Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1006/jmbi.1996.0864
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-2-HYDROXYISOCAPROATE DEHYDROGENASE333Lacticaseibacillus caseiMutation(s): 0 
EC: 1.1.1
Find proteins for P17584 (Lacticaseibacillus paracasei)
Explore P17584 
Go to UniProtKB:  P17584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17584
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata 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: 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
  • Version 1.5: 2023-08-09
    Changes: Database references, Other, Refinement description