Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, USA.
PLoS One. 2010 Jan 13;5(1):e8654. doi: 10.1371/journal.pone.0008654.
Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function.
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. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain.
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. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.
几丁质酶广泛存在于生命中，存在于包括古菌、细菌、真菌、植物和动物在内的物种中。它们分解几丁质，几丁质是仅次于纤维素的自然界中第二丰富的碳水化合物。因此，它们对于维持以不溶性几丁质形式被困在生物质中的碳和氮之间的平衡非常重要。几丁质酶分为两类，18 类和 19 类糖苷水解酶。除了催化结构域（三磷酸甘油醛异构酶桶）外，许多 18 家族几丁质酶还包含另一个模块，即几丁质酶插入结构域。虽然许多研究都集中在催化结构域在几丁质酶活性中的生物学作用上，但几丁质酶插入结构域的功能尚未完全了解。生物信息学提供了一个重要的途径，可以帮助理解几丁质酶插入结构域中残基在几丁质酶功能中的作用。
对包括四个实验确定结构在内的 27 个几丁质酶插入结构域序列进行了对齐和分析，使用了一种改进的序列熵参数。鉴定出 32 个具有保守残基的位置。通过对一些全酶的结构分析，探讨了这些保守残基的作用。氢键和范德华计算揭示了由四个保守残基组成的两个序列基序，它们与寡糖相互作用。其他保守残基可能是该结构域结构、折叠和稳定性的关键。
在进化框架内对几丁质酶插入结构域进行的序列和结构研究确定了四个明显与底物相互作用的保守残基。此外，进化研究提出了几丁质酶插入结构域的出现与 A 亚家族 18 家族几丁质酶功能之间的联系。
