› 3wfj

X-ray diffraction
2.8Å resolution

The complex structure of D-mandelate dehydrogenase with NADH

Released:
DOI: 10.2210/pdb3wfj/pdb
PDB entry 3wfj coloured by chain, front view.
PDB entry 3wfj coloured by chain, side view.
PDB entry 3wfj coloured by chain, top view.
Source organism: Enterococcus faecium
Primary publication:
The crystal structure of D-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase.
Miyanaga A, Fujisawa S, Furukawa N, Arai K, Nakajima M, Taguchi H
Biochem Biophys Res Commun 439 109-14 (2013)
PMID: 23954635

Function and Biology Details

Reaction catalysed: 
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122919 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-dehydropantoate 2-reductase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 312 amino acids
Theoretical weight: 34.37 KDa
Source organism: Enterococcus faecium
Expression system: Escherichia coli
UniProt:
  • Canonical: E3USM3 (Residues: 1-312; Coverage: 100%)
Gene names: AWT83_06180, B1P95_08245, B4W81_02790, CUN04_09550, FIU59_14170, GBM44_15605, GBM73_08440, HV425_00795, KYX88_01655, pLG1-0150
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 8 x NAD
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 115.65Å b: 103.44Å c: 119.74Å
α: 90° β: 90.01° γ: 90°
R-values:
R R work R free
0.242 0.239 0.306
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Diverse allosteric and catalytic functions of tetrameric d-lactate dehydrogenases from three Gram-negative bacteria.
Furukawa et al. (2014)
1 more

1 mention without citation

Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from Staphylococcus aureus.
Sanchez et al. (2015)