Difference between revisions of "Carbohydrate Binding Module Family 101"

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CAZy DB link
https://www.cazy.org/CBM101.html

Ligand specificities

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 [1]. 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 [2]. It is thus speculated that the weak affinity of WfCBM101 for porphyran is attributed to the structural heterogeneity of porphyran.

Structural Features

The predicted structure by AlphaFold2 shows that WfCBM101 displays a typical β-sandwich fold.

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 the red alga Gelidium amansii was realized by utilizing the fluorescent probe [1]. Taking WfCBM101 as the query sequence, 15 modules were retrieved from the NCBI database by the BLASTP program (E-value < e^-5). 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

First Identified

The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium Wenyingzhuangia fucanilytica CZ1127^T [3].

First Structural Characterization

No three-dimensional structure has been solved in this CBM family at present.

References

All Medline abstracts: PubMed

@@ Line 27: / Line 27: @@
 == 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 ==