Glycoside Hydrolase Family 64 - Revision history

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

2021-12-18T21:19:31Z

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

Julie Grondin: /* Family Firsts */

2020-07-21T21:11:48Z

Family Firsts

Julie Grondin at 03:26, 16 May 2020

2020-05-16T03:26:57Z

Julie Grondin at 03:25, 16 May 2020

2020-05-16T03:25:48Z

Julie Grondin at 03:25, 16 May 2020

2020-05-16T03:25:40Z

Julie Grondin at 03:22, 16 May 2020

2020-05-16T03:22:00Z

Julie Grondin at 03:21, 16 May 2020

2020-05-16T03:21:18Z

Harry Brumer at 00:33, 16 May 2020

2020-05-16T00:33:54Z

Harry Brumer: Curator approaved

2020-05-16T00:04:48Z

Curator approaved

Harry Brumer at 00:04, 16 May 2020

2020-05-16T00:04:15Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Julie Grondin^^^
+* [[Author]]: [[User:Julie Grondin|Julie Grondin]]
-* [[Responsible Curator]]:  ^^^Harry Brumer^^^
+* [[Responsible Curator]]:  [[User:Harry Brumer|Harry Brumer]]
 ----

@@ Line 48: / Line 48: @@
 ;First catalytic nucleophile identification: Laminaripentaose-producing &beta;-1,3-glucanase (LPHase) from ''Streptomyces matensis'' DIC-108 by site-directed mutagenesis, chemical rescue, and kinetic analysis <cite>Shrestha2011</cite>.
 ;First general acid/base residue identification: Laminaripentaose-producing &beta;-1,3-glucanase (LPHase) from ''Streptomyces matensis'' DIC-108 by site-directed mutagenesis, chemical rescue, and kinetic analysis <cite>Shrestha2011</cite>.
 ;First 3-D structure: Laminaripentaose-producing &beta;-1,3-glucanase (LPHase) from ''Streptomyces matensis'' DIC-108 by X-ray crystallography.<cite>Wu2009</cite>
 == References ==

@@ Line 40: / Line 40: @@
 Each three-dimensional GH64 structure characterized to date shares a crescent-like fold comprising of a barrel domain, and a mixed &alpha;/&beta; domain ('''Figure 1'''). This fold is unique among GHs; GH64s are not classified into any existing GH clans. In some instances, the GH64 may also contain a N-terminal [[CBM13]] or [[CBM56]], the latter of which has been shown to bind &beta;-1,3-glucans <cite>Qin2017</cite>.
-The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaripentaose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9]) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite>. To date, no significant conformational changes have been noted between ''apo'' and complex structures.
+The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaritetraose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9]) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite> (NB: In this case, LPHase was co-crystallized with laminaripentaose, however, density was only observed for four glycosyl residues). To date, no significant conformational changes have been noted between ''apo'' and complex structures.
 The three-dimensional structure of the catalytically-inactive Blg64A from ''Paenibacillus barengoltzii'', in complex with two laminarihexaose chains ([{{PDBlink}}5H9Y PDB ID 5H9Y]), provides the first structure-based evidence to explain how GH64s enzymes might bind to the triple-helical structure adopted by &beta;-1,3-glucans ''in vivo'' <cite>Qin2017</cite> ('''Figure 1'''). In this structure, the 40 Å-long groove containing the active site is 15 Å wide, and thus accommodates the two twisted laminarihexaose chains. The surface of the groove is also sufficiently large to accommodate the triple helix of linear &beta;-1,3-glucans  such as curdlan, however, the &beta;-1,6 branching typical of laminarin would be sterically hindered, explaining the lower activity of this enzyme on laminarin. To date, there is no experimental evidence to explain how the triple helix is hydrolyzed by GH64s.

@@ Line 40: / Line 40: @@
 Each three-dimensional GH64 structure characterized to date shares a crescent-like fold comprising of a barrel domain, and a mixed &alpha;/&beta; domain ('''Figure 1'''). This fold is unique among GHs; GH64s are not classified into any existing GH clans. In some instances, the GH64 may also contain a N-terminal [[CBM13]] or [[CBM56]], the latter of which has been shown to bind &beta;-1,3-glucans <cite>Qin2017</cite>.
-The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaritetraose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9], co-crystallized with laminaripentaose, but density was only observed for four glycosyl residues) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite>. To date, no significant conformational changes have been noted between ''apo'' and complex structures.
+The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaripentaose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9]) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite>. To date, no significant conformational changes have been noted between ''apo'' and complex structures.
 The three-dimensional structure of the catalytically-inactive Blg64A from ''Paenibacillus barengoltzii'', in complex with two laminarihexaose chains ([{{PDBlink}}5H9Y PDB ID 5H9Y]), provides the first structure-based evidence to explain how GH64s enzymes might bind to the triple-helical structure adopted by &beta;-1,3-glucans ''in vivo'' <cite>Qin2017</cite> ('''Figure 1'''). In this structure, the 40 Å-long groove containing the active site is 15 Å wide, and thus accommodates the two twisted laminarihexaose chains. The surface of the groove is also sufficiently large to accommodate the triple helix of linear &beta;-1,3-glucans  such as curdlan, however, the &beta;-1,6 branching typical of laminarin would be sterically hindered, explaining the lower activity of this enzyme on laminarin. To date, there is no experimental evidence to explain how the triple helix is hydrolyzed by GH64s.

@@ Line 40: / Line 40: @@
 Each three-dimensional GH64 structure characterized to date shares a crescent-like fold comprising of a barrel domain, and a mixed &alpha;/&beta; domain ('''Figure 1'''). This fold is unique among GHs; GH64s are not classified into any existing GH clans. In some instances, the GH64 may also contain a N-terminal [[CBM13]] or [[CBM56]], the latter of which has been shown to bind &beta;-1,3-glucans <cite>Qin2017</cite>.
-The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaripentaose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9]) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite>. To date, no significant conformational changes have been noted between ''apo'' and complex structures.
+The interface between the two domains forms a wide, electronegatively-charged groove, which contains the active site. Specifically, the proton donor and base are located in the center of this groove, on strands &beta;7 and &beta;9 of the barrel domain, approximately 7.5 Å apart. The laminaritetraose-bound structure of LPHase from ''Streptoymces matensis'' ([{{PDBlink}}3GD9 PDB ID 3GD9], co-crystallized with laminaripentaose, but density was only observed for four glycosyl residues) reveals that the barrel domain mediates most of the interactions between the sugar and the protein <cite>Wu2009</cite>. To date, no significant conformational changes have been noted between ''apo'' and complex structures.
 The three-dimensional structure of the catalytically-inactive Blg64A from ''Paenibacillus barengoltzii'', in complex with two laminarihexaose chains ([{{PDBlink}}5H9Y PDB ID 5H9Y]), provides the first structure-based evidence to explain how GH64s enzymes might bind to the triple-helical structure adopted by &beta;-1,3-glucans ''in vivo'' <cite>Qin2017</cite> ('''Figure 1'''). In this structure, the 40 Å-long groove containing the active site is 15 Å wide, and thus accommodates the two twisted laminarihexaose chains. The surface of the groove is also sufficiently large to accommodate the triple helix of linear &beta;-1,3-glucans  such as curdlan, however, the &beta;-1,6 branching typical of laminarin would be sterically hindered, explaining the lower activity of this enzyme on laminarin. To date, there is no experimental evidence to explain how the triple helix is hydrolyzed by GH64s.

@@ Line 52: / Line 52: @@
 == References ==
 <biblio>
-#Nakabayashi1998 Nakabayashi, M., Nishijima, T., Ehara, G., Nikaidou, N., Nishihashi, H., Watanabe, T. (1998) Structure of the gene encoding laminaripentaose-producing &beta;-1,3-glucanase (LPHase) of Streptomyces matensis DIC-108. ''J. Ferment. Bioengineer.'' '''85''', 459-464. [http://dx.doi.org/10.1016/s0922-338x(98)80062-7 DOI:10.1016/s0922-338x(98)80062-7]
+#Nakabayashi1998 Nakabayashi M, Nishijima T, Ehara G, Nikaidou N, Nishihashi H, and Watanabe T. (1998) Structure of the gene encoding laminaripentaose-producing &beta;-1,3-glucanase (LPHase) of Streptomyces matensis DIC-108. ''J. Ferment. Bioengineer.'' '''85''', 459-464. [http://dx.doi.org/10.1016/s0922-338x(98)80062-7 DOI:10.1016/s0922-338x(98)80062-7]
 #Palumbo2003 pmid=12867444
 #Wu2009 pmid=19640850

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-All characterized members of the GH64 family are laminaripentaose-producing &beta;-1,3-glucanases ([{{EClink}}3.2.1.39 EC 3.2.1.39]) from the GH64-TLP (thaumatin-like protein) superfamily. They are found in bacteria and fungal species, and are particularly abundant in the genomes of various ''Streptomyces'' and ''Fusarium'' species. Activity has been shown on insoluble and soluble &beta;-1,3-glucans, including curdlan <cite>Nakabayashi1998, Palumbo2003, Wu2009</cite>, colloidal pachyman <cite>Nakabayashi1998, Nishimura2001, Wu2009</cite>, laminarin <cite>Nakabayashi1998, Nishimura2001, Wu2009</cite>, and zymosan A <cite>Nakabayashi1998, Palumbo2003</cite>, a commercial preparation of partially-purified yeast cell walls (contains branched glucans).
+All characterized members of the GH64 family are laminaripentaose-producing &beta;(1,3)-glucanases ([{{EClink}}3.2.1.39 EC 3.2.1.39]) from the GH64-TLP (thaumatin-like protein) superfamily. They are found in bacteria and fungal species, and are particularly abundant in the genomes of various ''Streptomyces'' and ''Fusarium'' species. Activity has been shown on insoluble and soluble &beta;-1,3-glucans, including curdlan <cite>Nakabayashi1998, Palumbo2003, Wu2009</cite>, colloidal pachyman <cite>Nakabayashi1998, Nishimura2001, Wu2009</cite>, laminarin <cite>Nakabayashi1998, Nishimura2001, Wu2009</cite>, and zymosan A <cite>Nakabayashi1998, Palumbo2003</cite>, a commercial preparation of partially-purified yeast cell walls (contains branched glucans).
 == Kinetics and Mechanism ==

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