Crystal structure of the lysozyme from bacteriophage lambda and its relationship with V and C-type lysozymes

Abstract

Like other lysozymes, the bacteriophage lambda lysozyme is involved in the digestion of bacterial walls. This enzyme is remarkable in that its mechanism of action is different from the classical lysozyme's mechanism. From the point of view of protein evolution, it shows features of lysozymes from different classes.The crystal structure of the enzyme in which all tryptophan residues have been replaced by aza-tryptophan has been solved by X-ray crystallography at 2.3 Å using a combination of multiple isomorphous replacement, noncrystallographic symmetry averaging and density modification techniques. There are three molecules in the asymmetric unit. The characteristic structural elements of lysozymes are conserved: each molecule is organized in two domains connected by a helix and the essential catalytic residue (Glu19) is located in the depth of a cleft between the two domains. This cleft shows an open conformation in two of the independent molecules, while access to the cavity is much more restricted in the last one. A structural alignment with T4 lysozyme and hen egg white lysozyme allows us to superpose about 60 C α atoms with a rms distance close to 2 Å. The best alignments concern the helix preceding the catalytic residue, some parts of the β sheets and the helix joining the two domains. The results of sequence alignments with the V and C lysozymes, in which weak local similarities had been detected, are compared with the structural results.

Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis

“…A structure similarity search using the Dali server did not return any structures with significant similarity to the PGT domain. However, a secondary structure matching (SSM) search returned bacteriophage -lysozyme ( R; also known as LaL), which breaks the ␤(1,4) glycosidic linkages between NAM and NAG residues of peptidoglycan, the same bonds that the PGTs make (14,15). Terrak et al (16) have previously suggested that the PGTs might resemble the lysozymes.…”

The incorporation of a non-natural amino acid (aza-tryptophan) may help to crystallize a protein and to solve its crystal structure. Application to bacteriophage λ lysozyme.

“…The side chain of Trn73 is oriented outwards while that of Trn74 is completely buried, as shown in Table 1. In the interaction between molecules A and C in one column, the two clefts interpenetrate each other in a very symmetrical way, as previously described (Evrard et al, 1998). Since Trn73 is located close to the entrance to this cleft, it can be expected that the packing between the two molecules will considerably modify the accessibility of this side chain in molecules A and C. Indeed, Table 1 shows that when the two molecules are considered together, the accessible surface of the N 2 atoms is practically reduced to zero and the total accessibility of the residues is considerably lowered.…”

“…Synchrotron data at 2.3 A Ê were collected on beamline X31 at EMBL c/o DESY (Evrard et al, 1997). Solution of the crystal structure (Evrard et al, 1998) revealed the presence of three independent molecules in the asymmetric unit. The molecules are essentially composed of two domains connected by a long helix (H3).…”

“…The sequence of !L contains four tryptophan residues, in positions 17, 73, 74 and 124. It has been shown (Evrard et al, 1998) that the independent molecules A and C are very similar, while the conformation of molecule B is quite different from the two others in the region of the loops guarding the entrance to the active cleft. This modi®cation involves, for molecule B, the destruction of a ladder and the unwinding of one complete helix turn at the lower and the upper lip of this cleft, respectively.…”

“…lysozyme (!L). This structure has recently been solved (Evrard et al, 1998) by the multiple isomorphous replacement method and the application of non-crystallographic symmetry. The replacement of the tryptophan (Trp) residues by aza-tryptophans (Trn) was essential for crystallization, preparation of heavyatom derivatives and solution of the non-crystallographic symmetry.…”