3D3I

Crystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to glycoside hydrolase family 63

「2DS3」から置き換えられました

3D3I の概要

• エントリーDOI: 10.2210/pdb3d3i/pdb
• 関連するPDBエントリー: 3C67 3C68 3C69
• 分子名称: Uncharacterized protein ygjK, CALCIUM ION, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: gh63, processing alpha-glucosidase, alpha/alpha barrel, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 174007.24

構造登録者

Kurakata, Y.,Uechi, A.,Yoshida, H.,Kamitori, S.,Sakano, Y.,Nishikawa, A.,Tonozuka, T. (登録日: 2008-05-12, 公開日: 2008-06-03, 最終更新日: 2024-10-30)

主引用文献

Kurakata, Y.,Uechi, A.,Yoshida, H.,Kamitori, S.,Sakano, Y.,Nishikawa, A.,Tonozuka, T.
Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.
J.Mol.Biol., 381:116-128, 2008

PubMed Abstract: Proteins belonging to the glycoside hydrolase family 63 (GH63) are found in bacteria, archaea, and eukaryotes. Eukaryotic GH63 proteins are processing *-glucosidase I enzymes that hydrolyze an oligosaccharide precursor of eukaryotic N-linked glycoproteins. In contrast, the functions of the bacterial and archaeal GH63 proteins are unclear. Here we determined the crystal structure of a bacterial GH63 enzyme, Escherichia coli K12 YgjK, at 1.78 A resolution and investigated some properties of the enzyme. YgjK consists of the N-domain and the A-domain, joined by a linker region. The N-domain is composed of 18 antiparallel beta-strands and is classified as a super-beta-sandwich. The A-domain contains 16 *-helices, 12 of which form an (*/*)(6)-barrel; the remaining 4 *-helices are found in an extra structural unit that we designated as the A'-region. YgjK, a member of the glycoside hydrolase clan GH-G, shares structural similarity with glucoamylase (GH15) and chitobiose phosphorylase (GH94) [corrected] both of which belong to clan GH-L or GH-L-like [corrected] In crystal structures of YgjK in complex with glucose, mannose, and galactose, all of the glucose, mannose, and galactose units were located in the catalytic cleft. YgjK showed the highest activity for the *-1,3-glucosidic linkage of nigerose, but also hydrolyzed trehalose, kojibiose, and maltooligosaccharides from maltose to maltoheptaose, although the activities were low. These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars.

PubMed: 18586271
DOI: 10.1016/j.jmb.2008.05.061

実験手法

X-RAY DIFFRACTION (1.78 Å)