1LPN

ANALOGS OF REACTION INTERMEDIATES IDENTIFY A UNIQUE SUBSTRATE BINDING SITE IN CANDIDA RUGOSA LIPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

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This is version 2.0 of the entry. See complete history


Literature

Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase.

Grochulski, P.Bouthillier, F.Kazlauskas, R.J.Serreqi, A.N.Schrag, J.D.Ziomek, E.Cygler, M.

(1994) Biochemistry 33: 3494-3500

  • DOI: 10.1021/bi00178a005
  • Primary Citation of Related Structures:  
    1LPN, 1LPO, 1LPP

  • PubMed Abstract: 
  • The structures of Candida rugosa lipase-inhibitor complexes demonstrate that the scissile fatty acyl chain is bound in a narrow, hydrophobic tunnel which is unique among lipases studied to date. Modeling of triglyceride binding suggests that the bound lipid must adopt a "tuning fork" conformation ...

    The structures of Candida rugosa lipase-inhibitor complexes demonstrate that the scissile fatty acyl chain is bound in a narrow, hydrophobic tunnel which is unique among lipases studied to date. Modeling of triglyceride binding suggests that the bound lipid must adopt a "tuning fork" conformation. The complexes, analogs of tetrahedral intermediates of the acylation and deacylation steps of the reaction pathway, localize the components of the oxyanion hole and define the stereochemistry of ester hydrolysis. Comparison with other lipases suggests that the positioning of the scissile fatty acyl chain and ester bond and the stereochemistry of hydrolysis are the same in all lipases which share the alpha/beta-hydrolase fold.


    Related Citations: 
    • Two Conformational States of Candida Rugosa Lipase
      Grochulski, P., Li, Y., Schrag, J.D., Cygler, M.
      (1994) Protein Sci 3: 82
    • A Structural Basis for the Chiral Preferences of Lipases
      Cygler, M., Grochulski, P., Kazlauskas, R.J., Schrag, J.D., Bouthillier, F., Rubin, B., Serregi, A.N., Gupta, A.K.
      (1994) J Am Chem Soc 116: 3180
    • 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, Quebec.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIPASEA549Diutina rugosaMutation(s): 0 
Gene Names: LIP1
EC: 3.1.1.3
UniProt
Find proteins for P20261 (Diutina rugosa)
Explore P20261 
Go to UniProtKB:  P20261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20261
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSC
Query on DSC

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
DODECANESULFONATE ION
C12 H25 O3 S
LDMOEFOXLIZJOW-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65α = 90
b = 97.4β = 90
c = 176.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary