1HYH

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

Summary for 1HYH

• Entry DOI: 10.2210/pdb1hyh/pdb
• Descriptor: L-2-HYDROXYISOCAPROATE DEHYDROGENASE, SULFATE ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: l-2-hydroxycarboxylate dehydrogenase, l-lactate dehydrogenase, oxidoreductase (choh(d)-nad+(a))
• Biological source: Weissella confusa
• Total number of polymer chains: 4
• Total formula weight: 135358.45

Authors

Niefind, K.,Hecht, H.-J.,Schomburg, D. (deposition date: 1995-06-05, release date: 1995-10-15, Last modification date: 2024-05-22)

Primary citation

Niefind, K.,Hecht, H.J.,Schomburg, D.
Crystal structure of L-2-hydroxyisocaproate dehydrogenase from Lactobacillus confusus at 2.2 A resolution. An example of strong asymmetry between subunits.
J.Mol.Biol., 251:256-281, 1995

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+. 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.

PubMed: 7643402
DOI: 10.1006/jmbi.1995.0433

Experimental method

X-RAY DIFFRACTION (2.2 Å)