1TRH

TWO CONFORMATIONAL STATES OF CANDIDA RUGOSA LIPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two conformational states of Candida rugosa lipase.

Grochulski, P.Li, Y.Schrag, J.D.Cygler, M.

(1994) Protein Sci 3: 82-91

  • DOI: 10.1002/pro.5560030111
  • Primary Citation of Related Structures:  
    1TRH

  • PubMed Abstract: 
  • The structure of Candida rugosa lipase in a new crystal form has been determined and refined at 2.1 A resolution. The lipase molecule was found in an inactive conformation, with the active site shielded from the solvent by a part of the polypeptide chain-the flap ...

    The structure of Candida rugosa lipase in a new crystal form has been determined and refined at 2.1 A resolution. The lipase molecule was found in an inactive conformation, with the active site shielded from the solvent by a part of the polypeptide chain-the flap. Comparison of this structure with the previously determined "open" form of this lipase, in which the active site is accessible to the solvent and presumably the substrate, shows that the transition between these 2 states requires only movement of the flap. The backbone NH groups forming the putative oxyanion hole do not change position during this rearrangement, indicating that this feature is preformed in the inactive state. The 2 lipase conformations probably correspond to states at opposite ends of the pathway of interfacial activation. Quantitative analysis indicates a large increase of the hydrophobic surface in the vicinity of the active site. The flap undergoes a flexible rearrangement during which some of its secondary structure refolds. The interactions of the flap with the rest of the protein change from mostly hydrophobic in the inactive form to largely hydrophilic in the "open" conformation. Although the flap movement cannot be described as a rigid body motion, it has very definite hinge points at Glu 66 and at Pro 92. The rearrangement is accompanied by a cis-trans isomerization of this proline, which likely increases the energy required for the transition between the 2 states, and may play a role in the stabilization of the active conformation at the water/lipid interface. Carbohydrate attached at Asn 351 also provides stabilization for the open conformation of the flap.


    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
    • Cloning and Analysis of Candida Cylindracea Lipase Sequences
      Lotti, M., Grandori, R., Fusetti, F., Longhi, S., Brocca, S., Tramontano, A.
      (1993) Gene 124: 45
    • 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIPASE A534Diutina rugosaMutation(s): 0 
Gene Names: LIP1
EC: 3.1.1.3
Find proteins for P20261 (Diutina rugosa)
Explore P20261 
Go to UniProtKB:  P20261
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105α = 90
b = 106.7β = 94.8
c = 59.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary