Refined structure of baboon α-lactalbumin at 1.7 Å resolution: Comparison with C-type lysozyme

Abstract

The solution of the structure of α-lactalbumin from baboon milk ( Papio cynocephalus) at 4.5 Å resolution using the isomorphous replacement method has been reported previously. Initial refinement on the basis of these low-resolution studies was not successful because of the poor isomorphism of the best heavy-atom derivative. Because of the striking similarity between the structure of lysozyme and α-lactalbumin, a more cautious molecular replacement approach was tried to refine the model. Using hen egg-white lysozyme as the starting model, preliminary refinement was performed using heavily constrained least-squares minimization in reciprocal space. The model was further refined using stereochemical restraints at 1.7 Å resolution to a conventional crystallographic residual of 0.22 for 1141 protein atoms. In the final model, the root-mean-square deviation from ideality for bond distances is 0.015 Å, and for angle distances it is 0.027 Å. The refinement was carried out using the human α-lactalbumin sequence and “omit maps” calculated during the course of refinement indicated eight possible sequence changes in the baboon α-lactalbumin X-ray sequence. During the refinement, a tightly bound calcium ion and 150 water molecules, of which four are internal, have been located. Some of the water molecules were modelled for disordered side-chains. The co-ordination around the calcium is a slightly distorted pentagonal bipyramid. The Ca-O distances vary from 2.2 Å to 2.6 Å, representing a tight calcium-binding loop in the structure. The calcium-binding fold only superficially resembles the “EF-hand” and presumably has no evolutionary relationship with other EF-hand structures. The overall structure of α-lactalbumin is very similar to that of lysozyme. All large deviations occur in the loops where all sequence deletions and insertions are found. The C terminus appears to be rather flexible in α-lactalbumin compared to lysozyme. The experimental evidence supports the earlier predictions for the α-lactalbumin structure that were based upon the assumption that α-lactalbumin and lysozyme have similar three-dimensional structures, with minimal deletions and insertions. A detailed comparison of the two structures shows striking features as well as throwing some light on the evolution of these two proteins from a common precursor.