Glycoside Hydrolase Family 102 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:15:22Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 19:48, 26 August 2013

2013-08-26T19:48:49Z

Harry Brumer: updated CAZyDBlink

2012-09-10T16:45:30Z

updated CAZyDBlink

Bernard Henrissat: /* Kinetics and Mechanism */

2010-06-30T09:07:59Z

Kinetics and Mechanism

Spencer Williams at 12:19, 20 April 2010

2010-04-20T12:19:29Z

Spencer Williams at 10:44, 30 March 2010

2010-03-30T10:44:52Z

Harry Brumer at 17:51, 22 February 2010

2010-02-22T17:51:25Z

Harry Brumer at 17:49, 22 February 2010

2010-02-22T17:49:38Z

Harry Brumer at 17:48, 22 February 2010

2010-02-22T17:48:23Z

Anthony Clarke at 03:09, 20 February 2010

2010-02-20T03:09:02Z

@@ Line 1: / Line 1: @@
 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Anthony Clarke^^^
+* [[Author]]: [[User:Anthony Clarke|Anthony Clarke]]
-* [[Responsible Curator]]:  ^^^Anthony Clarke^^^
+* [[Responsible Curator]]:  [[User:Anthony Clarke|Anthony Clarke]]
 ----

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH102 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The [[glycoside hydrolase]]s of this family are lytic transglycosylases (also referred to as peptidoglycan lyases) of bacterial origin and they constitute family 2 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase A (MltA) from ''Escherichia coli.''  These enzymes cleave the β-1,4-linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1), but unlike the lytic transglycosylases of other families, they are active on peptidoglycan fragments lacking their stem peptides <cite>2</cite>.  No other activities have been observed.
+[[Image:LTreaction.jpg|thumb|400px|right|'''Figure 1.''' Reaction catalyzed by family GH102 enzymes. LT, lytic transglycosylase.]]The [[glycoside hydrolase]]s of this family are lytic transglycosylases (also referred to as peptidoglycan lyases) of bacterial origin and they constitute family 2 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase A (MltA) from ''Escherichia coli.''  These enzymes cleave the β-1,4-linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1), but unlike the lytic transglycosylases of other families, they are active on peptidoglycan fragments lacking their stem peptides <cite>2</cite>.  No other activities have been observed.
 == Kinetics and Mechanism ==
@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-[[Image:Mltamechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' MltA.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH103]], and [[GH104]]), the GH102 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue in ''E. coli'' MltA has been identified as Asp308 and, indeed, its replacement with Ala abolishes catalytic activity <cite>4</cite>.
+[[Image:Mltamechanism.jpg|thumb|400px|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' MltA.]]As with other lytic transglycosylases (families [[GH23]], [[GH103]], and [[GH104]]), the GH102 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue in ''E. coli'' MltA has been identified as Asp308 and, indeed, its replacement with Ala abolishes catalytic activity <cite>4</cite>.
 The mechanism of action of the family GH102 enzymes has yet to be proven experimentally, but examination of crystal structures of ''E. coli'' MltA complexed with chitohexoase has led to the proposal of a novel mechanism of action involving the stabilization of the putative [[intermediate]] [[oxocarbenium ion]] by an alpha-helix dipole <cite>5</cite>. Thus, the catalytic Asp308 is proposed to serve initially as an acid catalyst to donate a proton to the glycosidic oxygen of the linkage to be cleaved leading to the formation of an [[intermediate]] with [[oxocarbenium ion]] character (Figure 2).  In the absence of an anion/nucleophile in close proximity, this oxocarbenium [[intermediate]] is proposed to be stabilized by the negatively-charged side of the dipole that would exist at the C-terminal end of an alpha helix positioned just below the -1 binding subsite.  This would be followed by abstraction of the C-6 hydroxyl proton of the [[intermediate]] involving Asp308 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product.

@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH102.html
+| colspan="2" |{{CAZyDBlink}}GH102.html
 |}
 </div>

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-The lytic transglycosidases, strictly speaking, are [[retaining]] enzymes. They are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>3</cite>.   No detailed analyses involving both steady state and pre-steady state kinetic studies have been reported, but the Michaelis Menten (''K''<sub>M</sub> and ''V''<sub>max</sub>) parameters have been estimated for ''E. coli'' MltA acting on insoluble peptidoglycan sacculi <cite>2</cite>.
+The lytic transglycosidases, strictly speaking, are [[retaining]] enzymes. They are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhydromuramoyl product (Figure 1) thus lacking a reducing end <cite>3</cite>.   No detailed analyses involving both steady state and pre-steady state kinetic studies have been reported, but the Michaelis Menten (''K''<sub>M</sub> and ''V''<sub>max</sub>) parameters have been estimated for ''E. coli'' MltA acting on insoluble peptidoglycan sacculi <cite>2</cite>.
 == Catalytic Residues ==

@@ Line 37: / Line 37: @@
 [[Image:Mltamechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' MltA.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH103]], and [[GH104]]), the GH102 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue in ''E. coli'' MltA has been identified as Asp308 and, indeed, its replacement with Ala abolishes catalytic activity <cite>4</cite>.
-The mechanism of action of the family GH102 enzymes has yet to be proven experimentally, but examination of crystal structures of ''E. coli'' MltA complexed with chitohexoase has led to the proposal of a novel mechanism of action involving the stabilization of the putative [[intermediate]] oxocarbenium ion by an alpha-helix dipole <cite>5</cite>. Thus, the catalytic Asp308 is proposed to serve initially as an acid catalyst to donate a proton to the glycosidic oxygen of the linkage to be cleaved leading to the formation of an [[intermediate]] with oxocarbenium ion character (Figure 2).  In the absence of an anion/nucleophile in close proximity, this oxocarbenium [[intermediate]] is proposed to be stabilized by the negatively-charged side of the dipole that would exist at the C-terminal end of an alpha helix positioned just below the -1 binding subsite.  This would be followed by abstraction of the C-6 hydroxyl proton of the intermediate involving Asp308 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product.
+The mechanism of action of the family GH102 enzymes has yet to be proven experimentally, but examination of crystal structures of ''E. coli'' MltA complexed with chitohexoase has led to the proposal of a novel mechanism of action involving the stabilization of the putative [[intermediate]] [[oxocarbenium ion]] by an alpha-helix dipole <cite>5</cite>. Thus, the catalytic Asp308 is proposed to serve initially as an acid catalyst to donate a proton to the glycosidic oxygen of the linkage to be cleaved leading to the formation of an [[intermediate]] with [[oxocarbenium ion]] character (Figure 2).  In the absence of an anion/nucleophile in close proximity, this oxocarbenium [[intermediate]] is proposed to be stabilized by the negatively-charged side of the dipole that would exist at the C-terminal end of an alpha helix positioned just below the -1 binding subsite.  This would be followed by abstraction of the C-6 hydroxyl proton of the [[intermediate]] involving Asp308 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product.
 == Three-dimensional structures ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH102 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The glycoside hydrolases of this family are lytic transglyosylases (also referred to as peptidoglycan lyases) of bacterial origin and they constitute family 2 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase A (MltA) from ''Escherichia coli.''  These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1), but unlike the lytic transglycosylases of other families, they are active on peptidoglycan fragments lacking their stem peptides <cite>2</cite>.  No other activities have been observed.
+[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH102 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The [[glycoside hydrolase]]s of this family are lytic transglycosylases (also referred to as peptidoglycan lyases) of bacterial origin and they constitute family 2 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase A (MltA) from ''Escherichia coli.''  These enzymes cleave the β-1,4-linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1), but unlike the lytic transglycosylases of other families, they are active on peptidoglycan fragments lacking their stem peptides <cite>2</cite>.  No other activities have been observed.
 == Kinetics and Mechanism ==
-The lytic transglycosidases, strictly speaking, are retaining enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>3</cite>.   No detailed analyses involving both steady state and pre-steady state kinetic studies have been reported, but the Michaelis Menten (''K''<sub>M</sub> and ''V''<sub>max</sub>) parameters have been estimated for ''E. coli'' MltA acting on insoluble peptidoglycan sacculi <cite>2</cite>.
+The lytic transglycosidases, strictly speaking, are [[retaining]] enzymes. They are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>3</cite>.   No detailed analyses involving both steady state and pre-steady state kinetic studies have been reported, but the Michaelis Menten (''K''<sub>M</sub> and ''V''<sub>max</sub>) parameters have been estimated for ''E. coli'' MltA acting on insoluble peptidoglycan sacculi <cite>2</cite>.
 == Catalytic Residues ==
-[[Image:Mltamechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' MltA.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH103]], and [[GH104]]), the GH102 enzymes are thought to possess a single catalytic acid/base residue.   This residue in ''E. coli'' MltA has been identified as Asp308 and, indeed, its replacement with Ala abolishes catalytic activity <cite>4</cite>.
+[[Image:Mltamechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' MltA.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH103]], and [[GH104]]), the GH102 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue in ''E. coli'' MltA has been identified as Asp308 and, indeed, its replacement with Ala abolishes catalytic activity <cite>4</cite>.
-The mechanism of action of the family GH102 enzymes has yet to be proven experimentally, but examination of crystal structures of ''E. coli'' MltA complexed with chitohexoase has led to the proposal of a novel mechanism of action involving the stabilization of the putative transition state oxocarbenium ion by an alpha-helix dipole <cite>5</cite>. Thus, the catalytic Asp308 is proposed to serve initially as an acid catalyst to donate a proton to the glycosidic oxygen of the linkage to be cleaved leading to the formation of a  transition intermediate with oxocarbenium ion character (Figure 2).  In the absence of an anion/nucleophile in close proximity, this oxocarbenium intermediate is proposed to be stabilized by the negatively-charged side of the dipole that would exist at the C-terminal end of an alpha helix positioned just below the -1 binding subsite.  This would be followed by abstraction of the C-6 hydroxyl proton of the intermediate involving Asp308 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product.
+The mechanism of action of the family GH102 enzymes has yet to be proven experimentally, but examination of crystal structures of ''E. coli'' MltA complexed with chitohexoase has led to the proposal of a novel mechanism of action involving the stabilization of the putative [[intermediate]] oxocarbenium ion by an alpha-helix dipole <cite>5</cite>. Thus, the catalytic Asp308 is proposed to serve initially as an acid catalyst to donate a proton to the glycosidic oxygen of the linkage to be cleaved leading to the formation of an [[intermediate]] with oxocarbenium ion character (Figure 2).  In the absence of an anion/nucleophile in close proximity, this oxocarbenium [[intermediate]] is proposed to be stabilized by the negatively-charged side of the dipole that would exist at the C-terminal end of an alpha helix positioned just below the -1 binding subsite.  This would be followed by abstraction of the C-6 hydroxyl proton of the intermediate involving Asp308 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product.
 == Three-dimensional structures ==
@@ Line 44: / Line 44: @@
 == Family Firsts ==
 ;First identification of lytic transglycosylase: MltA from ''E. coli'' <cite>2</cite>.
-;First catalytic nucleophile identification: Not applicable for lytic transglycosylases.
+;First [[general acid/base]] residue identification: Inferred by X-ray crystallography of ''E. coli'' MltA <cite>4</cite>.
 ;First 3-D structure: ''E. coli'' MltA <cite>4</cite>.
 ;First identification as a lipoprotein: ''E. coli'' MltA <cite>7</cite>.

@@ Line 9: / Line 9: @@
 {| {{Prettytable}}
 |-
-|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
+|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH102'''
 |-
 |'''Clan'''
@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GHnn.html
+| colspan="2" |http://www.cazy.org/fam/GH102.html
 |}
 </div>

@@ Line 33: / Line 33: @@
 == Kinetics and Mechanism ==
 The lytic transglycosidases, strictly speaking, are retaining enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>3</cite>.   No detailed analyses involving both steady state and pre-steady state kinetic studies have been reported, but the Michaelis Menten (''K''<sub>M</sub> and ''V''<sub>max</sub>) parameters have been estimated for ''E. coli'' MltA acting on insoluble peptidoglycan sacculi <cite>2</cite>.
 == Catalytic Residues ==
@@ Line 42: / Line 41: @@
 == Three-dimensional structures ==
 Three-dimensional structures are available for several Family GH103 enzymes, the first solved being that of ''E. coli'' MltA <cite>4</cite>.   Unlike the other lytic transglycosylases of families [[GH23]], [[GH103]], and [[GH104]] which possesses the well characterized α+β “lysozyme fold,” these enzymes have a unique structure consisting of two domains. One has a double-ψ β-barrel fold similar to the catalytic domain of the family [[GH45]] endoglucanase V from ''Humicola insolens'' <cite>6</cite>.  The second and smaller domain has a β-barrel fold topology.  The large groove between the two domains serves as the active site cleft.
 == Family Firsts ==
@@ Line 63: / Line 61: @@
 #7 pmid=9287002
 #8 pmid=10037771
 </biblio>
-[[Category:Glycoside Hydrolase Families|GH102]
+[[Category:Glycoside Hydrolase Families|GH102]]

@@ Line 12: / Line 12: @@
 |-
 |'''Clan'''
-|None
+|none
 |-
 |'''Mechanism'''