5A6V

Open and closed conformations and protonation states of Candida antarctica Lipase B: Xenon complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Open and Closed States of Candida Antarctica Lipase B: Protonation and the Mechanism of Interfacial Activation.

Stauch, B.Fisher, S.J.Cianci, M.

(2015) J.Lipid Res. 56: 2348

  • DOI: 10.1194/jlr.M063388
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of consider ...

    Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or "interfacial activation," with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.


    Organizational Affiliation

    European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Robinson College, University of Cambridge, Cambridge CB3 9AN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIPASE B
A, B
317Pseudozyma antarcticaMutation(s): 0 
EC: 3.1.1.3
Find proteins for P41365 (Pseudozyma antarctica)
Go to UniProtKB:  P41365
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
XE
Query on XE

Download SDF File 
Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.139 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.656α = 87.80
b = 48.890β = 98.07
c = 71.680γ = 108.17
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection, Source and taxonomy
  • Version 1.3: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation