1JUD

L-2-HALOACID DEHALOGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.

Hisano, T.Hata, Y.Fujii, T.Liu, J.Q.Kurihara, T.Esaki, N.Soda, K.

(1996) J Biol Chem 271: 20322-20330

  • DOI: 10.1074/jbc.271.34.20322
  • Primary Citation of Related Structures:  
    1JUD

  • PubMed Abstract: 
  • L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. The crystal structure of the homodimeric enzyme from Pseudomonas sp. YL has been determined by a multiple isomorphous replacement method and refined at 2 ...

    L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. The crystal structure of the homodimeric enzyme from Pseudomonas sp. YL has been determined by a multiple isomorphous replacement method and refined at 2.5 A resolution to a crystallographic R-factor of 19.5%. The subunit consists of two structurally distinct domains: the core domain and the subdomain. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by five alpha-helices. The subdomain inserted into the core domain has a four helix bundle structure providing the greater part of the interface for dimer formation. There is an active site cavity between the domains. An experimentally identified nucleophilic residue, Asp-10, is located on a loop following the amino-terminal beta-strand in the core domain, and other functional residues, Thr-14, Arg-41, Ser-118, Lys-151, Tyr-157, Ser-175, Asn-177, and Asp-180, detected by a site-directed mutagenesis experiment, are arranged around the nucleophile in the active site. Although the enzyme is an alpha/beta-type hydrolase, it does not belong to the alpha/beta hydrolase fold family, from the viewpoint of the topological feature and the position of the nucleophile.


    Related Citations: 
    • Crystallization of L-2-Haloacid Dehalogenase from Pseudomonas Sp. Yl
      Hisano, T., Hata, Y., Fujii, T., Kurihara, T., Esaki, N., Soda, K.
      (1996) Proteins 24: 520

    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-2-HALOACID DEHALOGENASEA232Pseudomonas sp. YLMutation(s): 0 
Gene Names: L-DEX YL
EC: 3.8.1.2
UniProt
Find proteins for Q53464 (Pseudomonas sp. (strain YL))
Explore Q53464 
Go to UniProtKB:  Q53464
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.21α = 90
b = 62.78β = 122.4
c = 50.84γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
R-AXISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance