PROSITE documentation PDOC00737

Glycosyl hydrolases family 25 (GH25) active site signature and domain profile

It has been shown [1,2] that a number of cell-wall lytic enzymes (EC 3.2.1.17) are evolutionary related and can be classified into a single family:

• Lysozymes (lysin) from Streptococcus pneumoniae bacteriophages of the Cp family.
• Lysozyme (endolysin) from Lactococcus delbrueckii phage mv1.
• Autolytic lysozyme from Clostridium acetobutylicum.
• Lysozyme M1 from Streptomyces globisporus.
• N,O-diacetylmuramidase (lysozyme ch) from the fungus Chalaropsis.

These proteins belong to the Chalaropsis (Ch)-type lyzozymes or glycosyl hydrolases family 25 (GH25) [E1]. The Ch-type lysozymes family GH25 exhibits both β-1,4-N-acetylmuramidase and β-1,4-N,6-O-diacetylmuramidase activities and its evolutionary spread is diverse, comprising bacterial, viral (mainly phage) and eukaryotic representatives.

The Ch-type lysozyme domain is structurally unrelated to the other lysozyme folds. It has a β/α-barrel fold and is composed of eight β-strands and six α-helices, with the strands forming the staves of the barrel and the helices located around it (see <PDB:1JFX>). A conserved active-site DxE motif may be implicated in catalysis, which could proceed through an oxazoline intermediate. The aspartate residue has been proposed to be the catalytic acid/base, initially protonating the leaving group to facilitate its departure (general acid assistance) and subsequently acting as a general base to activate the hydrolytic water molecule. The glutamate residue acts to stabilize or deprotonate the oxazoline N atom [3,4]. A third residue, Asp6 of the profile, could also be involved in catalysis with the Glu of the DxE motif if the hydrolysis occurs via a net inversion of the anomeric configuration, with Asp6 acting as the general base, helping to activate the nucleophilic water molecule, and the Glu of the DxE motif acting as the general acid, protonating the departing oxygen atom in a concerted fashion as the bond cleaves [5,6].

Two residues, an aspartate and a glutamate, as well as some others in their vicinity are conserved in all proteins from this family and can be used as a signature pattern. We also developed a profile which covers the entire Ch-type lysozyme domain.