Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability

Abstract

AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.

Antimicrobial activity and mechanism of action of a novel cationic α‐helical octadecapeptide derived from α‐amylase of rice

“…The amino acid sequence of AmyI‐1 in the database constructed by The Institute for Genomic Research Rice Genome Annotation project (http://www.jcvi.org/cms/research/) was used to search for cationic α‐helical peptide sequences. On the basis of the three‐dimensional structure of AmyI‐1 reported for the first time by us, we determined the amino acid sequences of candidate AMPs having α‐helical propensity on the surface of the protein. Table shows the sequences and properties of candidate AMPs.…”

“…In this study, to identify novel and cationic α‐helical peptides that have a broad antimicrobial spectrum and high antimicrobial activity against human pathogens, we selected α‐amylase (AmyI‐1) from rice as a precursor of AMPs. Based on the crystal structure of AmyI‐1 that we recently determined, we searched the cationic α‐helical amino acid sequences on the surface of AmyI‐1. Surface features were selected because they contain both hydrophilic and hydrophobic amino acids necessary to generate the amphipathic properties essential for AMPs .…”

“…To better understand the molecular physiology and biological functions of α‐amylase (AmyI‐1: GenBank ID: BAF10134) which is expressed as a major isozyme in the scutellar epithelium and the aleurone layers during the germination process of rice seeds, we recently determined for the first time the crystal structure of AmyI‐1, which was expressed using a bacterial expression system and, therefore, lacked the N ‐glycosylated carbohydrate chain characteristic of plant α‐amylases . The overall structure, which includes 11‐helices and 15‐strands, is a typical scaffold that is highly conserved among α‐amylases from other organisms.…”

Raw starch degrading α-amylases: an unsolved riddle

“…Structure of twenty three different α-amylases have been determined [15] including recently published structures of a variant 'Termamyl-like' Geobacillus stearothermophilus α-amylase [36] and the α-amylase from Oryza sativa [37] from GH13 family.…”

New insight in cereal starch degradation: identification and structural characterization of four α-amylases in bread wheat

“…In plants, the role and number of α-amylase isoforms vary significantly across monocots and dicots. To date, there are at least four α-amylase categories in barley, from HvAMY1 to HvAMY4, while rice shows at least ten separate genes clustered into three subfamilies (OsAMY1, OsAMY2 and OsAMY3) [6,7]. All subfamilies in barley or rice have been demonstrated to be expressed at different grain developmental stages and in various tissues [8,9].…”