CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
 Totally new to the CAZy classification? Read this first.

Difference between revisions of "Carbohydrate Binding Module Family 99"

From CAZypedia
Jump to navigation Jump to search
m
Line 18: Line 18:
  
 
== Ligand specificities ==
 
== 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 CBM99 family is FvCBM99 <cite>Mei2023. The CBM FvCBM99 could bind to porphyran and displayed a weak affinity to agarose (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, FvCBM99 could bind to porphyran tetrasaccharide with an affinity constant of 1.9 × 10-4 M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran <cite>Chi2012, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays showed that FvCBM99 specifically binds to the major structural units 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 ==
 
== Structural Features ==
−
''Content in this section should include, in paragraph form, a description of:''
+
The predicted structure by AlphaFold2 showed that FvCBM99 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 ==  
 
== Functionalities ==  
−
''Content in this section should include, in paragraph form, a description of:''
+
To evaluate the feasibility of FvCBM99 as a tool in the in situ investigation of porphyran, a fluorescent probe was constructed by fusing FvCBM99 with a green fluorescent protein. The in situ visualization of porphyran in red alga Porphyra haitanensis was realized by utilizing the fluorescent probe <cite>Mei2023.
−
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
+
Most of the members of the CBM99 family are appended to the GH16_11, GH16_12, GH16_16, or GH16_26 subfamily, or GH86 family. As documented in the CAZy database, members of the four subfamilies and the GH86 family exhibit enzymatic activity for degrading porphyran. It suggests that multiple porphyran-binding CBMs might be present in the CBM99 family. Furthermore, the homologs of FvCBM99, including WP_102755601.1 (located from 770 to 859 amino acids) and WP_108602097.1 (located from 720 to 822 amino acids), were shown to bind to porphyran.  
−
* '''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 ==
 
== Family Firsts ==
 
;First Identified
 
;First Identified
−
:Insert archetype here, possibly including ''very brief'' synopsis.
+
The first member FvCBM99 is a component of a potential GH86 porphyranase (GenBank: AJW82063.1) from a marine bacterium Flammeovirga sp. OC4 [3].
 
;First Structural Characterization
 
;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 ==
 
== References ==
 
<biblio>
 
<biblio>
−
#Cantarel2009 pmid=18838391
+
#Mei2023 pmid= 37769778
−
#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
+
#Liu2015 pmid= 25683442
−
#Hashimoto2006 pmid=17131061
 
−
#Shoseyov2006 pmid=16760304
 
−
#Guillen2010 pmid=19908036
 
−
#Armenta2017 pmid=28547780
 
 
</biblio>
 
</biblio>
  
 
<!-- Do not delete this Category tag -->
 
<!-- Do not delete this Category tag -->
 
[[Category:Carbohydrate Binding Module Families|CBM099]]
 
[[Category:Carbohydrate Binding Module Families|CBM099]]

Revision as of 04:23, 2 January 2024

Under construction icon-blue-48px.png

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
https://www.cazy.org/CBM99.html

Ligand specificities

The first characterized member in the CBM99 family is FvCBM99 Mei2023. The CBM FvCBM99 could bind to porphyran and displayed a weak affinity to agarose (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, FvCBM99 could bind to porphyran tetrasaccharide with an affinity constant of 1.9 × 10-4 M, but not to agarose tetrasaccharide. Since agarose chains usually contain a few characteristic structural units of porphyran Chi2012, it was thus speculated that the weak affinity of FvCBM99 to agarose was attributed to the structural heterogeneity of agarose. The polysaccharide and oligosaccharide binding assays showed that FvCBM99 specifically binds to the major structural units of porphyran.

Structural Features

The predicted structure by AlphaFold2 showed that FvCBM99 displays a typical β-sandwich fold.

Functionalities

To evaluate the feasibility of FvCBM99 as a tool in the in situ investigation of porphyran, a fluorescent probe was constructed by fusing FvCBM99 with a green fluorescent protein. The in situ visualization of porphyran in red alga Porphyra haitanensis was realized by utilizing the fluorescent probe Mei2023. Most of the members of the CBM99 family are appended to the GH16_11, GH16_12, GH16_16, or GH16_26 subfamily, or GH86 family. As documented in the CAZy database, members of the four subfamilies and the GH86 family exhibit enzymatic activity for degrading porphyran. It suggests that multiple porphyran-binding CBMs might be present in the CBM99 family. Furthermore, the homologs of FvCBM99, including WP_102755601.1 (located from 770 to 859 amino acids) and WP_108602097.1 (located from 720 to 822 amino acids), were shown to bind to porphyran.


Family Firsts

First Identified

The first member FvCBM99 is a component of a potential GH86 porphyranase (GenBank: AJW82063.1) from a marine bacterium Flammeovirga sp. OC4 [3].

First Structural Characterization

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

References

  1. pmid= 37769778

    [Mei2023]

  2. pmid= 22526785

    [Chi2012]

  3. pmid= 25683442

    [Liu2015]
Retrieved from "http://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_99&oldid=17640"