Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains.

Abstract The three-dimensional structure of bovine liver rhodanese, a mitochondrial sulfurtransferase, has been determined at 2.5 A resolution using the multiple isomorphous replacement technique. The molecule consists of a single polypeptide chain of 293 residues. It is folded into an ellipsoid of 60 A × 50 A × 40 A with two domains which are of remarkably similar structure and are related by a pseudo 2-fold axis. It appears that the similarity in conformation of the domains is virtually not reflected in the amino acid sequence: the minimum base change per codon between the equivalent residues is 1.27 and only 13% of the equivalent amino acids are identical. Possible reasons for this intriguing observation are discussed. The core of each domain is a five-stranded parallel pleated sheet flanked by two helices on one side and three on the other. Two of the helices in each domain run anti-parallel to the neighbouring β-strands, giving rise to right-handed βαβ units. This architecture of proteins has been found in several other instances and the conformation of rhodanese is henceforth compared with the two nucleotide binding proteins, flavodoxin and alcohol dehydrogenase. It appears that the similarity of rhodanese with these two proteins hardly extends beyond the β-sheet. A comparison of the βαβ units within rhodanese shows them to be all very similar, particularly those within the first domain. The active site of rhodanese is a pocket in between the two domains. The essential Cys247 is located at the N-terminal end of a long helix in the second domain. As active sites or coenzyme binding sites frequently occur at helix termini, it is suggested that the dipole moment of an α-helix (Wada, 1976) is a factor involved in determining the properties of a protein molecule.