2ZVD

Crystal structure of Pseudomonas sp. MIS38 lipase in an open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids

Angkawidjaja, C.Matsumura, H.Koga, Y.Takano, K.Kanaya, S.

(2010) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2010.04.051
  • Primary Citation of Related Structures:  

  • 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 cr ...

    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.


    Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipase
A, C
617Pseudomonas sp. MIS38Mutation(s): 0 
Find proteins for Q9RBY1 (Pseudomonas sp. MIS38)
Go to UniProtKB:  Q9RBY1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.781α = 90.00
b = 104.781β = 90.00
c = 497.926γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
SPringdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance