Structural Analysis, Eighth Edition


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Molecular phylogenetic analyses of mammalian GH 18 chitinase and chitinase-like members suggest that active chitinases result from an early gene duplication event, which is followed by mutations, leading to chitinase-like proteins, such as chito-lectins [61]. Comprehensive genomic studies of animal GH 18 proteins showed a similar result [11].

Another phylogenetic analysis of catalytic domain sequences from various organisms showed that sequences of animal, fungi, and bacteria belong to different lineage; however, chitinase genes from lepidopteran insects and baculoviruses originated from bacteria and were maintained through evolution since they transferred laterally [62]. However, no evolutionary study has been conducted on the CID by itself.

To establish the phylogenetic relationships between the CIDs from different organisms, a preliminary phylogenetic tree was constructed based on the sixty sequences from five kingdoms Archaea, Bacteria, Fungi, Plantae, and Animalia Fig. Overall, the CID sequences grouped into five major clusters, each representing one kingdom as to be expected. In the cluster of Animalia, members from early eukaryotes and early Animalia branch out earlier than those from vertebrates and mammals.

The phylogenetic tree was constructed by the neighbour-joining method based on the CID sequences: five from Archaea, eighteen from Bacteria, twelve from Fungi, five from Plantae, three from early eukaryotes, eight from early Animalia, and nine from vertebrates V including six from mammals. The sequence names, corresponding GI numbers, and abbreviations are listed in Fig. In the study conducted by Nagano et al. A proposed evolution of the structure and function of family 18 chitinases and chitinase-like proteins in the subfamilies A and B can be potentially described as follows.

Due to divergent evolution, a TIM domain line may initially have evolved as hevamine, xylanase inhibitor protein, or seed storage protein e. Concanavalin B in some higher plants, as well as NAGase in some bacteria. One possible evolutionary scheme suggests that a TIM barrel evolved to a more potent family 18 chitinase in two routes: 1 with the incorporation of the CID to form a subfamily A chitinase and 2 with the other domains e.

In the first route, this double-domain chitinase evolved in archaea, bacteria, fungi, plants, and animals, as well as the triple-domain chitinase with the fusion of N- or C- terminal domain in S. Subsequently, the double-domain chitinase gene was mutated to have novel functions in animals [61]. Four conserved amino acids identified in this study are proposed to be essential for binding with the substrate and they form two distinguishable sequence motifs.

Because of the wide distribution in diverse organisms and the high conservation of the CID, we can identify the sequence and predict the structure of this domain in family 18 chitinases in the subfamily A. An evolutionary scheme is presented which places the emergence of the CID in the context of chitinase function; with the addition of the CID leading to an evolutionary shift of the protein from a non-chitinolytic protein, or a NAGase, to a subfamily A or B family 18 chitinase.

We also identify a group of conserved hydrophobic residues in the core which we propose are important for folding and structural stability. Research on the role of the CID in function to test this hypothesis can be carried out using a myriad of experimental and computational techniques such as molecular modelling, in vitro and in silico binding studies coupled to site-directed mutagenesis, enzymatic assays, and crystallization of the holo-proteins. The CID regions within the structures of three proteins: B.

They represent chitinases within the kingdoms of Bacteria, Fungi, and Animalia, respectively. A plant or archaeal structure was not available at the time however the PSI-BLAST searches did identify plant and archaeal chitinases for inclusion in our study. An initial multiple sequence alignment was made using MUSCLE - multiple protein sequence alignment program in Jalview Java alignment editor [67] , [68].

The alignment was created in order to enhance sequence variability and in this way, only the key conserved residues for structure, folding, and function could be identified. The boundary of the CID in each sequence was identified by aligning with the three model chitinases and the domain was further extracted from each chitinase sequence. The initial sequence alignment was compared with the initial structure alignment, and adjusted in Jalview to ensure the sequences with unknown structures were properly aligned with the known structures.

Since no structure from plant is available, the secondary structure of tobacco chitinase CID was predicted by the program of PSIPRED [70] , and the other sequences were aligned with it thereafter. A larger multiple sequence alignment of sixty sequences was generated using MUSCLE in Jalview, without being edited according to the three model structures. The number of each residue in each position was calculated and analyzed by SigmaPlot The entropy value was calculated by the following equation:.

P j i is the fractional occurence of amino acid type j at each site, and m is the number of amino acid types used in the particular analysis [72]. The positions with conservation values greater than 0. The positions which have more than one gap are considered non-conserved and therefore have a value of zero. The hydrophobicity scale of Nozaki and Tanford was used for our studies [74].


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Hydrogen bond calculations and van der Waals radii were determined with Insight II. The phylogenetic tree was constructed using the neighbour-joining algorithm as described by Saitou and Nei [76]. The tree was visualized and drawn with MEGA version 4. The structures were superimposed with the CE-MC method.


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The larger multiple sequence alignment of sixty CID sequences from various species. It is not edited according to the three model structures. The species names and GI numbers refer to Table S2. List of twenty-one family 18 chitinases and chitinase-like proteins from plants, bacteria, fungi, and animals.

Structures in bold are described and compared in the text. List of the sequence names, species name, and GI numbers of thirty-three more CID sequences that are included in the phylogenetic tree Fig.

Structural Analysis, 8th Edition

Janet M. We thank the reviewers for insightful comments which helped improve the quality of this manuscript. Competing Interests: The authors have declared that no competing interests exist. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. National Center for Biotechnology Information , U.

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PLoS One. Published online Jan Hai Li and Lesley H. Lesley H. Haibing Yang, Editor. Author information Article notes Copyright and License information Disclaimer. Received Jul 31; Accepted Dec 5. Copyright Li, Greene. 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 properly credited. This article has been cited by other articles in PMC. Table S1: List of twenty-one family 18 chitinases and chitinase-like proteins from plants, bacteria, fungi, and animals.

Abstract Background Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. Results Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter.

Conclusions Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Family 18 Chitinases Family 18 chitinases can be classified into three subfamilies A, B, and C, in terms of the amino acid sequence similarity [25].

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Figure 1. Structural analysis of the CID. Results and Discussion Structure-Based Sequence Alignment of the CID The representative family 18 chitinases and chitinase-like proteins from plants, bacteria, fungi, and animals whose three-dimensional structures have been determined by X-ray diffraction are listed in Table S1. Figure 2.

Structure-based multiple sequence alignment of the CID. Proposed Role of Conserved Residues on the CID Residues are often conserved in protein families because they either make critical stabilizing interactions or play important functional roles [41]. Figure 3.


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  7. Sequence conservation analysis of the CID. Figure 4. Structures of select family 18 chitinases with their substrates. A Interactions between select residues on E. B Interactions between some residues on S. The data are adapted from Waddling et al. Conserved residues on the CID from our conservation analysis are in bold.

    Figure 5. Phylogenetic analysis of the CID sequences from different lineages of organisms. Conclusions Four conserved amino acids identified in this study are proposed to be essential for binding with the substrate and they form two distinguishable sequence motifs. Conservation and Hydropathy Analysis The number of each residue in each position was calculated and analyzed by SigmaPlot Table S1 List of twenty-one family 18 chitinases and chitinase-like proteins from plants, bacteria, fungi, and animals. Footnotes Competing Interests: The authors have declared that no competing interests exist.

    References 1. Gooday GW. New York: Plenum Press; The ecology of chitin degradation. In: Advances in Microbial Ecology. Biotechnological aspects of chitinolytic enzymes: a review. Appl Microbiol Biotechnol. Li DC. Review of fungal chitinase.

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