Carbohydrate Binding Module Family 101 - Revision history

Elizabeth Ficko-Blean: /* Family Firsts */

2024-02-16T07:56:14Z

Family Firsts

Elizabeth Ficko-Blean: /* Structural Features */

2024-02-16T07:55:44Z

Structural Features

Elizabeth Ficko-Blean: /* Functionalities */

2024-01-29T16:09:20Z

Functionalities

Elizabeth Ficko-Blean: /* Structural Features */

2024-01-29T16:06:29Z

Structural Features

Elizabeth Ficko-Blean: /* Ligand specificities */

2024-01-29T16:06:12Z

Ligand specificities

Elizabeth Ficko-Blean: /* Ligand specificities */

2024-01-29T16:05:22Z

Ligand specificities

Yaoguang Chang at 06:45, 5 January 2024

2024-01-05T06:45:01Z

Xuanwei Mei at 13:43, 2 January 2024

2024-01-02T13:43:06Z

Xuanwei Mei at 13:25, 2 January 2024

2024-01-02T13:25:56Z

Xuanwei Mei at 13:20, 2 January 2024

2024-01-02T13:20:19Z

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 The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium ''Wenyingzhuangia fucanilytica'' CZ1127<sup>T</sup> <cite>Chen2016</cite>.
 ;First Structural Characterization
-No three-dimensional structure has been solved in this CBM family at present.
+No experimentally determined three-dimensional structure has been solved in this CBM family.
 == References ==

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 == Structural Features ==
-The predicted structure by AlphaFold2 shows that WfCBM101 displays a typical β-sandwich fold.
+An AlphaFold2 model predicts that WfCBM101 has a β-sandwich fold.
 == Functionalities ==

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 == Functionalities ==
-To evaluate the feasibility of WfCBM101 as a tool in the ''in situ'' investigation of porphyran, a fluorescent probe was constructed by fusing WfCBM101 with a green fluorescent protein. The ''in situ'' visualization of agarose in red alga ''Gelidium amansii'' was realized by utilizing the fluorescent probe <cite>Mei2023</cite>.
+To evaluate the feasibility of WfCBM101 as a tool in the ''in situ'' investigation of porphyran, a fluorescent probe was constructed by fusing WfCBM101 with a green fluorescent protein. The ''in situ'' visualization of agarose in the red alga ''Gelidium amansii'' was realized by utilizing the fluorescent probe <cite>Mei2023</cite>.
-Taking WfCBM101 as the query sequence, 15 modules were retrieved from the NCBI database by the BLASTP program (E-value < e<sup>-5</sup>). There are eight modules adjacent to catalytic domains which are divided into the GH16_16 subfamily or GH86 family respectively. According to the CAZy database, the GH16_16 subfamily and GH86 family members exhibit the activity for degrading agarose. It was thus implied that these eight modules might bind to agarose, which requires further investigation.
+Taking WfCBM101 as the query sequence, 15 modules were retrieved from the NCBI database by the BLASTP program (E-value < e<sup>-5</sup>). There are eight modules adjacent to catalytic domains which are divided into the [[GH16]]_16 subfamily or [[GH86]] family. According to the CAZy database, the [[GH16]_16 subfamily and [[GH86]] family have members that degrade agarose. This implies that these eight modules might bind to agarose; however, this requires further investigation.
 == Family Firsts ==

@@ Line 24: / Line 24: @@
 == Structural Features ==
-The predicted structure by AlphaFold2 showed that WfCBM101 displays a typical β-sandwich fold.
+The predicted structure by AlphaFold2 shows that WfCBM101 displays a typical β-sandwich fold.
 == Functionalities ==

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 == Ligand specificities ==
-[[File:Figure.png|thumb|'''Figure 1. Carbohydrate array assays of WfCBM101. ''' The binding of WfCBM101 to agarose and other galactans in red algae (A), and several other polysaccharides (B) was evaluated. 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. Three parallels were conducted for each polysaccharide.''' ]]
+[[File:Figure.png|thumb|'''Figure 1. Carbohydrate array assays of WfCBM101. ''' The binding of WfCBM101 to agarose and other galactans in red algae (A), and several other polysaccharides (B) was evaluated. 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. Three repeats were conducted for each polysaccharide.''' ]]
 The first characterized member in the CBM101 family is WfCBM101 <cite>Mei2023</cite>. The CBM WfCBM101 bound to agarose and displayed a weak affinity to porphyran (Fig. 1). It was incapable of binding to the other polysaccharides that were examined, including κ-carrageenan, ι-carrageenan, alginate, sulfated fucan, chondroitin sulfate A sodium salt, hyaluronic acid, and pectin. Furthermore, WfCBM101 bound to agarose tetrasaccharide, but not to porphyran tetrasaccharide. It was reported porphyran consists of approximately 30% structural units of agarose <cite>Chi2012</cite>. It is thus speculated that the weak affinity of WfCBM101 for porphyran is attributed to the structural heterogeneity of porphyran.

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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]]

← Older revision		Revision as of 13:20, 2 January 2024
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	== Ligand specificities ==		== Ligand specificities ==
		+
		+	[[File:Figure.png\|thumb\|'''Figure 1. Carbohydrate array assays of WfCBM101. ''' The binding of WfCBM101 to agarose and other galactans in red algae (A), and several other polysaccharides (B) was evaluated. 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. Three parallels were conducted for each polysaccharide.''' ]]
		+
	The first characterized member in the CBM101 family is WfCBM101 <cite>Mei2023</cite>. The CBM WfCBM101 could bind to agarose and displayed a weak affinity to porphyran (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, WfCBM101 could bind to agarose tetrasaccharide, but not to porphyran tetrasaccharide. It was reported that the backbone of porphyran consists of approximately 30% characteristic structural units of agarose <cite>Chi2012</cite>. It was thus speculated that the weak affinity of WfCBM101 to porphyran was attributed to the structural heterogeneity of porphyran.		The first characterized member in the CBM101 family is WfCBM101 <cite>Mei2023</cite>. The CBM WfCBM101 could bind to agarose and displayed a weak affinity to porphyran (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, WfCBM101 could bind to agarose tetrasaccharide, but not to porphyran tetrasaccharide. It was reported that the backbone of porphyran consists of approximately 30% characteristic structural units of agarose <cite>Chi2012</cite>. It was thus speculated that the weak affinity of WfCBM101 to porphyran was attributed to the structural heterogeneity of porphyran.