Structural and kinetic properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation

J Mol Biol. 2008 Oct 10;382(3):802-11. doi: 10.1016/j.jmb.2008.07.050. Epub 2008 Jul 25.

Abstract

2-(Hydroxymethyl)glutarate dehydrogenase, the fourth enzyme of the anaerobic nicotinate fermentation pathway of Eubacterium barkeri, catalyzes the NADH-dependent conversion between (S)-2-formylglutarate and (S)-2-(hydroxymethyl)glutarate. As shown by its 2.3-A crystal structure, this enzyme is a novel member of the beta-hydroxyacid dehydrogenase family and adopts a tetrameric architecture with monomers interacting via their C-terminal catalytic domains. The NAD-binding domains protrude heterogeneously from the central, tetrameric core with domain rotation angles differing up to 12 degrees. Kinetic properties of the enzyme, including NADH inhibition constants, were determined. A strong NADH binding in contrast to weaker NAD(+) binding of the protein was inferred from fluorometrically determined binding constants for the dinucleotide cofactor. The data support either an Iso Ordered Bi Bi mechanism or a more common Ordered Bi Bi mechanism as found in other dehydrogenases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Carbohydrate Dehydrogenases / chemistry*
  • Carbohydrate Dehydrogenases / genetics
  • Carbohydrate Dehydrogenases / metabolism*
  • Crystallography, X-Ray
  • Eubacterium / metabolism
  • Fermentation*
  • Humans
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • NAD / chemistry
  • NAD / metabolism
  • Niacin / chemistry
  • Niacin / metabolism*
  • Protein Conformation*
  • Sequence Alignment

Substances

  • Bacterial Proteins
  • NAD
  • Niacin
  • Carbohydrate Dehydrogenases
  • gulonate dehydrogenase

Associated data

  • PDB/3CKY