Carbohydrate Binding Module Family 75 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

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Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Elizabeth Ficko-Blean at 14:50, 3 July 2018

2018-07-03T14:50:46Z

Elizabeth Ficko-Blean at 15:33, 23 May 2018

2018-05-23T15:33:41Z

Elizabeth Ficko-Blean at 18:45, 22 May 2018

2018-05-22T18:45:20Z

Ana Luis at 21:52, 8 May 2018

2018-05-08T21:52:16Z

Harry Brumer at 08:43, 14 February 2018

2018-02-14T08:43:12Z

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

2018-02-13T10:34:46Z

Created page with "  {{UnderConstruc..."

New page

{{UnderConstruction}}
* [[Author]]: Ana De Jesus Vaz Luis
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM75.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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM075]]

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Ana Luis^^^
+* [[Author]]: [[User:Ana Luis|Ana Luis]]
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  [[User:Harry Gilbert|Harry Gilbert]]
 ----

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in ''Ruminococci''. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.
+CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.
 == Structural Features ==

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.
+CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in ''Ruminococci''. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.
 == Structural Features ==
@@ Line 23: / Line 23: @@
 == Functionalities ==
-''Ruminococcus flavefaciens'' CBM75<sub>RfGH43</sub>, is a biding module of a protein containing a glycoside hydrolase family 43 ([[GH43]]) and a C-terminal dockerin module <cite>Venditto2016</cite>. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases <cite>Mewis2016</cite>. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but do not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is usually consistent with the activity of the appended enzyme. Since CBM75<sub>RfGH43</sub> binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato <cite>Venditto2016</cite>.
+''Ruminococcus flavefaciens'' CBM75<sub>RfGH43</sub>, is a biding module of a protein containing a glycoside hydrolase family 43 ([[GH43]]) and a C-terminal dockerin module <cite>Venditto2016</cite>. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases <cite>Mewis2016</cite>. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but does not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is consistent with the activity of the appended enzyme. Since CBM75<sub>RfGH43</sub> binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato <cite>Venditto2016</cite>.
 == Family Firsts ==

@@ Line 17: / Line 17: @@
 == 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.
+CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+No three-dimensional structure has been solved for this CBM family.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+''Ruminococcus flavefaciens'' CBM75<sub>RfGH43</sub>, is a biding module of a protein containing a glycoside hydrolase family 43 ([[GH43]]) and a C-terminal dockerin module <cite>Venditto2016</cite>. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases <cite>Mewis2016</cite>. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but do not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is usually consistent with the activity of the appended enzyme. Since CBM75<sub>RfGH43</sub> binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato <cite>Venditto2016</cite>.
 == Family Firsts ==
-;First Identified
+;First Identified: CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization: No three-dimensional structure has been solved for this family.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Venditto2016 pmid=27298375
-#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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+#Mewis2016 pmid=26729713
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM075]]