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Difference between revisions of "Carbohydrate Binding Module Family 101"
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== Ligand specificities == | == Ligand specificities == | ||
| − | + | The first characterized member in the CBM101 family is WfCBM101 [1]. 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 [2]. It was thus speculated that the weak affinity of WfCBM101 to porphyran was attributed to the structural heterogeneity of porphyran. | |
| − | |||
| − | |||
== Structural Features == | == Structural Features == | ||
| − | + | The predicted structure by AlphaFold2 showed that WfCBM101 displays a typical β-sandwich fold. | |
| − | |||
| − | |||
| − | |||
== Functionalities == | == 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 [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 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. | |
| − | |||
| − | |||
== Family Firsts == | == Family Firsts == | ||
;First Identified | ;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| − | + | The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium Wenyingzhuangia fucanilytica CZ1127T [3].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 | ;First Structural Characterization | ||
| − | + | No three-dimensional structure has been solved in this CBM family at present. | |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Mei2023 pmid=38010608 |
| − | # | + | #Chi2012 pmid=22526785 |
| − | + | #Chen2016 pmid=27220912 | |
| − | |||
| − | |||
| − | |||
| − | # | ||
</biblio> | </biblio> | ||
<!-- Do not delete this Category tag --> | <!-- Do not delete this Category tag --> | ||
[[Category:Carbohydrate Binding Module Families|CBM101]] | [[Category:Carbohydrate Binding Module Families|CBM101]] | ||
Revision as of 06:15, 2 January 2024
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
| CAZy DB link | |
| http://www.cazy.org/CBM101.html |
Ligand specificities
The first characterized member in the CBM101 family is WfCBM101 [1]. 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 [2]. It was thus speculated that the weak affinity of WfCBM101 to porphyran was attributed to the structural heterogeneity of porphyran.
Structural Features
The predicted structure by AlphaFold2 showed 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 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 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.
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 three-dimensional structure has been solved in this CBM family at present.
References
- 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 |
- 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 |
- 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 |