2XT0

Dehalogenase DPpA from Plesiocystis pacifica SIR-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cloning, Functional Expression, Biochemical Characterization, and Structural Analysis of a Haloalkane Dehalogenase from Plesiocystis Pacifica Sir-1.

Hesseler, M.Bogdanovic, X.Hidalgo, A.Berenguer, J.Palm, G.J.Hinrichs, W.Bornscheuer, U.T.

(2011) Appl.Microbiol.Biotechnol. 91: 1049

  • DOI: 10.1007/s00253-011-3328-x

  • PubMed Abstract: 
  • A haloalkane dehalogenase (DppA) from Plesiocystis pacifica SIR-1 was identified by sequence comparison in the NCBI database, cloned, functionally expressed in Escherichia coli, purified, and biochemically characterized. The three-dimensional (3D) st ...

    A haloalkane dehalogenase (DppA) from Plesiocystis pacifica SIR-1 was identified by sequence comparison in the NCBI database, cloned, functionally expressed in Escherichia coli, purified, and biochemically characterized. The three-dimensional (3D) structure was determined by X-ray crystallography and has been refined at 1.95 Å resolution to an R-factor of 21.93%. The enzyme is composed of an α/β-hydrolase fold and a cap domain and the overall fold is similar to other known haloalkane dehalogenases. Active site residues were identified as Asp123, His278, and Asp249 and Trp124 and Trp163 as halide-stabilizing residues. DppA, like DhlA from Xanthobacter autotrophicus GJ10, is a member of the haloalkane dehalogenase subfamily HLD-I. As a consequence, these enzymes have in common the relative position of their catalytic residues within the structure and also show some similarities in the substrate specificity. The enzyme shows high preference for 1-bromobutane and does not accept chlorinated alkanes, halo acids, or halo alcohols. It is a monomeric protein with a molecular mass of 32.6 kDa and exhibits maximum activity between 33 and 37°C with a pH optimum between pH 8 and 9. The K(m) and k(cat) values for 1-bromobutane were 24.0 mM and 8.08 s(-1). Furthermore, from the 3D-structure of DppA, it was found that the enzyme possesses a large and open active site pocket. Docking experiments were performed to explain the experimentally determined substrate preferences.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Putative Haloalkane Dehalogenase Dppa from Plesiocystis Pacifica Sir-I.
      Bogdanovic, X.,Hesseler, M.,Palm, G.J.,Bornscheuer, U.T.,Hinrichs, W.
      (2010) Acta Crystallogr.,Sect.F 66: 828


    Organizational Affiliation

    Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HALOALKANE DEHALOGENASE
A
297Plesiocystis pacifica SIR-1Mutation(s): 0 
Find proteins for A6G7B1 (Plesiocystis pacifica SIR-1)
Go to UniProtKB:  A6G7B1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.262α = 90.00
b = 108.501β = 90.00
c = 67.312γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
CrystalCleardata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-09-21
    Type: Derived calculations