Glycoside Hydrolase Family 144 - Revision history

Masahiro Nakajima at 04:53, 12 July 2025

2025-07-12T04:53:20Z

Masahiro Nakajima at 04:50, 12 July 2025

2025-07-12T04:50:07Z

Masahiro Nakajima at 05:06, 2 February 2024

2024-02-02T05:06:51Z

Masahiro Nakajima at 05:02, 2 February 2024

2024-02-02T05:02:53Z

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

2021-12-18T21:14:59Z

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

Masahiro Nakajima at 00:10, 16 October 2019

2019-10-16T00:10:39Z

Masahiro Nakajima at 00:04, 16 October 2019

2019-10-16T00:04:18Z

Harry Brumer: Removed unpublished data reference, according to CAZypedia policy

2019-10-15T23:27:24Z

Removed unpublished data reference, according to CAZypedia policy

Harry Brumer: minor language edits

2019-10-15T23:26:32Z

minor language edits

Harry Brumer: standardized PDB links

2019-10-15T23:23:21Z

standardized PDB links

@@ Line 42: / Line 42: @@
 The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The SGL from Xanthomonas campestris pv. campestris in complex with sophoroheptaose provided a binding mode as a Michaelis complex <cite>Nakajima2025</cite>. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
-The unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized. Later, [[GH144]] is classified into clan GH-S with [[GH162]] based on structural similarity between them <cite>Tanaka2024</cite>.
+The unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized. Later, [[GH144]] is classified into clan GH-S with [[GH162]], [[GH192]], [[GH193]], and [[GH194]] based on structural similarity between them <cite>Nakajima2025</cite><cite>Tanaka2024</cite>.
 == Family Firsts ==

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of the glucose moieties in sophorotriose, nor are they proximal to the space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold ([[GH8]], [[GH15]], and [[GH162]]) did not provide clues to the assignment of the catalytic residues. These observation may imply that [[GH144]] enzymes have a non-canonical reaction mechanism.
+Mutational analysis of CpSGL indicated that Asp139, Glu142, and Glu211 play important roles in catalysis <cite>Abe2017</cite>. However, structural analysis of CpSGL showed that none of these residues are in positions that can directly transfer hydrogen to the O2 atoms of the glucose moieties in sophorotriose, nor are they proximal to the space between the bound glucose and sophorotriose. Comparison of topological positions of the conserved acidic residues in CpSGL with the catalytic residues in inverting GHs with a similar fold ([[GH8]], [[GH15]], and [[GH162]]) did not provide clues to the assignment of the catalytic residues. These observations may imply that [[GH144]] enzymes have a non-canonical reaction mechanism.
 == Three-dimensional structures ==
 The 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of [[GH162]] ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</cite>.
-The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
+The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The SGL from Xanthomonas campestris pv. campestris in complex with sophoroheptaose provided a binding mode as a Michaelis complex <cite>Nakajima2025</cite>. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
 The unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized. Later, [[GH144]] is classified into clan GH-S with [[GH162]] based on structural similarity between them <cite>Tanaka2024</cite>.
@@ Line 48: / Line 48: @@
 ;First general acid residue identification: Not known.
 ;First general base residue identification: Not known.
-;First 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (PDB ID [{{PDBlink}}3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (PDB IDs [{{PDBlink}}4gl3 4GL3] and [{{PDBlink}}4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there are no journal publications describing these proteins. The first published structures are those of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]), one of which ([{{PDBlink}}5gzh 5GZH]) captures sophorotriose and glucose.
+;First 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (PDB ID [{{PDBlink}}3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (PDB IDs [{{PDBlink}}4gl3 4GL3] and [{{PDBlink}}4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there are no journal publications describing these proteins. The first published structures are those of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]), one of which ([{{PDBlink}}5gzh 5GZH]) captures sophorotriose and glucose. In 2025, a complex with sophoroheptaose as a Michaelis complex is available (PDB ID [{{PDBlink}}5gzh 8XUL]).
 == References ==
@@ Line 56: / Line 56: @@
 #Tanaka2019 pmid=30926603
 #Tanaka2024 pmid=38300345
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH144]]

@@ Line 42: / Line 42: @@
 The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
-The unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.
+The unliganded crystal structures of [[GH144]] enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized. Later, [[GH144]] is classified into clan GH-S with [[GH162]] based on structural similarity between them <cite>Tanaka2024</cite>.
 == Family Firsts ==
@@ Line 55: / Line 55: @@
 #Shimizu2018 pmid=29763309
 #Tanaka2019 pmid=30926603
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH144]]

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

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

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolase]] family 144 contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064)  <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.
+[[Glycoside hydrolase]] family [[144]] contains β-1,2-glucan-hydrolyzing enzymes. The first characterized enzymes of this family are an ''endo''-β-1,2-glucanase ([{{EClink}}3.2.1.71 EC 3.2.1.71]) from ''Chitinophaga pinensis'' (CpSGL) and a sophorohydrolase (nonreducing end) (EC 3.2.1.-) from ''Parabacteroides distasonis'' (BDI_3064)  <cite>Abe2017, Shimizu2018</cite>. CpSGL hydrolyzes β-1,2-glucan and mainly releases β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of 3–5, whereas BDI_3064 efficiently hydrolyzes shorter β-1,2-glucooligosaccarides with DPs of more than 3 to produce sophorose (Glc-β-1,2-Glc) from the nonreducing end of β-1,2-glucooligosaccarides. These enzyme are highly specific for β-1,2-glucan or its shorter oligosaccharides.
 == Kinetics and Mechanism ==

@@ Line 40: / Line 40: @@
 The 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of [[GH162]] ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</cite>.
-The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
+The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the non-reducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
 The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-The 3-D structures of CpSGL ([https://www.rcsb.org/structure/5gzh 5GZH] and [https://www.rcsb.org/structure/5gzk 5GZK]) and BDI_3064 ([https://www.rcsb.org/structure/5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</cite>.
+The 3-D structures of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]) and BDI_3064 (PDB ID [{{PDBlink}}5z06 5Z06]) were determined by X-ray crystallography and showed an (α/α)<sub>6</sub>-fold of this family <cite>Abe2017</cite>. BDI_3064 possesses additional N-terminal domains 1 and 2, important for the substrate specificity of this enzyme, as described below. The overall structure of CpSGL is similar to that of GH162 ''endo''-β-1,2-glucanase (TfSGL) despite their low sequence similarity <cite>Tanaka2019</cite>.
 The crystal structure of CpSGL in complex with glucose and sophorotriose provided the structural basis for substrate recognition of this enzyme. CpSGL possesses the large cleft typical of ''endo''-acting enzymes. HPLC and ESI-MS analysis suggested that the bound glucose and sophorotriose occupies −3 subsite and +1 to +3 subsites, respectively. Docking analysis of CpSGL using sophoropentaose as a ligand supported the subsite assignment (unpublished data). The ligand-free crystal structure and docking analysis of BDI_3064 showed that Arg93 in the N-terminal domain 1 overlaps −3 subsite and completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharides <cite>Shimizu2018</cite>. This structural feature would make BDI_3064 an ''exo''-acting enzyme.
-The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species ([https://www.rcsb.org/structure/3eu8 3EU8], [https://www.rcsb.org/structure/4gl3 4GL3], and [https://www.rcsb.org/structure/4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.
+The unliganded crystal structures of GH144 enzymes from ''Bacteroides'' species (PDB IDs [{{PDBlink}}3eu8 3EU8], [{{PDBlink}}4gl3 4GL3], and [{{PDBlink}}4qt9 4QT9]) were deposited in the PDB database before the deposition of that of CpSGL. However, these ''Bacteroides'' enzymes have not been biochemically characterized.
 == Family Firsts ==
@@ Line 46: / Line 46: @@
 ;First general acid residue identification: Not known.
 ;First general base residue identification: Not known.
-;First 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 ([https://www.rcsb.org/structure/3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species ([https://www.rcsb.org/structure/4gl3 4GL3] and [https://www.rcsb.org/structure/4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there is no publication about these proteins. The first published structures are those of CpSGL ([https://www.rcsb.org/structure/5gzh 5GZH] and [https://www.rcsb.org/structure/5gzk 5GZK]), one of which (5GZK) captures sophorotriose and glucose.
+;First 3-D structure: The first deposited protein in the PDB database is BF9343_0330 protein from ''Bacteroides fragilis'' NCTC 9343 (PDB ID [{{PDBlink}}3eu8 3EU8]) followed by the deposition of BACUNI_03963 and BACCAC_03554 proteins from ''Bacteroides'' species (PDB IDs [{{PDBlink}}4gl3 4GL3] and [{{PDBlink}}4qt9 4QT9], respectively). These structures were determined by Joint Center for Structural Genomics in ligand-free form. However, there is no publication about these proteins. The first published structures are those of CpSGL (PDB IDs [{{PDBlink}}5gzh 5GZH] and [{{PDBlink}}5gzk 5GZK]), one of which ([{{PDBlink}}5gzh 5GZH]) captures sophorotriose and glucose.
 == References ==