1DXY

STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution.

Dengler, U.Niefind, K.Kiess, M.Schomburg, D.

(1997) J Mol Biol 267: 640-660

  • DOI: 10.1006/jmbi.1996.0864
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimer with 333 amino acids and a molecular mass of 37 kDa per subunit. The enzyme belongs to the protein family of NAD+-dependent D-2-hydroxycarboxylate dehydrogenases a ...

    D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimer with 333 amino acids and a molecular mass of 37 kDa per subunit. The enzyme belongs to the protein family of NAD+-dependent D-2-hydroxycarboxylate dehydrogenases and within this family to the subgroup of D-lactate dehydrogenases (D-LDHs). Compared with other D-LDHs D-HicDH is characterized by a very low specificity regarding size and chemical constitution of the accepted D-2-hydroxycarboxylates. Hexagonal crystals of recombinant D-HicDH in the presence of NAD+ and 2-oxoisocaproate (4-methyl-2-oxopentanoate) were grown with ammonium sulphate as precipitating agent. The structure of these crystals was solved by molecular replacement and refined to a final R-factor of 19.6% for all measured X-ray reflections in the resolution range (infinity to 1.86 A). Both NAD+ and 2-oxoisocaproate were identified in the electron density map; binding of the latter in the active site, however, competes with a sulphate ion, which is also defined by electron density. Additionally the final model contains 182 water molecules and a second sulphate ion. The binding of both an in vitro substrate and the natural cosubstrate in the active site provides substantial insight into the catalytic mechanism and allows us to assess previously published active site models for this enzyme family, in particular the two most controversial points, the role of the conserved Arg234 and substrate binding. Furthermore the overall topology and details of the D-HicDH structure are described, discussed against the background of homologous structures and compared with one closely and one distantly related protein.


    Related Citations: 
    • Crystallization and Preliminary Characterization of Crystals of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei
      Niefind, K., Hecht, H.J., Schomburg, D.
      (1994) J Mol Biol 240: 400
    • Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Confusus Alkalische Protease Aus Bacillus Alcalophilus/Variante Q59R
      Niefind, K.
      (1993) Thesis --: --
    • Potential of R-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei for Stereospecific Reductions
      Kallwass, H.K.W.
      (1992) Enzyme Microb Technol 14: 28
    • Cloning, Sequencing and Expression in Escherichia Coli of the D-2-Hydroxyisocaproate Dehydrogenase Gene of Lactobacillus Casei
      Lerch, H.P., Blocker, H., Kallwass, H., Hoppe, J., Tsai, H., Collins, J.
      (1989) Gene 78: 47
    • Crystallization and Molecular Properties of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei
      Kallwass, H., Tsai, H., Schuette, H.
      (1987) FEMS Microbiol Lett 43: 263
    • D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei. A New Enzyme Suitable for Stereospecific Reduction of 2-Ketocarboxylic Acids
      Hummel, W., Schuette, H., Kula, M.R.
      (1985) Appl Microbiol Biotechnol 21: 7

    Organizational Affiliation

    Gesellschaft fur Biotechnologische Forschung (GBF), Abteilung Molekulare Strukturforschung, Braunschweig, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-2-HYDROXYISOCAPROATE DEHYDROGENASE
A
333Lactobacillus caseiMutation(s): 0 
Gene Names: POTENTIAL
EC: 1.1.1
Find proteins for P17584 (Lactobacillus paracasei)
Go to UniProtKB:  P17584
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
COI
Query on COI

Download CCD File 
A
2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.1α = 90
b = 134.1β = 90
c = 125.1γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATA)data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-03-15
    Changes: Derived calculations