CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 47

2024-11-21T08:28:02Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', was the founding member of the CBM47 family <cite>Boraston2006</cite>. However, the ''Anguilla anguilla'' agglutinin (AAA) derived from the European eel, which was characterized earlier <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system. For instance, they are capable of recognizing and binding to specific carbohydrate structures on the surfaces of pathogens, such as L-fucose and D-galactose methylether derivatives, serving as vital immune recognition molecules. Furthermore, they can also recognize H and Lea antigens, which are used in determining ABO and Lewis blood group types <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to the [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane. These aggregates, through protein-protein interactions with the toxin, steer the toxin to accumulate at fucose-rich sites on the cell surface, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, as one of the structural molecules in the sea cucumber body wall, play an important role in the formation of the structure and quality of sea cucumber. A fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein, based on which the ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time <cite>Mei2022</cite>. It was observed that sulfated fucan existed as a ground substance in the extracellular matrix.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T08:26:24Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', was the founding member of the CBM47 family <cite>Boraston2006</cite>. However, the ''Anguilla anguilla'' agglutinin (AAA) derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system. For instance, they are capable of recognizing and binding to specific carbohydrate structures on the surfaces of pathogens, such as L-fucose and D-galactose methylether derivatives, serving as vital immune recognition molecules. Furthermore, they can also recognize H and Lea antigens, which are used in determining ABO and Lewis blood group types <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to the [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane. These aggregates, through protein-protein interactions with the toxin, steer the toxin to accumulate at fucose-rich sites on the cell surface, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, as one of the structural molecules in the sea cucumber body wall, play an important role in the formation of the structure and quality of sea cucumber. A fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein, based on which the ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time <cite>Mei2022</cite>. It was observed that sulfated fucan existed as a ground substance in the extracellular matrix.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T08:25:29Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', was the founding member of the CBM47 family <cite>Boraston2006</cite>. However, the ''Anguilla anguilla'' agglutinin (AAA) derived from the European eel, which was characterized earlier which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system. For instance, they are capable of recognizing and binding to specific carbohydrate structures on the surfaces of pathogens, such as L-fucose and D-galactose methylether derivatives, serving as vital immune recognition molecules. Furthermore, they can also recognize H and Lea antigens, which are used in determining ABO and Lewis blood group types <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to the [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane. These aggregates, through protein-protein interactions with the toxin, steer the toxin to accumulate at fucose-rich sites on the cell surface, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, as one of the structural molecules in the sea cucumber body wall, play an important role in the formation of the structure and quality of sea cucumber. A fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein, based on which the ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time <cite>Mei2022</cite>. It was observed that sulfated fucan existed as a ground substance in the extracellular matrix.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T08:21:35Z

Wenwen Tao: /* Functionalities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system. For instance, they are capable of recognizing and binding to specific carbohydrate structures on the surfaces of pathogens, such as L-fucose and D-galactose methylether derivatives, serving as vital immune recognition molecules. Furthermore, they can also recognize H and Lea antigens, which are used in determining ABO and Lewis blood group types <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to the [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane. These aggregates, through protein-protein interactions with the toxin, steer the toxin to accumulate at fucose-rich sites on the cell surface, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, as one of the structural molecules in the sea cucumber body wall, play an important role in the formation of the structure and quality of sea cucumber. A fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein, based on which the ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time <cite>Mei2022</cite>. It was observed that sulfated fucan existed as a ground substance in the extracellular matrix.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:42:07Z

Wenwen Tao: /* Functionalities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system. For instance, they are capable of recognizing and binding to specific carbohydrate structures on the surfaces of pathogens, such as L-fucose and D-galactose methylether derivatives, serving as vital immune recognition molecules. Furthermore, they can also recognize H and Lea antigens, which are used in determining ABO and Lewis blood group types <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to the [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane. These aggregates, through protein-protein interactions with the toxin, steer the toxin to accumulate at fucose-rich sites on the cell surface, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, as one of the structural molecules in the sea cucumber body wall, play an important role in the formation of the structure and quality of sea cucumber. A fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein, based on which the ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>. It was observed that sulfated fucan existed as a ground substance in the extracellular matrix.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:35:29Z

Wenwen Tao: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]).''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:27:28Z

Wenwen Tao: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA ([{{PDBlink}}1k12 PDB 1k12]) and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:26:23Z

Wenwen Tao: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability <cite>Boraston2006 Feil2012 Bianchet2002</cite>. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands <cite>Feil2012</cite>. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Additionally, the loop regions of MsaFBP32 are shorter than those of AAA, resulting in fewer steric hindrances, which facilitates easier contact with oligosaccharide molecules and the formation of stable binding, but concurrently may reduce binding specificity <cite>Bianchet2010</cite>.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:15:11Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite>, and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-21T06:13:38Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 106

2024-11-21T06:06:20Z

Wenwen Tao: /* Functionalities */

Carbohydrate Binding Module Family 96

2024-11-21T06:05:31Z

Wenwen Tao: /* Ligand specificities */

Carbohydrate Binding Module Family 47

2024-11-19T13:27:53Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3.''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM binds to the various sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-19T13:26:40Z

Wenwen Tao: /* Ligand specificities */

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The characterization of the C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin Sp[[GH98]], originating from the fucose utilization operon in ''Streptococcus pneumoniae'', first defined the CBM47 family <cite>Boraston2006</cite>. The CBM47 family was created after the discovery of SpX-1.2.3.''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and is also classified as an F-type lectin <cite>Bianchet2002</cite>, is also included in the CBM47 family. Several other members of the CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to carbohydrates containing fucose, which could be oligosaccharides (often trisaccharides or smaller) or parts of polysaccharides, such as the AAA, and a portion of CBM47 members have demonstrated binding to glycans containing galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, another CBM47 domain (named WfCBM47) was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127T, which is appended to the [[GH168]] family sequence. The CBM exhibited specific binding to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- are colored in cyan, yellow, white ,green and orange respectively.]]
All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>. The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds glycans through shallow grooves located within their complementarity-determining regions (CDRs); these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin Sp[[GH98]], was reported in 2006 and is considered the founding member of the CBM47 family <cite>Boraston2006</cite>. The F-type lectin AAA, discovered in the serum of European eel and reported in 2002, is also included in the CBM47 family <cite>Bianchet2002</cite>.
;First Structural Characterization: The first structural characterization was on the AAA ([{{PDBlink}}1k12 PDB 1k12]) prior to the founding of the CBM47 family <cite>Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 106

2024-11-19T13:19:51Z

Wenwen Tao:

Carbohydrate Binding Module Family 96

2024-11-19T13:17:00Z

Wenwen Tao:

Carbohydrate Binding Module Family 96

2024-11-19T13:08:54Z

Wenwen Tao:

Carbohydrate Binding Module Family 96

2024-11-19T13:06:30Z

Wenwen Tao: /* Structural Features */

Carbohydrate Binding Module Family 96

2024-11-19T12:57:37Z

Wenwen Tao: /* Structural Features */

Carbohydrate Binding Module Family 96

2024-11-19T12:54:33Z

Wenwen Tao: /* Ligand specificities */

Carbohydrate Binding Module Family 106

2024-11-19T12:42:45Z

Wenwen Tao:

File:CBM106 Fig.2.png

2024-11-19T12:38:12Z

Wenwen Tao:

Carbohydrate Binding Module Family 106

2024-11-19T12:36:33Z

Wenwen Tao:

Carbohydrate Binding Module Family 106

2024-11-19T12:13:51Z

Wenwen Tao: /* Ligand specificities */

Carbohydrate Binding Module Family 47

2024-11-01T13:19:39Z

Wenwen Tao:

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the [[GH168]] family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- were colored in cyan, yellow, white ,green and origin respectively.]]
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to [[GH98]] family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified
:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin SpGH98, was reported in 2006 and was initially proposed to constitute a member of the CBM47 family <cite>Boraston2006</cite>. However, F-type lectin AAA, discovered in the serum of European eel and reported in 2002, has also been included in the CBM47 family by CAZy database <cite>Bianchet2002</cite>.
;First Structural Characterization
:All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-01T13:18:47Z

Wenwen Tao:

{{CuratorApproved}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the [[GH168]] family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- were colored in cyan, yellow, white ,green and origin respectively.]]
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to GH98 family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified
:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin SpGH98, was reported in 2006 and was initially proposed to constitute a member of the CBM47 family <cite>Boraston2006</cite>. However, F-type lectin AAA, discovered in the serum of European eel and reported in 2002, has also been included in the CBM47 family by CAZy database <cite>Bianchet2002</cite>.
;First Structural Characterization
:All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

File:CBM47 Fig.1.png

2024-11-01T08:44:01Z

Wenwen Tao:

Carbohydrate Binding Module Family 47

2024-11-01T08:38:31Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the GH168 family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
[[File:CBM47_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of (A) AAA and (B) SpX-1.''' The strand, helix, loop, Ca2+ and Cl- were colored in cyan, yellow, white ,green and origin respectively.]]
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to GH98 family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified
:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin SpGH98, was reported in 2006 and was initially proposed to constitute a member of the CBM47 family <cite>Boraston2006</cite>. However, F-type lectin AAA, discovered in the serum of European eel and reported in 2002, has also been included in the CBM47 family by CAZy database <cite>Bianchet2002</cite>.
;First Structural Characterization
:All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-01T08:32:18Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the GH168 family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to GH98 family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified
:SpX-1.2.3, isolated from ''Streptococcus pneumoniae'' and associated with the toxin SpGH98, was reported in 2006 and was initially proposed to constitute a member of the CBM47 family <cite>Boraston2006</cite>. However, F-type lectin AAA, discovered in the serum of European eel and reported in 2002, has also been included in the CBM47 family by CAZy database <cite>Bianchet2002</cite>.
;First Structural Characterization
:All the fucose-binding proteins, SpX-1 ([{{PDBlink}}2j1r PDB 2j1r]), SpX-3 ([{{PDBlink}}2j22 PDB 2j22]) and AAA ([{{PDBlink}}1k12 PDB 1k12]), have had their tertiary structures determined through X-ray crystallography <cite>Boraston2006 Bianchet2002</cite>.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-01T08:27:23Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the GH168 family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
The AAA, discovered in the serum of European eel, and MsaFBP32, isolated from the plasma of the striped bass ''Morone saxatilis'', participate in the recognition of bacterial lipopolysaccharides by the animal innate immune system <cite>Bianchet2002 Bianchet2010</cite>.

Both LLYlec and SpX-1.2.3 are associated with bacterial toxins belonging to GH98 family. Under physiological conditions, these proteins form aggregates that bind to glycoproteins or glycolipids on the cell membrane and insert into the membrane, thereby enhancing the pore-forming activity of the toxins and accelerating cell lysis. Based on the binding specificity to fucoidan, the fluorescein isothiocyanate-labeled SpX-1.2.3 triplet was applied for in situ visualization of mouse lung tissue sections <cite>Boraston2006 Feil2012</cite>.

Sulfated fucans, constituting a pivotal structural component within the body wall of sea cucumbers, are important to the overall architecture and quality of these marine invertebrates. To evaluate the feasibility of WfCBM47 as a tool in the ''in situ'' investigation of sulfated fucan, a fluorescent probe was constructed by fusing WfCBM47 with a green fluorescent protein. The ''in situ'' visualization of sulfated fucan in the sea cucumber (''Apostichopus japonicus'') body wall was implemented for the first time by utilizing the probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-01T08:14:51Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the GH168 family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

== Structural Features ==
The core structures of the CBM47 family exhibit remarkable similarity, adopting an eight-stranded β-sandwich fold, which is comprised of a five-stranded anti-parallel β-sheet on one side and a three-stranded anti-parallel β-sheet on the other <cite>Boraston2006 Bianchet2002 Bianchet2010 Feil2012 Lawrence2012</cite>. Additionally, CBM47 typically exists as a dimer or trimer under physiological conditions, with Ca2+ playing a pivotal role in maintaining its conformational stability. The CBM47 family recognizes and binds polysaccharides through shallow grooves located within their complementarity-determining regions (CDRs), and these variable loops have been shown to exhibit a high degree of sequence and conformational variability among different CBM47s, enabling them to recognize diverse ligands. For instance, LLYlec and SpX-1 reveal smaller differences among their loops, permitting them to bind to a wide array of Lewis blood group oligosaccharides <cite>Boraston2006 Feil2012</cite>. While AAA features a particularly longer and rigid loop, which may account for its preference to form complexes with type 1 antigens while lacking affinity for type 2 antigens <cite>Bianchet2002</cite>. Polysaccharide binding via loop regions typically tends to be of shorter length.

== Functionalities ==
''Content in this section should include, in paragraph form, a description of:''
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 47

2024-11-01T07:47:29Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM47.html
|}
</div>


== Ligand specificities ==
The C-terminal triplet fucose-binding module (SpX-1.2.3) of protein toxin SpGH98, originating from the fucose utilization operon in ''Streptococcus pneumoniae'', has been firstly designated as CBM47 <cite>Boraston2006</cite>. ''Anguilla anguilla'' agglutinin (AAA), derived from the European eel, which was characterized earlier and initially classified as an F-type lectin <cite>Bianchet2002</cite>, was also included in the CBM47 family. Several other members of CBM47 family, such as MsaFBP32 <cite>Bianchet2010</cite>, LLYlec <cite>Feil2012</cite> and its mutant LLYlecY62H <cite>Lawrence2012</cite>, have been confirmed to possess the F-type lectin fold. The aforementioned proteins are all capable of binding to polysaccharides containing fucose, often trisaccharides or smaller, such as AAA, and a portion of CBM47 members has been demonstrated to bind to polysaccharides with galactose <cite>Bianchet2002</cite>. Both of these sugars are ubiquitous in glycoproteins and glycolipids on the cell surface, playing crucial roles in cellular bioactivity and functions. Furthermore, the CBM47 family exhibits specific binding to Lewis blood group oligosaccharides, which are characterized by fucosylation modifications. For instance, LLYlec binds to both Lewis y (Ley) antigen (type 1 antigen) and Lewis b (Leb) antigen (type 2 antigen) <cite>Feil2012</cite>, whereas AAA displays a preference for binding to the Ley antigen <cite>Bianchet2002</cite>. Consequently, the CBM47 family holds potential applications in immune recognition and disease diagnosis. Besides, a novel CBM47 domain was discovered from the marine bacterium ''Wenyingzhuangia fucanilytica'', which is appended to the GH168 family sequence. The CBM exhibited a specific binding capacity to sulfated fucans with the backbone composed of 1,3-α-L-fucopyranose residues <cite>Mei2022</cite>.

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010 Armenta2017</cite>.

== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
* '''Type:''' Include here Type A, B, or C and properties
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

== Functionalities ==
''Content in this section should include, in paragraph form, a description of:''
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Boraston2006 pmid=16987809
#Bianchet2002 pmid=12091873
#Bianchet2010 pmid=20561530
#Feil2012 pmid=22325774
#Lawrence2012 pmid=23181061
#Mei2022 pmid=34893209
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM047]]

Carbohydrate Binding Module Family 96

2024-11-01T07:42:34Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM96.html
|}
</div>


== Ligand specificities ==
Members of the CBM96 family are present within various CAZyme families, including [[PL8]], [[PL35]], [[GH16]], and [[GH136]], suggesting that they may possess a wide range of diverse activities. TM6-N4, originating from the marine thermophilic bacterium ''Defluviitalea phaphyphila'', and DmCBM96-1/DmCBM96-2, derived from the bacterium ''Dysgonomonas sp.'' HDW5A isolated from ''Hydrophilus acuminatus'' , are currently the characterized members of the CBM96 family. TM6-N4 is associated with the catalytic module of [[PL39]] alginate lyase, and its specific binding capability towards alginate was confirmed by affinity electrophoresis analysis. However, isothermal titration calorimetry analysis revealed that TM6-N4 exhibits no significant preference for mannuronate or guluronate oligosaccharides <cite>Ji2023</cite>. DmCBM96-1 and DmCBM96-2, which are consecutive CBMs linked to chondroitin sulfate (CS) lyase PL8_3, have been confirmed to bind to CS-A (chondroitin 4-sulfate), CS-C (chondroitin 6-sulfate), and Aj-fCS (consisting of CS-type backbone and sulfated fucose branches), but not to other polyuronic acids such as hyaluronic acid (HA), dermatan sulfate (DS), heparin (HS), pectin, and alginate. Comparatively, the relative affinity of both DmCBM96 proteins to CS-C are higher than CS-A <cite>Liu2024</cite>.

== Structural Features ==
[[File:CBM96_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of TM6-N4.''' The strand, helix, loop and Ca2+ were colored in cyan, yellow, white and green respectively.]]
Upon BLASTP analysis, DmCBM96-1 exhibits a relatively low sequence identity of approximately 32% when compared to TM6-N4, whereas the sequence identity between DmCBM96-2 and TM6-N4 is even lower, at 25%. The crystal structures of TM6-N4 (1.35 Å) and DmCBM96-1 (2.20 Å) reveal that they both exhibit a typical β-sandwich fold, comprising two antiparallel β-sheets consisting of 11 β-strands, but differ in helixes. The binding sites of both DmCBM96-1 and TM6-N4 are located within the loop regions. Site-directed mutagenesis assay revealed that the basic amino acids Arg27, Lys45, Arg53, Arg157, and the aromatic amino acid Tyr51 at the binding site of DmCBM96-1 are crucial for CS binding <cite>Liu2024</cite>. While , the amino acids located at the bottom or wall of the shallow groove of TM6-N4, including Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159, are essential for alginate binding <cite>Ji2023</cite>. Among these, the crucial amino acids Lys45 and Arg53 in DmCBM96-1 correspond to the key amino acids Lys27 and Arg36 in TM6-N4, respectively, and they are highly conserved within the CBM96 family, suggesting their pivotal roles in the ligand binding process.

== Functionalities ==
Members of the CBM96 family are annotated by dbCAN to be associated with several CAZyme families, and their presumed physiological role is to facilitate enzyme-carbohydrate interactions and enhance the local concentration of enzymes near substrates, thereby promoting the degradation of polysaccharides. Based on the polysaccharide-binding specificity of the CBM96 family, it may also have potential applications in the study of cellular structures or the detection of pathogenic bacteria. Furthermore, through fusion expression, CBM96 could potentially be utilized to optimize the properties of other CAZymes <cite>Ji2023</cite>.

== Family Firsts ==
;First Identified
:The TM6-N4 derived from the alginate lyase Dp0100 of marine bacterium ''Defluviitalea phaphyphila'', which was first reported in 2023, represents the first characterized member of the CBM96 family <cite>Ji2023</cite>.
;First Structural Characterization
:Alginate-binding protein TM6-N4 is the first member of the CBM96 family to undergo crystal structure characterization ([{{PDBlink}}7vbo PDB 7vbo]) <cite>Ji2023</cite>. Subsequently, CS-binding protein DmCBM96-1 was also characterized ([{{PDBlink}}2pqr PDB 2pqr]) <cite>Liu2024</cite>.

== References ==
<biblio>
#Ji2023 pmid=36592931
#Liu2024 pmid=38805590
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM096]]

Carbohydrate Binding Module Family 47

2024-11-01T07:27:44Z

Wenwen Tao:

User:Wenwen Tao

2024-10-31T02:49:23Z

Wenwen Tao:

[[Image:Wenwen_Tao.png|205px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
By now, she had helped establish CAZypedia pages for [[CBM47]], [[CBM96]], and [[CBM106]].

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-31T02:47:44Z

Wenwen Tao:

[[Image:Wenwen_Tao.png|100px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
By now, she had helped establish CAZypedia pages for [[CBM47]], [[CBM96]], and [[CBM106]].

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-31T02:47:33Z

Wenwen Tao:

[[Image:Wenwen_Tao.png|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
By now, she had helped establish CAZypedia pages for [[CBM47]], [[CBM96]], and [[CBM106]].

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-31T02:47:21Z

Wenwen Tao:

[[Image:Wenwen_Tao.png|1100px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
By now, she had helped establish CAZypedia pages for [[CBM47]], [[CBM96]], and [[CBM106]].

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-31T02:46:45Z

Wenwen Tao:

User:Wenwen Tao

2024-10-31T02:45:29Z

Wenwen Tao:

[[Image:Wenwen Tao.png|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>
By now, she had helped establish CAZypedia pages for [[CBM47]], [[CBM96]], and [[CBM106]].

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

File:Wenwen Tao.png

2024-10-31T02:41:10Z

Wenwen Tao: Wenwen Tao uploaded a new version of File:Wenwen Tao.png

User:Wenwen Tao

2024-10-31T02:40:02Z

Wenwen Tao:

User:Wenwen Tao

2024-10-30T12:25:49Z

Wenwen Tao:

[[Image:Wenwen_Tao.png|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-30T12:25:23Z

Wenwen Tao:

[[Image:Wenwen_Tao.jpg|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

File:Wenwen Tao.png

2024-10-30T12:25:21Z

Wenwen Tao:

User:Wenwen Tao

2024-10-30T12:19:43Z

Wenwen Tao:

[[Image:Wenwen Tao.png|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

User:Wenwen Tao

2024-10-30T12:18:07Z

Wenwen Tao:

[[Image:Blank_user-200px.png|200px|right]]
Wenwen Tao is currently a master student at the College of Food Science and Engineering, Ocean University of China, under the instruction of Prof. Yaoguang Chang. Her research focuses on the gene-mining and characterization of carbohydrate-binding modules. She discovered and characterized the first member of [[CBM106]] <cite>Mei2024</cite>:
*[[CBM106]]: VbCBM106 (alginate-binding CBM) <cite>Mei2024</cite>

----

<biblio>
#Mei2024 pmid=39069041

</biblio>


[[Category:Contributors|Tao,Wenwen]]

File:CBM96 Fig.1.png

2024-10-30T11:58:47Z

Wenwen Tao:

Carbohydrate Binding Module Family 96

2024-10-30T11:58:17Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM96.html
|}
</div>


== Ligand specificities ==
Members of the CBM96 family are present within various CAZyme families, including [[PL8]], [[PL35]], [[GH16]], and [[GH136]], suggesting that they may possess a wide range of diverse activities. TM6-N4, originating from the marine thermophilic bacterium ''Defluviitalea phaphyphila'', and DmCBM96-1/DmCBM96-2, derived from the bacterium ''Dysgonomonas sp.'' HDW5A isolated from ''Hydrophilus acuminatus'' , are currently the characterized members of the CBM96 family. TM6-N4 is associated with the catalytic module of [[PL39]] alginate lyase, and its specific binding capability towards alginate was confirmed by affinity electrophoresis analysis. However, isothermal titration calorimetry analysis revealed that TM6-N4 exhibits no significant preference for mannuronate or guluronate oligosaccharides <cite>Ji2023</cite>. DmCBM96-1 and DmCBM96-2, which are consecutive CBMs linked to chondroitin sulfate (CS) lyase PL8_3, have been confirmed to bind to CS-A (chondroitin 4-sulfate), CS-C (chondroitin 6-sulfate), and Aj-fCS (consisting of CS-type backbone and sulfated fucose branches), but not to other polyuronic acids such as hyaluronic acid (HA), dermatan sulfate (DS), heparin (HS), pectin, and alginate. Comparatively, the relative affinity of both DmCBM96 proteins to CS-C are higher than CS-A <cite>Liu2024</cite>.

== Structural Features ==
[[File:CBM96_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of TM6-N4.''' The strand, helix, loop and Ca2+ were colored in cyan, yellow, white and green respectively.]]
Upon BLASTP analysis, DmCBM96-1 exhibits a relatively low sequence identity of approximately 32% when compared to TM6-N4, whereas the sequence identity between DmCBM96-2 and TM6-N4 is even lower, at 25%. The crystal structures of TM6-N4 (1.35 Å) and DmCBM96-1 (2.20 Å) reveal that they both exhibit a typical β-sandwich fold, comprising two antiparallel β-sheets consisting of 11 β-strands, but differ in helixes. The binding sites of both DmCBM96-1 and TM6-N4 are located within the loop regions. Site-directed mutagenesis assay revealed that the basic amino acids Arg27, Lys45, Arg53, Arg157, and the aromatic amino acid Tyr51 at the binding site of DmCBM96-1 are crucial for CS binding <cite>Liu2024</cite>. While , the amino acids located at the bottom or wall of the shallow groove of TM6-N4, including Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159, are essential for alginate binding <cite>Ji2023</cite>. Among these, the crucial amino acids Lys45 and Arg53 in DmCBM96-1 correspond to the key amino acids Lys27 and Arg36 in TM6-N4, respectively, and they are highly conserved within the CBM96 family, suggesting their pivotal roles in the ligand binding process.

== Functionalities ==
Members of the CBM96 family are annotated by dbCAN to be associated with several CAZyme families, and their presumed physiological role is to facilitate enzyme-carbohydrate interactions and enhance the local concentration of enzymes near substrates, thereby promoting the degradation of polysaccharides. Based on the polysaccharide-binding specificity of the CBM96 family, it may also have potential applications in the study of cellular structures or the detection of pathogenic bacteria. Furthermore, through fusion expression, CBM96 could potentially be utilized to optimize the properties of other CAZymes <cite>Ji2023</cite>.

== Family Firsts ==
;First Identified
:The TM6-N4 derived from the alginate lyase Dp0100 of marine bacterium ''Defluviitalea phaphyphila'', which was first reported in 2023, represents the first characterized member of the CBM96 family <cite>Ji2023</cite>.
;First Structural Characterization
:Alginate-binding protein TM6-N4 is the first member of the CBM96 family to undergo crystal structure characterization ([{{PDBlink}}7vbo PDB 7vbo]) <cite>Ji2023</cite>. Subsequently, CS-binding protein DmCBM96-1 was also characterized ([{{PDBlink}}2pqr PDB 2pqr]) <cite>Liu2024</cite>.

== References ==
<biblio>
#Ji2023 pmid=36592931
#Liu2024 pmid=38805590
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM096]]

Carbohydrate Binding Module Family 96

2024-10-30T11:50:33Z

Wenwen Tao:

{{UnderConstruction}}
* [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM96.html
|}
</div>


== Ligand specificities ==
Members of the CBM96 family are present within various CAZyme families, including [[PL8]], [[PL35]], [[GH16]], and [[GH136]], suggesting that they may possess a wide range of diverse activities. TM6-N4, originating from the marine thermophilic bacterium ''Defluviitalea phaphyphila'', and DmCBM96-1/DmCBM96-2, derived from the bacterium ''Dysgonomonas sp.'' HDW5A isolated from ''Hydrophilus acuminatus'' , are currently the characterized members of the CBM96 family. TM6-N4 is associated with the catalytic module of [[PL39]] alginate lyase, and its specific binding capability towards alginate was confirmed by affinity electrophoresis analysis. However, isothermal titration calorimetry analysis revealed that TM6-N4 exhibits no significant preference for mannuronate or guluronate oligosaccharides <cite>Ji2023</cite>. DmCBM96-1 and DmCBM96-2, which are consecutive CBMs linked to chondroitin sulfate (CS) lyase PL8_3, have been confirmed to bind to CS-A (chondroitin 4-sulfate), CS-C (chondroitin 6-sulfate), and Aj-fCS (consisting of CS-type backbone and sulfated fucose branches), but not to other polyuronic acids such as hyaluronic acid (HA), dermatan sulfate (DS), heparin (HS), pectin, and alginate. Comparatively, the relative affinity of both DmCBM96 proteins to CS-C are higher than CS-A <cite>Liu2024</cite>.

== Structural Features ==
Upon BLASTP analysis, DmCBM96-1 exhibits a relatively low sequence identity of approximately 32% when compared to TM6-N4, whereas the sequence identity between DmCBM96-2 and TM6-N4 is even lower, at 25%. The crystal structures of TM6-N4 (1.35 Å) and DmCBM96-1 (2.20 Å) reveal that they both exhibit a typical β-sandwich fold, comprising two antiparallel β-sheets consisting of 11 β-strands, but differ in helixes. The binding sites of both DmCBM96-1 and TM6-N4 are located within the loop regions. Site-directed mutagenesis assay revealed that the basic amino acids Arg27, Lys45, Arg53, Arg157, and the aromatic amino acid Tyr51 at the binding site of DmCBM96-1 are crucial for CS binding <cite>Liu2024</cite>. While , the amino acids located at the bottom or wall of the shallow groove of TM6-N4, including Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159, are essential for alginate binding <cite>Ji2023</cite>. Among these, the crucial amino acids Lys45 and Arg53 in DmCBM96-1 correspond to the key amino acids Lys27 and Arg36 in TM6-N4, respectively, and they are highly conserved within the CBM96 family, suggesting their pivotal roles in the ligand binding process.

== Functionalities ==
Members of the CBM96 family are annotated by dbCAN to be associated with several CAZyme families, and their presumed physiological role is to facilitate enzyme-carbohydrate interactions and enhance the local concentration of enzymes near substrates, thereby promoting the degradation of polysaccharides. Based on the polysaccharide-binding specificity of the CBM96 family, it may also have potential applications in the study of cellular structures or the detection of pathogenic bacteria. Furthermore, through fusion expression, CBM96 could potentially be utilized to optimize the properties of other CAZymes <cite>Ji2023</cite>.

== Family Firsts ==
;First Identified
:The TM6-N4 derived from the alginate lyase Dp0100 of marine bacterium ''Defluviitalea phaphyphila'', which was first reported in 2023, represents the first characterized member of the CBM96 family <cite>Ji2023</cite>.
;First Structural Characterization
:Alginate-binding protein TM6-N4 is the first member of the CBM96 family to undergo crystal structure characterization ([{{PDBlink}}7vbo PDB 7vbo]) <cite>Ji2023</cite>. Subsequently, CS-binding protein DmCBM96-1 was also characterized ([{{PDBlink}}2pqr PDB 2pqr]) <cite>Liu2024</cite>.

== References ==
<biblio>
#Ji2023 pmid=36592931
#Liu2024 pmid=38805590
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM096]]