Glycoside Hydrolase Family 119 - Revision history

Eduardo Moreno Prieto at 10:06, 26 February 2024

2024-02-26T10:06:55Z

Stefan Janecek at 19:20, 12 February 2024

2024-02-12T19:20:52Z

Eduardo Moreno Prieto at 15:36, 12 February 2024

2024-02-12T15:36:51Z

Eduardo Moreno Prieto at 15:25, 12 February 2024

2024-02-12T15:25:36Z

Eduardo Moreno Prieto at 15:23, 12 February 2024

2024-02-12T15:23:04Z

Stefan Janecek at 15:44, 11 February 2024

2024-02-11T15:44:12Z

Stefan Janecek at 15:43, 11 February 2024

2024-02-11T15:43:35Z

Eduardo Moreno Prieto at 13:41, 11 February 2024

2024-02-11T13:41:05Z

Eduardo Moreno Prieto at 13:39, 11 February 2024

2024-02-11T13:39:56Z

Stefan Janecek at 11:43, 9 February 2024

2024-02-09T11:43:25Z

@@ Line 11: / Line 11: @@
 |-
 |'''Clan'''
-|GH-S
+|GH-T
 |-
 |'''Mechanism'''
@@ Line 39: / Line 39: @@
 == Catalytic Residues ==
-''In silico'' studies have revealed a close phylogenetic relationship between GH families 119 and 57 <cite>Janecek2012,Polacek2023</cite>. Through multiple sequence alignment (MSA) and superimposition of GH119 homology models and [[GH57]] crystallographic structures, it has been shown that GH119 sequences share the same five CSRs typical of [[GH57]] <cite>Janecek2012</cite>. The strictly conserved, catalytic residues of [[GH57]], namely a strand β4 glutamate serving as nucleophile and a β7 aspartate serving as acid/base <cite>Imamura2001,Imamura2003</cite> are located in CSR-3 and CSR-4, respectively. The equivalent residues in CocoGH119 (E225 and D369) have been found to be essential to catalysis by site-directed mutagenesis experiments resulting in complete abolishment of the enzyme’s activity <cite>Vuillemin2024</cite>. Furthermore, homology models of GH119 sequences suggest that their putative catalytic domain may adopt the (β/α)<sub>7</sub>-barrel (i.e., an incomplete TIM-barrel) fold followed by a bundle of α-helices also adopted by [[GH57]] <cite>Janecek2012,Polacek2023</cite>. Based on these differential features, GH119 and [[GH57]] define clan GH-S <cite>Vuillemin2024</cite>.
+''In silico'' studies have revealed a close phylogenetic relationship between GH families 119 and 57 <cite>Janecek2012,Polacek2023</cite>. Through multiple sequence alignment (MSA) and superimposition of GH119 homology models and [[GH57]] crystallographic structures, it has been shown that GH119 sequences share the same five CSRs typical of [[GH57]] <cite>Janecek2012</cite>. The strictly conserved, catalytic residues of [[GH57]], namely a strand β4 glutamate serving as nucleophile and a β7 aspartate serving as acid/base <cite>Imamura2001,Imamura2003</cite> are located in CSR-3 and CSR-4, respectively. The equivalent residues in CocoGH119 (E225 and D369) have been found to be essential to catalysis by site-directed mutagenesis experiments resulting in complete abolishment of the enzyme’s activity <cite>Vuillemin2024</cite>. Furthermore, homology models of GH119 sequences suggest that their putative catalytic domain may adopt the (β/α)<sub>7</sub>-barrel (i.e., an incomplete TIM-barrel) fold followed by a bundle of α-helices also adopted by [[GH57]] <cite>Janecek2012,Polacek2023</cite>. Based on these differential features, GH119 and [[GH57]] define clan GH-T <cite>Vuillemin2024</cite>.
 == Three-dimensional structures ==
 No 3D structure of a GH119 protein has been experimentally established so far. However, sequence comparisons indicate that several GH119 proteins exhibit a multi-modular architecture consisting of an N-terminal, putatively-catalytic, main domain followed by a variable number of additional domains, including carbohydrate-binding modules (CBM) of families [[CBM20]], CBM25 and CBM26, fibronectin type III (FN-III) and dockerin domains, among others <cite>Polacek2023, Vuillemin2024,Janecek2019</cite>. A phylogenetic tree of the family annotated with predicted domain architecture (Fig. 2) shows that different branches exhibit distinctive auxiliary domain patterns <cite>Vuillemin2024</cite>. Domain prediction for IgtZ suggests that this enzyme comprises an N-terminal, putative catalytic domain, followed by an FN-III, two [[CBM20]] in tandem and a C-terminal CBM25 <cite>Polacek2023</cite>.

@@ Line 31: / Line 31: @@
 In the CAZy database, the two largest amylolytic families, [[GH13]] and [[GH57]], are notably multi-specific, with α-amylase representing just one of more than 30 specificities in [[GH13]] <cite>Janecek2022</cite>. Family GH119 was predicted in 2012 <cite>Janecek2012</cite> to share its catalytic domain fold and catalytic machinery with those of the family [[GH57]] (Fig. 1). It had been also predicted that GH119 would be largely mono-specific, with α-amylase being the primary specificity <cite>Polacek2023</cite>. This was based on the composition of one of its conserved sequence regions (CSRs), specifically CSR-5 <cite>Janecek2011,Blesak2012</cite>.
-[[File:GH57 GH119 structure comparison.jpg|thumb|400px|right|'''Figure 1. Original structure comparison of families [[GH57]] and GH119<cite>Janecek2012</cite>.''' (a) Catalytic (β/α)<sub>7</sub>-barrel with succeeding α-helical bundle of ''Thermococcus litoralis'' [[GH57]] 4-α-glucanotransferase (red; PDB: [{{PDBlink}}1K1Y 1K1Y]; residues M1-Q381) superimposed with substantial part of the (β/α)<sub>7</sub>-barrel domain of ''Niallia circulans'' GH119 α-amylase IgtZ (blue; model; residues T121-D429). The rectangle indicates a detailed view on the right. (b) Focus on catalytic residues in [[GH57]] 4-α-glucanotransferase (Glu123 and Asp214) and the predicted catalytic machinery in GH119 α-amylase (Glu231 and Asp373). Acarbose occupying subsites -1 through +3 from the complex with [[GH57]] 4-α-glucanotransferase is also shown.]]
+[[File:GH57 GH119 structure comparison.jpg|thumb|400px|right|'''Figure 1. Original structure comparison of families [[GH57]] and GH119 <cite>Janecek2012</cite>.''' (a) Catalytic (β/α)<sub>7</sub>-barrel with succeeding α-helical bundle of ''Thermococcus litoralis'' [[GH57]] 4-α-glucanotransferase (red; PDB: [{{PDBlink}}1K1Y 1K1Y]; residues M1-Q381) superimposed with substantial part of the (β/α)<sub>7</sub>-barrel domain of ''Niallia circulans'' GH119 α-amylase IgtZ (blue; model; residues T121-D429). The rectangle indicates a detailed view on the right. (b) Focus on catalytic residues in [[GH57]] 4-α-glucanotransferase (Glu123 and Asp214) and the predicted catalytic machinery in GH119 α-amylase (Glu231 and Asp373). Acarbose occupying subsites -1 through +3 from the complex with [[GH57]] 4-α-glucanotransferase is also shown.]]
 Vuillemin ''et al.'' <cite>Vuillemin2024</cite> expressed recombinantly the core domain of five other GH119 sequences representing the major phylogenetic clades of family GH119. They all showed a specificity very similar to that of IgtZ: activity on glycogen, soluble starch, amylose and maltooligosaccharides with minimum DP5, but not on pullulan or dextran. This result confirmed the ''in silico'' prediction of uniform specificity. Their product profiles were also similar to IgtZ’s, except for that of α-amylase CocoGH119 from ''Corallococcus coralloides'' DSM 2259, which only produced DP2 and DP3 maltooligosaccharides from longer-chain substrates. This suggests that this enzyme is a maltogenic α-amylase <cite>Vuillemin2024</cite>.

@@ Line 30: / Line 30: @@
 Glycoside hydrolase family 119 (GH119) contains a relatively small number of exclusively bacterial sequences. The first experimentally-characterized member was the amylolytic enzyme IgtZ from ''Niallia circulans'' AM7 (formerly ''Bacillus circulans''). Watanabe ''et al.'' <cite>Watanabe2006</cite> expressed IgtZ’s full sequence and assayed it against a range of oligo- and polymeric α-glucans, demonstrating its ability to break down amylose and soluble starch but not pullulan or dextran. This suggests a strict specificity towards α-1,4 over α-1,6-glucan bonds. The enzyme also acts on maltooligosaccharides with a minimum degree of polymerization (DP) of 4 and maltooligosyl trehaloses with maltooligosaccharide portions of at least 4 monosaccharide units. The enzyme hydrolytic action yields primarily disaccharides (maltose or trehalose) accompanied by smaller amounts of glucose and other maltodextrins. The enzyme specificity increases with the DP of the substrate. Based on these findings, the authors categorized IgtZ as an α-amylase <cite>Watanabe2006</cite>.
-In the CAZy database, the two largest amylolytic families, [[GH13]] and [[GH57]], are notably multi-specific, with α-amylase representing just one of more than 30 specificities in [[GH13]] <cite>Janecek2022</cite>. Family GH119 was predicted in 2012 <cite>Janecek2012</cite> to share its catalytic domain fold and catalytic machinery with those of the family [[GH57]] (Fig. 1). It had been also predicted that GH119 would be largely mono-specific, with α-amylase being the primary specificity <cite>Polacek2023</cite>. This was based on the composition of one of its conserved sequence regions (CSRs), specifically CSR-5.<cite>Janecek2011,Blesak2012</cite>
+In the CAZy database, the two largest amylolytic families, [[GH13]] and [[GH57]], are notably multi-specific, with α-amylase representing just one of more than 30 specificities in [[GH13]] <cite>Janecek2022</cite>. Family GH119 was predicted in 2012 <cite>Janecek2012</cite> to share its catalytic domain fold and catalytic machinery with those of the family [[GH57]] (Fig. 1). It had been also predicted that GH119 would be largely mono-specific, with α-amylase being the primary specificity <cite>Polacek2023</cite>. This was based on the composition of one of its conserved sequence regions (CSRs), specifically CSR-5 <cite>Janecek2011,Blesak2012</cite>.
 [[File:GH57 GH119 structure comparison.jpg|thumb|400px|right|'''Figure 1. Original structure comparison of families [[GH57]] and GH119<cite>Janecek2012</cite>.''' (a) Catalytic (β/α)<sub>7</sub>-barrel with succeeding α-helical bundle of ''Thermococcus litoralis'' [[GH57]] 4-α-glucanotransferase (red; PDB: [{{PDBlink}}1K1Y 1K1Y]; residues M1-Q381) superimposed with substantial part of the (β/α)<sub>7</sub>-barrel domain of ''Niallia circulans'' GH119 α-amylase IgtZ (blue; model; residues T121-D429). The rectangle indicates a detailed view on the right. (b) Focus on catalytic residues in [[GH57]] 4-α-glucanotransferase (Glu123 and Asp214) and the predicted catalytic machinery in GH119 α-amylase (Glu231 and Asp373). Acarbose occupying subsites -1 through +3 from the complex with [[GH57]] 4-α-glucanotransferase is also shown.]]

@@ Line 41: / Line 41: @@
 ''In silico'' studies have revealed a close phylogenetic relationship between GH families 119 and 57 <cite>Janecek2012,Polacek2023</cite>. Through multiple sequence alignment (MSA) and superimposition of GH119 homology models and [[GH57]] crystallographic structures, it has been shown that GH119 sequences share the same five CSRs typical of [[GH57]] <cite>Janecek2012</cite>. The strictly conserved, catalytic residues of [[GH57]], namely a strand β4 glutamate serving as nucleophile and a β7 aspartate serving as acid/base <cite>Imamura2001,Imamura2003</cite> are located in CSR-3 and CSR-4, respectively. The equivalent residues in CocoGH119 (E225 and D369) have been found to be essential to catalysis by site-directed mutagenesis experiments resulting in complete abolishment of the enzyme’s activity <cite>Vuillemin2024</cite>. Furthermore, homology models of GH119 sequences suggest that their putative catalytic domain may adopt the (β/α)<sub>7</sub>-barrel (i.e., an incomplete TIM-barrel) fold followed by a bundle of α-helices also adopted by [[GH57]] <cite>Janecek2012,Polacek2023</cite>. Based on these differential features, GH119 and [[GH57]] define clan GH-S <cite>Vuillemin2024</cite>.
 == Three-dimensional structures ==
-No 3D structure of a GH119 protein has been experimentally established so far. However, domain prediction indicates that several GH119 proteins exhibit a multi-modular architecture consisting of an N-terminal, putatively-catalytic, main domain followed by a variable number of additional domains, including carbohydrate-binding modules (CBM) of families [[CBM20]], CBM25 and CBM26, fibronectin type III (FN-III) and dockerin domains, among others <cite>Polacek2023, Vuillemin2024,Janecek2019</cite>. A phylogenetic tree of the family annotated with predicted domain architecture (Fig. 2) shows that different branches exhibit distinctive auxiliary domain patterns <cite>Vuillemin2024</cite>. Domain prediction for IgtZ suggests that this enzyme comprises an N-terminal, putative catalytic domain, followed by an FN-III, two [[CBM20]] in tandem and a C-terminal CBM25 <cite>Polacek2023</cite>.
+No 3D structure of a GH119 protein has been experimentally established so far. However, sequence comparisons indicate that several GH119 proteins exhibit a multi-modular architecture consisting of an N-terminal, putatively-catalytic, main domain followed by a variable number of additional domains, including carbohydrate-binding modules (CBM) of families [[CBM20]], CBM25 and CBM26, fibronectin type III (FN-III) and dockerin domains, among others <cite>Polacek2023, Vuillemin2024,Janecek2019</cite>. A phylogenetic tree of the family annotated with predicted domain architecture (Fig. 2) shows that different branches exhibit distinctive auxiliary domain patterns <cite>Vuillemin2024</cite>. Domain prediction for IgtZ suggests that this enzyme comprises an N-terminal, putative catalytic domain, followed by an FN-III, two [[CBM20]] in tandem and a C-terminal CBM25 <cite>Polacek2023</cite>.
-[[File:GH119_phylogenetic_tree.jpg|thumb|400px|right|'''Figure 2. Phylogenetic tree representing 52 GH119 representative sequences <cite>Vuillemin2024</cite>.''' Tree branches in the same clade share the same colour. Stars mark experimentally characterised sequences. The remaining annotations to each branch, from left to right, include: NCBI accession number, source organism name coloured by phylum and predicted sequence domain composition.]]
+[[File:GH119_phylogenetic_tree.jpg|thumb|400px|right|'''Figure 2. Phylogenetic tree representing 52 GH119 representative sequences <cite>Vuillemin2024</cite>.''' Tree branches in the same clade share the same colour. Stars mark experimentally characterized sequences. The remaining annotations to each branch, from left to right, include: NCBI accession number, source organism name colored by phylum and predicted sequence domain composition.]]
 == Family Firsts ==
 ;First stereochemistry determination:The first evidence of a retaining mechanism within the family was presented by Watanabe ''et al.'' <cite>Watanabe2006</cite>, who conducted a polarimetry study of the maltooligosaccharide products resulting from the hydrolysis of maltopentaosyl trehalose by IgtZ.

@@ Line 30: / Line 30: @@
 Glycoside hydrolase family 119 (GH119) contains a relatively small number of exclusively bacterial sequences. The first experimentally-characterized member was the amylolytic enzyme IgtZ from ''Niallia circulans'' AM7 (formerly ''Bacillus circulans''). Watanabe ''et al.'' <cite>Watanabe2006</cite> expressed IgtZ’s full sequence and assayed it against a range of oligo- and polymeric α-glucans, demonstrating its ability to break down amylose and soluble starch but not pullulan or dextran. This suggests a strict specificity towards α-1,4 over α-1,6-glucan bonds. The enzyme also acts on maltooligosaccharides with a minimum degree of polymerization (DP) of 4 and maltooligosyl trehaloses with maltooligosaccharide portions of at least 4 monosaccharide units. The enzyme hydrolytic action yields primarily disaccharides (maltose or trehalose) accompanied by smaller amounts of glucose and other maltodextrins. The enzyme specificity increases with the DP of the substrate. Based on these findings, the authors categorized IgtZ as an α-amylase <cite>Watanabe2006</cite>.
-In the CAZy database, the two largest amylolytic families, [[GH13]] and [[GH57]], are notably multi-specific, with α-amylase representing just one of more than 30 specificities in [[GH13]] <cite>Janecek2022</cite>. Family GH119 was predicted in 2012 <cite>Janecek2012</cite> to share its catalytic domain fold and catalytic machinery with those of the family [[GH57]] (Fig. 1). It had been also predicted that GH119 would be largely mono-specific, with α-amylase being the primary specificity <cite>Polacek2023</cite>. This was based on the composition of one of its conserved sequence regions (CSRs), specifically CSR-5, which correlates with substrate specificity in families [[GH57]] and GH119 <cite>Janecek2011,Blesak2012</cite>.
+In the CAZy database, the two largest amylolytic families, [[GH13]] and [[GH57]], are notably multi-specific, with α-amylase representing just one of more than 30 specificities in [[GH13]] <cite>Janecek2022</cite>. Family GH119 was predicted in 2012 <cite>Janecek2012</cite> to share its catalytic domain fold and catalytic machinery with those of the family [[GH57]] (Fig. 1). It had been also predicted that GH119 would be largely mono-specific, with α-amylase being the primary specificity <cite>Polacek2023</cite>. This was based on the composition of one of its conserved sequence regions (CSRs), specifically CSR-5.<cite>Janecek2011,Blesak2012</cite>
-[[File:GH57 GH119 structure comparison.jpg|thumb|400px|right|'''Figure 1. Original structure comparison of families [[GH57]] and GH119 from 2012 <cite>Janecek2012</cite>.''' (a) Catalytic (β/α)<sub>7</sub>-barrel with succeeding α-helical bundle of ''Thermococcus litoralis'' [[GH57]] 4-α-glucanotransferase (red; PDB: [{{PDBlink}}1K1Y 1K1Y]; residues M1-Q381) superimposed with substantial part of the (β/α)<sub>7</sub>-barrel domain of ''Niallia circulans'' GH119 α-amylase IgtZ (blue; model; residues T121-D429). The rectangle indicates a detailed view on the right. (b) Focus on catalytic residues in [[GH57]] 4-α-glucanotransferase (Glu123 and Asp214) and the predicted catalytic machinery in GH119 α-amylase (Glu231 and Asp373). Acarbose occupying subsites -1 through +3 from the complex with [[GH57]] 4-α-glucanotransferase is also shown.]]
+[[File:GH57 GH119 structure comparison.jpg|thumb|400px|right|'''Figure 1. Original structure comparison of families [[GH57]] and GH119<cite>Janecek2012</cite>.''' (a) Catalytic (β/α)<sub>7</sub>-barrel with succeeding α-helical bundle of ''Thermococcus litoralis'' [[GH57]] 4-α-glucanotransferase (red; PDB: [{{PDBlink}}1K1Y 1K1Y]; residues M1-Q381) superimposed with substantial part of the (β/α)<sub>7</sub>-barrel domain of ''Niallia circulans'' GH119 α-amylase IgtZ (blue; model; residues T121-D429). The rectangle indicates a detailed view on the right. (b) Focus on catalytic residues in [[GH57]] 4-α-glucanotransferase (Glu123 and Asp214) and the predicted catalytic machinery in GH119 α-amylase (Glu231 and Asp373). Acarbose occupying subsites -1 through +3 from the complex with [[GH57]] 4-α-glucanotransferase is also shown.]]
-Vuillemin ''et al.'' <cite>Vuillemin2024</cite> expressed recombinantly the core domain of five other GH119 sequences representing the major phylogenetic clades of family GH119. They all showed a very similar specificity as IgtZ’s: activity on glycogen, soluble starch, amylose and maltooligosaccharides with minimum DP5, but not on pullulan or dextran. This result confirmed the ''in silico'' prediction of uniform specificity. Their product profiles were also similar to IgtZ’s, except for that of α-amylase CocoGH119 from ''Corallococcus coralloides'' DSM 2259, which only produced DP2 and DP3 maltooligosaccharides from longer-chain substrates. This suggests that this enzyme is a maltogenic α-amylase <cite>Vuillemin2024</cite>.
+Vuillemin ''et al.'' <cite>Vuillemin2024</cite> expressed recombinantly the core domain of five other GH119 sequences representing the major phylogenetic clades of family GH119. They all showed a specificity very similar to that of IgtZ: activity on glycogen, soluble starch, amylose and maltooligosaccharides with minimum DP5, but not on pullulan or dextran. This result confirmed the ''in silico'' prediction of uniform specificity. Their product profiles were also similar to IgtZ’s, except for that of α-amylase CocoGH119 from ''Corallococcus coralloides'' DSM 2259, which only produced DP2 and DP3 maltooligosaccharides from longer-chain substrates. This suggests that this enzyme is a maltogenic α-amylase <cite>Vuillemin2024</cite>.
 == Kinetics and Mechanism ==
@@ Line 39: / Line 39: @@
 == Catalytic Residues ==
-''In silico'' studies have revealed a close phylogenetic relationship between GH families 119 and 57 <cite>Janecek2012,Polacek2023</cite>. Through multiple sequence alignment (MSA) and superimposition of GH119 homology models and [[GH57]] crystallographic structures, it has been demonstrated that GH119 sequences share the same five CSRs typical of [[GH57]] <cite>Janecek2012</cite>. The strictly conserved, catalytic residues of [[GH57]], namely a strand β4 glutamate serving as nucleophile and a β7 aspartate serving as acid/base <cite>Imamura2001,Imamura2003</cite> are located in CSR-3 and CSR-4, respectively. The equivalent residues in CocoGH119 (E225 and D369) have been found to be essential to catalysis by site-directed mutagenesis experiments resulting in complete abolishment of the enzyme’s activity <cite>Vuillemin2024</cite>. Furthermore, homology models of GH119 sequences suggest that their putative catalytic domain may adopt a (β/α)<sub>7</sub>-barrel (i.e., an incomplete TIM-barrel) fold followed by a bundle of α-helices <cite>Janecek2012,Polacek2023</cite>.
+''In silico'' studies have revealed a close phylogenetic relationship between GH families 119 and 57 <cite>Janecek2012,Polacek2023</cite>. Through multiple sequence alignment (MSA) and superimposition of GH119 homology models and [[GH57]] crystallographic structures, it has been shown that GH119 sequences share the same five CSRs typical of [[GH57]] <cite>Janecek2012</cite>. The strictly conserved, catalytic residues of [[GH57]], namely a strand β4 glutamate serving as nucleophile and a β7 aspartate serving as acid/base <cite>Imamura2001,Imamura2003</cite> are located in CSR-3 and CSR-4, respectively. The equivalent residues in CocoGH119 (E225 and D369) have been found to be essential to catalysis by site-directed mutagenesis experiments resulting in complete abolishment of the enzyme’s activity <cite>Vuillemin2024</cite>. Furthermore, homology models of GH119 sequences suggest that their putative catalytic domain may adopt the (β/α)<sub>7</sub>-barrel (i.e., an incomplete TIM-barrel) fold followed by a bundle of α-helices also adopted by [[GH57]] <cite>Janecek2012,Polacek2023</cite>. Based on these differential features, GH119 and [[GH57]] define clan GH-S <cite>Vuillemin2024</cite>.
 == Three-dimensional structures ==
 No 3D structure of a GH119 protein has been experimentally established so far. However, domain prediction indicates that several GH119 proteins exhibit a multi-modular architecture consisting of an N-terminal, putatively-catalytic, main domain followed by a variable number of additional domains, including carbohydrate-binding modules (CBM) of families [[CBM20]], CBM25 and CBM26, fibronectin type III (FN-III) and dockerin domains, among others <cite>Polacek2023, Vuillemin2024,Janecek2019</cite>. A phylogenetic tree of the family annotated with predicted domain architecture (Fig. 2) shows that different branches exhibit distinctive auxiliary domain patterns <cite>Vuillemin2024</cite>. Domain prediction for IgtZ suggests that this enzyme comprises an N-terminal, putative catalytic domain, followed by an FN-III, two [[CBM20]] in tandem and a C-terminal CBM25 <cite>Polacek2023</cite>.

@@ Line 1: / Line 1: @@
-{{CuratoApproved}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Eduardo Moreno Prieto|Eduardo Moreno Prieto]]
 * [[Responsible Curator]]s: [[User:Stefan Janecek|Stefan Janecek]] and [[User:Bernard Henrissat|Bernard Henrissat]]