Crystal Structure of L-threonine dehydrogenase from Phytophthora infestans

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.238 

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This is version 1.2 of the entry. See complete history


Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans.

Yoneda, K.Nagano, R.Mikami, T.Sakuraba, H.Fukui, K.Araki, T.Ohshima, T.

(2020) Enzyme Microb Technol 140: 109627-109627

  • DOI: https://doi.org/10.1016/j.enzmictec.2020.109627
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD + and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.

  • Organizational Affiliation

    Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka, 535-8585, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-threonine 3-dehydrogenase, putative
A, B, C, D, E
A, B, C, D, E, F
345Phytophthora infestans T30-4Mutation(s): 0 
Gene Names: PITG_05140
Find proteins for D0N3N0 (Phytophthora infestans (strain T30-4))
Explore D0N3N0 
Go to UniProtKB:  D0N3N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0N3N0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
P [auth D]
S [auth E]
I [auth A],
K [auth B],
M [auth C],
P [auth D],
S [auth E],
U [auth F]
C21 H27 N7 O14 P2
Query on PE8

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H [auth A],
O [auth D]
C16 H34 O9
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth C]
N [auth D]
Q [auth E]
G [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth E],
R [auth E],
T [auth F]
C6 H5 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.207α = 90
b = 98.865β = 106.72
c = 152.515γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16K18689

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description