Glycoside Hydrolase Family 73 - Revision history

Florence Vincent: /* Catalytic Residues */

2022-12-27T11:48:54Z

Catalytic Residues

Florence Vincent at 11:47, 27 December 2022

2022-12-27T11:47:50Z

Florence Vincent at 11:43, 27 December 2022

2022-12-27T11:43:01Z

Florence Vincent at 11:40, 27 December 2022

2022-12-27T11:40:55Z

Florence Vincent at 11:40, 27 December 2022

2022-12-27T11:40:10Z

Florence Vincent at 11:39, 27 December 2022

2022-12-27T11:39:38Z

Florence Vincent at 11:39, 27 December 2022

2022-12-27T11:39:07Z

Florence Vincent at 11:34, 27 December 2022

2022-12-27T11:34:43Z

Florence Vincent at 11:33, 27 December 2022

2022-12-27T11:33:57Z

Florence Vincent at 11:30, 27 December 2022

2022-12-27T11:30:08Z

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 == Catalytic Residues ==
-[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' The motion performed by the β-hairpin to close on the active site is shown by comparing FlgJSt, Auto, and AtlA β-hairpin’s positionsn]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite>. Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite> (see figure 3).
+[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' The motion performed by the β-hairpin to close on the active site is shown by comparing FlgJSt, Auto, and AtlA β-hairpin’s positions]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite>. Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite> (see figure 3).
 On the other hand, significant residual activity was found when the putative nucleophile/base residue of  AcmA and AltWN were converted to glutamine or asparagine (for Asp1275 in AltWN), which is more compatible with substrate-assisted catalysis (also termed "[[neighboring group participation]]" mechanism) involving anchimeric assistance by the acetamido group of the GlcNAc moiety. In such a mechanism, a neighboring tyrosine is frequently involved. In family GH73, a Tyr residue is highly conserved  (Fig2: Tyr220 in Auto), in close proximity to the catalytic [[general acid]] Glu. Substitution of this Tyr residue in FlgJ, AcmA and AltWN was associated with a reduced activity similar to that resulting from the mutation of the [[general acid]] Glu <cite>Maruyama2010 Inagaki2009 Yokoi2008</cite>. The [[neighboring group participation]] mechanism involving the [[general acid]] Glu and the Tyr as essential catalytic residues found support from the sequence comparison of family GH73 with families [[GH20]], [[GH18]], [[GH23]] and [[GH56]], which do not have a catalytic nucleophile residue <cite>Inagaki2009</cite>.
 == Family Firsts ==
 ;First [[general acid/base]]/[[general acid]] residue identification: Glu 1238 in AltWN from ''Staphylococcus warneri'' M <cite>Yokoi2008</cite>

@@ Line 42: / Line 42: @@
 == Catalytic Residues ==
-[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' The motion performed by the β-hairpin to close on the active site is shown by comparing FlgJSt, Auto, and AtlA β-hairpin’s positions             ]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
+[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' The motion performed by the β-hairpin to close on the active site is shown by comparing FlgJSt, Auto, and AtlA β-hairpin’s positionsn]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite>. Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite> (see figure 3).
-Two main catalytic mechanisms are suggested for the GH73 family. On one hand,  the mutations of the putative distant nucleophile Glu156 in Auto <cite>Bublitz2009</cite> and Glu224 in FlgJ <cite>Maruyama2010</cite> were accompanied of a large decrease in the catalytic activity, compatible with the role of a base activating a water molecule for the nucleophilic attack on the opposite side of the sugar ring ([[inverting mechanism]]) <cite>Bublitz2009</cite>. recent work on AtlA from ''Enterococcus faecalis'' identifies key catalytic residues which together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
+On the other hand, significant residual activity was found when the putative nucleophile/base residue of  AcmA and AltWN were converted to glutamine or asparagine (for Asp1275 in AltWN), which is more compatible with substrate-assisted catalysis (also termed "[[neighboring group participation]]" mechanism) involving anchimeric assistance by the acetamido group of the GlcNAc moiety. In such a mechanism, a neighboring tyrosine is frequently involved. In family GH73, a Tyr residue is highly conserved  (Fig2: Tyr220 in Auto), in close proximity to the catalytic [[general acid]] Glu. Substitution of this Tyr residue in FlgJ, AcmA and AltWN was associated with a reduced activity similar to that resulting from the mutation of the [[general acid]] Glu <cite>Maruyama2010 Inagaki2009 Yokoi2008</cite>. The [[neighboring group participation]] mechanism involving the [[general acid]] Glu and the Tyr as essential catalytic residues found support from the sequence comparison of family GH73 with families [[GH20]], [[GH18]], [[GH23]] and [[GH56]], which do not have a catalytic nucleophile residue <cite>Inagaki2009</cite>.
 == Family Firsts ==
 ;First [[general acid/base]]/[[general acid]] residue identification: Glu 1238 in AltWN from ''Staphylococcus warneri'' M <cite>Yokoi2008</cite>

@@ Line 42: / Line 42: @@
 == Catalytic Residues ==
-[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' Comparison of Auto (in yellow) and HEWL (in grey) active sites. Catalytic residues are in italic for HEWL ([[GH22]])]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
+[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' The motion performed by the β-hairpin to close on the active site is shown by comparing FlgJSt, Auto, and AtlA β-hairpin’s positions             ]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
 Two main catalytic mechanisms are suggested for the GH73 family. On one hand,  the mutations of the putative distant nucleophile Glu156 in Auto <cite>Bublitz2009</cite> and Glu224 in FlgJ <cite>Maruyama2010</cite> were accompanied of a large decrease in the catalytic activity, compatible with the role of a base activating a water molecule for the nucleophilic attack on the opposite side of the sugar ring ([[inverting mechanism]]) <cite>Bublitz2009</cite>. recent work on AtlA from ''Enterococcus faecalis'' identifies key catalytic residues which together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.

@@ Line 42: / Line 42: @@
 == Catalytic Residues ==
-[[Image:GH73activesite.jpg|thumb|300px|right|'''Figure 3.''' Comparison of Auto (in yellow) and HEWL (in grey) active sites. Catalytic residues are in italic for HEWL ([[GH22]])]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
+[[File: FigurePourCazypedia2022.jpg|thumb|300px|right|'''Figure 3.''' Comparison of Auto (in yellow) and HEWL (in grey) active sites. Catalytic residues are in italic for HEWL ([[GH22]])]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
 Two main catalytic mechanisms are suggested for the GH73 family. On one hand,  the mutations of the putative distant nucleophile Glu156 in Auto <cite>Bublitz2009</cite> and Glu224 in FlgJ <cite>Maruyama2010</cite> were accompanied of a large decrease in the catalytic activity, compatible with the role of a base activating a water molecule for the nucleophilic attack on the opposite side of the sugar ring ([[inverting mechanism]]) <cite>Bublitz2009</cite>. recent work on AtlA from ''Enterococcus faecalis'' identifies key catalytic residues which together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.

@@ Line 42: / Line 42: @@
 == Catalytic Residues ==
-[[Image:GH73activesite.jpg|thumb|300px|right|'''Figure 3.''' Comparison of Auto (in yellow) and HEWL (in grey) active sites. Catalytic residues are in italic for HEWL ([[GH22]])]]. The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
+[[Image:GH73activesite.jpg|thumb|300px|right|'''Figure 3.''' Comparison of Auto (in yellow) and HEWL (in grey) active sites. Catalytic residues are in italic for HEWL ([[GH22]])]] The catalytic [[general acid]] is a glutamate, strictly conserved in the GH73 family. Its catalytic role has been evidenced in FlgJ <cite>Maruyama2010</cite>, Auto <cite>Bublitz2009</cite>, AcmA <cite>Inagaki2009</cite> and AltWN <cite>Yokoi2008</cite>. Glu185 in FlgJ  and Glu122 in Auto have also been identified through structural comparison with the actives sites of [[GH19]], [[GH22]] and [[GH23]] enzymes <cite>Hashimoto2009 Bublitz2009 </cite>.  However, in contrast to [[GH22]] lysozymes, the structures of FlgJ and Auto both lack a nearby second catalytic carboxylate such as Asp52 in hen egg white lysozyme (HEWL), which represents the [[catalytic nucleophile]] <cite>Vocadlo2001</cite> (see figure 3). Interestingly this amino acid is strictly conserved in the sequences of GH73 enzymes but it is situated 13Å away from the Glu [[general acid]] in the active site. Recent work on AtlA from ''Enterococcus faecalis'' identifies key conserved catalytic residues and together with a closed conformation of the active site groove confirms a  ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.
 Two main catalytic mechanisms are suggested for the GH73 family. On one hand,  the mutations of the putative distant nucleophile Glu156 in Auto <cite>Bublitz2009</cite> and Glu224 in FlgJ <cite>Maruyama2010</cite> were accompanied of a large decrease in the catalytic activity, compatible with the role of a base activating a water molecule for the nucleophilic attack on the opposite side of the sugar ring ([[inverting mechanism]]) <cite>Bublitz2009</cite>. recent work on AtlA from ''Enterococcus faecalis'' identifies key catalytic residues which together with a closed conformation of the active site groove confirms the ([[inverting mechanism]])<cite>Roig-Zamboni2022</cite>.