Abstract
Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid–base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid–base activities of phosphate derivatives are comparable to the Brønsted acid–base activities of amino acid side chains.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Cane, D. E. Isoprenoid biosynthesis. Stereochemistry of the cyclization of allylic pyrophosphates. Acc. Chem. Res. 18, 220–226 (1985).
Croteau, R. & Cane, D. E. Monoterpene and sesquiterpene cyclases. Methods Enzymol. 110, 383–405 (1985).
Cane, D. E. Enzymatic formation of sesquiterpenes. Chem. Rev. 90, 1089–1103 (1990).
Allemann, R. K. Chemical wizardry? The generation of diversity in terpenoid biosynthesis. Pure Appl. Chem. 80, 1791–1798 (2008).
Austin, M. B., O’Maille, P. E. & Noel, J. P. Evolving biosynthetic tangos negotiate mechanistic landscapes. Nat. Chem. Biol. 4, 217–222 (2008).
Wendt, K. U. & Schulz, G. E. Isoprenoid biosynthesis: manifold chemistry catalyzed by similar enzymes. Structure 6, 127–133 (1998).
Lesburg, C. A., Caruthers, J. M., Paschall, C. M. & Christianson, D. W. Managing and manipulating carbocations in biology: terpenoid cyclase structure and mechanism. Curr. Opin. Struct. Biol. 8, 695–703 (1998).
Tholl, D. Terpene synthases and the regulation, diversity and biological roles of terpene metabolism. Curr. Opin. Plant Biol. 9, 297–304 (2006).
Christianson, D. W. Structural biology and chemistry of the terpenoid cyclases. Chem. Rev. 106, 3412–3442 (2006).
Christianson, D. W. Unearthing the roots of the terpenome. Curr. Opin. Chem. Biol. 12, 141–150 (2008).
Cane, D. E., Rossi, T., Tillman, A. M. & Pachlatko, J. P. Stereochemical studies of isoprenoid biosynthesis. Biosynthesis of pentalenolactone from [U-13C6]glucose and [6-2H2]glucose. J. Am. Chem. Soc. 103, 1838–1843 (1981).
Cane, D. E. & Tillman, A. M. Pentalenene biosynthesis and the enzymatic cyclization of farnesyl pyrophosphate. J. Am. Chem. Soc. 105, 122–124 (1983).
Cane, D. E. et al. Biosynthesis of pentalenene and pentalenolactone. J. Am. Chem. Soc. 112, 4513–4524 (1990).
Koe, B. K., Sobin, B. A. & Celmer, W. D. PA 132, a new antibiotic. I. Isolation and chemical properties. Antibiot. Annu. 672–675 (1957).
Hartmann, S., Neeff, J., Heer, U. & Mecke, D. Arenaemycin (pentalenolactone): a specific inhibitor of glycolysis. FEBS Lett. 93, 339–342 (1978).
Mann, K. & Mecke, D. Inhibition of spinach glyceraldehyde-3-phosphate dehydrogenases by pentalenolactone. Nature 282, 535–536 (1979).
Cane, D. E., Abell, C. & Tillman, A. M. Pentalenene biosynthesis and the enzymatic cyclization of farnesyl pyrophosphate: proof that the cyclization is catalyzed by a single enzyme. Bioorg. Chem. 12, 312–328 (1984).
Cane, D. E. et al. Pentalenene synthase. Purification, molecular cloning, sequencing, and high-level expression in Escherichia coli of a terpenoid cyclase from Streptomyces UC5319. Biochemistry 33, 5846–5857 (1994).
Lesburg, C. A., Zhai, G., Cane, D. E. & Christianson, D. W. Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology. Science 277, 1820–1824 (1997).
Seemann, M., Zhai, G., Umezawa, K. & Cane, D. Pentalenene Synthase. Histidine-309 is not required for catalytic activity. J. Am. Chem. Soc. 121, 591–592 (1999).
Starks, C. M., Back, K., Chappell, J. & Noel, J. P. Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Science 277, 1815–1820 (1997).
Seemann, M. et al. Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis. J. Am. Chem. Soc. 124, 7681–7689 (2002).
Caruthers, J. M., Kang, I., Rynkiewicz, M. J., Cane, D. E. & Christianson, D. W. Crystal structure determination of aristolochene synthase from the blue cheese mold, Penicillium roqueforti . J. Biol. Chem. 275, 25533–25539 (2000).
Felicetti, B. & Cane, D. E. Aristolochene synthase: mechanistic analysis of active site residues by site-directed mutagenesis. J. Am. Chem. Soc. 126, 7212–7221 (2004).
Shishova, E. Y., Di Costanzo, L., Cane, D. E. & Christianson, D. W. X-ray crystal structure of aristolochene synthase from Aspergillus terreus and evolution of templates for the cyclization of farnesyl diphosphate. Biochemistry 46, 1941–1951 (2007).
Miller, D. J. & Allemann, R. K. Sesquiterpene synthases: passive catalysts or active players? Nat. Prod. Rep. 29, 60–71 (2012).
Faraldos, J. A., Gonzalez, V. & Allemann, R. K. The role of aristolochene synthase in diphosphate activation. Chem. Commun. 48, 3230–3232 (2012).
Köksal, M., Zimmer, I., Schnitzler, J.-P. & Christianson, D. W. Structure of isoprene synthase illuminates the chemical mechanism of teragram atmospheric carbon emission. J. Mol. Biol. 402, 363–373 (2010).
Faraldos, J. A. et al. Probing the mechanism of 1,4-conjugate elimination reactions catalyzed by terpene synthases. J. Am. Chem. Soc. 134, 20844–20848 (2012).
Aaron, J. A. & Christianson, D. W. Trinuclear metal clusters in catalysis by terpenoid synthases. Pure Appl. Chem. 82, 1585–1597 (2010).
Rynkiewicz, M. J., Cane, D. E. & Christianson, D. W. Structure of trichodiene synthase from Fusarium sporotrichiodes provides mechanistic inferences on the terpene cyclization cascade. Proc. Natl Acad. Sci. USA 98, 13543–13548 (2001).
Hosfield, D. J. et al. Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis. J. Biol. Chem. 279, 8526–8529 (2004).
Tarshis, L. C., Yan, M., Poulter, C. D. & Sacchettini, J. C. Crystal structure of recombinant farnesyl diphosphate synthase at 2.6-Å resolution. Biochemistry 33, 10871–10877 (1994).
Chen, M. et al. Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase. Biochemistry 52, 5441–5453 (2013).
Tymoczko, J. L., Berg, J. M. & Stryer, L. Biochemistry: A Short Course, 2nd edn p. A3 (W. H. Freeman and Company, New York, USA, (2013).
Phillips, R. S., Sundararaju, B. & Koushik, S. V. The catalytic mechanism of kynureninase from Pseudomonas fluorescens: evidence for transient quinonoid and ketimine intermediates from rapid-scanning stopped-flow spectrophotometry. Biochemistry 37, 8783–8789 (1998).
Phillips, R. S. & Dua, R. Stereochemistry and mechanism of aldol reactions catalyzed by kynureninase. J. Am. Chem. Soc. 113, 7385–7388 (1991).
Koushik, S. V., Moore, J. A. III, Sundararaju, B. & Phillips, R. S. The catalytic mechanism of kynureninase from Pseudomonas fluorescens: insights from the effects of pH and isotopic substitution on steady-state and pre-steady-state kinetics. Biochemistry 37, 1376–1382 (1998).
Gawandi, V. B., Liskey, D., Lima, S. & Phillips, R. S. Reaction of Pseudomonas fluorescens kynureninase with β-benzoyl-L-alanine: detection of a new reaction intermediate and a change in rate-determining step. Biochemistry 43, 3230–3237 (2004).
Kumar, S., Gawandi, V. B., Capito, N. & Phillips, R. S. Substituent effects on the reaction of β-benzoylalanines with Pseudomonas fluorescens kynureninase. Biochemistry 49, 7913–7919 (2010).
Lima, S., Kumar, S., Gawanadi, B., Momany, C. & Phillips, R. S. Crystal structure of the Homo sapiens kynurenine-3-hydroxyhippuric acid inhibitor complex: Insights into the molecular basis of kynurenine substrate specificity. J. Med. Chem. 52, 389–396 (2009).
Lima, S., Khristoforov, R., Momany, C. & Phillips, R. S. Crystal structure of Homo sapiens kynureninase. Biochemistry 46, 2735–2744 (2007).
Momany, C., Levdikov, V., Blagova, L., Lima, S. & Phillips, R. S. Three-dimensional structure of kynureninase from Pseudomonas fluorescens . Biochemistry 43, 1193–1203 (2004).
Phillips, R. S., Scott, I., Paulose, R., Patel, A. & Barron, T. C. The phosphate of pyridoxal-5’-phosphate is an acid/base catalyst in the mechanism of Pseudomonas fluorescens kynureninase. FEBS J. 281, 1100–1109 (2014).
Phillips, R. S. Structure and mechanism of kynureninase. Arch. Biochem. Biophys. 544, 69–74 (2014).
Phillips, R. S. Chemistry and diversity of pyridoxal-5’-phosphate dependent enzymes. Biochim. Biophys. Acta 1854, 1167–1174 (2015).
Flint, D. H. & Allen, R. M. Iron-sulfur proteins with nonredox functions. Chem. Rev. 96, 2315–2334 (1996).
Hwang, B. Y., Cho, B. K., Yun, K., Koteshwar, K. & Kim, B. G. Revisit of aminotransferases in the genomic era and its application to biocatalysis. J. Mol. Catal. B Enzym. 37, 47–55 (2005).
Urusova, D. V. et al. Crystal Structure of D-serine dehydratase from Escherichia coli . Biochim. Biophys. Acta. 1824, 422–432 (2012).
Yamada, T. et al. Crystal structure of serine dehydratase from rat liver. Biochemistry 42, 12854–12865 (2003).
Johnson, L. N., Hu, S.-H. & Barford, D. Catalytic mechanism of glycogen phosphorylase. Faraday Discuss 93, 131–142 (1992).
Kantrowitz, E. R. Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase. Arch. Biochem. Biophys. 519, 81–90 (2012).
Lipscomb, W. N. & Kantrowitz, E. R. Structure and mechanisms of Escherichia coli aspartate transcarbamoylase. Acc. Chem. Res. 45, 444–453 (2012).
Lipscomb, W. N. Aspartate transcarbamylase from Escherichia coli: activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol. 68, 67–151 (1994).
Krause, K. L., Volz, K. W. & Lipscomb, W. N. 2.5 Å structure of aspartate carbamoyltransferase complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate. J. Mol. Biol. 193, 527–553 (1987).
Gouaux, J. E., Krause, K. L. & Lipscomb, W. N. The catalytic mechanism of Escherichia coli aspartate carbamoyltransferase: a molecular modelling study. Biochem. Biophys. Res. Commun. 142, 893–897 (1987).
Zhou, H., Liao, X & Cook, J. M. Regiospecific, enantiospecific total synthesis of the 12-alkoxy-substituted indole alkaloids, (+)-12-methoxy-N a-methylvellosimine, (+)-12-methoxyaffinisine, and (–)-fuchsiaefoline. Org. Lett. 6, 249–252 (2004).
Maresh, J. J. et al. Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme. J. Am. Chem. Soc. 130, 710–723 (2008).
Seayad, J., Seayad, A. M. & List, B. Catalytic asymmetric Pictet-Spengler reaction. J. Am. Chem. Soc. 128, 1086–1087 (2006).
Holloway, C. A., Muratore, M. E., Storer, R. I. & Dixon, D. J. Direct enantioselective Brønsted acid catalyzed N-acyliminium cyclization cascades of tryptamines and ketoacids. Org. Lett. 12, 4720–4723 (2010).
Overvoorde, L. M., Grayson, M. N., Luo, Y. & Goodman, J. M. Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction. J. Org. Chem. 80, 2634–2640 (2015).
Rynkiewicz, M. J., Cane, D. E. & Christianson, D. W. X-ray crystal structures of D100E trichodiene synthase and its pyrophosphate complex reveal the basis for terpene product diversity. Biochemistry 41, 1732–1741 (2002).
Köksal, M., Jin, Y., Coates, R. M., Croteau, R. & Christianson, D. W. Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis. Nature 469, 116–120 (2011).
Zu, L. et al. Effect of isotopically sensitive branching on product distribution for pentalenene synthase: support for a mechanism predicted by quantum chemistry. J. Am. Chem. Soc. 134, 11369–11371 (2012).
Gutta, P. & Tantillo, D. J. Theoretical studies on farnesyl cation cyclization: pathways to pentalenene. J. Am. Chem. Soc. 128, 6172–6179 (2006).
Hong, Y. J. & Tantillo, D. J. Feasibility of intramolecular proton transfers in terpene biosynthesis—guiding principles. J. Am. Chem. Soc. 137, 4134–4140 (2015).
Miller, D. J. et al. Stereochemistry of eudesmane cation formation during catalysis by aristolochene synthase from Penicillium roqueforti . Org. Biomol. Chem. 6, 2346–2354 (2008).
Acknowledgements
We thank the National Institutes of Health for grant GM56838 in support of this research. DWC thanks the Radcliffe Institute for Advanced Study for the Elizabeth S and Richard M Cashin Fellowship.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Dedicated to Professor David E Cane, with profound gratitude for sharing his wisdom and friendship in more than two decades of collaboration on the structural biology and chemistry of terpenoid biosynthesis.
Rights and permissions
About this article
Cite this article
Pemberton, T., Christianson, D. General base-general acid catalysis by terpenoid cyclases. J Antibiot 69, 486–493 (2016). https://doi.org/10.1038/ja.2016.39
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/ja.2016.39
This article is cited by
-
The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry
Nature Communications (2019)
