3ZWQ

HYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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This is version 1.1 of the entry. See complete history


Literature

The Crystal Structure of an Esterase from the Hyperthermophilic Microorganism Pyrobaculum Calidifontis Va1 Supports Explanation of its Enantioselectivity.

Palm, G.J.Fernandez-Alvaro, E.Bogdanovic, X.Bartsch, S.Sczodrok, J.Singh, R.K.Boettcher, D.Atomi, H.Bornscheuer, U.T.Hinrichs, W.

(2011) Appl Microbiol Biotechnol 91: 1061

  • DOI: 10.1007/s00253-011-3337-9
  • Primary Citation of Related Structures:  
    2YH2, 3ZWQ

  • PubMed Abstract: 
  • The highly thermostable esterase from the hyperthermophilic archaeon Pyrobaculum calidifontis VA1 (PestE) shows high enantioselectivity (E > 100) in the kinetic resolution of racemic chiral carboxylic acids, but little selectivity towards acetates of tertiary alcohols (E = 2-4) ...

    The highly thermostable esterase from the hyperthermophilic archaeon Pyrobaculum calidifontis VA1 (PestE) shows high enantioselectivity (E > 100) in the kinetic resolution of racemic chiral carboxylic acids, but little selectivity towards acetates of tertiary alcohols (E = 2-4). To explain these unique properties, its crystal structure has been determined at 2.0 Å resolution. The enzyme is a member of the hormone-sensitive lipase group (group H) of the esterase/lipase superfamily on the basis of the amino acid sequence identity. The PestE structure shows a canonical α/β-hydrolase fold as core domain with a cap structure at the C-terminal end of the β-sheet. A tetramer in the crystal packing is formed of two dimers; the dimeric form is observed in solution. Conserved dimers and even tetramers are found in other group H proteins. The amino acid residues Ser157, His284, and Asp254 form the catalytic triad, which is typically found in α/β-hydrolases. The oxyanion hole is composed of Gly85 and Gly86 within the conserved sequence motif HGGG(M,F,W) (amino acid residues 83-87) and Ala158. With the elucidated structure, experimental results about enantioselectivity towards the two model substrate classes (as exemplified for 3-phenylbutanoic acid ethyl ester and 1,1,1-trifluoro-2-phenylbut-3-yn-2-yl acetate) could be explained by molecular modeling. For both enantiomers of the tertiary alcohol, orientations in two binding pockets were obtained without significant energy differences corresponding to the observed low enantioselectivity due to missing steric repulsions. In contrast, for the carboxylic acid ester, two different orientations with significant energy differences for each enantiomer were found matching the high E values.


    Related Citations: 
    • Extremely Stable and Versatile Carboxylesterase from a Hyperthermophilic Archaeon.
      Hotta, Y., Ezaki, S., Atomi, H., Imanaka, T.
      (2002) Appl Environ Microbiol 68: 3925

    Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Biochemistry, Greifswald University, Felix-Hausdorff Str. 4, 17487 Greifswald, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEINA, B313Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
Gene Names: Pcal_1307
EC: 3.1.1.1
Find proteins for A3MVR4 (Pyrobaculum calidifontis (strain JCM 11548 / VA1))
Explore A3MVR4 
Go to UniProtKB:  A3MVR4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.919α = 90
b = 127.271β = 90
c = 93.727γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references