Difference between revisions of "Carbohydrate Binding Module Family 91"

Latest revision as of 04:55, 29 July 2025

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CAZy DB link
https://www.cazy.org/CBM91.html

Ligand specificities

PxCBM91 from Paenibacillus xynaniclasticus bound to oat spelt xylan with K_a value of 2.0×10^-5 M^-1, and bound birchwood xylan [1]. It did not bind to lichenan or the cellulosic substrates carboxymethyl-cellulose or ball-milled cellulose [1]. Therefore, PxCBM91 can recognize and bind to insoluble xylan [1].

Structural Features

Figure 1. The structure of PxXyl43A and PxCBM91 [2]. The structure prediction by Alpha Fold 2 of PxCBM91 (red). This CBM91 is appended to the catalytic domain of PxXyl43A (green).

Alpha Fold 2 structural analysis of PxCBM91 exhibited a β-sandwich fold consisted of 12 β-strands and two opposing antiparallel beta sheets [2]. 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 [2]. Another CBM91 study suggests the CBM91 may contribute a small loop to extend the enzyme active site [3].

Functionalities

Paenibacillus xylaniclastuicus was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source [4, 5]. P. xylaniclastuicus likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like PxXyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended PxCBM91 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) (see 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 [3].

Family Firsts

First Identified: Xylan binding was first identified in PxCBM91 from PxXyl43A of Paenibacillus xynaniclasticus strain TW1 [1].
First Structural Characterization: β-D-xylosidase, a family 43 glycoside hydrolase from Clostridium acetobutylicum ATCC 824 (Released: 2005-01-25) PDB ID 1Y7B [6].

References

Error fetching PMID 36312872:
Error fetching PMID 38556222:

Error fetching PMID 36312872: [Ito2022]
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
[Ito2023]
Error fetching PMID 38556222: [Pang2024]
C. Tachaapaikoon, S. Tanasupawat, P. Pason, S. Sornyotha, R. Waeonukul, K.L. Kyu and K. Ratanakhanockchai: Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester. J.Microbiol., 50, 394–400 (2012) DOI:10.1007/s12275-012-1480-3
[Tachaapaikoon2012]
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) DOI:10.1556/ABiol.63.2012.2.10
[Ratanakhanockchai2012]
Teplyakov, A., Fedorov, E., Gilliland, G.L., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)
[StructuralGenomics]

All Medline abstracts: PubMed

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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]]
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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. But it did not bind to cellulosic substrates (carboxymethyl-cellulose, ball-milled cellulose and lichnan). 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.
+[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and ''Px''CBM91 <cite>Ito2023</cite>.
-'''The prediction structure 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 structure 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 possesse several hydrophobic amino acid residues, the surface is expected to be the binding site.
+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 ==
-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.
+''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 anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source.
-Xylosidases, like GH43, which produce xylose from xylan and xylooligosaccharides and connects to CBM91  is one of vial enzymes. Therefore,  CM91 would contribute to produce the carbon sources for the growth of xylolytic bacteria.
+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>.
 == 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 [{{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 ==
 <biblio>
+#Tachaapaikoon2012 C. Tachaapaikoon, S. Tanasupawat, P. Pason, S. Sornyotha, R. Waeonukul, K.L. Kyu and K. Ratanakhanockchai: ''Paenibacillus xylaniclasticus'' sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester. J.Microbiol., 50, 394–400 (2012) [https://doi.org/10.1007/s12275-012-1480-3 DOI:10.1007/s12275-012-1480-3]
 #Ito2022 pmid=36312872
-</biblio>
+#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
-<biblio>
-#Ito2023 Ito, D., 2023. Characterization of plant cell wall degrading enzymes from Paenibacillus sp. Ph. D. Mie University.https://dl.ndl.go.jp/pid/12910195/1/1
+#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)
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM091]]