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Online Journal of Bioinformatics©
Volume 5 :
32-48, 2004
Phylogenetic Clustering and Secondary structural analysis
of Plant Terpenoid Synthases
Singh IV1,
Agrawal S2, Khan3 F, Mishra BN4
1,3,4 Department of Biotechnology,
Institute of Engineering & Technology, Uttar Pradesh, 2 Bioinformatics Division,
Indian Institute of Information Technology, Allahabad, India
Singh
IV, Agrawal S, Khan F, Mishra
BN Phylogenetic Clustering and Secondary structural
analysis of Plant Terpenoid Synthases
Online J Bioinformatics 5:32-48, 2004. The present work describes the evolutionary,
secondary structural and functional relationship among 95 plant derived terpene synthases. Amino acid
sequences of selected plant terpene synthases were retrieved from the NCBI data bank. Tree Top
(TT) and Conserve Domain Database (CDD) programs were used for phylogenetic analysis, and domain identification and
creation of phylogenetic trees, respectively. The phylogenetic tree of primary sequences revealed significant
synteny in individual groups as well as groups in
combinations, whereas the secondary structure analysis in terms of a helix, b
extended sheets and random coils showed almost similar percentage of occurrence
with varying structural arrangements in the individual classes of enzyme. Most
of the members in each class of the terpenoid synthases were functionally analyzed to have common
conserved domain(s). Henceforth, secondary structural and functional
relatedness could be established both in terpenoid synthases as a whole as well as in individual class.
KEY WORDS: Isoprenoids,
Terpenoids, Terpene synthases, Phylogenetic
clustering, Secondary structure analysis