3A6Z

Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation following dialysis against Ca-free buffer

Summary for 3A6Z

• Entry DOI: 10.2210/pdb3a6z/pdb
• Related: 2Z8X 2Z8Z 2ZJ6 2ZJ7 2ZVD 3A70
• Descriptor: Lipase, CALCIUM ION (3 entities in total)
• Functional Keywords: family i.3 lipase, beta-roll, open conformation, hydrolase
• Biological source: Pseudomonas
• Total number of polymer chains: 2
• Total formula weight: 129809.04

Authors

Angkawidjaja, C.,Matsumura, H.,Koga, Y.,Takano, K.,Kanaya, S. (deposition date: 2009-09-10, release date: 2010-05-26, Last modification date: 2023-11-01)

Primary citation

Angkawidjaja, C.,Matsumura, H.,Koga, Y.,Takano, K.,Kanaya, S.
X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids
J.Mol.Biol., 2010

PubMed Abstract: The interfacial activation mechanism of family I.3 lipase from Pseudomonas sp. MIS38 (PML), which has two alpha-helical lids (lid1 and lid2), was investigated using a combination of X-ray crystallography and molecular dynamics (MD) simulation. The crystal structure of PML in an open conformation was determined at 2.1 A resolution in the presence of Ca(2+) and Triton X-100. Comparison of this structure with that in the closed conformation indicates that both lids greatly change their positions and lid1 is anchored by the calcium ion (Ca1) in the open conformation. This structure was not seriously changed even when the protein was dialyzed extensively against the Ca(2+)-free buffer containing Triton X-100 before crystallization, indicating that the open conformation is fairly stable unless a micellar substance is removed. The crystal structure of the PML derivative, in which the active site serine residue (Ser207) is diethylphosphorylated by soaking the crystal of PML in the open conformation in a solution containing diethyl p-nitrophenyl phosphate, was also determined. This structure greatly resembles that in the open conformation, indicating that PML structure in the open conformation represents that in the active form. MD simulation of PML in the open conformation in the absence of micelles showed that lid2 closes first, while lid1 maintains its open conformation. Likewise, MD simulation of PML in the closed conformation in the absence of Ca(2+) and in the presence of octane or trilaurin micelles showed that lid1 opens, while lid2 remains closed. These results suggest that Ca1 functions as a hook for stabilization of a fully opened conformation of lid1 and for initiation of subsequent opening of lid2.

PubMed: 20438738
DOI: 10.1016/j.jmb.2010.04.051

Experimental method

X-RAY DIFFRACTION (2.15 Å)