3VAY

Crystal structure of 2-Haloacid Dehalogenase from Pseudomonas syringae pv. Tomato DC3000


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.979 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of 2-haloacid dehalogenase from Pseudomonas syringae pv. tomato DC3000

Hou, Z.Zhang, H.Li, M.Chang, W.

(2013) Acta Crystallogr.,Sect.D 69: 1108-1114

  • DOI: 10.1107/S0907444913006021

  • PubMed Abstract: 
  • 2-Haloacid dehalogenases (2-HADs) catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the C(α)-atom position and releasing a halogen atom. These enzymes are of interest for their potential use in bioreme ...

    2-Haloacid dehalogenases (2-HADs) catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the C(α)-atom position and releasing a halogen atom. These enzymes are of interest for their potential use in bioremediation and in the synthesis of industrial chemicals. Here, the crystal structure of 2-HAD from Pseudomonas syringae pv. tomato DC3000 (ps-2-HAD) at 1.98 Å resolution solved using the single-wavelength anomalous dispersion method is reported. The ps-2-HAD molecule consists of two structurally distinct domains: the core domain and the subdomain. Enzymatic activity analysis of ps-2-HAD revealed its capacity to catalyse the dehalogenation of both L- and D-substrates; however, the structure of ps-2-HAD is completely different from that of DehI, which is the only DL-2-HAD enzyme that has been structurally characterized, but shows similar overall folding to L-HADs. Single mutations of four amino-acid residues at the putative active site showed that they are related to its enzymatic activity, yet three of them are nonconserved among HADs. These observations imply that ps-2-HAD has a novel active site and a unique catalytic behaviour compared with other HADs. This study provides a structural basis and biochemical evidence for further elucidation of the catalytic mechanism of 2-HAD.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HAD-superfamily hydrolase
A, B
230Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
Find proteins for Q88B12 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Go to UniProtKB:  Q88B12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.979 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.325α = 90.00
b = 92.274β = 108.13
c = 70.191γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description