Biochemistry, Vol. 269, Issue 14 https://doi.org/10.1046/j.1432-1033.2002.03044.x	journal	July 2002
Cooperativity in monomeric enzymes with single ligand-binding sites Porter, Carol M.; Miller, Brian G. Bioorganic Chemistry, Vol. 43 https://doi.org/10.1016/j.bioorg.2011.11.001	journal	August 2012
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
Substrate channeling between the human dihydrofolate reductase and thymidylate synthase: Substrate Channeling Between the Human DHFR and TS Wang, Nuo; McCammon, J. Andrew Protein Science, Vol. 25, Issue 1 https://doi.org/10.1002/pro.2720	journal	June 2015
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
Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase Chen, Mengbin; Chou, Wayne K. W.; Toyomasu, Tomonobu ACS Chemical Biology, Vol. 11, Issue 4 https://doi.org/10.1021/acschembio.5b00960	journal	January 2016
CTFFIND4: Fast and accurate defocus estimation from electron micrographs Rohou, Alexis; Grigorieff, Nikolaus Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.008	journal	November 2015
Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy Naydenova, Katerina; Russo, Christopher J. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00782-3	journal	September 2017
Fusicoccanes: diterpenes with surprising biological functions de Boer, Albertus H.; Leeuwen, Ingrid J. de Vries-van Trends in Plant Science, Vol. 17, Issue 6 https://doi.org/10.1016/j.tplants.2012.02.007	journal	June 2012
New tools for automated high-resolution cryo-EM structure determination in RELION-3 Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O. eLife, Vol. 7 https://doi.org/10.7554/eLife.42166	journal	November 2018
Releasing the potential power of terpene synthases by a robust precursor supply platform Bian, Guangkai; Han, Yichao; Hou, Anwei Metabolic Engineering, Vol. 42 https://doi.org/10.1016/j.ymben.2017.04.006	journal	July 2017
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4193	journal	February 2017
Enzyme clustering accelerates processing of intermediates through metabolic channeling Castellana, Michele; Wilson, Maxwell Z.; Xu, Yifan Nature Biotechnology, Vol. 32, Issue 10 https://doi.org/10.1038/nbt.3018	journal	September 2014
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Identification of Chimeric αβγ Diterpene Synthases Possessing both Type II Terpene Cyclase and Prenyltransferase Activities Mitsuhashi, Takaaki; Okada, Masahiro; Abe, Ikuro ChemBioChem, Vol. 18, Issue 21 https://doi.org/10.1002/cbic.201700445	journal	September 2017
Analysis of Interactions Stabilized by Fusicoccin A Reveals an Expanded Suite of Potential 14–3–3 Binding Partners Sengupta, Ananya; Liriano, Josue; Miller, Brian G. ACS Chemical Biology, Vol. 15, Issue 2 https://doi.org/10.1021/acschembio.9b00795	journal	January 2020
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
An electrostatic highway Stroud, Robert M. Nature Structural Biology, Vol. 1, Issue 3 https://doi.org/10.1038/nsb0394-131	journal	March 1994
Small-Molecule Stabilization of 14-3-3 Protein-Protein Interactions Stimulates Axon Regeneration Kaplan, Andrew; Morquette, Barbara; Kroner, Antje Neuron, Vol. 93, Issue 5 https://doi.org/10.1016/j.neuron.2017.02.018	journal	March 2017
Substrate channelling as an approach to cascade reactions Wheeldon, Ian; Minteer, Shelley D.; Banta, Scott Nature Chemistry, Vol. 8, Issue 4 https://doi.org/10.1038/nchem.2459	journal	March 2016
The Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Reveals a Novel Hexameric Arrangement and Inhibitory Product Binding Kavanagh, Kathryn L.; Dunford, James E.; Bunkoczi, Gabor Journal of Biological Chemistry, Vol. 281, Issue 31 https://doi.org/10.1074/jbc.M602603200	journal	August 2006
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
Stabilization and Inhibition of Protein–Protein Interactions: The 14-3-3 Case Study Milroy, Lech-Gustav; Brunsveld, Luc; Ottmann, Christian ACS Chemical Biology, Vol. 8, Issue 1 https://doi.org/10.1021/cb300599t	journal	December 2012
EMAN2: An extensible image processing suite for electron microscopy Tang, Guang; Peng, Liwei; Baldwin, Philip R. Journal of Structural Biology, Vol. 157, Issue 1 https://doi.org/10.1016/j.jsb.2006.05.009	journal	January 2007
Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics Bauler, Patricia; Huber, Gary; Leyh, Thomas The Journal of Physical Chemistry Letters, Vol. 1, Issue 9 https://doi.org/10.1021/jz1002007	journal	April 2010
The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation Sweetlove, Lee J.; Fernie, Alisdair R. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04543-8	journal	May 2018
Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data Sheng, Quanhu; Li, Rongxia; Dai, Jie Molecular & Cellular Proteomics, Vol. 14, Issue 2 https://doi.org/10.1074/mcp.O114.041376	journal	February 2015
The Molecular Basis of Substrate Channeling Miles, Edith Wilson; Rhee, Sangkee; Davies, David R. Journal of Biological Chemistry, Vol. 274, Issue 18 https://doi.org/10.1074/jbc.274.18.12193	journal	April 1999
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
Integrative structure modeling with the Integrative Modeling Platform: Integrative Structure Modeling with IMP Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3311	journal	October 2017
Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis Götze, Michael; Pettelkau, Jens; Fritzsche, Romy Journal of The American Society for Mass Spectrometry, Vol. 26, Issue 1 https://doi.org/10.1007/s13361-014-1001-1	journal	September 2014
Complexes of Sequential Metabolic Enzymes Srere, Paul A. Annual Review of Biochemistry, Vol. 56, Issue 1 https://doi.org/10.1146/annurev.bi.56.070187.000513	journal	June 1987
Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases Pemberton, Travis A.; Chen, Mengbin; Harris, Golda G. Biochemistry, Vol. 56, Issue 14 https://doi.org/10.1021/acs.biochem.7b00137	journal	March 2017
Glutaraldehyde: behavior in aqueous solution, reaction with proteins, and application to enzyme crosslinking Migneault, Isabelle; Dartiguenave, Catherine; Bertrand, Michel J. BioTechniques, Vol. 37, Issue 5 https://doi.org/10.2144/04375RV01	journal	November 2004
CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins Holehouse, Alex S.; Das, Rahul K.; Ahad, James N. Biophysical Journal, Vol. 112, Issue 1 https://doi.org/10.1016/j.bpj.2016.11.3200	journal	January 2017
Fusicoccins are biosynthesized by an unusual chimera diterpene synthase in fungi Toyomasu, T.; Tsukahara, M.; Kaneko, A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 9 https://doi.org/10.1073/pnas.0608426104	journal	February 2007
Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering Helfrich, Eric J. N.; Lin, Geng-Min; Voigt, Christopher A. Beilstein Journal of Organic Chemistry, Vol. 15 https://doi.org/10.3762/bjoc.15.283	journal	January 2019
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Punjani, Ali; Rubinstein, John L.; Fleet, David J. Nature Methods, Vol. 14, Issue 3 https://doi.org/10.1038/nmeth.4169	journal	February 2017
Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures Viswanath, Shruthi; Chemmama, Ilan E.; Cimermancic, Peter Biophysical Journal, Vol. 113, Issue 11 https://doi.org/10.1016/j.bpj.2017.10.005	journal	December 2017
A model study of sequential enzyme reactions and electrostatic channeling Eun, Changsun; Kekenes-Huskey, Peter M.; Metzger, Vincent T. The Journal of Chemical Physics, Vol. 140, Issue 10 https://doi.org/10.1063/1.4867286	journal	March 2014
Structural Insight on Assembly-Line Catalysis in Terpene Biosynthesis Faylo, Jacque L.; van Eeuwen, Trevor; Kim, Hee Jong Zenodo https://doi.org/10.5281/zenodo.4709849	text	January 2021
Software tools for automated transmission electron microscopy Schorb, Martin; Haberbosch, Isabella; Hagen, Wim J. H. Nature Methods, Vol. 16, Issue 6 https://doi.org/10.1038/s41592-019-0396-9	journal	May 2019
Sampling the conformational space of the catalytic subunit of human γ-secretase Bai, Xiao-chen; Rajendra, Eeson; Yang, Guanghui eLife, Vol. 4 https://doi.org/10.7554/eLife.11182	journal	December 2015
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
Human Geranylgeranyl Diphosphate Synthase Kuzuguchi, Tsuyoshi; Morita, Yuiko; Sagami, Ikuko Journal of Biological Chemistry, Vol. 274, Issue 9 https://doi.org/10.1074/jbc.274.9.5888	journal	February 1999

Similar Records

Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase

Journal Article · Wed Jan 06 00:00:00 EST 2016 · ACS Chemical Biology · OSTI ID:1816540

Chen, Mengbin; Chou, Wayne K. W.; Toyomasu, Tomonobu; +2 more

Taxadiene Synthase Structure and Evolution of Modular Architecture in Terpene Biosynthesis

Journal Article · Sat Dec 31 00:00:00 EST 2011 · Nature · OSTI ID:1816540

Köksal, M; Jin, Y; Coates, R; +2 more

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 · Mon Oct 02 00:00:00 EDT 2017 · Biochemistry · OSTI ID:1816540

Blank, Patrick N.; Barrow, Golda H.; Chou, Wayne K. W.; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
cryoelectron microscopy
enzyme mechanisms
multienzyme complexes

Title: Structural insight on assembly-line catalysis in terpene biosynthesis

Citation Formats

References (53)

Similar Records

Related Subjects