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In silico Analysis of Pectin Lyase and Pectinase Sequences

P. K. Yadav1,2, V. K. Singh3, S. Yadav2, K. D. S. Yadav2, and D. Yadav1,3*

1Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur (U. P.), India; E-mail: dinesh_yad@rediffmail.com; pramod0231@rediffmail.com

2Department of Chemistry, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur (U. P.), India

3Department of Molecular Biology and Genetic Engineering, CBSH, G. B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand), India

* To whom correspondence should be addressed.

Received October 13, 2008; Revision received December 22, 2008
A total of 48 full-length protein sequences of pectin lyases from different source organisms available in NCBI were subjected to multiple sequence alignment, domain analysis, and phylogenetic tree construction. A phylogenetic tree constructed on the basis of the protein sequences revealed two distinct clusters representing pectin lyases from bacterial and fungal sources. Similarly, the multiple accessions of different source organisms representing bacterial and fungal pectin lyases also formed distinct clusters, showing sequence level homology. The sequence level similarities among different groups of pectinase enzymes, viz. pectin lyase, pectate lyase, polygalacturonase, and pectin esterase, were also analyzed by subjecting a single protein sequence from each group with common source organism to tree construction. Four distinct clusters representing different groups of pectinases with common source organisms were observed, indicating the existing sequence level similarity among them. Multiple sequence alignment of pectin lyase protein sequence of different source organisms along with pectinases with common source organisms revealed a conserved region, indicating homology at sequence level. A conserved domain Pec_Lyase_C was frequently observed in the protein sequences of pectin lyases and pectate lyases, while Glyco_hydro_28 domains and Pectate lyase-like β-helix clan domain are frequently observed in polygalacturonases and pectin esterases, respectively. The signature amino acid sequence of 41 amino acids, i.e. TYDNAGVLPITVNSNKSLIGEGSKGVIKGKGLRIVSGAKNI, related with the Pec_Lyase_C is frequently observed in pectin lyase protein sequences and might be related with the structure and enzymatic function.
KEY WORDS: pectin lyase, pectate lyase, polygalacturonase, pectin esterase, domain analysis

DOI: 10.1134/S0006297909090144