1ALC

REFINED STRUCTURE OF BABOON ALPHA-LACTALBUMIN AT 1.7 ANGSTROMS RESOLUTION. COMPARISON WITH C-TYPE LYSOZYME

Summary for 1ALC

• Entry DOI: 10.2210/pdb1alc/pdb
• Descriptor: ALPHA-LACTALBUMIN, CALCIUM ION (3 entities in total)
• Functional Keywords: calcium binding protein
• Biological source: Papio cynocephalus (yellow baboon)
• Total number of polymer chains: 1
• Total formula weight: 14229.10

Authors

Acharya, K.R.,Stuart, D.I.,Phillips, D.C. (deposition date: 1989-08-14, release date: 1989-10-15, Last modification date: 2024-10-30)

Primary citation

Acharya, K.R.,Stuart, D.I.,Walker, N.P.,Lewis, M.,Phillips, D.C.
Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme.
J.Mol.Biol., 208:99-127, 1989

PubMed Abstract: The solution of the structure of alpha-lactalbumin from baboon milk (Papio cynocephalus) at 4.5 A 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 alpha-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 A 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 A, and for angle distances it is 0.027 A. The refinement was carried out using the human alpha-lactalbumin sequence and "omit maps" calculated during the course of refinement indicated eight possible sequence changes in the baboon alpha-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 A to 2.6 A, 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 alpha-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 alpha-lactalbumin compared to lysozyme. The experimental evidence supports the earlier predictions for the alpha-lactalbumin structure that were based upon the assumption that alpha-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.

PubMed: 2769757
DOI: 10.1016/0022-2836(89)90091-0

Experimental method

X-RAY DIFFRACTION (1.7 Å)