1THG

1.8 ANGSTROMS REFINED STRUCTURE OF THE LIPASE FROM GEOTRICHUM CANDIDUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

1.8 A refined structure of the lipase from Geotrichum candidum.

Schrag, J.D.Cygler, M.

(1993) J.Mol.Biol. 230: 575-591

  • DOI: 10.1006/jmbi.1993.1171

  • PubMed Abstract: 
  • A lipase from the fungus Geotrichum candidum is one of only three interfacially activated lipases whose structures have been reported to date. We have previously reported the partially refined 2.2 A structure of this enzyme. We have subsequently exte ...

    A lipase from the fungus Geotrichum candidum is one of only three interfacially activated lipases whose structures have been reported to date. We have previously reported the partially refined 2.2 A structure of this enzyme. We have subsequently extended the resolution and here report the fully refined 1.8 A structure of this lipase. The structure observed in the crystal is apparently not the lipolytic conformation, as the active site is not accessible from the surface of the molecule. A single large cavity is found in the interior of the molecule and extends from the catalytic Ser to two surface helices, suggesting that this face may be the region that interacts with the lipid interface. The mobility of local segments on this face is indicated by temperature factors larger than elsewhere in the molecule and by the observation of several residues whose side-chains are discretely disordered. These observations strongly suggest that this portion of the molecule is involved in interfacial and substrate binding, but the exact nature of the conformational changes induced by binding to the lipid interface can not be determined.


    Related Citations: 
    • Structure of Human Pancreatic Lipase
      Winkler, F.K.,D'Arcy, A.,Hunziker, W.
      (1990) Nature 343: 771
    • Pancreatic Lipases: Evolutionary Intermediates in a Positional Change of Catalytic Carboxylates?
      Schrag, J.D.,Winkler, F.K.,Cygler, M.
      (1992) J.Biol.Chem. 267: 4300
    • Multiple Crystal Forms of Lipases from Geotrichum Candidum
      Schrag, J.D.,Li, Y.,Wu, S.,Cygler, M.
      (1991) J.Mol.Biol. 220: 541
    • Ser-His-Glu Triad Forms the Catalytic Site of the Lipase from Geotrichum Candidum
      Schrag, J.D.,Li, Y.,Wu, S.,Cygler, M.
      (1991) Nature 351: 761
    • Insights Into Interfacial Activation from an Open Structure of Candida Rugosa Lipase
      Grochulski, P.,Li, Y.,Schrag, J.D.,Bouthillier, F.,Smith, P.,Harrison, D.,Rubin, B.,Cygler, M.
      (1993) J.Biol.Chem. 268: 12843


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipase 2
A
544Geotrichum candidumGene Names: LIP2
EC: 3.1.1.3
Find proteins for P22394 (Geotrichum candidum)
Go to UniProtKB:  P22394
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.400α = 90.00
b = 84.000β = 100.10
c = 56.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2016-01-13
    Type: Source and taxonomy
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other