1THG

1.8 ANGSTROMS REFINED STRUCTURE OF THE LIPASE FROM GEOTRICHUM CANDIDUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    1THG

  • 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: 
    • 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
    • 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
    • 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
    • Multiple Crystal Forms of Lipases from Geotrichum Candidum
      Schrag, J.D., Li, Y., Wu, S., Cygler, M.
      (1991) J Mol Biol 220: 541
    • Structure of Human Pancreatic Lipase
      Winkler, F.K., D'Arcy, A., Hunziker, W.
      (1990) Nature 343: 771

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipase 2A544Geotrichum candidumMutation(s): 0 
Gene Names: LIP2
EC: 3.1.1.3
Find proteins for P22394 (Geotrichum candidum)
Explore P22394 
Go to UniProtKB:  P22394
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NDG
Query on NDG

Download CCD File 
A
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.4α = 90
b = 84β = 100.1
c = 56γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2016-01-13
    Changes: Source and taxonomy
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary