Carbohydrate Binding Module Family 77 - Revision history

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

2021-12-18T21:14:12Z

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

Elizabeth Ficko-Blean at 14:51, 3 July 2018

2018-07-03T14:51:44Z

Elizabeth Ficko-Blean at 18:59, 22 May 2018

2018-05-22T18:59:02Z

Ana Luis at 22:22, 13 May 2018

2018-05-13T22:22:22Z

Harry Brumer at 08:44, 14 February 2018

2018-02-14T08:44:51Z

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

2018-02-13T10:37:48Z

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}}CBM77.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|CBM077]]

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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 ==
-CBM77 is a bacterial family of binding modules that comprises around 110 amino acids. Only the founding member of this family, CBM77<sub>RfPL1/9</sub> has been characterized. This binding module found in ''Ruminococcus flavefaciens'' binds exclusively to homogalacturonan (pectin) with low degrees of methyl esterification (DE) <cite>Venditto2016</cite>. By isothermal titration calorimetry, CBM77<sub>RfPL1/9</sub> displays high affinity for low DE pectins such as, lime DE 11% and citrus pectin DE 30% (K<sub>A</sub> 1.8 x 10<sup>5</sup> M<sup>-1</sup> and 1.1 x 10<sup>4</sup> M<sup>-1</sup>, respectively). This binding module displays a reduction in affinity as the DE of the ligand increase. Indeed CBM77<sub>RfPL1/9</sub> exhibits no binding to polygalacturonic acid with a DE ≥80%. This binding module displays optimum binding to oligosaccharides of α1,4-D-Galacturonic acid (GalA) with a degree of polymerization of 7 to 8. Additionally, the presence of a chelating agent (EDTA) did not influence CBM77<sub>RfPL1/9</sub> affinity indicating a metal independent binding mechanism <cite>Venditto2016</cite>. The only other example of a CBM that binds to homogalacturonan backbone is [[CBM32]] from ''Yersinia enterolitica'' (YeCBM32) (which is not a component of an enzyme) <cite>Abbott2007</cite>.
+CBM77 is a bacterial family of binding modules that comprises around 110 amino acids. Only the founding member of this family, CBM77<sub>RfPL1/9</sub> has been characterized. This carbohydrate-binding module found in ''Ruminococcus flavefaciens'' binds exclusively to homogalacturonan (pectin) with low degrees of methyl esterification (DE) <cite>Venditto2016</cite>. By isothermal titration calorimetry, CBM77<sub>RfPL1/9</sub> displays high affinity for low DE pectins such as, lime DE 11% and citrus pectin DE 30% (K<sub>A</sub> 1.8 x 10<sup>5</sup> M<sup>-1</sup> and 1.1 x 10<sup>4</sup> M<sup>-1</sup>, respectively). This binding module displays a reduction in affinity as the DE of the ligand increase. Indeed CBM77<sub>RfPL1/9</sub> exhibits no binding to polygalacturonic acid with a DE ≥80%. This binding module displays optimum binding to oligosaccharides of α-1,4-D-Galacturonic acid (GalA) with a degree of polymerization of 7 to 8. Additionally, the presence of a chelating agent (EDTA) did not influence CBM77<sub>RfPL1/9</sub> affinity indicating a divalent cation independent binding mechanism <cite>Venditto2016</cite>. The only other example of a CBM that binds to homogalacturonan backbone is [[CBM32]] from ''Yersinia enterolitica'' (YeCBM32) (which is not a component of an enzyme) <cite>Abbott2007</cite>.
 == Structural Features ==
@@ Line 24: / Line 24: @@
 The three-dimensional structure of ''Ruminoccocus'' CBM77<sub>RfPL1/9</sub> ([{{PDBlink}}5FU5 5FU5]) solved using X-ray displays a beta-sandwich fold in which the 13 antiparallel β-strands are organized in two β-sheets <cite>Venditto2016</cite>.
-The key residues implicated in substrate binding were identified by site-direct mutagenesis. The canonical ligand binding site of a endo-active [[Carbohydrate-binding_modules#Types|type B]] CBM adopts a cleft-like structure. However, in CBM77<sub>RfPL1/9</sub>, the alanine mutation of aromatic or basic amino acids in the concave surface had no effect on ligand binding. Only the alanine mutation of three invariant basic residues (Lys1092, Lys1107, and Lys1162) located at the convex surface of CBM77<sub>RfPL1/9</sub> abrogated binding to polygalacturonic acid (PGA), showing the location of the binding site. The single alanine mutants of two distal basic residues (Lys1136 and Lys1141) displayed only a modest reduction in affinity for PGA when compared with the wild-type protein. However, the double mutation Lys1136A/Lys1141A resulted in complete loss of binding indicating that these lysines display functional redundancy. Additionally, based on the mutant binding data, the CBM77<sub>RfPL1/9</sub> ligand recognition surface is ~ 25 Å suggesting that the binding site can accommodate a hexasaccharide <cite>Venditto2016</cite>.
+The key residues implicated in ligand binding were identified by site-direct mutagenesis. The canonical ligand binding site of an endo-binding [[Carbohydrate-binding_modules#Types|type B]] CBM adopts a cleft-like structure. However, in CBM77<sub>RfPL1/9</sub>, the alanine mutation of aromatic or basic amino acids in the concave surface had no effect on ligand binding. Only the alanine mutation of three invariant basic residues (Lys1092, Lys1107, and Lys1162) located at the convex surface of CBM77<sub>RfPL1/9</sub> abrogated binding to polygalacturonic acid (PGA), showing the location of the binding site. The single alanine mutants of two distal basic residues (Lys1136 and Lys1141) displayed only a modest reduction in affinity for PGA when compared with the wild-type protein; however, the double mutation Lys1136A/Lys1141A resulted in complete loss of binding indicating that these lysines display functional redundancy. Additionally, based on the mutant binding data, the CBM77<sub>RfPL1/9</sub> ligand recognition surface is ~ 25 Å suggesting that the binding site can accommodate a hexasaccharide <cite>Venditto2016</cite>.
 The CBM77<sub>RfPL1/9</sub> ligand recognition mediated by basic polar residues is distinct from other CBMs where aromatic residues play a central role in glycan recognition, but resembles glycosaminoglycan binding proteins, where ligand recognition is also mediated by basic residues (arginine and lysines) <cite>Hileman1998</cite>.
 == Functionalities ==
-''Ruminoccocus flavefaciens'' CBM77<sub>RfPL1/9</sub> is a component of an enzyme that contains two catalytic modules, belonging to polysaccharide lyase families 1 ([[PL1]]) and 9 ([[PL9]]) and a C-terminal dockerin module. Consistent with the CBM77<sub>RfPL1/9</sub>, both PL enzymes display pectate lyase activity <cite>Venditto2016</cite>.
+''Ruminoccocus flavefaciens'' CBM77<sub>RfPL1/9</sub> is a component of an enzyme that contains two catalytic modules, belonging to polysaccharide lyase families 1 ([[PL1]]) and 9 ([[PL9]]) and a C-terminal dockerin module. Consistent with the CBM77<sub>RfPL1/9</sub> specificity, both PL enzymes display pectate lyase activity <cite>Venditto2016</cite>.
 This CBM family contains 26 members from a range of bacteria suggesting a general role in pectin degradation that is not specific to the cellulosome organization or the rumen environment. In the majority of the proteins, the CBM77 is appended to PL1 catalytic modules although PL9 sequences are also present <cite>Venditto2016</cite>.
@@ Line 37: / Line 37: @@
 == Family Firsts ==
 ;First Identified: CBM77<sub>RfPL1/9</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.
-;First Structural Characterization:  The first available crystal was CBM77<sub>RfPL1/9</sub> <cite>Venditto2016</cite>.
 == References ==

@@ 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.
+CBM77 is a bacterial family of binding modules that comprises around 110 amino acids. Only the founding member of this family, CBM77<sub>RfPL1/9</sub> has been characterized. This binding module found in ''Ruminococcus flavefaciens'' binds exclusively to homogalacturonan (pectin) with low degrees of methyl esterification (DE) <cite>Venditto2016</cite>. By isothermal titration calorimetry, CBM77<sub>RfPL1/9</sub> displays high affinity for low DE pectins such as, lime DE 11% and citrus pectin DE 30% (K<sub>A</sub> 1.8 x 10<sup>5</sup> M<sup>-1</sup> and 1.1 x 10<sup>4</sup> M<sup>-1</sup>, respectively). This binding module displays a reduction in affinity as the DE of the ligand increase. Indeed CBM77<sub>RfPL1/9</sub> exhibits no binding to polygalacturonic acid with a DE ≥80%. This binding module displays optimum binding to oligosaccharides of α1,4-D-Galacturonic acid (GalA) with a degree of polymerization of 7 to 8. Additionally, the presence of a chelating agent (EDTA) did not influence CBM77<sub>RfPL1/9</sub> affinity indicating a metal independent binding mechanism <cite>Venditto2016</cite>. The only other example of a CBM that binds to homogalacturonan backbone is [[CBM32]] from ''Yersinia enterolitica'' (YeCBM32) (which is not a component of an enzyme) <cite>Abbott2007</cite>.
-''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 ==
+The CBM77<sub>RfPL1/9</sub> ligand recognition mediated by basic polar residues is distinct from other CBMs where aromatic residues play a central role in glycan recognition, but resembles glycosaminoglycan binding proteins, where ligand recognition is also mediated by basic residues (arginine and lysines) <cite>Hileman1998</cite>.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+''Ruminoccocus flavefaciens'' CBM77<sub>RfPL1/9</sub> is a component of an enzyme that contains two catalytic modules, belonging to polysaccharide lyase families 1 ([[PL1]]) and 9 ([[PL9]]) and a C-terminal dockerin module. Consistent with the CBM77<sub>RfPL1/9</sub>, both PL enzymes display pectate lyase activity <cite>Venditto2016</cite>.
-* '''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.)
+This CBM family contains 26 members from a range of bacteria suggesting a general role in pectin degradation that is not specific to the cellulosome organization or the rumen environment. In the majority of the proteins, the CBM77 is appended to PL1 catalytic modules although PL9 sequences are also present <cite>Venditto2016</cite>.
-* '''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: CBM77<sub>RfPL1/9</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization:  The first available crystal was CBM77<sub>RfPL1/9</sub> <cite>Venditto2016</cite>.
 == 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].
+#Abbott2007 pmid=17292916
-#Boraston2004 pmid=15214846
+#Hileman1998 pmid=9631661
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM077]]