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Difference between revisions of "Carbohydrate Binding Module Family 101"

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* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]]
 
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]]
 
* [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]
 
* [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]
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== Ligand specificities ==
 
== Ligand specificities ==
  
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[[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.''' ]]
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[[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.''' ]]
  
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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.
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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.
  
 
== Structural Features ==
 
== Structural Features ==
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The predicted structure by AlphaFold2 showed that WfCBM101 displays a typical β-sandwich fold.  
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An AlphaFold2 model predicts that WfCBM101 has a β-sandwich fold.
  
 
== Functionalities ==  
 
== Functionalities ==  
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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>.
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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>.
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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 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.
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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 ==
 
== Family Firsts ==
 
;First Identified
 
;First Identified
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The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium Wenyingzhuangia fucanilytica CZ1127T <cite>Chen2016</cite>.
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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
 
;First Structural Characterization
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No three-dimensional structure has been solved in this CBM family at present.
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No experimentally determined three-dimensional structure has been solved in this CBM family.
  
 
== References ==
 
== References ==

Latest revision as of 23:56, 15 February 2024

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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

An AlphaFold2 model predicts that WfCBM101 has a 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 CZ1127T [3].

First Structural Characterization

No experimentally determined three-dimensional structure has been solved in this CBM family.

References

  1. Mei X, Zhang Y, Jiang X, Liu G, Shen J, Xue C, Xiao H, and Chang Y. (2024). Discovery and characterization of a novel carbohydrate-binding module: a favorable tool for investigating agarose. J Sci Food Agric. 2024;104(5):2792-2797. DOI:10.1002/jsfa.13164 | PubMed ID:38010608 [Mei2023]
  2. Chi WJ, Chang YK, and Hong SK. (2012). Agar degradation by microorganisms and agar-degrading enzymes. Appl Microbiol Biotechnol. 2012;94(4):917-30. DOI:10.1007/s00253-012-4023-2 | PubMed ID:22526785 [Chi2012]
  3. Chen F, Chang Y, Dong S, and Xue C. (2016). Wenyingzhuangia fucanilytica sp. nov., a sulfated fucan utilizing bacterium isolated from shallow coastal seawater. Int J Syst Evol Microbiol. 2016;66(9):3270-3275. DOI:10.1099/ijsem.0.001184 | PubMed ID:27220912 [Chen2016]

All Medline abstracts: PubMed

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