Crystal structure of a HSL-like carboxylesterase from Sulfolobus tokodaii complexed with paraoxon

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobustokodaii

Angkawidjaja, C.Koga, Y.Takano, K.Kanaya, S.

(2012) FEBS J 279: 3071-3084

  • DOI: https://doi.org/10.1111/j.1742-4658.2012.08687.x
  • Primary Citation of Related Structures:  
    3AIK, 3AIL, 3AIM, 3AIN, 3AIO

  • PubMed Abstract: 

    The hormone-sensitive lipase (HSL) family is comprised of carboxylesterases and lipases with similarity to mammalian HSL. Thermophilic enzymes of this family have a high potential for use in biocatalysis. We prepared and crystallized a carboxylesterase of the HSL family from Sulfolobus tokodaii (Sto-Est), and determined its structures in the presence and absence of an inhibitor. Sto-Est forms a dimer in solution and the crystal structure suggests the presence of a stable biological dimer. We identified a residue close to the dimer interface, R267, which is conserved in archaeal enzymes of HSL family and is in close proximity to the same residue from the other monomer. Mutations of R267 to Glu, Gly and Lys were conducted and the resultant R267 mutants were characterized and crystallized. The structures of R267E, R267G and R267K are highly similar to that of Sto-Est with only slight differences in atomic coordinates. The dimerized states of R267E and R267G are unstable under denaturing conditions or at high temperature, as shown by a urea-induced dimer dissociation experiment and molecular dynamics simulation. R267E is the most unstable mutant protein, followed by R267G and R267K, as shown by the thermal denaturation curve and optimum temperature for activity. From the data, we discuss the importance of R267 in maintaining the dimer integrity of Sto-Est.

  • Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan. clement@bio.mls.eng.osaka-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
303aa long hypothetical esterase
A, B, C, D
323Sulfurisphaera tokodaiiMutation(s): 0 
Gene Names: ST0071
Find proteins for Q976W8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q976W8 
Go to UniProtKB:  Q976W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ976W8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DEP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
O [auth D]
C4 H11 O3 P
Query on MRD

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
M [auth C]
C6 H14 O2
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
N [auth C],
P [auth D]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.323α = 90
b = 114.367β = 108.44
c = 101.892γ = 90
Software Package:
Software NamePurpose
BL38B1data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description