The conformation of mitochondrial malate dehydrogenase derived from an electron density map at 5.3-A resolution

A monoclinic form of crystalline porcine heart mitochondrial malate dehydrogenase has been prepared and contains two dimers in the asymmetric unit. The analysis of single crystal x-ray data shows that the two dimers are packed in the crystal lattice as a tetramer with approximate 222-point symmetry. Heavy atom derivatives using the compounds ethylmercurithiosalicylic acid and IrCl3 have been characterized and multiple isomorphous replacement methods have been used to obtain an electron density map at 5.3-A resolution. The phasing of the x-ray data was aided by including contributions from crystal forms with and without the coenzyme, NAD+. By using electron density averaging methods, the quality of the low resolution electron density map was improved to the point where it was possible to establish the overall conformation of mitochondrial malate dehydrogenase. The results confirm the proposed similarities between the mitochondrial and cytoplasmic forms of the malate dehydrogenases. Studies using x-ray data from the apo- and holo-forms of the enzyme describe the location of the active site as well as the arrangement of subunits in the tetrameric crystalline form of the enzyme.