3VDR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.176 

Starting Model: experimental
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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

  • DOI: https://doi.org/10.1107/S1744309109008537
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-hydroxybutyrate dehydrogenase
A, B, C, D
260Alcaligenes faecalisMutation(s): 0 
EC: 1.1.1.30
UniProt
Find proteins for D0VWQ0 (Alcaligenes faecalis)
Explore D0VWQ0 
Go to UniProtKB:  D0VWQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWQ0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
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
Query on NAD

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G [auth A],
M [auth B],
Q [auth C],
V [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
3HR
Query on 3HR

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I [auth A],
O [auth B],
S [auth C],
X [auth D]
(3R)-3-hydroxybutanoic acid
C4 H8 O3
WHBMMWSBFZVSSR-GSVOUGTGSA-N
AAE
Query on AAE

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J [auth A],
P [auth B],
T [auth C],
Y [auth D]
ACETOACETIC ACID
C4 H6 O3
WDJHALXBUFZDSR-UHFFFAOYSA-N
CA
Query on CA

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E [auth A],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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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 
  • R-Value Work: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.1α = 90
b = 91.1β = 90
c = 262γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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