Carbohydrate Binding Module Family 83 - Revision history

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

2021-12-18T21:20:39Z

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

Elizabeth Ficko-Blean: /* Ligand specificities */

2019-05-14T06:16:25Z

Ligand specificities

Darrell Cockburn at 20:31, 13 May 2019

2019-05-13T20:31:54Z

Elizabeth Ficko-Blean: /* Family Firsts */

2019-05-13T08:51:27Z

Family Firsts

Elizabeth Ficko-Blean at 08:50, 13 May 2019

2019-05-13T08:50:33Z

Nicole Koropatkin at 16:45, 9 May 2019

2019-05-09T16:45:27Z

Darrell Cockburn at 15:30, 9 May 2019

2019-05-09T15:30:35Z

Darrell Cockburn at 20:09, 8 May 2019

2019-05-08T20:09:23Z

Elizabeth Ficko-Blean at 14:32, 30 August 2018

2018-08-30T14:32:32Z

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

2018-08-30T12:35:46Z

Created page with "  {{UnderConstruc..."

New page

{{UnderConstruction}}
* [[Author]]: ^^^XX^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM83.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|CBM083]]

@@ Line 2: / Line 2: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Darrell Cockburn^^^
+* [[Author]]: [[User:Darrell Cockburn|Darrell Cockburn]]
-* [[Responsible Curator]]:  ^^^Nicole Koropatkin^^^
+* [[Responsible Curator]]:  [[User:Nicole Koropatkin|Nicole Koropatkin]]
 ----

@@ Line 19: / Line 19: @@
 == Ligand specificities ==
 [[File:Amy13K_CBM83_highlight.jpg|thumb|600px|right|'''Figure 1. Domain architecture of ''E. rectale'' Amy13K''' The CBM and GH families are indicated. The 'S' is the signal sequence and the 'anchor' is a cell wall anchoring motif. The CBM83 domain is bolded. The 'unknown' domain has no known function, however, its deletion eliminates all activity of the enzyme <cite>Cockburn2018</cite>]]
-The founding member and first to be characterized of this family is the fifth CBM found in the cell-wall anchored Amy13K from ''Eubacterium rectale'' (Fig1). It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
+The founding member and first to be characterized of this family is the fifth CBM found in the cell-wall anchored [[GH13]] enzyme Amy13K from ''Eubacterium rectale'' (Fig1). It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
 <cite>Cockburn2018</cite>.

@@ Line 23: / Line 23: @@
 == Structural Features ==
-Secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the [[CBM41]] family.
+Secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the [[CBM41]] family <cite>Cockburn2018</cite>.
 == Functionalities ==
-This family has been found to be exclusively associated with [[GH13]] family amylases from a quite narrow taxonomic range within ''Roseburia'' and ''Eubacterium rectale''. Removal of the only CBM83 from the ''E. rectale'' Amy13K enzyme had little effect on its activity towards amylopectin and potato starch, but resulted in a 2-fold decrease in the activity towards corn starch granules, suggesting an important role in activity towards this substrate  <cite>Cockburn2018</cite>
+This family has been found to be exclusively associated with [[GH13]] family amylases from a quite narrow taxonomic range within ''Roseburia'' and ''Eubacterium rectale'' <cite>Cockburn2018</cite>. Removal of the only CBM83 from the ''E. rectale'' Amy13K enzyme had little effect on its activity towards amylopectin and potato starch, but resulted in a 2-fold decrease in the activity towards corn starch granules, suggesting an important role in activity towards this substrate  <cite>Cockburn2018</cite>
 == Family Firsts ==

@@ Line 16: / Line 16: @@
 </div>
 <!-- This is the end of the table -->
-[[File:Amy13K_CBM83_highlight.jpg|thumb|750px|right|'''Figure 1. Domain architecture of E. rectale Amy13K''' The CBM and GH families are indicated. The 'S' is the signal sequence and the 'anchor' is a cell wall anchoring motif. The CBM83 domain is bolded. The 'unknown' domain has no known function, however, its deletion eliminates all activity of the enzyme <cite>Cockburn2018</cite>]]
 == Ligand specificities ==
 The founding member and first to be characterized of this family is the fifth CBM found in the cell-wall anchored Amy13K from ''Eubacterium rectale'' (Fig1). It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
 <cite>Cockburn2018</cite>.

@@ Line 16: / Line 16: @@
 </div>
 <!-- This is the end of the table -->
+[[File:Amy13K_CBM83_highlight.jpg|thumb|750px|right|'''Figure 1. Domain architecture of E. rectale Amy13K''' The CBM and GH families are indicated. The 'S' is the signal sequence and the 'anchor' is a cell wall anchoring motif. The CBM83 domain is bolded. The 'unknown' domain has no known function, however, its deletion eliminates all activity of the enzyme <cite>Cockburn2018</cite>]]
 == Ligand specificities ==
-Only one member of this family has been characterized to date, the fifth CBM found in the cell-wall anchored Amy13K from ''Eubacterium rectale''. It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
+The founding member and first to be characterized of this family is the fifth CBM found in the cell-wall anchored Amy13K from ''Eubacterium rectale'' (Fig1). It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
 <cite>Cockburn2018</cite>.
 == Structural Features ==
-There is currently no structures solved for this family, however, secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the [[CBM41]] family.
+There is currently no structure solved for this family, however, secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the [[CBM41]] family.
 == Functionalities ==

@@ Line 29: / Line 29: @@
 == Family Firsts ==
-;First Identified
+;First Identified: In ''Roseburia inulinivorans'' as a predicted CBM <cite>Ramsay2006</cite>
 == References ==

@@ 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.
+Only one member of this family has been characterized to date, the fifth CBM found in the cell-wall anchored Amy13K from ''Eubacterium rectale''. It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis.
+<cite>Cockburn2018</cite>.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+There is currently no structures solved for this family, however, secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the [[CBM41]] family.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+This family has been found to be exclusively associated with [[GH13]] family amylases from a quite narrow taxonomic range within ''Roseburia'' and ''Eubacterium rectale''. Removal of the only CBM83 from the ''E. rectale'' Amy13K enzyme had little effect on its activity towards amylopectin and potato starch, but resulted in a 2-fold decrease in the activity towards corn starch granules, suggesting an important role in activity towards this substrate  <cite>Cockburn2018</cite>
 == Family Firsts ==
 ;First Identified
-:Insert archetype here, possibly including ''very brief'' synopsis.
+In ''Roseburia inulinivorans'' as a predicted CBM <cite>Ramsay2006</cite>
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Characterized
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Cockburn2018 pmid=29139580
-#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].
+#Ramsay2006 pmid=17074899
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM083]] <!-- 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. -->