Difference between revisions of "Carbohydrate Binding Module Family 91"

Latest revision as of 10:35, 31 August 2024

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

Ligand specificities

CBM91 from Paenibacillus xynaniclasticus bound to oat spelt xylan with K_a value of 2.0×10^-5 M^-1, 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 [1].

Structural Features

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

Alpha Fold 2 structure 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 possesse several hydrophobic amino acid residues, the surface is expected to be the binding site.

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 anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source [3, 4]. 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.

Family Firsts

First Identified: 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.

References

Ito D, Nakano E, Karita S, Umekawa M, Ratanakhanokchai K, and Tachaapaikoon C. (2022). Characterization of a GH Family 43 β-Xylosidase Having a Novel Carbohydrate-binding Module from Paenibacillus xylaniclasticus Strain TW1. J Appl Glycosci (1999). 2022;69(3):65-71. DOI:10.5458/jag.jag.JAG-2022_0001 | PubMed ID:36312872 [Ito2022]
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
[Ito2023]
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]

@@ Line 18: / Line 18: @@
 == Ligand specificities ==
-CBM91 bind oat spelt xylan with ''K''<sub>a</sub> value of 2.0×10<sup>-5</sup> M<sup>-1</sup>, and can bind birchwood xylan. But it does not bind to cellulosic substrates, carboxymethyl-cellulose, ball-milled cellulose and lichnan. So, CBM91 can recognize and bind to insoluble xylan <cite>Ito2022</cite>.
+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>.
 == Structural Features ==
-[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure. The structure of CBM91.
+[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and 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 prediction structure by Alpha Fold 2 of CBM91(red).  This CBM91 is appended to the catalytic domain of ''Px''Xyl43A(green).]]
-* '''Fold: β-sandwich '''
+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.
-* '''Type: Type B '''
 == Functionalities ==
-CBM91 often is found in the β-xylosidases, for example GH43. These seem not to need CBMs because the substrates, xylobiose and/or xylo-oligosaccharides, are soluble. So, it is likely that the binding ability may not be involved in β-xylosidase activity of catalytic domain. β-xylosidases would utilize CBM91 as a tool for efficient saccharification by combination with other enzymes and xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates. CBM91 binds to the substrates and would places the catalytic domain at the vicinity of substrates in which substrate concentration is high.
+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 anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012 Ratanakhanockchai2012</cite>.
+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.
 == Family Firsts ==
-;First Identified
+;First Identified:''Px''CBM91 from ''Px''Xyl43A of ''Paenibacillus xynaniclasticus'' strain TW1 <cite>Ito2022</cite>.
-:CBM91 from ''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 [{{PDBlink}}1Y7B PDB ID 1Y7B].
 == 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
+#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
+#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>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM091]]