Sequence and Structural Analysis of the Chitinase Insertion Domain Reveals Two Conserved Motifs Involved in Chitin-Binding

Abstract

BackgroundChitinases 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.ResultsTwenty-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.ConclusionsSequence 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.

Molecular cloning and expression of drought-induced protein 3 (DIP3) encoding a class III chitinase in upland rice

“…The characteristic catalytic domain is called the glycosyl hydrolase (GH) domain, which consists of about 220 to 230 amino acid residues (Liu et al, 2010). The catalytic domain is grouped into two families: glycosyl hydolase family 18 (GH18) and glycosyl hydrolase family 19 (GH19) (Li and Greene, 2010). Chitinases belong to the GH18 family including class III and V chitinases (Takenaka et al, 2009).…”

Overexpression, purification, and characterization of Paenibacillus cell surface-expressed chitinase ChiW with two catalytic domains

“…1) that function to allow the enzyme access to tightly packed chitin and assist in catalysis. 13) Members of the family GH-18 chitinase subfamily A have an extra domain with a small α + β domain (chitinase insertion domain, CID) inserted into the core TIM-barrel fold, 8,11,40) while chitinase subfamilies B and C have no such domain. 7,8,41) BLAST 27) and ClustalW 28) analysis revealed that the amino acid sequence of the 1st GH-18 domain was 56% identical to the 2nd GH-18 domain; 42% identical to the catalytic domain of chitinase A1 from Bacillus circulans WL-12, 40) belonging to subfamily A judged by its primary and three dimensional structures; 11% identical to catalytic domains of chitinase from Bacillus cereus NCTU2, belonging to subfamily B also based on its primary and three dimensional structures 41) ; and 10% identical to chitinase C1 from Serratia marcescens 2170, which belongs to subfamily C based on its amino acid sequence 7) (Fig.…”

“…6) The bacterial chitinases of family GH-18 are classified into three subfamilies: A, B, and C. 7,8) The GH-18 chitinases have a triosephosphate isomerase (TIM-barrel) fold as a catalytic domain and have a retaining mechanism, 9) while the GH-19 chitinases are comprised of lysozyme-like (α + β)-folds and use an inverting mechanism. 10) Some chitinases are multi-modular in structure, composed of more than one functional domain, such as a catalytic domain and a carbohydrate binding module (CBM) to bind and assist in long chitin chain degradation.…”

Diverse chitinases are invoked during the activity-dormancy transition in spruce

“…Chitinases are typified by the presence of a glycosyl hydrolase domain which corresponds to the catalytic domain. The chitinase family can be subdivided into two main groups-glycoside hydrolase family 18 (GH 18) and glycoside hydrolase family 19 (GH 19)-based on differences in this domain (Davies and Henrissat 1995;Iseli et al 1996;Li and Greene 2010). Biochemically, chitinases are grouped into classes I to VII, based on their primary structure and the presence of one or more diagnostic motifs (Collinge et al 1993;Neuhaus 1999;Grover 2012).…”