3ILN

X-ray structure of the laminarinase from Rhodothermus marinus

Summary for 3ILN

• Entry DOI: 10.2210/pdb3iln/pdb
• Descriptor: Laminarinase, GLYCEROL, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: jelly row, hydrolase, family 16 glycosyl hydrolase
• Biological source: Rhodothermus marinus (Rhodothermus obamensis)
• Total number of polymer chains: 2
• Total formula weight: 58947.31

Authors

Bleicher, L.,Golubev, A.,Rojas, A.L.,Nascimento, A.S.,Polikarpov, I. (deposition date: 2009-08-07, release date: 2010-08-18, Last modification date: 2023-09-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.95 Å)