1D07

Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 1IZ8


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

  • DOI: 10.1021/bi001539c
  • Primary Citation of Related Structures:  
    1CV2, 1D07

  • 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 aliphatic compounds ...

    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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HALOALKANE DEHALOGENASEA296Sphingomonas paucimobilisMutation(s): 0 
EC: 3.8.1.5
UniProt
Find proteins for D4Z2G1 (Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S))
Explore D4Z2G1 
Go to UniProtKB:  D4Z2G1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
PDO
Query on PDO

Download Ideal Coordinates CCD File 
D [auth A]1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.274 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.227α = 90
b = 71.721β = 90
c = 73.319γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXLrefinement
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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