Glycoside Hydrolase Family 103 - Revision history

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

2021-12-18T21:16:07Z

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

Harry Brumer: updated CAZyDBlink

2012-09-10T16:45:48Z

updated CAZyDBlink

Spencer Williams: /* Catalytic Residues */

2010-04-20T12:20:03Z

Catalytic Residues

Spencer Williams: /* Family Firsts */

2010-04-20T12:17:22Z

Family Firsts

Spencer Williams: /* Catalytic Residues */

2010-04-20T12:16:58Z

Catalytic Residues

Spencer Williams at 12:15, 20 April 2010

2010-04-20T12:15:50Z

Harry Brumer at 17:50, 22 February 2010

2010-02-22T17:50:41Z

Harry Brumer at 17:50, 22 February 2010

2010-02-22T17:50:10Z

Anthony Clarke at 03:09, 20 February 2010

2010-02-20T03:09:33Z

Anthony Clarke at 03:07, 20 February 2010

2010-02-20T03:07:42Z

@@ 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 23: / Line 23: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH103.html
+| colspan="2" |{{CAZyDBlink}}GH103.html
 |}
 </div>

@@ Line 39: / Line 39: @@
 [[Image:MltBmechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' and ''P. aeruginosa'' MltB.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH104]]), the GH103 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue has been identified as Glu162 in MltB from both ''E. coli'' and ''P. aeruginosa'' and, indeed, its replacement abolishes catalytic activity <cite>4 5</cite>. The mechanism of action of family GH103 enzymes has been investigated the most compared to the lytic transglycosylases of the other families ([[GH23]],[[GH102]], and [[GH104]]).
-Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic residue at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a two-step [[neighboring group participation]] mechanism involving substrate-assisted catalysis has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic residue Glu162 is proposed to serve initially as a [[general acid]] to donate a proton to the glycosidic oxygen of the linkage to be cleaved. At the same time the MurNAc 2-acetamido group acts as a nucleophile and attacks the anomeric centre. The [[transition state]] leading to the [[intermediate]] possesses oxocarbenium ion character (Figure 2). In the second step abstraction of the C-6 hydroxyl proton of the oxazolinium species by Glu162 which now serves as a [[general base]] leads to nucleophilic attack and the formation of 1,6-anhydromuramic acid product, again through a [[transition state]] with [[oxocarbenium ion]] character. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion [[intermediate]] <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
+Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic residue at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a two-step [[neighboring group participation]] mechanism involving substrate-assisted catalysis has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic residue Glu162 is proposed to serve initially as a [[general acid]] to donate a proton to the glycosidic oxygen of the linkage to be cleaved. At the same time the MurNAc 2-acetamido group acts as a nucleophile and attacks the anomeric centre. The [[transition state]] leading to the [[intermediate]] possesses [[oxocarbenium ion]] character (Figure 2). In the second step abstraction of the C-6 hydroxyl proton of the oxazolinium species by Glu162 which now serves as a [[general base]] leads to nucleophilic attack and the formation of 1,6-anhydromuramic acid product, again through a [[transition state]] with [[oxocarbenium ion]] character. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an [[oxazolinium ion]] [[intermediate]] <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
 == Three-dimensional structures ==

@@ Line 46: / Line 46: @@
 == Family Firsts ==
 ;First identification of lytic transglycosylase: MltB from ''E. coli'' <cite>2</cite>.
-;First [[catalytic nucleophile]] identification: Uses [[neighboring group participation mechanism]].
+;First [[catalytic nucleophile]] identification: Uses [[neighboring group participation]] mechanism.
 ;First [[general acid/base]] residue identification: Inferred by X-ray crystallography of ''E. coli'' MltB <cite>5</cite>.
 ;First 3-D structure: ''E. coli'' MltB <cite>5</cite>.

@@ Line 39: / Line 39: @@
 [[Image:MltBmechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' and ''P. aeruginosa'' MltB.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH104]]), the GH103 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue has been identified as Glu162 in MltB from both ''E. coli'' and ''P. aeruginosa'' and, indeed, its replacement abolishes catalytic activity <cite>4 5</cite>. The mechanism of action of family GH103 enzymes has been investigated the most compared to the lytic transglycosylases of the other families ([[GH23]],[[GH102]], and [[GH104]]).
-Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic residue at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a two-step [[neighboring group participation mechanism]] involving substrate-assisted catalysis has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic residue Glu162 is proposed to serve initially as a [[general acid]] to donate a proton to the glycosidic oxygen of the linkage to be cleaved. At the same time the MurNAc 2-acetamido group acts as a nucleophile and attacks the anomeric centre. The [[transition state]] leading to the [[intermediate]] possesses oxocarbenium ion character (Figure 2). In the second step abstraction of the C-6 hydroxyl proton of the oxazolinium species by Glu162 which now serves as a [[general base]] leads to nucleophilic attack and the formation of 1,6-anhydromuramic acid product, again through a [[transition state]] with [[oxocarbenium ion]] character. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion [[intermediate]] <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
+Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic residue at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a two-step [[neighboring group participation]] mechanism involving substrate-assisted catalysis has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic residue Glu162 is proposed to serve initially as a [[general acid]] to donate a proton to the glycosidic oxygen of the linkage to be cleaved. At the same time the MurNAc 2-acetamido group acts as a nucleophile and attacks the anomeric centre. The [[transition state]] leading to the [[intermediate]] possesses oxocarbenium ion character (Figure 2). In the second step abstraction of the C-6 hydroxyl proton of the oxazolinium species by Glu162 which now serves as a [[general base]] leads to nucleophilic attack and the formation of 1,6-anhydromuramic acid product, again through a [[transition state]] with [[oxocarbenium ion]] character. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion [[intermediate]] <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
 == Three-dimensional structures ==

@@ Line 31: / Line 31: @@
 == Substrate specificities ==
-[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH103 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 3 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase B (MltB) from ''Escherichia coli'' <cite>2</cite>.  These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1),  No other activities have been observed.
+[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH103 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The [[glycoside hydrolases]] of this family are in fact lytic transglycosylases (also referred to as peptidoglycan lyases) of bacterial origin and they constitute family 3 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  The prototype for this family is membrane-bound lytic transglycosylase B (MltB) from ''Escherichia coli'' <cite>2</cite>.  These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1).  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 ''Pseudomonas aeruginosa'' MltB acting on insoluble peptidoglycan sacculi <cite>4</cite>.
+The lytic transglycosidases, strictly speaking, are [[retaining]] enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transfer reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhydromuramoyl product (Figure 1) that lacks 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 ''Pseudomonas aeruginosa'' MltB acting on insoluble peptidoglycan sacculi <cite>4</cite>.
 == Catalytic Residues ==
-[[Image:MltBmechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' and ''P. aeruginosa'' MltB.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH104]]), the GH103 enzymes are thought to possess a single catalytic acid/base residue.   This residue has been identified as Glu162 in MltB from both ''E. coli'' and ''P. aeruginosa'' and, indeed, its replacement abolishes catalytic activity <cite>4 5</cite>. The mechanism of action of family GH103 enzymes has been investigated the most compared to the lytic transglycosylases of the other families ([[GH23]],[[GH102]], and [[GH104]]).
+[[Image:MltBmechanism.jpg|thumb|right|'''Figure 2.''' Reaction mechanism proposed for ''E. coli'' and ''P. aeruginosa'' MltB.  (''click to enlarge'').]]As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH104]]), the GH103 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue has been identified as Glu162 in MltB from both ''E. coli'' and ''P. aeruginosa'' and, indeed, its replacement abolishes catalytic activity <cite>4 5</cite>. The mechanism of action of family GH103 enzymes has been investigated the most compared to the lytic transglycosylases of the other families ([[GH23]],[[GH102]], and [[GH104]]).
-Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a  substrate-assisted mechanism has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic Glu162 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 to stabilize this oxocarbenium intermediate,  the lytic transglycosylases would employ anchimeric assistance of the MurNAc 2-acetamido group resulting in the formation an oxazolinium ion intermediate.  This would be followed by abstraction of the C-6 hydroxyl proton of the oxazolinium species involving Glu162 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion intermediate <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
+Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic residue at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a two-step [[neighboring group participation mechanism]] involving substrate-assisted catalysis has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic residue Glu162 is proposed to serve initially as a [[general acid]] to donate a proton to the glycosidic oxygen of the linkage to be cleaved. At the same time the MurNAc 2-acetamido group acts as a nucleophile and attacks the anomeric centre. The [[transition state]] leading to the [[intermediate]] possesses oxocarbenium ion character (Figure 2). In the second step abstraction of the C-6 hydroxyl proton of the oxazolinium species by Glu162 which now serves as a [[general base]] leads to nucleophilic attack and the formation of 1,6-anhydromuramic acid product, again through a [[transition state]] with [[oxocarbenium ion]] character. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion [[intermediate]] <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
 == Three-dimensional structures ==
@@ Line 46: / Line 46: @@
 == Family Firsts ==
 ;First identification of lytic transglycosylase: MltB from ''E. coli'' <cite>2</cite>.
-;First catalytic nucleophile identification: Not applicable for lytic transglycosylases.
+;First [[catalytic nucleophile]] identification: Uses [[neighboring group participation mechanism]].
-;First general acid/base residue identification: Inferred by X-ray crystallography of ''E. coli'' MltB <cite>5</cite>.
+;First [[general acid/base]] residue identification: Inferred by X-ray crystallography of ''E. coli'' MltB <cite>5</cite>.
 ;First 3-D structure: ''E. coli'' MltB <cite>5</cite>.
 ;First identification as a lipoprotein: ''E. coli'' MltB <cite>9</cite>.

@@ Line 9: / Line 9: @@
 {| {{Prettytable}}
 |-
-|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
+|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH103'''
 |-
 |'''Clan'''
@@ Line 23: / Line 23: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GHnn.html
+| colspan="2" |http://www.cazy.org/fam/GH103.html
 |}
 </div>

@@ Line 35: / Line 35: @@
 == 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 ''Pseudomonas aeruginosa'' MltB acting on insoluble peptidoglycan sacculi <cite>4</cite>.
 == Catalytic Residues ==
@@ Line 41: / Line 40: @@
 Examination of crystal structures of ''E. coli'' Slt35 (a soluble proteolytic derivative of MltB) and theoretical considerations led to the proposal of a mechanism that accommodates a single catalytic at its active site.  Thus, based on the complexes formed with murodipeptide, chitobiose, and the inhibitor bulgecin, a  substrate-assisted mechanism has been invoked analogous to the family [[GH18]] chitinases and chitobiases, family [[GH20]] ''N''-acetyl-β-hexosaminidases, and family [[GH23]] lytic transglycosylases <cite>6</cite>.  Thus, the catalytic Glu162 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 to stabilize this oxocarbenium intermediate,  the lytic transglycosylases would employ anchimeric assistance of the MurNAc 2-acetamido group resulting in the formation an oxazolinium ion intermediate.  This would be followed by abstraction of the C-6 hydroxyl proton of the oxazolinium species involving Glu162 which now serves as the base catalyst leading to nucleophilic attack and the formation of 1,6-anhydromuramic acid product. The β-hexosaminidase inhibitor NAG-thiazoline (Figure 2) was found to inhibit ''P. aeruginosa'' MltB thus supporting the proposal for the formation of an oxazolinium ion intermediate <cite>7</cite>, and the results of a site-directed mutagenesis study suggest that Ser216 orients the N-acetyl group on MurNAc at the -1 subsite of MltB for its participation in a substrate-assisted mechanism of action <cite>8</cite>.
 == Three-dimensional structures ==
 Three-dimensional structures are available for several family GH103 enzymes, the first solved being that of ''E. coli'' MltB (Slt35) <cite>5</cite>.  The catalytic domain of the enyzmes possesses the well characterized α+β "lysozyme fold."
 == Family Firsts ==
@@ Line 55: / Line 52: @@
 ;First identification of localization to outer membrane: ''E. coli'' MltB <cite>9</cite>.
 ;Frist demonstration of molecular interactions between GH103 enzymes and penicillin-binding proteins:''E. coli'' MltB <cite>10</cite>.
 == References ==
@@ Line 69: / Line 65: @@
 #9 pmid=7476170
 #10 pmid=9158739
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH103]]

@@ Line 12: / Line 12: @@
 |-
 |'''Clan'''
-|None
+|none
 α+β "lysozyme fold"
 |-