Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 angstrom resolution

The three-dimensional structure of the R form of rabbit liver fructose 1,6- bisphosphatase (Fru-1,6-Pase; E.C. 3.1.3.11) has been determined by a combi nation of heavy-atom and molecular-replacement methods. A model, which incl udes 2394 protein atoms and 86 water molecules, has been refined at 2.3 Ang strom resolution to a crystallographic R factor of 0.177. The root-mean-squ are deviations of bond distances and angles from standard geometry are 0.01 2 Angstrom and 1.7 degrees, respectively. This structural result, in conjun ction with recently redetermined amino-acid sequence data, unequivocally es tablishes that the rabbit liver enzyme is not an aberrant bisphosphatase as once believed, but is indeed homologous to other Fru-1,6-Pases. The root-m ean-square deviation of the C alpha atoms in the rabbit liver structure fro m the homologous atoms in the pig kidney structure complexed with the produ ct, fructose 6-phosphate, is 0.7 Angstrom. Fru-1,6-Pases are homotetramers, and the rabbit liver protein crystallizes in space group I222 with one mon omer in the asymmetric unit. The structure contains a single endogenous Mg2 + ion coordinated by Glu97, Asp118, Asp121 and Glu280 at the site designate d metal site 1 in pig kidney Fru-1,6-Pase R-form complexes. In addition, tw o sulfate ions, which are found at the positions normally occupied by the 6 -phosphate group of the substrate, as well as the phosphate of the alloster ic inhibitor AMP appear to provide stability. Met177, which has hydrophobic contacts with the adenine moiety of AMP in pig kidney T-form complexes, is replaced by glycine. Binding of a non-hydrolyzable substrate analog, beta- methyl-fructose 1,6-bisphosphate, at the catalytic site is also examined.