3A28

Crystal structure of L-2,3-butanediol dehydrogenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 

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Literature

Structural basis for chiral substrate recognition by two 2,3-butanediol dehydrogenases

Otagiri, M., Ui, S., Takusagawa, Y., Ohtsuki, T., Kurisu, G., Kusunoki, M.

(2010) FEBS Lett 584: 219-223

  • DOI: https://doi.org/10.1016/j.febslet.2009.11.068
  • Primary Citation of Related Structures:  
    3A28

  • PubMed Abstract: 

    2,3-butanediol dehydrogenase (BDH) catalyzes the NAD-dependent redox reaction between acetoin and 2,3-butanediol. There are three types of homologous BDH, each stereospecific for both substrate and product. To establish how these homologous enzymes possess differential stereospecificities, we determined the crystal structure of l-BDH with a bound inhibitor at 2.0 A. Comparison with the inhibitor binding mode of meso-BDH highlights the role of a hydrogen-bond from a conserved Trp residue(192). Site-directed mutagenesis of three active site residues of meso-BDH, including Trp(190), which corresponds to Trp(192) of L-BDH, converted its stereospecificity to that of L-BDH. This result confirms the importance of conserved residues in modifying the stereospecificity of homologous enzymes.

    • Organizational Affiliation: 

    Laboratory of Environmental Molecular Biology, RIKEN, Tsurumi-ward, Kanagawa, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-2.3-butanediol dehydrogenase258Corynebacterium glutamicumMutation(s): 0 
UniProt
Find proteins for Q9ZNN8 (Corynebacterium glutamicum)
Explore Q9ZNN8 
Go to UniProtKB:  Q9ZNN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZNN8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
AA [auth H]
I [auth C]
L [auth D]
O [auth A]
Q [auth B]
AA [auth H],
I [auth C],
L [auth D],
O [auth A],
Q [auth B],
S [auth E],
V [auth F],
Y [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
BME
Query on BME
Download Ideal Coordinates CCD File 
BA [auth H]
J [auth C]
M [auth D]
P [auth A]
R [auth B]
BA [auth H],
J [auth C],
M [auth D],
P [auth A],
R [auth B],
T [auth E],
W [auth F],
Z [auth G]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
K [auth C],
N [auth D],
U [auth E],
X [auth F]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.8α = 96.1
b = 69.2β = 100.2
c = 127.4γ = 109.6
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description