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› 5z21

X-ray diffraction
2.3Å resolution

The ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH and oxamate

Released:
DOI: 10.2210/pdb5z21/pdb
Model geometry
Fit model/data
PDB entry 5z21 coloured by chain, front view.
PDB entry 5z21 coloured by chain, side view.
PDB entry 5z21 coloured by chain, top view.
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
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 + H(+).
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-185983 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-lactate dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 358 amino acids
Theoretical weight: 40.79 KDa
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RG11 (Residues: 1-335; Coverage: 100%)
Gene name: FN0511
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAI 4 x NAI
1 bound ligand:
Ligand OXM 4 x OXM
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21212
Unit cell:
a: 117.23Å b: 159.74Å c: 90Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.225 0.251
Expression system: Escherichia coli

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Citations

3 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)
2 more

3 mentions without citation

Identification and characterization of the LRR repeats in plant LRR-RLKs.
Chen T. (2021)
2 more