{PDOC00737}
{PS00953; GLYCOSYL_HYDROL_F25_1}
{PS51904; GLYCOSYL_HYDROL_F25_2}
{BEGIN}
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* Glycosyl hydrolases family 25 (GH25) active site signature and domain profile *
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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 beta-1,4-N-acetylmuramidase     and     beta-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 beta/alpha-barrel fold and is composed of eight beta-strands
and six  alpha-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.

-Consensus pattern: D-[LIVM]-x(3)-[NQ]-[PGE]-x(9,15)-[GR]-x(4)-[LIVMFY](2)-K-
                    x-[ST]-E-[GS]-x(2)-[FYL]-x-[DN]
                    [D is an active site residue]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Expert(s) to contact by email:
           Henrissat B.; bernie@afmb.cnrs-mrs.fr

-Last update: August 2019 / Text revised; profile added.

[ 1] Croux C., Garcia J.L.
     "Sequence of the lyc gene encoding the autolytic lysozyme of
     Clostridium acetobutylicum ATCC824: comparison with other lytic
     enzymes."
     Gene 104:25-31(1991).
     PubMed=1916274
[ 2] Henrissat B.
     "A classification of glycosyl hydrolases based on amino acid sequence
     similarities."
     Biochem. J. 280:309-316(1991).
     PubMed=1747104
[ 3] Rau A., Hogg T., Marquardt R., Hilgenfeld R.
     "A new lysozyme fold. Crystal structure of the muramidase from
     Streptomyces coelicolor at 1.65 A resolution."
     J. Biol. Chem. 276:31994-31999(2001).
     PubMed=11427528; DOI=10.1074/jbc.M102591200
[ 4] Korczynska J.E., Danielsen S., Schagerloef U., Turkenburg J.P.,
     Davies G.J., Wilson K.S., Taylor E.J.
     "The structure of a family GH25 lysozyme from Aspergillus fumigatus."
     Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 66:973-977(2010).
     PubMed=20823508; DOI=10.1107/S1744309110025601
[ 5] Hermoso J.A., Monterroso B., Albert A., Galan B., Ahrazem O.,
     Garcia P., Martinez-Ripoll M., Garcia J.L., Menendez M.
     "Structural basis for selective recognition of pneumococcal cell wall
     by modular endolysin from phage Cp-1."
     Structure 11:1239-1249(2003).
     PubMed=14527392
[ 6] Al-Riyami B., Uestok F.I., Stott K., Chirgadze D.Y., Christie G.
     "The crystal structure of Clostridium perfringens SleM, a muramidase
     involved in cortical hydrolysis during spore germination."
     Proteins 84:1681-1689(2016).
     PubMed=27488615; DOI=10.1002/prot.25112
[E1] http://www.cazy.org/GH25.html

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