Carbohydrate Binding Module Family 103 - Revision history

Marie-Katherin Zuehlke: /* Functionalities */

2024-11-07T09:31:36Z

Functionalities

Marie-Katherin Zuehlke: /* Structural Features */

2024-11-07T08:45:34Z

Structural Features

Elizabeth Ficko-Blean: /* Functionalities */

2024-10-25T14:35:36Z

Functionalities

Elizabeth Ficko-Blean at 14:35, 25 October 2024

2024-10-25T14:35:07Z

Elizabeth Ficko-Blean at 14:28, 25 October 2024

2024-10-25T14:28:22Z

Elizabeth Ficko-Blean at 14:22, 25 October 2024

2024-10-25T14:22:38Z

Marie-Katherin Zuehlke at 14:11, 12 September 2024

2024-09-12T14:11:47Z

Marie-Katherin Zuehlke at 15:16, 9 September 2024

2024-09-09T15:16:23Z

Elizabeth Ficko-Blean: Created page with " {{UnderConstruc..."

2024-09-05T14:32:31Z

Created page with "  {{UnderConstruc..."

New page

{{UnderConstruction}}
* [[Author]]: [[User:Marie-Katherin Zuehlke|Marie-Katherin Zühlke]]
* [[Responsible Curator]]: [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]
----


<div style="float:right">
{| {{Prettytable}}
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM103.html
|}
</div>


== 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>.

== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
* '''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:''
* '''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
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#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>


[[Category:Carbohydrate Binding Module Families|CBM103]]

@@ Line 30: / Line 30: @@
 == Functionalities ==
-The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and recruitment to the bacterial cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum Bacteroidota and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-[[GH16]]_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-[[GH5]]_46 combination. In ''C. forsetii'', the CBM103 is attached to a [[GH16]]_3, which was suggested to increase catalysis <cite>Zuehlke2024</cite>.
+The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and recruitment to the bacterial cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum Bacteroidota and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-[[GH16]]_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-[[GH5]]_46 combination. In ''C. forsetii'', the CBM103 is attached to a [[GH16]]_3, which was suggested to increase enzyme concentration and thus catalysis <cite>Zuehlke2024</cite>.
 == Family Firsts ==

@@ Line 23: / Line 23: @@
 == Structural Features ==
-The CBM103 of the ''B. fluxus'' SGBP (BfSGBP-B) displays a β-barrel fold with an additional β-strand pair and two short α-helices <cite>Tamura2021</cite> (Figure 1). 3D crystal structures showed that reducing ends of laminarin- or MLG-derived oligosaccharides bind on the top face of the β-barrel, which provides a 'shallow binding canyon'. Therefore, CBM103 classifies as a [[Carbohydrate-binding_modules|type C CBM]]. Polar- and CH-π-interactions mediate binding to trioses derived from laminarin and MLG, with Trp164 (third subsite), Trp165, Lys172 and Asp221 (all terminal subsite) demonstrated to be indispensable <cite>Tamura2021</cite>. In the ''B. fluxus'' SGBP, the CBM103 follows an N-terminal ‘PKD’ domain.
+The CBM103 of the ''B. fluxus'' SGBP (BfSGBP-B) displays a β-barrel fold with an additional β-strand pair and two short α-helices <cite>Tamura2021</cite> (Figure 1a). 3D crystal structures showed that reducing ends of laminarin- or MLG-derived oligosaccharides bind on the top face of the β-barrel, which provides a 'shallow binding canyon'. Therefore, CBM103 classifies as a [[Carbohydrate-binding_modules|type C CBM]]. Polar- and CH-π-interactions mediate binding to trioses derived from laminarin and MLG. Trp164, which interacts with the glucose residue at the third subsite (Figure 1b), and Trp165, Lys172 and Asp221, which interact with the reducing-end glucose at the terminal subsite, were essential for binding <cite>Tamura2021</cite>. Replacing the individual residues with alanine abolished binding in each case, as shown by affinity gel electrophoresis.
-[[File:Bfluxus.png|thumb|'''Figure 1.''' 3D crystal structure of the CBM103-containing SGBP of ''Bacteroides fluxus'', which is preceded by an N-terminal 'PKD' domain (light violet) <cite>Tamura2021</cite>. Mixed-linkage glucotriose (pink) binds on a platform of CBM103 (PDB ID [{{PDBlink}}7KV6 7KV6])]]
+In the ''B. fluxus'' SGBP, the CBM103 follows an N-terminal ‘PKD’ domain (Figure 1a).
 == Functionalities ==

@@ Line 28: / Line 28: @@
 == Functionalities ==
-The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and recruitment to the bacterial cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum ''Bacteroidota'' and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-[[GH16]]_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-[[GH5]]_46 combination. In ''C. forsetii'', the CBM103 is attached to a [[GH16]]_3, which was suggested to increase catalysis <cite>Zuehlke2024</cite>.
+The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and recruitment to the bacterial cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum Bacteroidota and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-[[GH16]]_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-[[GH5]]_46 combination. In ''C. forsetii'', the CBM103 is attached to a [[GH16]]_3, which was suggested to increase catalysis <cite>Zuehlke2024</cite>.
 == Family Firsts ==

@@ Line 25: / Line 25: @@
 The CBM103 of the ''B. fluxus'' SGBP (BfSGBP-B) displays a β-barrel fold with an additional β-strand pair and two short α-helices <cite>Tamura2021</cite> (Figure 1). 3D crystal structures showed that reducing ends of laminarin- or MLG-derived oligosaccharides bind on the top face of the β-barrel, which provides a 'shallow binding canyon'. Therefore, CBM103 classifies as a [[Carbohydrate-binding_modules|type C CBM]]. Polar- and CH-π-interactions mediate binding to trioses derived from laminarin and MLG, with Trp164 (third subsite), Trp165, Lys172 and Asp221 (all terminal subsite) demonstrated to be indispensable <cite>Tamura2021</cite>. In the ''B. fluxus'' SGBP, the CBM103 follows an N-terminal ‘PKD’ domain.
-[[File:Bfluxus.png|thumb|'''Figure 1.''' 3D crystal structure of the CBM103-containing SGBP of ''Bacteroides fluxus'', which is preceded by an N-terminal 'PKD' domain (light blue) <cite>Tamura2021</cite>. Mixed-linkage glucotriose (pink) binds on a platform of CBM103 (PDB ID [{{PDBlink}}7KV6 7KV6])]]
+[[File:Bfluxus.png|thumb|'''Figure 1.''' 3D crystal structure of the CBM103-containing SGBP of ''Bacteroides fluxus'', which is preceded by an N-terminal 'PKD' domain (light violet) <cite>Tamura2021</cite>. Mixed-linkage glucotriose (pink) binds on a platform of CBM103 (PDB ID [{{PDBlink}}7KV6 7KV6])]]
 == Functionalities ==
-The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and its recruiting to the cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum ''Bacteroidota'' and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-GH16_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-GH5_46 combination. In ''C. forsetii'', the CBM103 is attached to a GH16_3, which was suggested to increase catalysis <cite>Zuehlke2024</cite>.
+The CBM103-containing SGBP of ''B. fluxus'' (BfSGBP-B) was suggested to support glycan recognition and recruitment to the bacterial cellular surface in the human intestinal tract <cite>Tamura2021</cite>. Similarly, in 555 representative bacterial metagenome assembled genomes retrieved from phytoplankton blooms of three respective years (2016, 2018 and 2020) in the North Sea, 43 CBM103-only sequences were identified, some of which might function as SGBPs <cite>Zuehlke2024</cite>. All detected CBM103-containing sequences (82) belonged to the phylum ''Bacteroidota'' and covered also 17 CBM103-[[Carbohydrate_Binding_Module_Family_102|CBM102]] combinations, 21 CBM103-[[GH16]]_3 combinations as well as one CBM103-[[Carbohydrate_Binding_Module_Family_6|CBM6]]-[[GH5]]_46 combination. In ''C. forsetii'', the CBM103 is attached to a [[GH16]]_3, which was suggested to increase catalysis <cite>Zuehlke2024</cite>.
 == Family Firsts ==
-;First Identified: CBM103 was first identified in an SGBP of ''B. fluxus'' (BfSGBP-B) <cite>Tamura2021</cite>, although binding of the SGBP to β-glucans was shown before <cite>Dejean2020</cite>. Later, a CBM103-containing GH16_3 of ''C. forsetii'' led to the creation of the CBM family 103 <cite>Zuehlke2024</cite>.
+;First Identified: CBM103 was first identified in an SGBP of ''B. fluxus'' (BfSGBP-B) <cite>Tamura2021</cite>, although binding of the SGBP to β-glucans was shown before <cite>Dejean2020</cite>. Later, a CBM103-containing [[GH16]]_3 of ''C. forsetii'' led to the creation of the CBM family 103 <cite>Zuehlke2024</cite>.
 ;First Structural Characterization: The CBM103-containing SGBP of ''B. fluxus'' represents the first 3D crystal structure, with and without ligands (PDB ID [https://www.rcsb.org/structure/7KV5 7KV5] without ligand, PDB ID [https://www.rcsb.org/structure/7KV6 7KV6] with DP3 from MLG, PDB ID [https://www.rcsb.org/structure/7KV7 7KV7] with DP3 from laminarin) <cite>Tamura2021</cite>.

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-The CBM103-containing surface glycan-binding protein (SGBP) of ''Bacteroides fluxus ''(BfSGBP-B), a strain from the human intestinal tract, binds laminarin (''Laminaria digitata'') and mixed-linkage β(1,3)/β(1,4)-glucans (MLG, from Barley) as well as oligosaccharides thereof <cite>Dejean2020 Tamura2021</cite>. The protein binds laminarin and MLG with similar affinity (K<sub>a</sub> 8.63 X 10<sup>4</sup> M<sup>-1</sup> and K<sub>a</sub> 8.56 X 10<sup>4</sup> M<sup>-1</sup>, respectively) <cite>Dejean2020</cite>. Binding of laminarin-derived oligosaccharides required a degree of polymerization (DP) of more than two and affinities ranged from K<sub>d</sub> 3.63-7.61 x 10<sup>-5</sup> M (DP3-6) <cite>Tamura2021</cite>. DP3 and DP4 derived from MLG were binding with similar affinities (K<sub>d</sub> 1.23 x 10<sup>-5</sup> M or 1.16 x 10<sup>-5</sup> M, respectively), but a β(1,3)-glucosyl linkage at the reducing end was essential for binding.
+The CBM103-containing surface glycan-binding protein (SGBP) of ''Bacteroides fluxus ''(BfSGBP-B), a strain from the human intestinal tract, binds laminarin (''Laminaria digitata'') and mixed-linkage β(1,3)/β(1,4)-glucans (MLG, from Barley) as well as MLG oligosaccharides <cite>Dejean2020 Tamura2021</cite>. The protein binds laminarin and MLG with similar affinity (K<sub>a</sub> 8.63 X 10<sup>4</sup> M<sup>-1</sup> and K<sub>a</sub> 8.56 X 10<sup>4</sup> M<sup>-1</sup>, respectively) <cite>Dejean2020</cite>. Binding of laminarin-derived oligosaccharides required a degree of polymerization (DP) of more than two and affinities ranged from K<sub>d</sub> 3.63-7.61 x 10<sup>-5</sup> M (for DP 3-6) <cite>Tamura2021</cite>. DP3 and DP4 derived from MLG bound with similar affinities (K<sub>d</sub> 1.23 x 10<sup>-5</sup> M or 1.16 x 10<sup>-5</sup> M, respectively), but a β(1,3)-glucosyl linkage at the reducing end was essential for binding.
 == Structural Features ==
 The CBM103 of the ''B. fluxus'' SGBP (BfSGBP-B) displays a β-barrel fold with an additional β-strand pair and two short α-helices <cite>Tamura2021</cite> (Figure 1). 3D crystal structures showed that reducing ends of laminarin- or MLG-derived oligosaccharides bind on the top face of the β-barrel, which provides a 'shallow binding canyon'. Therefore, CBM103 classifies as a [[Carbohydrate-binding_modules|type C CBM]]. Polar- and CH-π-interactions mediate binding to trioses derived from laminarin and MLG, with Trp164 (third subsite), Trp165, Lys172 and Asp221 (all terminal subsite) demonstrated to be indispensable <cite>Tamura2021</cite>. In the ''B. fluxus'' SGBP, the CBM103 follows an N-terminal ‘PKD’ domain.
@@ Line 30: / Line 31: @@
 == Family Firsts ==
-;First Identified
+;First Identified: CBM103 was first identified in an SGBP of ''B. fluxus'' (BfSGBP-B) <cite>Tamura2021</cite>, although binding of the SGBP to β-glucans was shown before <cite>Dejean2020</cite>. Later, a CBM103-containing GH16_3 of ''C. forsetii'' led to the creation of the CBM family 103 <cite>Zuehlke2024</cite>.
-;First Structural Characterization
+;First Structural Characterization: The CBM103-containing SGBP of ''B. fluxus'' represents the first 3D crystal structure, with and without ligands (PDB ID [https://www.rcsb.org/structure/7KV5 7KV5] without ligand, PDB ID [https://www.rcsb.org/structure/7KV6 7KV6] with DP3 from MLG, PDB ID [https://www.rcsb.org/structure/7KV7 7KV7] with DP3 from laminarin) <cite>Tamura2021</cite>.
 == References ==
 <biblio>
 #Dejean2020 pmid=32265336
 #Tamura2021 pmid=33587952
 #Zuehlke2024 pmid=38757353
 </biblio>

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Marie-Katherin Zuehlke|Marie-Katherin Zühlke]]
 * [[Responsible Curator]]:  [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]