Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation

The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an int...

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Main Authors: Muralidharan K S, Roopa Lalitha, Shanmugam Girija, Pravin Kumar R, Akshai P S, Meghana N Swamy, Nayana M, Malaiyandi Jayanthi
Format: Article
Language:English
Published: MDPI AG 2020-03-01
Series:Catalysts
Subjects:
Online Access:https://www.mdpi.com/2073-4344/10/3/280
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author Muralidharan K S
Roopa Lalitha
Shanmugam Girija
Pravin Kumar R
Akshai P S
Meghana N Swamy
Nayana M
Malaiyandi Jayanthi
author_facet Muralidharan K S
Roopa Lalitha
Shanmugam Girija
Pravin Kumar R
Akshai P S
Meghana N Swamy
Nayana M
Malaiyandi Jayanthi
author_sort Muralidharan K S
collection DOAJ
description The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two.
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spelling doaj.art-0998a74d8d174c20b90d452e3388dadc2022-12-22T03:02:52ZengMDPI AGCatalysts2073-43442020-03-0110328010.3390/catal10030280catal10030280Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics SimulationMuralidharan K S0Roopa Lalitha1Shanmugam Girija2Pravin Kumar R3Akshai P S4Meghana N Swamy5Nayana M6Malaiyandi Jayanthi7Research and Development Centre, Bharathiar University, Coimbatore 641046, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaDepartment of Biotechnology, Bharathiar University, Coimbatore 641046 IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaKcat Enzymatic Pvt Ltd, #16, Ramakrishnappa Road, Cox Town, Bengaluru 560005, IndiaDepartment of Biotechnology, Bharathiar University, Coimbatore 641046 IndiaThe biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two.https://www.mdpi.com/2073-4344/10/3/280plumbaginnaphthoate synthasethioesterasemolecular dynamics simulationquantum mechanics
spellingShingle Muralidharan K S
Roopa Lalitha
Shanmugam Girija
Pravin Kumar R
Akshai P S
Meghana N Swamy
Nayana M
Malaiyandi Jayanthi
Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
Catalysts
plumbagin
naphthoate synthase
thioesterase
molecular dynamics simulation
quantum mechanics
title Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
title_full Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
title_fullStr Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
title_full_unstemmed Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
title_short Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation
title_sort identification of a reaction intermediate and mechanism of action of intermediary enzymes in plumbagin biosynthetic pathway using molecular dynamics simulation
topic plumbagin
naphthoate synthase
thioesterase
molecular dynamics simulation
quantum mechanics
url https://www.mdpi.com/2073-4344/10/3/280
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