3ATG

endo-1,3-beta-glucanase from Cellulosimicrobium cellulans

3ATG の概要

• エントリーDOI: 10.2210/pdb3atg/pdb
• 分子名称: GLUCANASE, PHOSPHATE ION, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: beta-sandwich fold, hydrolase, carbohydrate/sugar binding
• 由来する生物種: Cellulosimicrobium cellulans
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 28498.50

構造登録者

Tanabe, Y.,Pang, Z.,Oda, M.,Mikami, B. (登録日: 2011-01-04, 公開日: 2012-01-18, 最終更新日: 2024-03-13)

主引用文献

Oda, M.,Inaba, S.,Kamiya, N.,Bekker, G.J.,Mikami, B.
Structural and thermodynamic characterization of endo-1,3-beta-glucanase: Insights into the substrate recognition mechanism.
Biochim. Biophys. Acta, 1866:415-425, 2018

PubMed Abstract: Endo-1,3-β-glucanase from Cellulosimicrobium cellulans is composed of a catalytic domain and a carbohydrate-binding module. We have determined the X-ray crystal structure of the catalytic domain at a high resolution of 1.66Å. The overall fold is a sandwich-like β-jelly roll architecture like the enzymes in the glycoside hydrolase family 16. The substrate-binding cleft has a length and a width of ~28 and ~15Å, respectively, which is thought to be capable of accommodating at least six glucopyranose units. Laminarihexaose was placed into the substrate-binding cleft, namely at the subsites +2 to -4 from the reducing end, and the complex structure was analyzed using molecular dynamics simulations (MD) and using a rotamer search of the pocket. During the MD simulations, the substrate fluctuated more than the enzyme, where the residues at the subsites toward the non-reducing end fluctuated more than those toward the reducing end. Little conformational change of the protein was observed for the subsites +1 and +2, indicating that the glucose's position could be tightly restricted inside the pocket. Substrate binding experiments using isothermal titration calorimetry showed that the binding affinity of laminaritriose was higher than that of laminaribiose and similar to those of other longer laminarioligosaccharides. Taken together, the substrates mainly bind to the subsites -1 to -3 with the highest affinity, while the part bound to the reducing end would be hydrolyzed.

PubMed: 29246508
DOI: 10.1016/j.bbapap.2017.12.004

実験手法

X-RAY DIFFRACTION (1.66 Å)