3ILN

X-ray structure of the laminarinase from Rhodothermus marinus

3ILN の概要

• エントリーDOI: 10.2210/pdb3iln/pdb
• 分子名称: Laminarinase, GLYCEROL, CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: jelly row, hydrolase, family 16 glycosyl hydrolase
• 由来する生物種: Rhodothermus marinus (Rhodothermus obamensis)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 58947.31

構造登録者

Bleicher, L.,Golubev, A.,Rojas, A.L.,Nascimento, A.S.,Polikarpov, I. (登録日: 2009-08-07, 公開日: 2010-08-18, 最終更新日: 2023-09-06)

主引用文献

Bleicher, L.,Prates, E.T.,Gomes, T.C.,Silveira, R.L.,Nascimento, A.S.,Rojas, A.L.,Golubev, A.,Martinez, L.,Skaf, M.S.,Polikarpov, I.
Molecular basis of the thermostability and thermophilicity of laminarinases: X-ray structure of the hyperthermostable laminarinase from Rhodothermus marinus and molecular dynamics simulations.
J.Phys.Chem.B, 115:7940-7949, 2011

PubMed Abstract: Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 Å resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting β-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

PubMed: 21619042
DOI: 10.1021/jp200330z

実験手法

X-RAY DIFFRACTION (1.95 Å)