3VDR | pdb_00003vdr

Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)

• PDB DOI: https://doi.org/10.2210/pdb3VDR/pdb
• Entry: 3VDR supersedes: 3EEW

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Mutation(s): No 


• Deposited: 2012-01-06 Released: 2012-02-08 
• Deposition Author(s): Hoque, M.M., Shimizu, S., Juan, E.C.M., Sato, Y., Hossain, M.T., Yamamoto, T., Imamura, S., Amano, H., Suzuki, K., Sekiguchi, T., Tsunoda, M., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 

Starting Model: experimental

Literature

Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.

Hoque, M.M., Shimizu, S., Juan, E.C.M., Sato, Y., Hossain, M.T., Yamamoto, T., Imamura, S., Suzuki, K., Amano, H., Sekiguchi, T., Tsunoda, M., Takenaka, A.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 331-335

• PubMed: 19342772 
• DOI: https://doi.org/10.1107/S1744309109008537
• Primary Citation Related Structures: 
  3VDR


• PubMed Abstract: 
  

  D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between D-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate D-3-hydroxybutyrate and the cofactor NAD(+) at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD(+) and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of D-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure.

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Organizational Affiliation: 
• Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 114.8 kDa 
• Atom Count: 8,281 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-hydroxybutyrate dehydrogenase	A, B, C, D	260	Alcaligenes faecalis	Mutation(s): 0  EC: 1.1.1.30
UniProt
Find proteins for D0VWQ0 (Alcaligenes faecalis) Explore D0VWQ0  Go to UniProtKB:  D0VWQ0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	H [auth A], N [auth B], R [auth C], W [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
NAD	G [auth A], M [auth B], Q [auth C], V [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
3HR	I [auth A], O [auth B], S [auth C], X [auth D]	(3R)-3-hydroxybutanoic acid C4 H8 O3 WHBMMWSBFZVSSR-GSVOUGTGSA-N
AAE	J [auth A], P [auth B], T [auth C], Y [auth D]	ACETOACETIC ACID C4 H6 O3 WDJHALXBUFZDSR-UHFFFAOYSA-N
CA	E [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], L [auth B], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.241 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.1	α = 90
b = 91.1	β = 90
c = 262	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Hoque, M.M., Shimizu, S., Juan, E.C.M., Sato, Y., Hossain, M.T., Yamamoto, T., Imamura, S., Amano, H., Suzuki, K., Sekiguchi, T., Tsunoda, M., Takenaka, A.
• This entry supersedes: 3EEW

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description