Lysozyme amino acid sequence

Lysozyme from bacteriophage T4 is a 164 amino acid polypeptide chain that folds into two domains (Figure 17.3) There are no disulfide bridges the two cysteine residues in the amino acid sequence, Cys 54 and Cys 97, are far apart in the folded structure. The stability of both the wild-type and mutant proteins is expressed as the melting temperature, Tm, which is the temperature at which 50% of the enzyme is inactivated during reversible beat denat-uration. For the wild-type T4 lysozyme the Tm is 41.9 °C. 

Bovine a-lactalbumin is one of the two enzymes in lactose synthetase, and its amino acid sequence shows striking similarities to that of lysozyme.118 A model based on the lysozyme model has been built, and the side-chain interactions found are convincing, showing that the model is essentially correct. The active cleft in the crystal is, however, shorter than that in the model, and is consistent with a mono- or di-saccharide as the substrate. Thus, the lysozyme structure may serve as a model for some enzymes that synthesize and hydrolyze carbohydrates. 

Use the BLAST tool to compare the amino acid sequences for human a-lactalbumin and lysozyme. Repeat the process using BLAST to compare the nucleotide sequences for the genes coding for human a-lactalbumin and lysozyme. 

Figure 25-15 Lysozyme from hen egg-white showing the amino-acid sequence (primary structure) and the four intrachain disulfide bridges. [Adapted from D. C. Phillips, Sc/. Amer. 5, 215 (1966).]...

Stanford Moore Rockefeller Univ., amino acid sequence of lysozyme... 

Figure 4.5. PIR format for amino acid sequence of chicken egg-white lysozyme.

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 10,6. Prediction of exons with FEX at Sanger Centre. The nucleotide sequence of DNA encoding human lysozyme (5648 bp) is submitted to Sanger Centre for exon prediction with FEX. The output shows number of predicted exons, locations, and amino acid sequences of translates.

Figure 11.6. Amino acid sequence alignment at EBI. Amino acid sequences of type C lysozyme are submitted to ClustalW tool of EBI, and the alignment is retrieved from the notified URL...

Figure 12.9. Protein structure prediction with PHD. The amino acid sequence of chicken lysozyme precursor (147 amino acids) is submitted to PredictProtein server for PHD structure predictions. The returned e-mail reports protein class based on secondary structures, predicted secondary structure composition (%H, %E, and %L), residue composition, data interpretation, and predicted data in two levels (brief and normal of which the normal is shown). Search for the database can be performed by making choice(s) from the list(s) of pop-up box(es).

Retrieve the amino acid sequences of type C lysozymes from twelve biological sources. Perform ClustalW multiple sequence alignment and WebPhylip parsimony analysis to draw a cladogram of the consensus tree. 

Figure 15.1. Workspace of Swiss-PDB Viewer. The workspace of Swiss-PDB Viewer (SPBBV) consists of main windows (with menu bars, icons, and display window), control panel (with listing of amino acid residues), and align window (with amino acid sequence of the displayed molecule). Lysozyme (1 lyz.pdb) with highlighted catalytic residues (Glu35 and Asp52) is displayed.

Canfield, R. 1963. The amino acid sequence of egg white lysozyme. J Biol Chem 238 2698-2707. 

Figure 2. (a) The amino acid sequence of the enzyme lysozyme (from egg white). Blocks enclosing two cysteines (Cys) denote intramolecular covalent cross-links (disulfide bonds). This molecule in crystalline form has the three-dimensional structure sketched in part (b). Note the helical subdomains and sheet substructures formed by nearby extended segments. Reprinted by permission from C. C. F. Blake, Structure of Hen Egg-White Lysozyme, Nature vol. 206 p. 757. Copyright (c) 1967 Macmillan Magazines Ltd. 

TABLE I Primary Amino Acid Sequences of Evolutionary Variant Lysozymes ... 

TABLE 14.2. Cationic residues in the amino acid sequence of lysozyme and cytochrome c [19]. 

In 1958 Yasunobu and Wilcox drew attention to certain similarities between a-lactalbumin and lysozyme (see Gordon, 1971). A few years later Brew and Campbell (1967) also drew attention to their marked similarity in molecular weights, amino acid composition, and the amino-and carboxy-terminal amino acid residues. They stated, To the extent that the properties mentioned reflect similar primary structures, the a-lactalbumins may have evolved by gradual modification from lysozyme, which is found in the milk of many species (p. 263). This proposal prompted Brew etal. (1967, 1970) to determine the amino acid sequence of bovine a-lactalbumin, which proved to have a high level of sequence identity with domestic hen egg-white lysozyme. Thus, these studies were in accordance with the proposal that the two proteins had diverged from a common ancestor (see also Hill etal., 1969, 1974). They stated that although lysozyme does not participate in lactose synthesis and a-lactalbu-... 

Because of the high level of identity in amino acid sequence between lysozyme and a-lactalbumin (see Fig. 10), it was inevitable that interest turned to the three-dimensional structure of a-lactalbumin when the structure of lysozyme was determined in 1965 by the group at the Royal Institution. However, there were unforeseen difficulties in the direct experimental determination, as discussed below. Hence, attention was directed to models for the a-lactalbumin structure based on the coordinates for lysozyme and on energy minimization programs. 

On the basis of monomer molecular weights (from sedimentation-equilibrium and sedimentation—diffusion studies, amino acid sequences and compositions), the a-lactalbumins, with one exception (rat a-lactalbumin, 140 residues, see Section VII,B), have a single chain of — 123 residues and values of —14,000. The mammalian lysozymes have 128-130 residues and values of —14,400, except echidna lysozyme, which has —125 residues. The c-type hen egg-white lysozymes have -127—131 residues, in contrast to the g type, which has —185 residues. 

The assignment for residue 57 was discussed by Teahan (1986). She pointed out that KDII and PDl lysozymes have identical amino acid sequences, except for residue 57, which is given as Glu by Hermann et al. (1971) for KDIII and as Gin by Kondo et al. (1982) for PDl. Prager and Wilson (1972) have shown that both proteins have identical electrophoretic mobilities. Thus, it is likely that KDII has Gin in position 57. This is in accord with the later view of Rodriguez et al. (1987). Further, we note that all other c-type lysozymes and all a-lactalbumins have Gin in this position. Hence, we conclude that KDII and KDIII have Gin in position 57, as shown in Fig. 10. This, then, means that KDII and PDl are identical. 

Phylogenetic analysis of amino acid sequences of c-type egg-white lysozymes from a variety of birds is generally in accord with taxonomic classification. However, there are some differences For example, the chachalaca is classified normally in the order Galliformes, but its lysozyme differs more in sequence from those of pheasandike birds than do the c-type lysozymes of ducks (for a discussion of this and other examples, see Jolles and Jolles, 1984). 

In Section VII,B and Fig. 10 we compared the sequences of 13 a-lactalbumins (if the bovine A variant, equine B and C variants, and ovine variant are included), 23 mammalian c-type lysozymes (if donkey, mouse M, bovine stomach 1 and 3, caprine 1 and 2, ovine 1-3, camel 1, deer 2, echidna II, and porcine 1 and 2 are included), and 13 avian c-type lysozymes (if KDIII and PD2 and PD3 are included). Analysis of the sequence differences indicates that, with the recent considerable increase in the number of lysozymes sequenced, there has been an appreciable decrease in the numbers of residues that are invariant in lysozymes as well as for both proteins. Nevertheless, there is still significant overall homology (—35%) between a-lactalbumin and c-type lysozyme. From the similarities in amino acid sequences, three-dimensional structures, intron—exon patterns, etc., there can be little doubt that the concept of divergence is still valid for these proteins. What is controversial are the rate of evolution and the details of the way in which ct-lactalbumin arose, although it is conceded generally that the mechanism involves gene duplication. 

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