Difference between revisions of "Carbohydrate Binding Module Family 101"

Revision as of 05:15, 2 January 2024

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CAZy DB link
https://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The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium Wenyingzhuangia fucanilytica CZ1127T [3].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

All Medline abstracts: PubMed

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.
+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.
-''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010 Armenta2017</cite>.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+The predicted structure by AlphaFold2 showed that WfCBM101 displays a typical β-sandwich fold.
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
-* '''Type:''' Include here Type A, B, or C and properties
-* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+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].
-* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
+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.
-* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
-* '''Novel Applications:'''  Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.
 == Family Firsts ==
 ;First Identified
-:Insert archetype here, possibly including ''very brief'' synopsis.
+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
-:Insert archetype here, possibly including ''very brief'' synopsis.
+No three-dimensional structure has been solved in this CBM family at present.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Mei2023 pmid=38010608
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 DOI:10.1042/BIO03004026].
+#Chi2012 pmid=22526785
-#Boraston2004 pmid=15214846
+#Chen2016 pmid=27220912
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM101]]