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OJB©
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 Onl J Bioinform.,
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.