1CIJ

HALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase.

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

(1999) Biochemistry 38: 12052-12061


  • PubMed Abstract: 
  • Haloalkane dehalogenase (DhlA) converts haloalkanes to their corresponding alcohols and halide ions. The rate-limiting step in the reaction of DhlA is the release of the halide ion. The kinetics of halide release have been analyzed by measuring halid ...

    Haloalkane dehalogenase (DhlA) converts haloalkanes to their corresponding alcohols and halide ions. The rate-limiting step in the reaction of DhlA is the release of the halide ion. The kinetics of halide release have been analyzed by measuring halide binding with stopped-flow fluorescence experiments. At high halide concentrations, halide import occurs predominantly via the rapid formation of a weak initial collision complex, followed by transport of the ion to the active site. To obtain more insight in this collision complex, we determined the X-ray structure of DhlA in the presence of bromide and investigated the kinetics of mutants that were constructed on the basis of this structure. The X-ray structure revealed one bromide ion firmly bound in the active site and two bromide ions weakly bound on the surface of the enzyme. One of the weakly bound ions is close to Thr197 and Phe294, near the entrance of the earlier proposed tunnel for substrate import. Kinetic analysis of bromide import by the Thr197Ala and Phe294Ala mutants of DhlA at high halide concentration showed that the rate constants for halide binding no longer displayed a wild-type-like parabolic increase with increasing bromide concentrations. This is in agreement with an elimination or a decrease in affinity of the surface-located halide-binding site. Likewise, chloride binding kinetics of the mutants indicated significant differences with wild-type enzyme. The results indicate that Thr197 and Phe294 are involved in the formation of an initial collision complex for halide import in DhlA and provide experimental evidence for the role of the tunnel in substrate and product transport.


    Related Citations: 
    • Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism.
      Verschueren, K.H.,Franken, S.M.,Rozeboom, H.J.,Kalk, K.H.,Dijkstra, B.W.
      (1993) J.Mol.Biol. 232: 856
    • Crystallization of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
      Rozeboom, H.J.,Kingma, J.,Janssen, D.B.,Dijkstra, B.W.
      (1988) J.Mol.Biol. 200: 611
    • Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes.
      Franken, S.M.,Rozeboom, H.J.,Kalk, K.H.,Dijkstra, B.W.
      (1991) Embo J. 10: 1297
    • Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.
      Verschueren, K.H.,Seljee, F.,Rozeboom, H.J.,Kalk, K.H.,Dijkstra, B.W.
      (1993) Nature 363: 693


    Organizational Affiliation

    Laboratory of Biochemistry, BIOSON Research Institute, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HALOALKANE DEHALOGENASE)
A
310Xanthobacter autotrophicusMutation(s): 0 
Gene Names: dhlA
EC: 3.8.1.5
Find proteins for P22643 (Xanthobacter autotrophicus)
Go to UniProtKB:  P22643
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.407α = 90.00
b = 71.964β = 90.00
c = 40.968γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2019-11-20
    Type: Database references