D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate

Matsumoto, Y.Yasutake, Y.Takeda, Y.Tamura, T.Yokota, A.Wada, M.

(2015) Appl Microbiol Biotechnol 99: 7137-7150

  • DOI: https://doi.org/10.1007/s00253-015-6479-3
  • Primary Citation of Related Structures:  
    3WQC, 3WQD, 3WQE, 3WQF, 3WQG, 4PB3, 4PB4, 4PB5

  • PubMed Abstract: 

    D-threo-3-Hydroxyaspartate dehydratase (D-THA DH) is a fold-type III pyridoxal 5'-phosphate-dependent enzyme, isolated from a soil bacterium of Delftia sp. HT23. It catalyzes the dehydration of D-threo-3-hydroxyaspartate (D-THA) and L-erythro-3-hydroxyaspartate (L-EHA). To elucidate the mechanism of substrate stereospecificity, crystal structures of D-THA DH were determined in complex with various ligands, such as an inhibitor (D-erythro-3-hydroxyaspartate (D-EHA)), a substrate (L-EHA), and the reaction intermediate (2-amino maleic acid). The C (β) -OH of L-EHA occupied a position close to the active-site Mg(2+), clearly indicating a possibility of metal-assisted C (β) -OH elimination from the substrate. In contrast, the C (β) -OH of an inhibitor was bound far from the active-site Mg(2+). This suggests that the substrate specificity of D-THA DH is determined by the orientation of the C (β) -OH at the active site, whose spatial arrangement is compatible with the 3R configuration of 3-hydroxyaspartate. We also report an optically pure synthesis of L-threo-3-hydroxyaspartate (L-THA) and D-EHA, promising intermediates for the synthesis of β-benzyloxyaspartate, by using a purified D-THA DH as a biocatalyst for the resolution of racemic DL-threo-3-hydroxyaspartate (DL-THA) and DL-erythro-3-hydroxyaspartate (DL-EHA). Considering 50 % of the theoretical maximum, efficient yields of L-THA (38.9 %) and D-EHA (48.9 %) as isolated crystals were achieved with >99 % enantiomeric excess (e.e.). The results of nuclear magnetic resonance signals verified the chemical purity of the products. We were directly able to isolate analytically pure compounds by the recrystallization of acidified reaction mixtures (pH 2.0) and thus avoiding the use of environmentally harmful organic solvents for the chromatographic purification.

  • Organizational Affiliation

    Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, 060-8589, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-threo-3-hydroxyaspartate dehydratase
A, B
390Delftia sp. HT23Mutation(s): 0 
Gene Names: dthadh
Find proteins for B2DFG5 (Delftia sp. (strain HT23))
Explore B2DFG5 
Go to UniProtKB:  B2DFG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2DFG5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C8 H10 N O6 P
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A],
K [auth B],
M [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.689α = 90
b = 157.689β = 90
c = 158.784γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXEmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-08-26
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description