1HYH

CRYSTAL STRUCTURE OF L-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS CONFUSUS AT 2.2 ANGSTROMS RESOLUTION-AN EXAMPLE OF STRONG ASYMMETRY BETWEEN SUBUNITS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of L-2-hydroxyisocaproate dehydrogenase from Lactobacillus confusus at 2.2 A resolution. An example of strong asymmetry between subunits.

Niefind, K.Hecht, H.J.Schomburg, D.

(1995) J Mol Biol 251: 256-281

  • DOI: 10.1006/jmbi.1995.0433
  • Primary Citation of Related Structures:  
    1HYH

  • PubMed Abstract: 
  • L-2-Hydroxyisocaproate dehydrogenase (L-HicDH) from Lactobacillus confusus, a homotetramer with a molecular mass of 33 kDa per subunit, belongs to the protein family of the NAD(+)-dependent L-2-hydroxycarboxylate dehydrogenases. L-HicDH was crystallized with ammonium sulphate as precipitant in the presence of NAD+ ...

    L-2-Hydroxyisocaproate dehydrogenase (L-HicDH) from Lactobacillus confusus, a homotetramer with a molecular mass of 33 kDa per subunit, belongs to the protein family of the NAD(+)-dependent L-2-hydroxycarboxylate dehydrogenases. L-HicDH was crystallized with ammonium sulphate as precipitant in the presence of NAD+. The crystals belong to the trigonal space group P3(2)21, with a = 135.9 A and c = 205.9 A, and diffract X-rays to 2.2 A resolution. The crystal structure was solved by Patterson search and molecular replacement techniques and refined to an R-value of 21.4% (2.2 to 8 A). The final structure model contains one NAD+ molecule and one sulphate ion per subunit, with 309 water molecules. An unusual feature of this crystal structure is the deviation of the protein subunits from non-crystallographic symmetry, which is so strong that it can be detected globally by self-rotation calculations in reciprocal space. This asymmetry is especially pronounced in the environment of the active site; it is reflected also in the nicotinamide conformation of NAD+ and allows some conclusions to be drawn about the catalytic mechanism. In this context, an "inner active site loop" is identified as a structural element of fundamental functional importance. Furthermore, with knowledge of the crystal structure of L-HicDH the differences in substrate specificity between L-HicDH and the L-lactate dehydrogenases can be partly explained.


    Related Citations: 
    • Deletion Variants of L-Hydroxyisocaproate Dehydrogenase-Probing Substrate Specificity
      Feil, I.K., Lerch, H.-P., Schomburg, D.
      (1994) Eur J Biochem 223: 857
    • 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(Slash)Variante Q59R (German, with English Summary)
      Niefind, K.
      (1993) Thesis --: --
    • Cloning, Sequencing and Expression of the L-2-Hydroxyisocaproate Dehydrogenase-Encoding Gene of Lactobacillus Confusus in Escherichia Coli
      Lerch, H.-P., Frank, R., Collins, J.
      (1989) Gene 83: 263
    • L-2-Hydroxyisocaproate Dehydrogenase-A New Enzyme from Lactobacillus Confusus for the Stereospecific Reduction of 2-Ketocarboxylic Acids
      Schuette, H., Hummel, W., Kula, M.-R.
      (1984) Appl Microbiol Biotechnol 19: 167

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-2-HYDROXYISOCAPROATE DEHYDROGENASEABCD309Weissella confusaMutation(s): 0 
EC: 1.1.1.27 (PDB Primary Data), 1.1.1 (UniProt)
Find proteins for P14295 (Weissella confusa)
Explore P14295 
Go to UniProtKB:  P14295
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Observed: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.9α = 90
b = 135.9β = 90
c = 205.9γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Database references, Derived calculations, Other