Title
Detection, Characterization and Evolution of Internal Repeats in Chitinases of Known 3-D Structure
Document Type
Article
Abstract
Chitinase proteins have evolved and diversified almost in all organisms ranging from prokaryotes to eukaryotes. During evolution, internal repeats may appear in amino acid sequences of proteins which alter the structural and functional features. Here we deciphered the internal repeats from Chitinase and characterized the structural similarities between them. Out of 24 diverse Chitinase sequences selected, six sequences (2CJL, 2DSK, 2XVP, 2Z37, 3EBV and 3HBE) did not contain any internal repeats of amino acid sequences. Ten sequences contained repeats of length <50, and the remaining 8 sequences contained repeat length between 50 and 100 residues. Two Chitinase sequences, 1ITX and 3SIM, were found to be structurally similar when analyzed using secondary structure of Chitinase from secondary and 3-Dimensional structure database of Protein Data Bank. Internal repeats of 3N17 and 1O6I were also involved in the ligand-binding site of those Chitinase proteins, respectively. Our analyses enhance our understanding towards the identification of structural characteristics of internal repeats in Chitinase proteins.
Disciplines
Biochemistry, Biophysics, and Structural Biology
Recommended Citation
Sivaji M, Sadasivam V, Narayanasamy J, Samuel S, Fan C (2014) Detection, Characterization and Evolution of Internal Repeats in Chitinases of Known 3-D Structure. PLoS ONE 9(3): e91915. doi: 10.1371/journal.pone.0091915
Figure S1. Multiple sequence alignment of 18 TIM barrel fold Chitinases with the repeats regions marked. doi:10.1371/journal.pone.0091915.s001
Figure_S2.pdf (82 kB)
Figure S2. Multiple sequence alignment of 6 Endochitinase fold Chitinases with the repeats regions marked. doi:10.1371/journal.pone.0091915.s002
Figure_S3.tif (164 kB)
Figure S3. Phylogenetic relationship of Endochitinase fold Chitinases. Bootstrap support value (%) >50 is showed above branch. doi:10.1371/journal.pone.0091915.s003
Figure_S4.tif (396 kB)
Figure S4. Phylogenetic relationship of TIM barrel fold Chitinases. Bootstrap support value (%) >50 is showed above branch. doi:10.1371/journal.pone.0091915.s004
Table_S1.pdf (70 kB)
Table S1. Alignment scores of different pairs of Chitinases. doi:10.1371/journal.pone.0091915.s005
Table_S2.pdf (49 kB)
Table S2. RMSD and Z-scores of structural superposition of proteins belonging to the TIM fold. doi:10.1371/journal.pone.0091915.s006
Table_S3.pdf (128 kB)
Table S3. RMSD and Z-scores of structural superposition of proteins belonging to the Endochitinase fold. doi:10.1371/journal.pone.0091915.s007
Comments
© 2014 Sivaji et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.