Glycoside Hydrolase Family 25 - Revision history

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

2021-12-18T21:20:39Z

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

Harry Brumer: updated reference identifiers to standard AuthorYear format to make future editing easier

2011-05-27T12:41:19Z

updated reference identifiers to standard AuthorYear format to make future editing easier

Spencer Williams at 00:58, 20 June 2010

2010-06-20T00:58:44Z

Spencer Williams: /* Family Firsts */

2010-06-19T23:49:24Z

Family Firsts

Spencer Williams at 23:48, 19 June 2010

2010-06-19T23:48:41Z

Spencer Williams at 23:44, 19 June 2010

2010-06-19T23:44:09Z

Spencer Williams at 01:25, 9 June 2010

2010-06-09T01:25:20Z

Spencer Williams at 01:23, 9 June 2010

2010-06-09T01:23:58Z

Spencer Williams at 01:23, 9 June 2010

2010-06-09T01:23:36Z

Harry Brumer at 11:38, 29 May 2010

2010-05-29T11:38:32Z

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

@@ Line 15: / Line 15: @@
 |-
 |'''Mechanism'''
-|unknown, likely retaining<br>by analogy with<br>GH18,20,56,84,85 <cite>REF3</cite>
+|unknown, likely retaining<br>by analogy with<br>GH18,20,56,84,85 <cite>MartinezFleites2009</cite>
 |-
 |'''Active site residues'''
@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH25.html
+| colspan="2" |{{CAZyDBlink}}GH25.html
 |}
 </div>
@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolase]]s of family GH25 are lysozymes otherwise known as the Chalaropsis (CH) type of lysozymes (from their initial characterisation from Chalaropsis species of fungus <cite>REF1</cite>). They cleave the β-1,4-glycosidic bond between ''N''-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in the carbohydrate backbone of bacterial peptidoglycan.  The characterized lysozymes from this family exhibit both β-1,4-''N''-acetyl- and β-1,4-''N'',6-O-diacetylmuramidase activities and are able to degrade  O-acetylated peptidoglycan present in ''Staphylococcus aureus'' and other pathogens <cite>REF2</cite>. The activity of GH25 enzymes appears to fulfil two main biological roles in bacteria. These roles are the re-modelling of peptidoglycan in cellular process such as division and the dissemination of phage progeny toward the end of the phage lytic cycle, which is achieved by lysis of the bacterial cell. For this reason many GH25 proteins are found to be chromosomal, phage or prophage encoded. The majority of the GH25 family is comprised of bacterial or prokaryotic viral (phage) members. There are however a few eukaryotic representatives, but these are so far restricted to the fungal kingdom.   The roles of these fungal enzymes are less clear, many possess signal secretion peptides indicating a likely extracellular location, possibly for the purpose of obtaining or gaining assess to nutrients or even as a selective agent against bacteria.
+[[Glycoside hydrolase]]s of family GH25 are lysozymes otherwise known as the Chalaropsis (CH) type of lysozymes (from their initial characterisation from Chalaropsis species of fungus <cite>Hash1967</cite>). They cleave the β-1,4-glycosidic bond between ''N''-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in the carbohydrate backbone of bacterial peptidoglycan.  The characterized lysozymes from this family exhibit both β-1,4-''N''-acetyl- and β-1,4-''N'',6-O-diacetylmuramidase activities and are able to degrade  O-acetylated peptidoglycan present in ''Staphylococcus aureus'' and other pathogens <cite>Vollmer2008b</cite>. The activity of GH25 enzymes appears to fulfil two main biological roles in bacteria. These roles are the re-modelling of peptidoglycan in cellular process such as division and the dissemination of phage progeny toward the end of the phage lytic cycle, which is achieved by lysis of the bacterial cell. For this reason many GH25 proteins are found to be chromosomal, phage or prophage encoded. The majority of the GH25 family is comprised of bacterial or prokaryotic viral (phage) members. There are however a few eukaryotic representatives, but these are so far restricted to the fungal kingdom.   The roles of these fungal enzymes are less clear, many possess signal secretion peptides indicating a likely extracellular location, possibly for the purpose of obtaining or gaining assess to nutrients or even as a selective agent against bacteria.
 == Kinetics and Mechanism ==
-The lack of activity on chitooligosaccharides and the difficulty of producing defined synthetic peptidoglycan substrates, has inevitably hampered the determination of kinetic parameters. Structural studies have shown the active-centre is closely similar to those from [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] implying that, in the absence of evidence to the contrary, GH25 enzymes are [[retaining]] glycoside hydrolases that use a [[neighboring group participation]] mechanism common to this “super-family” of enzymes <cite>REF3</cite>.
+The lack of activity on chitooligosaccharides and the difficulty of producing defined synthetic peptidoglycan substrates, has inevitably hampered the determination of kinetic parameters. Structural studies have shown the active-centre is closely similar to those from [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] implying that, in the absence of evidence to the contrary, GH25 enzymes are [[retaining]] glycoside hydrolases that use a [[neighboring group participation]] mechanism common to this “super-family” of enzymes <cite>MartinezFleites2009</cite>.
 == Catalytic Residues ==
-The super-family comprised of families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD moitif <cite>REF4 REF5</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>REF6</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline (or [[oxazolinium ion]]) [[intermediate]].
+The super-family comprised of families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD motif <cite>Ling2009 Abbott2009</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>VocadloDavies2008</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline (or [[oxazolinium ion]]) [[intermediate]].
 == Three-dimensional structures ==
-So far four members of this family of enzymes have been structural characterized, that of the ''Streptomyces coelicolor'' enzyme “cellosyl” <cite>REF7</cite>, the bacteriophage lysine PlyB <cite>REF8</cite>, and Clp-1lysozyme from a ''Streptococcus pneumoniae '' phage <cite>REF9 REF10</cite>, whose structure was also obtained in complex with fragments of peptidoglycan analogues 10 and  BaGh25c from ''Bacillus anthracis'' str. Ames <cite>REF3</cite>. The GH25 lysozymes,  are structurally unrelated to the [[GH22]], [[GH23]], [[GH24]], [[GH73]] and [[GH108]] lysozyme folds and instead these enzymes display a modified α -barrel-like fold that, like the classical “TIM-barrel” is composed of a eight-stranded β-barrel, but which is flanked by just three (as opposed to the normal eight) α-helices <cite>REF7</cite>.There is a prominent, long groove, very likely the substrate binding site, located on the C-terminal face. This groove culminates in a deep hole of a highly negative electrostatic potential forming the catalytic site <cite>REF11</cite>.
+So far four members of this family of enzymes have been structural characterized, that of the ''Streptomyces coelicolor'' enzyme “cellosyl” <cite>Rau2001</cite>, the bacteriophage lysine PlyB <cite>Porter2007</cite>, and Clp-1lysozyme from a ''Streptococcus pneumoniae '' phage <cite>Hermoso2003 PerezDorado2007</cite>, whose structure was also obtained in complex with fragments of peptidoglycan analogues 10 and  BaGh25c from ''Bacillus anthracis'' str. Ames <cite>MartinezFleites2009</cite>. The GH25 lysozymes,  are structurally unrelated to the [[GH22]], [[GH23]], [[GH24]], [[GH73]] and [[GH108]] lysozyme folds and instead these enzymes display a modified α -barrel-like fold that, like the classical “TIM-barrel” is composed of a eight-stranded β-barrel, but which is flanked by just three (as opposed to the normal eight) α-helices <cite>Rau2001</cite>. There is a prominent, long groove, very likely the substrate binding site, located on the C-terminal face. This groove culminates in a deep hole of a highly negative electrostatic potential forming the catalytic site <cite>Vollmer2008a</cite>.
 == Family Firsts ==
 ;First sterochemistry determination: Has yet to be experimentally determined.
-;First catalytic nucleophile identification: This remains to be experimentally proven. Inverting mechanisms have been proposed <cite>REF9</cite>, but it is perhaps more likely that the enzyme is [[retaining]] and that the nucleophile is not enzyme-derived, but is provided by the substrate in a [[neighboring group participation]] mechanism <cite>REF3</cite>. This is based upon the considerable active centre structural similarity with other neighboring group enzymes in GH18, 20, 56, 84 and also 85.
+;First catalytic nucleophile identification: This remains to be experimentally proven. Inverting mechanisms have been proposed <cite>Hermoso2003</cite>, but it is perhaps more likely that the enzyme is [[retaining]] and that the nucleophile is not enzyme-derived, but is provided by the substrate in a [[neighboring group participation]] mechanism <cite>MartinezFleites2009</cite>. This is based upon the considerable active centre structural similarity with other neighboring group enzymes in GH18, 20, 56, 84 and also 85.
-;First [[general acid/base]] residue identification: Has yet to be fully experimentally determined but again structural similarity strongly implicates the second carboxylate in the DXE motif described previously. In the case of the ''Bacillus anthracis'' enzyme this is Glu107 <cite>REF3</cite>.
+;First [[general acid/base]] residue identification: Has yet to be fully experimentally determined but again structural similarity strongly implicates the second carboxylate in the DXE motif described previously. In the case of the ''Bacillus anthracis'' enzyme this is Glu107 <cite>MartinezFleites2009</cite>.
-;First 3-D structure: The ''Streptomyces coelicolor'' enzyme "cellosyl" <cite>REF7</cite> was the first GH25 structure to be described in 2001.
+;First 3-D structure: The ''Streptomyces coelicolor'' enzyme "cellosyl" <cite>Rau2001</cite> was the first GH25 structure to be described in 2001.
 == References ==
 <biblio>
-#REF1 pmid=12325376
+#Hash1967 pmid=12325376
-#REF2 pmid=18070068
+#Vollmer2008a pmid=18266855
-#REF3 pmid=19595298
+#Vollmer2008b pmid=18070068
-#REF4 pmid=19327363
+#MartinezFleites2009 pmid=19595298
-#REF5 pmid=19181667
+#Ling2009 pmid=19327363
-#REF6 pmid=18558099
+#Abbott2009 pmid=19181667
-#REF7 pmid=11427528
+#VocadloDavies2008 pmid=18558099
-#REF8 pmid=17182056
+#Rau2001 pmid=11427528
-#REF9 pmid=14527392
+#Porter2007 pmid=17182056
-#REF10 pmid=17581815
+#Hermoso2003 pmid=14527392
-#REF11 pmid=18266855
+#PerezDorado2007 pmid=17581815
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH025]]

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-The super-family comprised of families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD moitif <cite>REF4 REF5</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>REF6</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline (or oxazolinium ion) [[intermediate]].
+The super-family comprised of families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD moitif <cite>REF4 REF5</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>REF6</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline (or [[oxazolinium ion]]) [[intermediate]].
 == Three-dimensional structures ==

@@ Line 42: / Line 42: @@
 == Family Firsts ==
 ;First sterochemistry determination: Has yet to be experimentally determined.
-;First catalytic nucleophile identification: This remains to be experimentally proven. Inverting mechanisms have been proposed <cite>REF9</cite>, but it is perhaps more likely that the enzyme is [[retaining]] and that the nucleophile is not enzyme-derived, but is provided by the substrate in a “neighboring group" participation reaction <cite>REF3</cite>. This is based upon the considerable active centre structural similarity with other neighboring group enzymes in GH18, 20, 56, 84 and also 85.
+;First catalytic nucleophile identification: This remains to be experimentally proven. Inverting mechanisms have been proposed <cite>REF9</cite>, but it is perhaps more likely that the enzyme is [[retaining]] and that the nucleophile is not enzyme-derived, but is provided by the substrate in a [[neighboring group participation]] mechanism <cite>REF3</cite>. This is based upon the considerable active centre structural similarity with other neighboring group enzymes in GH18, 20, 56, 84 and also 85.
 ;First [[general acid/base]] residue identification: Has yet to be fully experimentally determined but again structural similarity strongly implicates the second carboxylate in the DXE motif described previously. In the case of the ''Bacillus anthracis'' enzyme this is Glu107 <cite>REF3</cite>.
 ;First 3-D structure: The ''Streptomyces coelicolor'' enzyme "cellosyl" <cite>REF7</cite> was the first GH25 structure to be described in 2001.

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolase]]s of family GH25 are lysozymes otherwise known as the Chalaropsis (CH) type of lysozymes (from their initial characterisation from Chalaropsis species of fungus <cite>REF1</cite>). They cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in the carbohydrate backbone of bacterial peptidoglycan.  The characterized lysozymes from this family exhibit both β-1,4-N-acetyl- and β-1,4- N ,6-O-diacetylmuramidase activities and are able to degrade  O-acetylated peptidoglycan present in ''Staphylococcus aureus'' and other pathogens <cite>REF2</cite>. The activity of GH25 enzymes appears to fulfil two main biological roles in bacteria. These roles are the re-modelling of peptidoglycan in cellular process such as division and the dissemination of phage progeny toward the end of the phage lytic cycle, which is achieved by lysis of the bacterial cell. For this reason many GH25 proteins are found to be chromosomal, phage or prophage encoded. The majority of the GH25 family is comprised of bacterial or prokaryotic viral (phage) members. There are however a few eukaryotic representatives, but these are so far restricted to the fungal kingdom.   The roles of these fungal enzymes are less clear, many possess signal secretion peptides indicating a likely extracellular location, possibly for the purpose of obtaining or gaining assess to nutrients or even as a selective agent against bacteria.
+[[Glycoside hydrolase]]s of family GH25 are lysozymes otherwise known as the Chalaropsis (CH) type of lysozymes (from their initial characterisation from Chalaropsis species of fungus <cite>REF1</cite>). They cleave the β-1,4-glycosidic bond between ''N''-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in the carbohydrate backbone of bacterial peptidoglycan.  The characterized lysozymes from this family exhibit both β-1,4-''N''-acetyl- and β-1,4-''N'',6-O-diacetylmuramidase activities and are able to degrade  O-acetylated peptidoglycan present in ''Staphylococcus aureus'' and other pathogens <cite>REF2</cite>. The activity of GH25 enzymes appears to fulfil two main biological roles in bacteria. These roles are the re-modelling of peptidoglycan in cellular process such as division and the dissemination of phage progeny toward the end of the phage lytic cycle, which is achieved by lysis of the bacterial cell. For this reason many GH25 proteins are found to be chromosomal, phage or prophage encoded. The majority of the GH25 family is comprised of bacterial or prokaryotic viral (phage) members. There are however a few eukaryotic representatives, but these are so far restricted to the fungal kingdom.   The roles of these fungal enzymes are less clear, many possess signal secretion peptides indicating a likely extracellular location, possibly for the purpose of obtaining or gaining assess to nutrients or even as a selective agent against bacteria.
 == Kinetics and Mechanism ==

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-The lack of activity on chitooligosaccharides and complexity in producing defined synthetic peptidoglycan substrates, has inevitably hampered the determination of kinetic parameters. Structural studies have shown the active-centre is closely similar to those from GH18, 20, 56, 84 and 85 implying that, in the absence of evidence to the contrary, GH25 enzymes are [[retaining]] glycoside hydrolases that use a [[neighboring group participation]] mechanism common to this “super-family” of enzymes <cite>REF3</cite>.
+The lack of activity on chitooligosaccharides and complexity in producing defined synthetic peptidoglycan substrates, has inevitably hampered the determination of kinetic parameters. Structural studies have shown the active-centre is closely similar to those from [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] implying that, in the absence of evidence to the contrary, GH25 enzymes are [[retaining]] glycoside hydrolases that use a [[neighboring group participation]] mechanism common to this “super-family” of enzymes <cite>REF3</cite>.
 == Catalytic Residues ==
-The super-family comprised of families GH18, 20, 56, 84 and 85 has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD moitif <cite>REF4 REF5</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>REF6</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline intermediate.
+The super-family comprised of families [[GH18]], [[GH20]], [[GH56]], [[GH84]] and [[GH85]] has been shown to use an active site DE or DXE sequence motif (or exceptionally in the case of GH85 a NXD moitif <cite>REF4 REF5</cite>).  This carboxylate pair promotes a double displacement mechanism in which the catalytic nucleophile is not enzyme-derived but is provided by the substrate in an  intramolecular “neighboring group” attack of the N-acetyl carbonyl group <cite>REF6</cite>. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline intermediate.
 == Three-dimensional structures ==