7OL1

The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.

• PDB DOI: https://doi.org/10.2210/pdb7OL1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-18 Released: 2021-06-16 
• Deposition Author(s): Guo, J., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.

Adjogatse, E., Bennett, J., Guo, J., Erskine, P.T., Wood, S.P., Wren, B.W., Cooper, J.B.

(2021) Acta Crystallogr F Struct Biol Commun 77: 269-274

• PubMed: 34341193 
• DOI: https://doi.org/10.1107/S2053230X21007135
• Primary Citation of Related Structures:  
  7OL1


• PubMed Abstract: 
  

  In many prokaryotes, the first step of threonine metabolism is catalysed by the enzyme threonine dehydrogenase (TDH), which uses NAD ⁺ to oxidize its substrate to 2-amino-3-ketobutyrate. The absence of a functional TDH gene in humans suggests that inhibitors of this enzyme may have therapeutic potential against pathogens which are reliant on this enzyme. Here, TDH from Clostridium difficile has been cloned and overexpressed, and the X-ray structure of the apoenzyme form has been determined at 2.6 Å resolution.

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Organizational Affiliation: 

Division of Medicine, UCL, Gower Street, London WC1E 6BT, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.42 kDa 
• Atom Count: 5,142 
• Modelled Residue Count: 638 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine 3-dehydrogenase	A, B	339	Clostridioides difficile	Mutation(s): 0  Gene Names: cdgr_08060, NCTC13307_02322, SAMEA1402406_00083, SAMEA3375037_00176 EC: 1.1.1.103
UniProt
Find proteins for Q187A2 (Clostridioides difficile (strain 630)) Explore Q187A2  Go to UniProtKB:  Q187A2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.5281/zenodo.4771118

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.87	α = 90
b = 180.87	β = 90
c = 88.35	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Guo, J., Cooper, J.B.

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description