Polypeptide conformation of cytoplasmic malate dehydrogenase from an electron density map at 3.0 Å resolution

Abstract

The polypeptide chain conformation of both subunits of eytoplasmic malate dehydrogenase has been determined from an electron density map at 3.0 Å resolution. The two polypeptide chains are believed to be sequentially identical, but in the crystals studied, only one subunit will bind additional coenzyme, nicotinamide adenine dinucleotide. The present interpretation of the chain-folding places 665 alpha carbons in the dirner. A least-squares fit of these alpha carbon positions indicates that the two subunits in the dimer are closely related by 2-fold rotational symmetry. The folding of the polypeptide chains of malate dehydrogenase involves considerable amounts of secondary structure. The first 150 residues from the amino terminal end of the chain involve alternating parallel extended and helical conformations. The parallel-extended segments form a twisted sheet, one region of which includes the active site. The remaining polypeptide chain cannot be described in such a regular manner. It does, however, include helical segments and regions of anti-parallel extended polypeptide chain. The interface between the two subunits consists of three helical regions from each subunit. The polypeptide conformation of malate dehydrogenase is remarkably similar to that of dogfish lactate dehydrogenase. While the atomic co-ordinates of malate dehydrogenase will be improved by a higher resolution electron density map, it is already clear that these two different enzymes have fundamentally the same conformation. The one exception to the structural homology is the absence of the lactate dehydrogenase extended arm in the malate dehydrogenase structure. This arm in lactate dehydrogenase contains the first 22 amino acids at the N-terminal. In addition to the structural homology in the polypeptide conformation, both enzymes bind nicotinamide adenine dinucleotide in structurally homologous regions.