5MAL

Crystal structure of extracelular lipase from Streptomyces rimosus at 1.7A resolution

Summary for 5MAL

• Entry DOI: 10.2210/pdb5mal/pdb
• Descriptor: Lipase (2 entities in total)
• Functional Keywords: sgnh hydrolase, multifunctional enzyme from streptomyces rimosus, quantum-mechanical study, catalytic mechanism, catalytic dyad - ser /his, hydrolase
• Biological source: Streptomyces rimosus
• Cellular location: Secreted {ECO:0000269|Ref: Q93MW7
• Total number of polymer chains: 2
• Total formula weight: 48387.48

Authors

Stefanic, Z. (deposition date: 2016-11-03, release date: 2017-06-14, Last modification date: 2024-10-16)

Primary citation

Lescic Asler, I.,Stefanic, Z.,Marsavelski, A.,Vianello, R.,Kojic-Prodic, B.
Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus.
ACS Chem. Biol., 12:1928-1936, 2017

PubMed Abstract: SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer αβα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···O═C-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG = 17.9 kcal mol, being in reasonable agreement with the experimental value of 14.5 kcal mol, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.

PubMed: 28558229
DOI: 10.1021/acschembio.6b01140

Experimental method

X-RAY DIFFRACTION (1.708 Å)