It has been shown [1,2] that a number of cell-wall lytic enzymes (EC 220.127.116.11)
are evolutionary related and can be classified into a single family:
- Lysozymes (lysin) from Streptococcus pneumoniae bacteriophages of the Cp
- 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
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
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