3WN6

Crystal structure of alpha-amylase AmyI-1 from Oryza sativa

Summary for 3WN6

• Entry DOI: 10.2210/pdb3wn6/pdb
• Descriptor: Alpha-amylase, CALCIUM ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: (alpha/beta)8-barrel, hydrolase, carbohydrate/sugar binding, glycosylation
• Biological source: Oryza sativa Japonica Group (Japonica rice)
• Total number of polymer chains: 4
• Total formula weight: 184323.44

Authors

Ochiai, A.,Sugai, H.,Harada, K.,Tanaka, S.,Ishiyama, Y.,Ito, K.,Tanaka, T.,Uchiumi, T.,Taniguchi, M.,Mitsui, T. (deposition date: 2013-12-05, release date: 2014-09-10, Last modification date: 2023-11-08)

Primary citation

Ochiai, A.,Sugai, H.,Harada, K.,Tanaka, S.,Ishiyama, Y.,Ito, K.,Tanaka, T.,Uchiumi, T.,Taniguchi, M.,Mitsui, T.
Crystal structure of alpha-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability
Biosci.Biotechnol.Biochem., 78:989-997, 2014

PubMed 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.

PubMed: 25036124
DOI: 10.1080/09168451.2014.917261

Experimental method

X-RAY DIFFRACTION (2.16 Å)