1AQ6

STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate.

Ridder, I.S.Rozeboom, H.J.Kalk, K.H.Janssen, D.B.Dijkstra, B.W.

(1997) J.Biol.Chem. 272: 33015-33022


  • PubMed Abstract: 
  • The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Its crystal st ...

    The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Its crystal structure was solved by the method of multiple isomorphous replacement with incorporation of anomalous scattering information and solvent flattening, and was refined at 1.95-A resolution to an R factor of 21.3%. The three-dimensional structure is similar to that of the homologous L-2-haloacid dehalogenase from Pseudomonas sp. YL (1), but the X. autotrophicus enzyme has an extra dimerization domain, an active site cavity that is completely shielded from the solvent, and a different orientation of several catalytically important amino acid residues. Moreover, under the conditions used, a formate ion is bound in the active site. The position of this substrate-analogue provides valuable information on the reaction mechanism and explains the limited substrate specificity of the Xanthobacter L-2-haloacid dehalogenase.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of L-2-Haloacid Dehalogenase from Xanthobacter Autotrophicus Gj10
      Ridder, I.S.,Rozeboom, H.J.,Kingma, J.,Janssen, D.B.,Dijkstra, B.W.
      (1995) Protein Sci. 4: 2619


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-2-HALOACID DEHALOGENASE
A, B
253Xanthobacter autotrophicusGene Names: dhlB
EC: 3.8.1.2
Find proteins for Q60099 (Xanthobacter autotrophicus)
Go to UniProtKB:  Q60099
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.246α = 90.00
b = 84.160β = 90.00
c = 91.487γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASESphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance