Difference between revisions of "Carbohydrate Binding Module Family 100"

Revision as of 18:53, 4 January 2024

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CAZy DB link
https://www.cazy.org/CBM100.html

Ligand specificities

Figure 1. Domain analysis of the parent enzyme of PhCBM100.The enzyme consists of a signal peptide (1-23 amino acids), a PL29 domain (68-399 amino acids), a CBM100 domain (viz., PhCBM100; 555-785 amino acids) and a C-terminal sorting domain (786-851 amino acids).

The first characterized member of the CBM100 family, PhCBM100[1], was found in a PL29 putative chondroitin lyase from Polaribacter haliotis. PhCBM100 bound specifically to chondroitin sulfates (CSs) including CS-A, CS-C and fucosylated chondroitin sulfate from sea cucumber Apostichopus japonicus, whereas incapable of binding to other glycosaminoglycans or polyuronic acids. By affinity electrophoresis assays, PhCBM100 displays high affinity for CS-A and CS-C with the Ka values of 2.1×10⁶ M^-1 and 6.0×10⁶ M^-1, respectively.

Structural Features

Figure 2. Structure of PhCBM100. (A) Schematic representation of PhCBM100 showing helices in yellow and strands in cyan. (B) Detailed view of the putative PhCBM100 binding site. The surface is colored by electrostatic potential, from blue (positive charge) to red (negative charge).

The 1.55 Å resolution X-ray crystal structure of PhCBM100 (PDB ID 8JIY) exhibited a β-sandwich fold formed by two antiparallel comprised of 10 β-strands and 2 helices. A groove with both a distinct positive charge and a high degree of conserved residues is proposed as the binding site, enriched with hydrophilic amino acids. As the result of molecular docking, the basic amino acid residues (e.g., Lys-40, Arg-122 and Arg-201) of PhCBM100 may contribute to CS binding through the ionic contacts.

Functionalities

PhCBM100 is a component of a PL29 enzyme that displays chondroitin-sulfate ABC endolyase activity, consistent with the PhCBM100 specificity. The in situ visualization of chondroitin sulfate in animal tissues (e.g., chicken cartilage, bovine muscle, and porcine laryngeal cartilage) was realized by utilizing a fluorescent probe constructed by fusing PhCBM100 with a green fluorescent protein.

Family Firsts

First Identified: The chondroitin sulfate binding PhCBM100 from the P. haliotis PL29 putative chondroitin lyase was the first member of the family to be identified and characterized.
First Structural Characterization: PhCBM100 was also the first structurally characterized CBM100.

References

Liu G, Chang Y, Mei X, Chen G, Zhang Y, Jiang X, Tao W, and Xue C. (2024). Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100. Int J Biol Macromol. 2024;255:127959. DOI:10.1016/j.ijbiomac.2023.127959 | PubMed ID:37951443 [Liu2024]

@@ 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.
+[[File:Fig.1 300.png|thumb|300px|right|'''Figure 1. Domain analysis of the parent enzyme of PhCBM100.'''The enzyme consists of a signal peptide (1-23 amino acids), a PL29 domain (68-399 amino acids), a CBM100 domain (viz., PhCBM100; 555-785 amino acids) and a C-terminal sorting domain (786-851 amino acids).]]
+The first characterized member of the CBM100 family, PhCBM100<cite>Liu2024</cite>, was found in a PL29 putative chondroitin lyase from ''Polaribacter haliotis''. PhCBM100 bound specifically to chondroitin sulfates (CSs) including CS-A, CS-C and fucosylated chondroitin sulfate from sea cucumber ''Apostichopus japonicus'', whereas incapable of binding to other glycosaminoglycans or polyuronic acids. By affinity electrophoresis assays, PhCBM100 displays high affinity for CS-A and CS-C with the Ka values of 2.1×10<sup>6</sup> M<sup>-1</sup> and 6.0×10<sup>6</sup> M<sup>-1</sup>, respectively.
-''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:''
+[[File:Fig.2 300.png|thumb|300px|right|'''Figure 2. Structure of PhCBM100.''' (A) Schematic representation of PhCBM100 showing helices in yellow and strands in cyan. (B) Detailed view of the putative PhCBM100 binding site. The surface is colored by electrostatic potential, from blue (positive charge) to red (negative charge).]]
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+The 1.55 Å resolution X-ray crystal structure of PhCBM100 (PDB ID 8JIY) exhibited a β-sandwich fold formed by two antiparallel comprised of 10 β-strands and 2 helices.
-* '''Type:''' Include here Type A, B, or C and properties
+A groove with both a distinct positive charge and a high degree of conserved residues is proposed as the binding site, enriched with hydrophilic amino acids. As the result of molecular docking, the basic amino acid residues (e.g., Lys-40, Arg-122 and Arg-201) of PhCBM100 may contribute to CS binding through the ionic contacts.
-* '''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:''
+PhCBM100 is a component of a PL29 enzyme that displays chondroitin-sulfate ABC endolyase activity, consistent with the PhCBM100 specificity. The ''in situ'' visualization of chondroitin sulfate in animal tissues (e.g., chicken cartilage, bovine muscle, and porcine laryngeal cartilage) was realized by utilizing a fluorescent probe constructed by fusing PhCBM100 with a green fluorescent protein.
-* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
-* '''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
+;First Identified:The chondroitin sulfate binding PhCBM100 from the ''P. haliotis'' PL29 putative chondroitin lyase was the first member of the family to be identified and characterized.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization:PhCBM100 was also the first structurally characterized CBM100.
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Liu2024 pmid=37951443
-#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].
-#Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM100]]