› 5lc1

X-ray diffraction
2.1Å resolution

L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.

Released:
DOI: 10.2210/pdb5lc1/pdb
PDB entry 5lc1 coloured by chain, front view.
PDB entry 5lc1 coloured by chain, side view.
PDB entry 5lc1 coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations.
Adjogatse E, Erskine P, Wells SA, Kelly JM, Wilden JD, Chan AWE, Selwood D, Coker A, Wood S, Cooper JB
Acta Crystallogr D Struct Biol 74 861-876 (2018)
PMID: 30198897

Function and Biology Details

Reaction catalysed: 
L-threonine + NAD(+) = L-2-amino-3-oxobutanoate + NADH
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182221 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent epimerase/dehydratase domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 321 amino acids
Theoretical weight: 35.85 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7YW97 (Residues: 14-332; Coverage: 100%)
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 6 x NAD
4 bound ligands:
Ligand PYR 6 x PYR
Ligand BME 2 x BME
Ligand ACT 3 x ACT
Ligand NA 6 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21212
Unit cell:
a: 132.04Å b: 276.49Å c: 55.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.147 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Why is manganese so valuable to bacterial pathogens?
Čapek et al. (2023)

1 mention without citation

The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
Adjogatse et al. (2021)