3WFJ image
Deposition Date 2013-07-19
Release Date 2014-07-23
Last Version Date 2023-11-08
Entry Detail
PDB ID:
3WFJ
Keywords:
OXIDOREDUCTASE
Title:
The complex structure of D-mandelate dehydrogenase with NADH
Biological Source:
Source Organism:
Enterococcus faecium (Taxon ID: 1352)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.80 Å
R-Value Free:
0.30
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
P 1 21 1
3WFJ validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:2-dehydropantoate 2-reductase
Gene (Uniprot):AWT83_06180, B1P95_08245, CUN04_09550, CYQ77_12020, DKP91_09695, GBM73_08440, HV480_00795, KYX88_01655, P6Z85_14490, pLG1-0150
Chain IDs:A, B, C, D, E, F, G, H
Chain Length:312
Number of Molecules:8
Biological Source:Enterococcus faecium
UniProt ID:E3USM3 Pfam ID:PF02558, PF08546 EC:1.1.1.345
Ligand Molecules
NAD
Primary Citation
The crystal structure of D-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase.
Biochem.Biophys.Res.Commun. 439 109 114 (2013)
PMID: 23954635 DOI: 10.1016/j.bbrc.2013.08.019

Abstact

D-Mandelate dehydrogenases (D-ManDHs), belonging to a new d-2-hydroxyacid dehydrogenase family, catalyze the conversion between benzoylformate and d-mandelate using NAD as a coenzyme. We determined the first D-ManDH structure, that of ManDH2 from Enterococcus faecalis IAM10071. The overall structure showed ManDH2 has a similar fold to 2-ketopantoate reductase (KPR), which catalyzes the conversion of 2-ketopantoate to d-pantoate using NADP as a coenzyme. They share conserved catalytic residues, indicating ManDH2 has the same reaction mechanism as KPR. However, ManDH2 exhibits significant structural variations in the coenzyme and substrate binding sites compared to KPR. These structural observations could explain their different coenzyme and substrate specificities.

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Chemical

Disease

Primary Citation of related structures
3WFI