Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach

Tian, Bo Xue; Wallrapp, Frank; Holiday, Gemma L.; Chow, Jeng Yeong; Babbitt, Patricia C.; Poulter, C. Dale; Jacobson, Matthew P.

doi:10.1371/journal.pcbi.1003874

Cited by 24 publications

(24 citation statements)

References 89 publications

(91 reference statements)

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“…Again, only one cyclized intermediate, with the best docking score, was retained in round 1. Thus, in rounds 0 and 1, the algorithm predicts the first cyclized intermediate, in a manner similar to our previous reaction channel prediction for the triterpenoid synthases (25).…”

Section: Methodsmentioning

confidence: 76%

“…QM/MM calculations, which take the enzyme structures into account, are computationally too expensive for making predictions, i.e., for uncharacterized enzymes, because the product chemical space for terpene synthases is huge. We recently described a mechanism-based carbocation docking approach to predict functions of triterpene synthases (25). However, the approach is limited because the carbocation library used for docking contains only known carbocations believed to participate in characterized terpene synthase reactions, implying that novel functions will not be predicted.…”

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confidence: 99%

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Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

Chow

Tian

Ramamoorthy

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Terpenoids are a large structurally diverse group of natural products with an array of functions in their hosts. The large amount of genomic information from recent sequencing efforts provides opportunities and challenges for the functional assignment of terpene synthases that construct the carbon skeletons of these compounds. Inferring function from the sequence and/or structure of these enzymes is not trivial because of the large number of possible reaction channels and products. We tackle this problem by developing an algorithm to enumerate possible carbocations derived from the farnesyl cation, the first reactive intermediate of the substrate, and evaluating their steric and electrostatic compatibility with the active site. The homology model of a putative pentalenene synthase (Uniprot: B5GLM7) from Streptomyces clavuligerus was used in an automated computational workflow for product prediction. Surprisingly, the workflow predicted a linear triquinane scaffold as the top product skeleton for B5GLM7. Biochemical characterization of B5GLM7 reveals the major product as (5S,7S,10R,11S)-cucumene, a sesquiterpene with a linear triquinane scaffold. To our knowledge, this is the first documentation of a terpene synthase involved in the synthesis of a linear triquinane. The success of our prediction for B5GLM7 suggests that this approach can be used to facilitate the functional assignment of novel terpene synthases.T erpenoid compounds form a large group of natural products synthesized by many species of plants, fungi, and bacteria. To date, more than 70,000 of these compounds have been identified, comprising ∼25% of all of the known natural products (Dictionary of Natural Products database, dnp.chemnetbase.com/intro/ index.jsp). Terpenoids and molecules containing terpenoid fragments are produced from two basic five-carbon building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (1, 2). IPP and DMAPP are then converted into a series of terpenoid diphosphate esters of increasing chain lengths by chain length selective polyprenyl diphosphate synthases to give geranyl diphosphate (GPP, C 10 ), farnesyl diphosphate (FPP, C 15 ), geranylgeranyl diphosphate (GGPP, C 20 ), and higher five-carbon homologs (3). These molecules are substrates for terpene synthases, which catalyze hydroxylation, elimination, cyclization, and rearrangement reactions to produce much of the structural diversity of terpenoid molecules found in nature (4, 5).The two main classes of terpene synthases (class I and class II) are distinguished from one another by the mechanisms they use to initiate carbocationic cyclization and rearrangement reactions and by their respective folds (6, 7). Class I terpene synthases use active site Mg 2+ ions to bind and activate the diphosphate moieties of their substrates as leaving groups to generate highly reactive allylic carbocations. In those terpene synthases that catalyze cyclization reactions, the carbocations alkylate distal double bonds in the hydrocarbon chain. The initial cycliza...

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Section: Methodsmentioning

confidence: 76%

mentioning

confidence: 99%

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

Chow

Tian

Ramamoorthy

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Given the size of the substrate, a 30-carbon linear achiral isoprenoid, the role of the cyclase active site as a template to enforce a productive substrate conformation is critically important. Triterpene cyclization mechanisms have been exhaustively reviewed, 10 and computational approaches for studying evolutionary relationships and cyclization specificity have been described, 438 so structure–mechanism relationships are only briefly reviewed here for squalene-hopene cyclase and oxidosqualene cyclase.…”

Section: Class II Terpenoid Cyclasesmentioning

confidence: 99%

Structural and Chemical Biology of Terpenoid Cyclases

2017

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The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function.

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“…Each of the 67 TSSs was then docked into EIZS (PDB ID 3KB9) using the Fast Rigid Exhaustive Docking (FRED) program in the Openeye software suite. 38 – 41 The pyrophosphate group lost in step IV was considered to be part of the enzyme active site and was held fixed in these docking simulations. Rankings and docking scores (here, reflecting primarily shape complementarity) 38 – 40 for all TSSs can be found in the ESI, † but results for the TSSs that lead to the relative stereochemistry in epi -isozizaene if the reaction proceeds without significant post-step VI conformational changes ( TS1b–TS1d , Fig.…”

Section: Resultsmentioning

confidence: 99%

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase

Pemberton

Tantillo

2015

Chem. Sci.

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Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach

Cited by 24 publications

References 89 publications

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

Structural and Chemical Biology of Terpenoid Cyclases

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase

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