Difference between revisions of "Carbohydrate Binding Module Family 101"

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The first member WfCBM101 is a component of a GH86 β-agarase (unpublished data) from a marine bacterium Wenyingzhuangia fucanilytica CZ1127^T [3].

First Structural Characterization

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

References

All Medline abstracts: PubMed

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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]]
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 == 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.
-''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>.
+[[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.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+An AlphaFold2 model predicts that WfCBM101 has a 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 the red alga ''Gelidium amansii'' was realized by utilizing the fluorescent probe <cite>Mei2023</cite>.
-* '''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<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.
-* '''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'' CZ1127<sup>T</sup> <cite>Chen2016</cite>.
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+No experimentally determined three-dimensional structure has been solved in this CBM family.
 == 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]]
-<!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. -->