{{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}}CBM106.html
|}
</div>


== Ligand specificities ==
VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase found in the marine bacteria ''Vibrio breoganii''. The CBM showed the favorable specificity to alginate, while it could not bind to other polyuronic acids, such as hyaluronic acid, chondroitin sulfates, dermatan sulfate, and pectin, as well as other polysaccharides from brown algae including laminarin and fucoidan <cite>Mei2024</cite>.

== Structural Features ==
[[File:CBM106_Fig.1.png|thumb|250px|right|'''Figure 1. Crystal structure of VbCBM106.''' The strand, helix, and loop were colored in cyan, yellow, and white respectively. The sequential order of these strands and helices was depicted from P4 through to G200.]]
The crystal structure (1.55 Å) of VbCBM106 exhibits a typical β-sandwich fold, which is composed of two antiparallel β-sheets formed by 11 β-strands and 4 helixes (Fig.1). Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 <cite>Mei2024</cite>.

== Functionalities ==
VbCBM106 and some of its homologous sequences are linked to the catalytic modules of the PL6 family or its subfamily PL6_1. In the natural environments, VbCBM106 might enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domains and alginate <cite>Mei2024</cite>.

== Family Firsts ==
;First Identified: The first member VbCBM106 is a component of a potential [[PL6]] alginate lyase from a marine bacterium ''Vibrio breoganii'' <cite>Mei2024</cite>.
;First Structural Characterization: VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]) is the first and currently only member of the CBM106 family with the structural information <cite>Mei2024</cite>.

== References ==
<biblio>
#Mei2024 pmid=39069041
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM106]]

Carbohydrate Binding Module Family 106

2024-11-08T15:01:31Z

Elizabeth Ficko-Blean: /* 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}}CBM106.html
|}
</div>


== Ligand specificities ==
VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase found in the marine bacteria ''Vibrio breoganii''. The CBM showed the favorable specificity to alginate, while it could not bind to other polyuronic acids, such as hyaluronic acid, chondroitin sulfates, dermatan sulfate, and pectin, as well as other polysaccharides from brown algae including laminarin and fucoidan <cite>Mei2024</cite>.

== Structural Features ==
[[File:CBM106_Fig.1.png|thumb|350px|right|'''Figure 1. Crystal structure of VbCBM106.''' The strand, helix, and loop were colored in cyan, yellow, and white respectively. The sequential order of these strands and helices was depicted from P4 through to G200.]]
The crystal structure (1.55 Å) of VbCBM106 exhibits a typical β-sandwich fold, which is composed of two antiparallel β-sheets formed by 11 β-strands and 4 helixes (Fig.1). Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 <cite>Mei2024</cite>.

== Functionalities ==
VbCBM106 and some of its homologous sequences are linked to the catalytic modules of the PL6 family or its subfamily PL6_1. In the natural environments, VbCBM106 might enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domains and alginate <cite>Mei2024</cite>.

== Family Firsts ==
;First Identified: The first member VbCBM106 is a component of a potential [[PL6]] alginate lyase from a marine bacterium ''Vibrio breoganii'' <cite>Mei2024</cite>.
;First Structural Characterization: VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]) is the first and currently only member of the CBM106 family with the structural information <cite>Mei2024</cite>.

== References ==
<biblio>
#Mei2024 pmid=39069041
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM106]]

Carbohydrate Binding Module Family 96

2024-11-08T14:53:18Z

Elizabeth Ficko-Blean: /* Family Firsts */

{{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}}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 Ca<Sup>2+</Sup> 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 X-ray crystallography structural 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]]