Carbohydrate Binding Module Family 106 - Revision history

Wenwen Tao: /* Functionalities */

2024-11-21T06:06:20Z

Functionalities

Wenwen Tao at 13:19, 19 November 2024

2024-11-19T13:19:51Z

Wenwen Tao at 12:42, 19 November 2024

2024-11-19T12:42:45Z

Wenwen Tao at 12:36, 19 November 2024

2024-11-19T12:36:33Z

Wenwen Tao: /* Ligand specificities */

2024-11-19T12:13:51Z

Ligand specificities

Elizabeth Ficko-Blean: /* Structural Features */

2024-11-08T15:07:33Z

Structural Features

Elizabeth Ficko-Blean: /* Functionalities */

2024-11-08T15:01:31Z

Functionalities

Elizabeth Ficko-Blean: /* Family Firsts */

2024-11-04T08:35:22Z

Family Firsts

Yaoguang Chang at 12:55, 1 November 2024

2024-11-01T12:55:44Z

Wenwen Tao at 11:28, 30 October 2024

2024-10-30T11:28:43Z

@@ Line 26: / Line 26: @@
 Since VbCBM106 is capable of binding to soluble alginate polysaccharides, it is suggested that it belongs to type B <cite>Boraston2004</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 domain and alginate, similar to the role of the CBM13 domain in alginate lyase<cite>Li2015</cite>.
+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 domain and alginate, similar to the role of the CBM13 domain in alginate lyase <cite>Li2015</cite>.
 == Family Firsts ==

@@ Line 21: / Line 21: @@
 == Structural Features ==
-[[File:CBM106_Fig.1.png|thumb|250px|right|'''Figure 1. Crystal structure of VbCBM106.([{{PDBlink}}8zqf PDB 8zqf]) ''' 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.]]
+[[File:CBM106_Fig.1.png|thumb|250px|right|'''Figure 1. Crystal structure of VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]).''' 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.]]
 [[File:CBM106_Fig.2.png|thumb|250px|right|'''Figure 2. Detailed view of the predicted binding site of VbCBM106.''' The potential critical residues and their side chains are shown.]]
 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). Several conserved residues were identified, including S47, S57, R59, R61, F62, K63, Y95, K100, K139, F142, K143, R190, and D192. The conserved residues are spatially adjacent, situated on the concave of one β-sheet and the apical loop region (Fig.2). 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>.

@@ Line 21: / Line 21: @@
 == 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.]]
+[[File:CBM106_Fig.1.png|thumb|250px|right|'''Figure 1. Crystal structure of VbCBM106.([{{PDBlink}}8zqf PDB 8zqf]) ''' 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.]]
 [[File:CBM106_Fig.2.png|thumb|250px|right|'''Figure 2. Detailed view of the predicted binding site of VbCBM106.''' The potential critical residues and their side chains are shown.]]
 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). Several conserved residues were identified, including S47, S57, R59, R61, F62, K63, Y95, K100, K139, F142, K143, R190, and D192. The conserved residues are spatially adjacent, situated on the concave of one β-sheet and the apical loop region (Fig.2). 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>.
 Since VbCBM106 is capable of binding to soluble alginate polysaccharides, it is suggested that it belongs to type B <cite>Boraston2004</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>.
+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 domain and alginate, similar to the role of the CBM13 domain in alginate lyase<cite>Li2015</cite>.
 == Family Firsts ==
@@ Line 37: / Line 37: @@
 #Mei2024 pmid=39069041
 #Boraston2004 pmid=15214846
 </biblio>

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase (GenBank: ANO33061.1) from the marine bacterium ''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>.
+VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase (GenBank: ANO33061.1) from the marine bacterium ''Vibrio breoganii'' <cite>Hidalgo2009</cite>. 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>.
+[[File:CBM106_Fig.2.png|thumb|250px|right|'''Figure 2. Detailed view of the predicted binding site of VbCBM106.''' The potential critical residues and their side chains are shown.]]
+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). Several conserved residues were identified, including S47, S57, R59, R61, F62, K63, Y95, K100, K139, F142, K143, R190, and D192. The conserved residues are spatially adjacent, situated on the concave of one β-sheet and the apical loop region (Fig.2). 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>.
@@ Line 33: / Line 34: @@
 == References ==
 <biblio>
 #Mei2024 pmid=39069041
 </biblio>

@@ Line 18: / Line 18: @@
 == 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>.
+VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase (GenBank: ANO33061.1) from the marine bacterium ''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 ==

@@ Line 28: / Line 28: @@
 == Family Firsts ==
-;First Identified
+;First Identified: The first member VbCBM106 is a component of a potential [[PL6]] alginate lyase from a marine bacterium ''Vibrio breoganii'' <cite>Mei2024</cite>.
-: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 ==

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 * [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]