Carbohydrate Binding Module Family 91 - Revision history

Elizabeth Ficko-Blean: /* References */

2025-07-29T12:55:05Z

References

Elizabeth Ficko-Blean: /* Functionalities */

2025-07-29T12:53:27Z

Functionalities

Elizabeth Ficko-Blean: /* Structural Features */

2025-07-29T12:52:33Z

Structural Features

Elizabeth Ficko-Blean at 12:50, 29 July 2025

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Elizabeth Ficko-Blean at 09:30, 29 July 2025

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Elizabeth Ficko-Blean at 09:29, 29 July 2025

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Elizabeth Ficko-Blean at 09:28, 29 July 2025

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Elizabeth Ficko-Blean at 09:19, 29 July 2025

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Elizabeth Ficko-Blean at 09:11, 29 July 2025

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Elizabeth Ficko-Blean at 07:36, 29 July 2025

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 #Ito2023 Ito, D., 2023. Characterization of plant cell wall degrading enzymes from Paenibacillus sp., 2023, Mie University, Ph. D. thesis. https://dl.ndl.go.jp/pid/12910195/1/1
-#Pang2024 PMID=38556222
+#Pang2024 pmid=38556222
 #Ratanakhanockchai2012 K. Ratanakhanockchai, C. Tachaapaikoon, K.L. Kyu and P. Pason: A novel multienzyme complex from a newly isolated facultative anaerobic bacterium, ''Paenibacillus'' sp. TW1. Act. Biol. Hung., 63, 288–300 (2012) [https://doi.org/10.1556/ABiol.63.2012.2.10 DOI:10.1556/ABiol.63.2012.2.10]
 #StructuralGenomics Teplyakov, A., Fedorov, E., Gilliland, G.L., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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 CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]) (see [http://www.cazy.org/CBM91_structure.html CBM91 page of the CAZy Database]). CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.
-In the ''Physcomitrellae patens'' β-xylosidase/α-L-arabinofuranosidase bifunctional [[GH43]] enzyme the CBM91 at its C-terminus was essential for catalytic activity on artificial substrates and the deletion mutant greatly reduced activity on natural substrates <cite>Pang2024</cite>. The authors suggest a small CBM91 loop may contribute to the enzyme active site <cite>Pang2024</cite>.
+In the ''Physcomitrellae patens'' β-xylosidase/α-L-arabinofuranosidase bifunctional [[GH43]] enzyme the CBM91 at its C-terminus was essential for catalytic activity on artificial substrates and the deletion mutant greatly reduced activity on natural substrates <cite>Pang2024</cite>.
 == Family Firsts ==

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 [[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and ''Px''CBM91 <cite>Ito2023</cite>.
 '''The structure prediction by Alpha Fold 2 of ''Px''CBM91 (red).  This CBM91 is appended to the catalytic domain of ''Px''Xyl43A (green).]]
-Alpha Fold 2 structural analysis of ''Px''CBM91 exhibited a β-sandwich fold consisted of 12 β-strands and two opposing antiparallel beta sheets <cite>Ito2023</cite>. The concave surface and loops around it connecting the β-strands possess several hydrophobic amino acid residues, the surface is expected to be the binding site<cite>Ito2023</cite>.
+Alpha Fold 2 structural analysis of ''Px''CBM91 exhibited a β-sandwich fold consisted of 12 β-strands and two opposing antiparallel beta sheets <cite>Ito2023</cite>. The concave surface and loops around it connecting the β-strands possess several hydrophobic amino acid residues, the surface is expected to be the binding site <cite>Ito2023</cite>.  Another CBM91 study suggests the CBM91 may contribute a small loop to extend the enzyme active site <cite>Pang2024</cite>.
 == Functionalities ==

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 CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]) (see [http://www.cazy.org/CBM91_structure.html CBM91 page of the CAZy Database]). CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.
 == Family Firsts ==
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 #Ito2022 pmid=36312872
 #Ito2023 Ito, D., 2023. Characterization of plant cell wall degrading enzymes from Paenibacillus sp., 2023, Mie University, Ph. D. thesis. https://dl.ndl.go.jp/pid/12910195/1/1
 #Ratanakhanockchai2012 K. Ratanakhanockchai, C. Tachaapaikoon, K.L. Kyu and P. Pason: A novel multienzyme complex from a newly isolated facultative anaerobic bacterium, ''Paenibacillus'' sp. TW1. Act. Biol. Hung., 63, 288–300 (2012) [https://doi.org/10.1556/ABiol.63.2012.2.10 DOI:10.1556/ABiol.63.2012.2.10]
 #StructuralGenomics Teplyakov, A., Fedorov, E., Gilliland, G.L., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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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:Daichi Ito|Daichi Ito]]
 * [[Responsible Curator]]:  [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]

← Older revision		Revision as of 09:29, 29 July 2025
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	''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus'' likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like ''Px''Xyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended ''Px''CBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.		''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus'' likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like ''Px''Xyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended ''Px''CBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.

−	CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]) [http://www.cazy.org/CBM91_structure.html CBM91 page of the CAZy Database]. CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.	+	CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]) (see [http://www.cazy.org/CBM91_structure.html CBM91 page of the CAZy Database]). CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.

← Older revision		Revision as of 09:28, 29 July 2025
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	''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus'' likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like ''Px''Xyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended ''Px''CBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.		''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus'' likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like ''Px''Xyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended ''Px''CBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.

−	CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]). CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.	+	CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]) [http://www.cazy.org/CBM91_structure.html CBM91 page of the CAZy Database]. CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.

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 == Family Firsts ==
-;First Identified:''Px''CBM91 from ''Px''Xyl43A of ''Paenibacillus xynaniclasticus'' strain TW1 <cite>Ito2022</cite>.
+;First Identified: Xylan binding was first identified in ''Px''CBM91 from ''Px''Xyl43A of ''Paenibacillus xynaniclasticus'' strain TW1 <cite>Ito2022</cite>.
-;First Structural Characterization: β-D-xylosidase, a family 43 glycoside hydrolase from ''Clostridium acetobutylicum'' ATCC 824 (Released: 2005-01-25) [{{PDBlink}}1Y7B PDB ID 1Y7B].
+;First Structural Characterization: β-D-xylosidase, a family 43 glycoside hydrolase from ''Clostridium acetobutylicum'' ATCC 824 (Released: 2005-01-25) [{{PDBlink}}1Y7B PDB ID 1Y7B] <cite>StructuralGenomics</cite>.
 == References ==
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 #Ito2023 Ito, D., 2023. Characterization of plant cell wall degrading enzymes from Paenibacillus sp., 2023, Mie University, Ph. D. thesis. https://dl.ndl.go.jp/pid/12910195/1/1
 #Ratanakhanockchai2012 K. Ratanakhanockchai, C. Tachaapaikoon, K.L. Kyu and P. Pason: A novel multienzyme complex from a newly isolated facultative anaerobic bacterium, ''Paenibacillus'' sp. TW1. Act. Biol. Hung., 63, 288–300 (2012) [https://doi.org/10.1556/ABiol.63.2012.2.10 DOI:10.1556/ABiol.63.2012.2.10]
 </biblio>

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 == Functionalities ==
-CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]). CBM91 binds to the substrates and would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.
+''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus''  likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like ''Px''Xyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended ''Px''CBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.
-''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus''  is supposed to degrade xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like GH43, which produce xylose from xylan and xylooligosaccharides and connects to CBM91 is one of vial enzymes. Therefore, CBM91 would contribute to produce the carbon sources for the growth of xylolytic bacteria.
 == Family Firsts ==

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 == Ligand specificities ==
-CBM91 from ''Paenibacillus xynaniclasticus'' bound to oat spelt xylan with ''K''<sub>a</sub> value of 2.0×10<sup>-5</sup> M<sup>-1</sup>, and bound birchwood xylan <cite>Ito2022</cite>. It did not bind to lichenan or the cellulosic substrates carboxymethyl-cellulose or ball-milled cellulose  <cite>Ito2022</cite>. Therefore, CBM91 can recognize and bind to insoluble xylan <cite>Ito2022</cite>.
+''Px''CBM91 from ''Paenibacillus xynaniclasticus'' bound to oat spelt xylan with ''K''<sub>a</sub> value of 2.0×10<sup>-5</sup> M<sup>-1</sup>, and bound birchwood xylan <cite>Ito2022</cite>. It did not bind to lichenan or the cellulosic substrates carboxymethyl-cellulose or ball-milled cellulose  <cite>Ito2022</cite>. Therefore, ''Px''CBM91 can recognize and bind to insoluble xylan <cite>Ito2022</cite>.
 == Structural Features ==
-[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and CBM91 <cite>Ito2023</cite>.
+[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and ''Px''CBM91 <cite>Ito2023</cite>.
-'''The structure prediction by Alpha Fold 2 of CBM91 (red).  This CBM91 is appended to the catalytic domain of ''Px''Xyl43A (green).]]
+'''The structure prediction by Alpha Fold 2 of ''Px''CBM91 (red).  This CBM91 is appended to the catalytic domain of ''Px''Xyl43A (green).]]
 Alpha Fold 2 structural analysis of ''Px''CBM91 exhibited a β-sandwich fold consisted of 12 β-strands and two opposing antiparallel beta sheets <cite>Ito2023</cite>. The concave surface and loops around it connecting the β-strands possess several hydrophobic amino acid residues, the surface is expected to be the binding site<cite>Ito2023</cite>.
 == Functionalities ==
-CBM91 often is connected to the β-xylosidases belonging to glycoside hydrolase family 43 ([GH43]). CBM91 binds to the substrates and would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.
+CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 ([[GH43]]). CBM91 binds to the substrates and would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.
-''Paenibacillus xylaniclastuicus'' was isolated from anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012 Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus''  is supposed to degrade xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like GH43, which produce xylose from xylan and xylooligosaccharides and connects to CBM91 is one of vial enzymes. Therefore, CBM91 would contribute to produce the carbon sources for the growth of xylolytic bacteria.
+''Paenibacillus xylaniclastuicus'' was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012, Ratanakhanockchai2012</cite>. ''P. xylaniclastuicus''  is supposed to degrade xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like GH43, which produce xylose from xylan and xylooligosaccharides and connects to CBM91 is one of vial enzymes. Therefore, CBM91 would contribute to produce the carbon sources for the growth of xylolytic bacteria.
 == Family Firsts ==