3WI7

Crystal Structure of the Novel Haloalkane Dehalogenase DatA from Agrobacterium tumefaciens C58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism.

Guan, L.Yabuki, H.Okai, M.Ohtsuka, J.Tanokura, M.

(2014) Appl.Microbiol.Biotechnol. --: --

  • DOI: 10.1007/s00253-014-5751-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 belongs to the HLD-II subfamily and hydrolyzes brominated and iodinated compounds, leading to the generation of the corresponding alcohol, a halide ion, and a proton. Because Dat ...

    A novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 belongs to the HLD-II subfamily and hydrolyzes brominated and iodinated compounds, leading to the generation of the corresponding alcohol, a halide ion, and a proton. Because DatA possesses a unique Asn-Tyr pair instead of the Asn-Trp pair conserved among the subfamily members, which was proposed to keep the released halide ion stable, the structural basis for its reaction mechanism should be elucidated. Here, we determined the crystal structures of DatA and its Y109W mutant at 1.70 and 1.95 Å, respectively, and confirmed the location of the active site by using its novel competitive inhibitor. The structural information from these two crystal structures and the docking simulation suggested that (i) the replacement of the Asn-Tyr pair with the Asn-Trp pair increases the binding affinity for some halogenated compounds, such as 1,3-dibromopropane, mainly due to the electrostatic interaction between Trp109 and halogenated compounds and the change of substrate-binding mode caused by the interaction and (ii) the primary halide-stabilizing residue is only Asn43 in the wild-type DatA, while Tyr109 is a secondary halide-stabilizing residue. Furthermore, docking simulation using the crystal structures of DatA indicated that its enantioselectivity is determined by the large and small spaces around the halogen-binding site.


    Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Haloalkane dehalogenase
A, B
304Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: dhaA (dha)
EC: 3.8.1.5
Find proteins for Q8U671 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q8U671
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download SDF File 
Download CCD File 
A, B
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.700α = 90.00
b = 123.700β = 90.00
c = 88.070γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release