1CV2

Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.211 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.

Marek, J.Vevodova, J.Smatanova, I.K.Nagata, Y.Svensson, L.A.Newman, J.Takagi, M.Damborsky, J.

(2000) Biochemistry 39: 14082-14086

  • Primary Citation of Related Structures:  1D07
  • Also Cited By: 2BFN

  • PubMed Abstract: 
  • The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliph ...

    The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Haloalkane Dehalogenase Linb from Sphingomonas Paucimobilis Ut26
      Smatanova, I.,Nagata, Y.,Svensson, L.A.,Takagi, M.,Marek, J.
      (1999) Acta Crystallogr.,Sect.D 53: 1231


    Organizational Affiliation

    Laboratory of Biomolecular Structure and Dynamics, and Department of Inorganic Chemistry, Faculty of Science, Masaryk University, Kotlárská 2, CZ 611 37 Brno, Czech Republic. marek@chemi.muni.cz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HALOALKANE DEHALOGENASE
A
296Sphingomonas paucimobilisGene Names: linB
EC: 3.8.1.5
Find proteins for P51698 (Sphingomonas paucimobilis)
Go to UniProtKB:  P51698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.264α = 90.00
b = 71.669β = 90.00
c = 72.698γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Data collection, Refinement description