Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2 ',5 ')adenosine

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic -like ribonuclease superfamily. The native enzyme is a mixture of two dimer ic forms with distinct structural features. The most abundant form is chara cterized by the swapping of N-terminal fragments. In this paper, the crysta l structure of the complex between the swapping dimer and uridylyl(2'5')ade nosine is reported at 2.06 Angstrom resolution. The refined model has a cry stallographic R-factor of 0.184 and good stereochemistry. The quality of th e electron density maps enables the structure of both the inhibitor and act ive site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts a n extended conformation with the pyrimidine and purine base interacting wit h Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His 119, and Phe 120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specif ic water molecules believed to be relevant to catalytic activity. Upon bind ing of the dinucleotide, small but significant modifications of the tertiar y and quaternary structure of the protein are observed. The ensuing correla tion of these modifications with the catalytic activity of the enzyme is di scussed.