3-D structure modelling of theStaphylococcus simulanslipase: conformational changes, substrate specificity and novel structural features

Abstract

We have modelled, using the CHARMM27 energy force field, the structures of closed and open forms of Staphylococcus simulans lipase (SSL) on the basis of the crystal structures of Bacillus stearothermophilus and Staphylococcus hyicus lipases, respectively. The models suggested the presence of a main lid and a second lid that may act with the former as a double door to control the access to the active site. Superimposition of both closed and open forms of SSL allowed us to determine the hinge regions allowing the movements of the main and the second lid upon lipase activation. The flexibility of these hinge regions was checked by molecular dynamics simulations. The SSL models also allowed us to identify key residues involved in binding substrates, calcium or zinc ions.

Lipase from Pseudomonas stutzeri: Purification, homology modelling and rational explanation of the substrate binding mode

“…The presence of the double lid motif has been also observed in the 3D crystalline structure of the lipase from P. aeruginosa [59], the template used in out homology modelling, and in some other crystallized lipases, such as those ones from S. hyicus [51], Staphylococcus simulans [60], Geobacillus thermocatenolatus [50], Serratia marcesens [61], Pseudomonas sp. MIS38 [62] or lipase T1 from G. zalihae [63], therefore making these lipases very attractive for modelling studies to simulate lid movements upon solvent effects [64], which will be commented in next section.…”

Asymmetric hydrolysis of dimethyl-3-phenylglutarate in sequential batch reactor operation catalyzed by immobilized Geobacillus thermocatenulatus lipase

“…They recognize a wide variety of substrates while exhibiting high stereoselectivity in many instances [1]. Lipase from Geobacillus thermocatenulatus (BTL2) is a non-commercial intracellular enzyme presenting two "lids" covering the active site, a feature also reported for lipases from Pseudomonas stutzeri [2], Pseudomonas aeruginosa [3], Staphylococcus simulans [4], Serratia marcenses [5], Pseudomonas sp MIS38 [6] and T1 from Geobacillus zalihae [7]. The interest in this lipase is based on its stability at high pH and temperature and in the presence of organic solvents, and the ability to carry out selective reactions [8,9].…”