Hen’s egg-white lysozyme

WJ Browne, ACT North, DC Phillips, K Brew, TC Vanaman, RC Hill. A possible three-dimensional stnicture of bovine a-lactalbumin based on that of hen s egg-white lysozyme. J Mol Biol 42 65-86, 1969. 

Detection of hen s egg white lysozyme in milk and dairy products... 

Each set of coordinates deposited with the PDB becomes a separate entry. Each entry is associated with an accession PDB code with a unique set of four alphanumeric characters. PDB and its mirror sites offer a text search engine that uses an index of all the textual information in each PDB record (e.g., PDB ID) an example of such an index is 1LYZ for hen s egg-white lysozyme. The first character is a version number. An identifier beginning with the number 0 signifies that the entry is purely bibliographic. The pdb file is a text file with an explanatory header followed by a set of atomic coordinates. The atomic coordinates are subjected to a set of standard stereochemical checks and are translated into a standard entry format for example, Figure 4.10 shows partial coordinate file for ILYZ.pdb or pdblLYZ.ent. 

Figure 4.10. PDB file (partial) for 3D structure of hen s egg-white lysozyme (ILYZ.pdb). The abbreviated file shows partial atomic coordinates for residues 34-36. Informational lines such as AUTHOR (contributing authors of the 3D structure), REVDAT, JRNL (primary bibliographic citation), REMARK (other references, corrections, refinements, resolution and missing residues in the structure), SEQRES (amino acid sequence), FTNOTE (list of possible hydrogen bonds), HELIX (initial and final residues of a-helices), SHEET (initial and final residues of / -sheets), TURN (initial and final residues of turns, types of turns), and SSBOND (disulfide linkages) are deleted here for brevity. Atomic coordinates for amino acid residues are listed sequentially on ATOM lines. The following HETATM lines list atomic coordinates of water and/or ligand molecules.

Figure 4.11. Graphic representations of protein 3D structure. Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first and second rows, ILYZ.pdb) and Cn3D (third row, ILYZ.val) are shown from left to right (color type) in wireframe (atom), spacefill (atom), dots (residue), backbone (residue), ribbons (secondary structure), strands (secondary structure), secondary structure (secondary structure), ball-and-stick (residue), and tubular (domain) representations.

Figure 4.17. Graphic display of KineMage in ribbon representation. The Ca chain of hen s egg-white lysozyme (ILYZ.kin derived from ILYZ.pdb) is displayed in ribbons showing secondary structure features.

Figure 15.9. Superimposition of 3D protein structures at CE server. The opening graphic window for the superimposition of the modeled (homology modeling with SPDBV) pigeon lysozyme (USR2 in pink) and hen s egg-white lysozyme, ILYZ.pdb (USR1 in blue). The superimposed structures are displayed with the alignment summary (e.g., sequence identity, rms deviation).

Figure 8 X-ray diffraction images, (a) A precession photograph of muconate lactonizing enzyme. The fourfold symmetry in the diffraction pattern is clearly visible. This gives an undistorted view of the reciprocal lattice but are no longer used because they are not as efficient as rotation images, (b) A rotation image of hen s egg white lysozyme. This easily obtainable image gives a distorted projection of the reciprocal lattice, but this is no obstacle for modern programs.

Structural characterization of glycosidases has a long history, with the very first crystal structure of an enzyme being that of hen s egg white lysozyme. Of the current 112 families of glycosidases, more than 60 families already have at least one representative structure determined. An important feature emerging from these structural studies is the occurrence of widely diversified structural scaffolds, despite the fact that all these... 

Hen s egg-white lysozyme (Tir.WI.) T. reesei /3-Side TIF.WL complexed with a product, MurNAc-GlcNAc-MurNAc,shows the ligand bound at subsites B-D.There is no room at subsite D for the -anomer of MurNAc as its axial 1-OH would clash with Asp52 and other residues in the region. These structural features confirm that water and other acceptors reach the reaction center only from the /3-side.1 The complex with o-iodobenzyl l-thio-/3-cellobioside shows no ordered water... 

Over the past few decades the reactions of a number of retaining gly-cosylases have been reported to involve an oxocarbonium ion rather than a covalent intermediate. During the same period, however, a revised version of the traditional double-displacement mechanism has become widely accepted as the way retaining glycosidases function. Here, the required covalent intermediate is reached via an oxocarbonium ionlike transition state in which the anomeric C-l atom remains partly bonded to its original axial or equatorial substituent, with a second transition state intervening between the intermediate and cosubstrate. According to this model, the idea of an ion-pair intermediate is untenable—with the questionable exception of hen s egg-white lysozyme.13715... 

Brodbeck and Ebner found that the soluble lactose synthetase from milk can be separated into two protein components, A and B, which individually do not exhibit any catalytic activity however, their recombination restores full lactose synthetase activity. The B fraction has been crystallized from bovine skim milk and bovine mammary tissue, and was identified as a-lactalbumin. It was thus found that a-lactalbumin can be substituted for the B protein of lactose synthetase. Lactose synthetases from the milk of sheep, goats, pigs, and humans were also resolved into A and B proteins, and the fractions from these species were shown to be qualitatively interchangeable in the rate assay of lactose synthesis. Determination of the amino acid sequence of a-lactalbumin (B fraction) has shown a distinct homology in the sequence of amino acids of a-lactalbumin and hen s egg-white lysozyme, suggesting that lysozyme and a-lactalbumin have evolved from a common ancestral gene. 

Figure 5.1 Common representations of the three-dimensional structures of proteins Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first row, ILYZ.pdb) are displayed in wireframe (residue type), spacefill (atom type) and backbone (structure type). The Cj, mainchain with side chain residues is displayed with KineMage (second raw left). The secondary structure representations (a helices and P-sheets) are visualized with KineMage (lLYZ.kin) in ribbons and arrows (second raw center), and Cn3D (ILYZ.cnS) in cylinders and arrows (second raw right).

Selection of a suitable template is very important the better the sequence identity (and similarity), the better the protein model. Here we selected hen s egg white lysozyme as the template in contrast to the other candidates explored by Browne et al., Perutz, " and Perutz et Our selection... 

A Possible Three-Dimensional Structure of Bovine a-Lactalbumin Based on that of Hen s Egg-White Lysozyme. 

J. Jauregui-Adell, J. Joll s and P. Jolles, The Disulphide Bridges in Hen s Egg-white Lysozyme, Biochim. biophys. Acta 107, 97-111 (1965). 

The 3, 4 -epoxybutyl-)8-D-glycoside of (Glc NAc) 2 inhibits hen s egg-white lysozyme at a similar rate to the epoxypropyl analog, but the 5, 6 -epoxyhexyl analog is much less effective. ... 

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