Carbohydrate Binding Module Family 99 - Revision history

Elizabeth Ficko-Blean at 07:54, 16 February 2024

2024-02-16T07:54:04Z

Elizabeth Ficko-Blean at 15:29, 29 January 2024

2024-01-29T15:29:51Z

Elizabeth Ficko-Blean at 15:21, 29 January 2024

2024-01-29T15:21:46Z

Elizabeth Ficko-Blean at 15:19, 29 January 2024

2024-01-29T15:19:21Z

Yaoguang Chang at 06:41, 5 January 2024

2024-01-05T06:41:56Z

Xuanwei Mei at 13:34, 2 January 2024

2024-01-02T13:34:55Z

Xuanwei Mei at 13:23, 2 January 2024

2024-01-02T13:23:23Z

Xuanwei Mei at 13:22, 2 January 2024

2024-01-02T13:22:56Z

Xuanwei Mei at 13:21, 2 January 2024

2024-01-02T13:21:42Z

Xuanwei Mei at 12:55, 2 January 2024

2024-01-02T12:55:17Z

@@ Line 24: / Line 24: @@
 == Structural Features ==
-The predicted structure by AlphaFold2 shows that FvCBM99 displays a typical β-sandwich fold.
+An AlphaFold2 model predicts that FvCBM99 has a β-sandwich fold <cite>Mei2023</cite>.
 == Functionalities ==
@@ Line 33: / Line 33: @@
 == Family Firsts ==
 ;First Identified: The first member FvCBM99 is a component of a potential [[GH86]] porphyranase (GenBank: AJW82063.1) from a marine bacterium ''Flammeovirga sp''. OC4 <cite>Liu2015</cite>.
-;First Structural Characterization: No three-dimensional structure has been solved in this CBM family.
+;First Structural Characterization: No experimental three-dimensional structure has been solved in this family.
 == References ==

@@ Line 32: / Line 32: @@
 == Family Firsts ==
-;First Identified
+;First Identified: The first member FvCBM99 is a component of a potential [[GH86]] porphyranase (GenBank: AJW82063.1) from a marine bacterium ''Flammeovirga sp''. OC4 <cite>Liu2015</cite>.
-The first member FvCBM99 is a component of a potential [[GH86]] porphyranase (GenBank: AJW82063.1) from a marine bacterium ''Flammeovirga sp''. OC4 <cite>Liu2015</cite>.
+;First Structural Characterization: No three-dimensional structure has been solved in this CBM family.
 == References ==

@@ Line 19: / Line 19: @@
 == Ligand specificities ==
-[[File:Figure1.png|thumb|'''Figure 1. Carbohydrate array assay results of FvCBM99. ''' Binding analysis with porphyran and other galactans in red algae (A), and other polysaccharides (B). κ-Car, κ-carrageenan. ι-Car, ι-carrageenan. Alg, alginate. An-FUC, sulfated fucan from ''Ascophyllum nodosum''. CSA, chondroitin sulfate A sodium salt. HA, hyaluronic acid. Pec, pectin. Each polysaccharide performed three parallels. The values (noted at the bottom) were the average gray intensities of the triplicates. The value binding to porphyran was set to 100, and the other values were normalized accordingly.''' ]]
+[[File:Figure1.png|thumb|'''Figure 1. Carbohydrate array assay results of FvCBM99. ''' Binding analysis with porphyran and other galactans from red algae (A), and other polysaccharides (B). κ-Car, κ-carrageenan. ι-Car, ι-carrageenan. Alg, alginate. An-FUC, sulfated fucan from ''Ascophyllum nodosum''. CSA, chondroitin sulfate A sodium salt. HA, hyaluronic acid. Pec, pectin. Each polysaccharide performed three parallels. The values (noted at the bottom) were the average gray intensities of the triplicates. The value binding to porphyran was set to 100, and the other values were normalized accordingly.''' ]]
 The first characterized member in the CBM99 family is FvCBM99 <cite>Mei2023</cite>. The CBM FvCBM99 bound to porphyran and displayed a weak affinity to agarose (Fig. 1). It was incapable of binding to the other examined polysaccharides, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, and pectin. Furthermore, FvCBM99 bound to porphyran tetrasaccharide with an affinity constant of 1.9 × 10<sup>-4</sup> M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012</cite>, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays show that FvCBM99 specifically binds to the major structural units of porphyran.

@@ Line 21: / Line 21: @@
 [[File:Figure1.png|thumb|'''Figure 1. Carbohydrate array assay results of FvCBM99. ''' Binding analysis with porphyran and other galactans in red algae (A), and other polysaccharides (B). κ-Car, κ-carrageenan. ι-Car, ι-carrageenan. Alg, alginate. An-FUC, sulfated fucan from ''Ascophyllum nodosum''. CSA, chondroitin sulfate A sodium salt. HA, hyaluronic acid. Pec, pectin. Each polysaccharide performed three parallels. The values (noted at the bottom) were the average gray intensities of the triplicates. The value binding to porphyran was set to 100, and the other values were normalized accordingly.''' ]]
-The first characterized member in the CBM99 family is FvCBM99 <cite>Mei2023</cite>. The CBM FvCBM99 could bind to porphyran and displayed a weak affinity to agarose (Fig. 1). While it was incapable of binding to the other examined polysaccharides, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, or pectin. Furthermore, FvCBM99 could bind to porphyran tetrasaccharide with an affinity constant of 1.9 × 10<sup>-4</sup> M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012</cite>, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays showed that FvCBM99 specifically binds to the major structural units of porphyran.
+The first characterized member in the CBM99 family is FvCBM99 <cite>Mei2023</cite>. The CBM FvCBM99 bound to porphyran and displayed a weak affinity to agarose (Fig. 1). It was incapable of binding to the other examined polysaccharides, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, and pectin. Furthermore, FvCBM99 bound to porphyran tetrasaccharide with an affinity constant of 1.9 × 10<sup>-4</sup> M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012</cite>, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays show that FvCBM99 specifically binds to the major structural units of porphyran.
 == Structural Features ==
-The predicted structure by AlphaFold2 showed that FvCBM99 displays a typical β-sandwich fold.
+The predicted structure by AlphaFold2 shows that FvCBM99 displays a typical β-sandwich fold.
 == Functionalities ==
 To evaluate the feasibility of FvCBM99 as a tool in the ''in situ'' investigation of porphyran, a fluorescent probe was constructed by fusing FvCBM99 with a green fluorescent protein. The ''in situ'' visualization of porphyran in red alga ''Porphyra haitanensis'' was realized by utilizing the fluorescent probe <cite>Mei2023</cite>.
-Most of the members of the CBM99 family are appended to the GH16_11, GH16_12, GH16_16, or GH16_26 subfamily, or GH86 family. As documented in the CAZy database, members of the four subfamilies and the GH86 family exhibit enzymatic activity for degrading porphyran. It suggests that multiple porphyran-binding CBMs might be present in the CBM99 family. Furthermore, the homologs of FvCBM99, including WP_102755601.1 (located from 770 to 859 amino acids) and WP_108602097.1 (located from 720 to 822 amino acids), were shown to bind to porphyran.
 == Family Firsts ==
 ;First Identified
-The first member FvCBM99 is a component of a potential GH86 porphyranase (GenBank: AJW82063.1) from a marine bacterium ''Flammeovirga sp''. OC4 <cite>Liu2015</cite>.
+The first member FvCBM99 is a component of a potential [[GH86]] porphyranase (GenBank: AJW82063.1) from a marine bacterium ''Flammeovirga sp''. OC4 <cite>Liu2015</cite>.
 ;First Structural Characterization
-No three-dimensional structure has been solved in this CBM family at present.
+No three-dimensional structure has been solved in this CBM family.
 == References ==

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]

@@ Line 21: / Line 21: @@
 [[File:Figure1.png|thumb|'''Figure 1. Carbohydrate array assay results of FvCBM99. ''' Binding analysis with porphyran and other galactans in red algae (A), and other polysaccharides (B). κ-Car, κ-carrageenan. ι-Car, ι-carrageenan. Alg, alginate. An-FUC, sulfated fucan from Ascophyllum nodosum. CSA, chondroitin sulfate A sodium salt. HA, hyaluronic acid. Pec, pectin. Each polysaccharide performed three parallels. The values (noted at the bottom) were the average gray intensities of the triplicates. The value binding to porphyran was set to 100, and the other values were normalized accordingly.''' ]]
-The first characterized member in the CBM99 family is FvCBM99 <cite>Mei2023</cite>. The CBM FvCBM99 could bind to porphyran and displayed a weak affinity to agarose (Fig. 1). While it was incapable of binding to the other examined polysaccharides, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, or pectin. Furthermore, FvCBM99 could bind to porphyran tetrasaccharide with an affinity constant of 1.9 × 10-4 M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012</cite>, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays showed that FvCBM99 specifically binds to the major structural units of porphyran.
+The first characterized member in the CBM99 family is FvCBM99 <cite>Mei2023</cite>. The CBM FvCBM99 could bind to porphyran and displayed a weak affinity to agarose (Fig. 1). While it was incapable of binding to the other examined polysaccharides, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, or pectin. Furthermore, FvCBM99 could bind to porphyran tetrasaccharide with an affinity constant of 1.9 × 10 <sup>-4</sup> M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012</cite>, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays showed that FvCBM99 specifically binds to the major structural units of porphyran.
 == Structural Features ==