› 5z20

X-ray diffraction
2.2Å resolution

The ternary structure of D-lactate dehydrogenase from Pseudomonas aeruginosa with NADH and oxamate

Released:
DOI: 10.2210/pdb5z20/pdb
PDB entry 5z20 coloured by chain, front view.
PDB entry 5z20 coloured by chain, side view.
PDB entry 5z20 coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria.
Furukawa N, Miyanaga A, Nakajima M, Taguchi H
Biochemistry 57 5388-5406 (2018)
PMID: 30149697

Function and Biology Details

Reaction catalysed: 
(R)-lactate + NAD(+) = pyruvate + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191401 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-lactate dehydrogenase (Fermentative) Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 345 amino acids
Theoretical weight: 37.83 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I530 (Residues: 1-329; Coverage: 100%)
Gene names: PA0927, ldhA
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAI 6 x NAI
5 bound ligands:
Ligand FMT 2 x FMT
Ligand OXM 6 x OXM
Ligand PGE 4 x PGE
Ligand PEG 1 x PEG
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P3121
Unit cell:
a: 155.69Å b: 155.69Å c: 230.011Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.171 0.199
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus.
Lück et al. (2022)
3 more

1 mention without citation

Structural Basis of Sequential and Concerted Cooperativity.
Morea et al. (2022)