1GZ7

Crystal structure of the closed state of lipase 2 from Candida rugosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights Into the Lipase/Esterase Behavior in the Candida Rugosa Lipases Family: Crystal Structure of the Lipase 2 Isoenzyme at 1.97A Resolution

Mancheno, J.M.Pernas, M.A.Martinez, M.J.Ochoa, B.Rua, M.L.Hermoso, J.A.

(2003) J.Mol.Biol. 332: 1059


  • PubMed Abstract: 
  • The yeast Candida rugosa produces several closely related extracellular lipases that differ in their substrate specificity. Here, we report the crystal structure of the isoenzyme lipase 2 at 1.97A resolution in its closed conformation. Lipase 2 shows ...

    The yeast Candida rugosa produces several closely related extracellular lipases that differ in their substrate specificity. Here, we report the crystal structure of the isoenzyme lipase 2 at 1.97A resolution in its closed conformation. Lipase 2 shows a 79.4% amino acid sequence identity with lipase 1 and 82.2% with lipase 3, which makes it relevant to compare these three isoenzymes. Despite this high level of sequence identity, structural comparisons reveal several amino acid changes affecting the flap (residue 69), the substrate-binding pocket (residues 127, 132 and 450) and the mouth of the hydrophobic tunnel (residues 296 and 344), which may be responsible for the different substrate specificity and catalytic properties of this group of enzymes. Also, these comparisons reveal two distinct regions in the hydrophobic tunnel: a phenylalanyl-rich region and an aliphatic-rich region. Whereas this last region is essentially identical in the three isoenzymes, the phenylalanyl content in the first one is specific for each lipase, resulting in a different environment of the catalytic triad residues, which probably tunes finely their lipase/esterase character. The greater structural similarity observed between the monomeric form of lipase 3 and lipase 2 concerning the above-mentioned key residues led us to propose a significant esterase activity for this last protein. This enzymatic activity has been confirmed with biochemical experiments using cholesteryl [1-14C]oleate as substrate. Surprisingly, lipase 2 is a more efficient esterase than lipase 3, showing a twofold specific activity against cholesteryl [1-14C]oleate in our experimental conditions. These results show that subtle amino acid changes within a highly conserved protein fold may produce protein variants endowed with new enzymatic properties.


    Related Citations: 
    • Cloning, Sequencing, and Expression of Candida Rugosa Lipases
      Alberghina, L.,Lotti, M.
      (1997) Methods Enzymol. 284: 246
    • The Codon Cug is Read as Serine in an Asporogenic Yeast Candida Cylindracea
      Kawaguchi, Y.,Honda, H.,Taniguchi-Morimura, J.,Iwasaki, S.
      (1989) Nature 341: 164


    Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano C.S.I.C., Serrano 119, 28006, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPASE 2
A, B, C, D
534Diutina rugosaMutation(s): 0 
Gene Names: LIP2
EC: 3.1.1.3
Find proteins for P32946 (Diutina rugosa)
Go to UniProtKB:  P32946
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.150α = 90.78
b = 91.140β = 106.31
c = 108.460γ = 86.91
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-12
    Type: Initial release
  • Version 1.1: 2011-10-19
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance