3WFI | pdb_00003wfi

The crystal structure of D-mandelate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb3WFI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-19 Released: 2014-07-23 
• Deposition Author(s): Miyanaga, A., Fujisawa, S., Furukawa, N., Arai, K., Nakajima, M., Taguchi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

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.

(2013) Biochem Biophys Res Commun 439: 109-114

• PubMed: 23954635 
• DOI: https://doi.org/10.1016/j.bbrc.2013.08.019
• Primary Citation Related Structures: 
  3WFI, 3WFJ


• PubMed Abstract: 
  

  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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Organizational Affiliation: 
• Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.74 kDa 
• Atom Count: 5,121 
• Modeled Residue Count: 623 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B	312	Enterococcus faecium	Mutation(s): 0  Gene Names: pLG1-0150 EC: 1.1.1.169
UniProt
Find proteins for E3USM3 (Enterococcus faecium) Explore E3USM3  Go to UniProtKB:  E3USM3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.8	α = 90
b = 40.68	β = 105.47
c = 88.94	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Miyanaga, A., Fujisawa, S., Furukawa, N., Arai, K., Nakajima, M., Taguchi, H.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description