Biological Crystallography Structures of the B1 Domain of Protein L from Peptostreptococcus Magnus with a Tyrosine to Tryptophan Substitution

The three-dimensional structure of a tryptophan-containing variant of the IgG-binding B1 domain of protein L has been solved in two crystal forms to 1.7 and 1.8 A resolution. In one of the crystal forms, the entire N-terminal histidine-tag region was immobilized through the coordination of zinc ions and its structural conformation along with the zinc coordination scheme were determined. However, the ordering of the histidine tag by zinc does not affect the overall structure of the rest of the protein. Structural comparisons of the tryptophan-containing variant with an NMR-derived wild-type structure, which contains a tyrosine at position 47, reveals a common fold, although the overall backbone root-mean-square difference is 1.5 A. The Y47W substitution only caused local rearrangement of several side chains, the most prominent of which is the rotation of the Tyr34 side chain, resulting in a 6 A displacement of its hydroxyl group. A small methyl-sized cavity bounded by beta-strands 1, 2 and 4 and the alpha-helix was found in the structures of the Y47W-substituted protein L B1 domain. This cavity may be created as the result of subsequent side-chain rearrangements caused by the Y47W substitution. These high-resolution structures of the tryptophan-containing variant provide a reference frame for the analysis of thermodynamic and kinetic data derived from a series of mutational studies of the protein L B1 domain.

[1]  L. Björck,et al.  Proton nuclear magnetic resonance sequential assignments and secondary structure of an immunoglobulin light chain-binding domain of protein L. , 1993, Biochemistry.

[2]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[3]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[4]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[5]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[6]  E. Nielsen,et al.  Protein L, a bacterial immunoglobulin-binding protein and possible virulence determinant , 1990 .

[7]  A. Fersht,et al.  Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. , 1993, Biochemistry.

[8]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[9]  D Baker,et al.  Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. , 1997, Journal of molecular biology.

[10]  L. Björck,et al.  Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein L. Comparison with the IgG-binding domains of protein G. , 1994, Biochemistry.

[11]  A. Fersht,et al.  Crystal structural analysis of mutations in the hydrophobic cores of barnase. , 1994, Journal of molecular biology.

[12]  A. Fersht,et al.  Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. , 1996, Biochemistry.

[13]  J M Thornton,et al.  SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. , 1990, Journal of molecular biology.

[14]  D Baker,et al.  Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. , 1997, Biochemistry.

[15]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[16]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[17]  B. Matthews,et al.  A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene , 1993, Nature.

[18]  B. Matthews,et al.  Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. , 1992, Science.

[19]  V. Cofman.  Biophysical chemistry. Part II , 1929 .

[20]  D Baker,et al.  A breakdown of symmetry in the folding transition state of protein L. , 2000, Journal of molecular biology.

[21]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[22]  D. McRee,et al.  A visual protein crystallographic software system for X11/Xview , 1992 .