3CKY

Structural and Kinetic Properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation

Summary for 3CKY

• Entry DOI: 10.2210/pdb3cky/pdb
• Descriptor: 2-hydroxymethyl glutarate dehydrogenase (2 entities in total)
• Functional Keywords: rossmann fold, two domain enzyme, oxidoreductase
• Biological source: Eubacterium barkeri (Clostridium barkeri)
• Total number of polymer chains: 4
• Total formula weight: 123595.48

Authors

Reitz, S.,Alhapel, A.,Pierik, A.J.,Essen, L.-O. (deposition date: 2008-03-18, release date: 2008-08-26, Last modification date: 2024-02-21)

Primary citation

Reitz, S.,Alhapel, A.,Essen, L.O.,Pierik, A.J.
Structural and Kinetic Properties of a beta-Hydroxyacid Dehydrogenase Involved in Nicotinate Fermentation.
J.Mol.Biol., 382:802-811, 2008

PubMed 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.

PubMed: 18680749
DOI: 10.1016/j.jmb.2008.07.050

Experimental method

X-RAY DIFFRACTION (2.3 Å)