Carbohydrate Binding Module Family 8 - Revision history

Harry Brumer: Adjusted spacing before in-text citatations

2024-05-02T15:00:17Z

Adjusted spacing before in-text citatations

Elizabeth Ficko-Blean at 13:51, 2 May 2024

2024-05-02T13:51:17Z

Elizabeth Ficko-Blean: /* Functionalities */

2024-05-02T13:12:17Z

Functionalities

Elizabeth Ficko-Blean: /* Structural Features */

2024-05-02T13:11:43Z

Structural Features

Elizabeth Ficko-Blean: /* Ligand specificities */

2024-05-02T13:10:52Z

Ligand specificities

Elizabeth Ficko-Blean: /* Family Firsts */

2024-05-02T13:09:02Z

Family Firsts

Elizabeth Ficko-Blean: /* Family Firsts */

2024-05-02T13:08:25Z

Family Firsts

Elizabeth Ficko-Blean at 09:44, 2 May 2024

2024-05-02T09:44:35Z

Elizabeth Ficko-Blean at 09:30, 2 May 2024

2024-05-02T09:30:48Z

Elizabeth Ficko-Blean at 09:09, 2 May 2024

2024-05-02T09:09:39Z

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 == Ligand specificities ==
-These CBMs were originally called CBDVIII (family 8 cellulose-binding domains). DdCBM8, from the slime mold ''Dictyostelium discoideum''  CelA enzyme (270-6) binds xyloglucan, glucomannan, β-glucan, hydroxyethyl cellulose (HEC) and insoluble forms of cellulose, but not xylan<cite>Liberato2022</cite>. Binding was detected using affinity gel electrophoresis, ITC and intrinsic fluorescence microscopy<cite>Liberato2022</cite>. There is no evidence for binding to oligosaccharides<cite>Liberato2022</cite>.
+These CBMs were originally called CBDVIII (family 8 cellulose-binding domains). DdCBM8, from the slime mold ''Dictyostelium discoideum''  CelA enzyme (270-6) binds xyloglucan, glucomannan, β-glucan, hydroxyethyl cellulose (HEC) and insoluble forms of cellulose, but not xylan <cite>Liberato2022</cite>. Binding was detected using affinity gel electrophoresis, ITC and intrinsic fluorescence microscopy <cite>Liberato2022</cite>. There is no evidence for binding to oligosaccharides <cite>Liberato2022</cite>.
 == Structural Features ==
 [[File:DdCBM8.png|thumb|300px|right|'''Figure 1.'''  A secondary structure representation of the ''Dictyostelium discoideum'' DdCBM8 from the CelA enzyme [{{PDBlink}}7T7Z 7T7Z] showing the hydrophobic platform which is its predicted planar binding site <cite>Liberato2022</cite>.]]
-DdCBM8 is found C-terminal to the [[GH9]] endo-(1,4)-beta-D-glucanase (cellulase) catalytic module of the CelA enzyme (270–6) and connected via a Thr-Glu-Thr-Pro type repeat linker<cite>Ramalingam1992, Liberato2022</cite>.
+DdCBM8 is found C-terminal to the [[GH9]] endo-(1,4)-beta-D-glucanase (cellulase) catalytic module of the CelA enzyme (270–6) and connected via a Thr-Glu-Thr-Pro type repeat linker <cite>Ramalingam1992, Liberato2022</cite>.
-DdCBM8 has a beta-sandwich fold which supports the planar surface formed by W572, W574, and Y600, akin to [[Carbohydrate-binding_modules#Types|type A]] CBMs<cite>Liberato2022</cite>. These residues align with the [[CBM29]]-2 [{{PDBlink}}1GWM 1GWM] binding site<cite>Charnock2002</cite>, the residues R634 and Q686 from DdCBM8 are also conserved with binding residues from [[CBM29]]-2<cite>Liberato2022</cite>. Alanine mutations were made in DdCBM8 for W572, Y600, F608, R634, and Q686 and glycan binding was assessed using affinity gel electrophoresis<cite>Liberato2022</cite>.  The mutations W572A and Y600A abolished binding. The researchers were unable to produce the protein for the mutation W574A<cite>Liberato2022</cite>. No shift in gel mobility was detected for F608A or R634A, though the mutation Q686A did have an effect confirming its role in ligand binding<cite>Liberato2022</cite>. The W572,W574, Y600, and Q686 residues are highly conserved in the CBM8 family<cite>Liberato2022</cite>.
+DdCBM8 has a beta-sandwich fold which supports the planar surface formed by W572, W574, and Y600, akin to [[Carbohydrate-binding_modules#Types|type A]] CBMs <cite>Liberato2022</cite>. These residues align with the [[CBM29]]-2 [{{PDBlink}}1GWM 1GWM] binding site <cite>Charnock2002</cite>, the residues R634 and Q686 from DdCBM8 are also conserved with binding residues from [[CBM29]]-2 <cite>Liberato2022</cite>. Alanine mutations were made in DdCBM8 for W572, Y600, F608, R634, and Q686 and glycan binding was assessed using affinity gel electrophoresis <cite>Liberato2022</cite>.  The mutations W572A and Y600A abolished binding. The researchers were unable to produce the protein for the mutation W574A <cite>Liberato2022</cite>. No shift in gel mobility was detected for F608A or R634A, though the mutation Q686A did have an effect confirming its role in ligand binding <cite>Liberato2022</cite>. The W572,W574, Y600, and Q686 residues are highly conserved in the CBM8 family <cite>Liberato2022</cite>.
-DdCBM8 appears to be broadly specific with both [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM characteristics as it binds crystalline cellulose with a planar binding site, but has higher affinity for soluble glycans<cite>Liberato2022</cite>.
+DdCBM8 appears to be broadly specific with both [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM characteristics as it binds crystalline cellulose with a planar binding site, but has higher affinity for soluble glycans <cite>Liberato2022</cite>.
 == Functionalities ==
-DdCBM8 is appended to the [[GH9]] endo-(1,4)-beta-D-glucanase CelA<cite>Ramalingam1992</cite>. DdCBM8 shows fairly promiscuous binding so it may bring the enzyme in proximity to substrate (it is unlikely target to specific motifs).
+DdCBM8 is appended to the [[GH9]] endo-(1,4)-beta-D-glucanase CelA <cite>Ramalingam1992</cite>. DdCBM8 shows fairly promiscuous binding so it may bring the enzyme in proximity to substrate (it is unlikely target to specific motifs).
-CelA and CelB (a cellulose binding domain with no known cellulase activity<cite>Ramalingam1997</cite>) from ''Dictyostelium discoideum'' are predicted to be important for amoebae release from spores as transcriptomic experiments show that their mRNA levels are low in dormant spores, they rise during germination and then rapidly disappear after germination<cite>Ramalingam1992</cite>. Cellulase activities from differently sized cellulases are also shown to increase during spore germination<cite>Blume1991</cite>. It is suggested that CelB might improve the substrate accessibility for CelA due to their concomitant expression during germination<cite>Ramalingam1997</cite>.
+CelA and CelB (a cellulose binding domain with no known cellulase activity <cite>Ramalingam1997</cite>) from ''Dictyostelium discoideum'' are predicted to be important for amoebae release from spores as transcriptomic experiments show that their mRNA levels are low in dormant spores, they rise during germination and then rapidly disappear after germination <cite>Ramalingam1992</cite>. Cellulase activities from differently sized cellulases are also shown to increase during spore germination <cite>Blume1991</cite>. It is suggested that CelB might improve the substrate accessibility for CelA due to their concomitant expression during germination <cite>Ramalingam1997</cite>.
 == Family Firsts ==
 ;First Identified
-:The first suggestion of binding to cellulose for the CBM8 family was determined by affinity gels in the absence of the DdCBM8 from CelA from ''Dictyostelium discoideum''<cite>Ramalingam1992</cite>.  Detailed binding studies are presented in <cite>Liberato2022</cite>.
+:The first suggestion of binding to cellulose for the CBM8 family was determined by affinity gels in the absence of the DdCBM8 from CelA from ''Dictyostelium discoideum'' <cite>Ramalingam1992</cite>.  Detailed binding studies are presented in ref. <cite>Liberato2022</cite>.
 ;First Structural Characterization
-:The first crystal structures are from DdCBM8, from the slime mold ''Dictyostelium discoideum''<cite>Liberato2022</cite>, see [{{PDBlink}}7T7Y 7T7Y]  and [{{PDBlink}}7T7Z 7T7Z].
+:The first crystal structures are from DdCBM8, from the slime mold ''Dictyostelium discoideum'' <cite>Liberato2022</cite>, see [{{PDBlink}}7T7Y 7T7Y]  and [{{PDBlink}}7T7Z 7T7Z].
 == References ==

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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |{{CAZyDBlink}}CBM08.html
+| colspan="2" |{{CAZyDBlink}}CBM8.html
 |}
 </div>

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 DdCBM8 is appended to the [[GH9]] endo-(1,4)-beta-D-glucanase CelA<cite>Ramalingam1992</cite>. DdCBM8 shows fairly promiscuous binding so it may bring the enzyme in proximity to substrate (it is unlikely target to specific motifs).
-CelA and CelB (a cellulose binding domain with no known cellulase activity<cite>Ramalingam1997</cite>) from ''Dictyostelium discoideum'' are predicted to be important for amoebae release from spores as transcriptomic experiments show that their mRNA levels are low in dormant spores, they rise during germination and then rapidly disappear after germination <cite>Ramalingam1992</cite>. Cellulase activities from differently sized cellulases are also shown to increase during spore germination <cite>Blume1991</cite>. It is suggested that CelB might improve the substrate accessibility for CelA due to their concomitant expression during germination <cite>Ramalingam1997</cite>.
+CelA and CelB (a cellulose binding domain with no known cellulase activity<cite>Ramalingam1997</cite>) from ''Dictyostelium discoideum'' are predicted to be important for amoebae release from spores as transcriptomic experiments show that their mRNA levels are low in dormant spores, they rise during germination and then rapidly disappear after germination<cite>Ramalingam1992</cite>. Cellulase activities from differently sized cellulases are also shown to increase during spore germination<cite>Blume1991</cite>. It is suggested that CelB might improve the substrate accessibility for CelA due to their concomitant expression during germination<cite>Ramalingam1997</cite>.
 == Family Firsts ==

@@ Line 23: / Line 23: @@
 [[File:DdCBM8.png|thumb|300px|right|'''Figure 1.'''  A secondary structure representation of the ''Dictyostelium discoideum'' DdCBM8 from the CelA enzyme [{{PDBlink}}7T7Z 7T7Z] showing the hydrophobic platform which is its predicted planar binding site <cite>Liberato2022</cite>.]]
-DdCBM8 is found C-terminal to the [[GH9]] endo-(1,4)-beta-D-glucanase (cellulase) catalytic module of the CelA enzyme (270–6) and connected via a Thr-Glu-Thr-Pro type repeat linker <cite>Ramalingam1992, Liberato2022</cite>.
+DdCBM8 is found C-terminal to the [[GH9]] endo-(1,4)-beta-D-glucanase (cellulase) catalytic module of the CelA enzyme (270–6) and connected via a Thr-Glu-Thr-Pro type repeat linker<cite>Ramalingam1992, Liberato2022</cite>.
 DdCBM8 has a beta-sandwich fold which supports the planar surface formed by W572, W574, and Y600, akin to [[Carbohydrate-binding_modules#Types|type A]] CBMs<cite>Liberato2022</cite>. These residues align with the [[CBM29]]-2 [{{PDBlink}}1GWM 1GWM] binding site<cite>Charnock2002</cite>, the residues R634 and Q686 from DdCBM8 are also conserved with binding residues from [[CBM29]]-2<cite>Liberato2022</cite>. Alanine mutations were made in DdCBM8 for W572, Y600, F608, R634, and Q686 and glycan binding was assessed using affinity gel electrophoresis<cite>Liberato2022</cite>.  The mutations W572A and Y600A abolished binding. The researchers were unable to produce the protein for the mutation W574A<cite>Liberato2022</cite>. No shift in gel mobility was detected for F608A or R634A, though the mutation Q686A did have an effect confirming its role in ligand binding<cite>Liberato2022</cite>. The W572,W574, Y600, and Q686 residues are highly conserved in the CBM8 family<cite>Liberato2022</cite>.
 DdCBM8 appears to be broadly specific with both [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM characteristics as it binds crystalline cellulose with a planar binding site, but has higher affinity for soluble glycans<cite>Liberato2022</cite>.
 == Functionalities ==

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-These CBMs were originally called CBDVIII (family 8 cellulose-binding domains). DdCBM8, from the slime mold ''Dictyostelium discoideum''  CelA enzyme (270-6) binds insoluble forms of cellulose and xyloglucan, glucomannan, β-glucan, and hydroxyethyl cellulose (HEC), but not xylan<cite>Liberato2022</cite>. Binding was detected using affinity gel electrophoresis, ITC and intrinsic fluorescence microscopy<cite>Liberato2022</cite>. There is no evidence for binding to oligosaccharides <cite>Liberato2022</cite>.
+These CBMs were originally called CBDVIII (family 8 cellulose-binding domains). DdCBM8, from the slime mold ''Dictyostelium discoideum''  CelA enzyme (270-6) binds xyloglucan, glucomannan, β-glucan, hydroxyethyl cellulose (HEC) and insoluble forms of cellulose, but not xylan<cite>Liberato2022</cite>. Binding was detected using affinity gel electrophoresis, ITC and intrinsic fluorescence microscopy<cite>Liberato2022</cite>. There is no evidence for binding to oligosaccharides<cite>Liberato2022</cite>.
 == Structural Features ==

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