Journal Article

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

Bo-Xue Tian, Gurusankar Ramamoorthy, Ronald D. Seidel, Brandan S. Hillerich, Matthew P. Jacobson, C. Dale Poulter, Steven C. Almo, Jeng-Yeong Chow

2015

Overview

Significance This paper describes a novel strategy for predicting the function of terpene synthases. Functional assignment of terpene synthases is a daunting task because product selectivity is not high in many terpene synthases, and mutations in and near the active sites of selective enzyme can result in synthesis of different products. Using a homology model of an unknown terpene synthase, we developed an algorithm that predicted the enzyme synthesizes a linear triquinane. We confirmed this prediction; specifically, the enzyme converts farnesyl diphosphate to a linear triquinine sesquiterpene: (5 S ,7 S ,10 R ,11 S )-cucumene. The findings highlight the potential for using computational approaches to assist in the discovery and characterization of unknown terpene synthases. 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 (5 S ,7 S ,10 R ,11 S )-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.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: active sites / Algorithms / Alkyl and Aryl Transferases - chemistry / Biological Sciences / Carbon / Carbon - chemistry / Catalytic Domain / Cations / Cluster Analysis / Computational Biology / Computer Simulation / Enzymes / Genomics / Gram-positive bacteria / mutation / Organic chemicals / prediction / Protein Structure, Tertiary / sesquiterpenoids / Software / Streptomyces - enzymology / Streptomyces clavuligerus / Structure-Activity Relationship