CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
 Totally new to the CAZy classification? Read this first.

Difference between revisions of "Carbohydrate Binding Module Family 91"

From CAZypedia
Jump to navigation Jump to search
m
 
(32 intermediate revisions by 2 users not shown)
Line 18: Line 18:
  
 
== Ligand specificities ==
 
== 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.
+
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>.
−
 
 
−
''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 ==
−
''Content in this section should include, in paragraph form, a description of:''
+
[[Image:The_structure_of_PxXyl43A.png|thumb|300px|right|'''Figure 1. The structure of ''Px''Xyl43A and CBM91 <cite>Ito2023</cite>.
−
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+
'''The prediction structure by Alpha Fold 2 of CBM91(red).  This CBM91 is appended to the catalytic domain of ''Px''Xyl43A(green).]]
−
* '''Type:''' Include here Type A, B, or C and properties
+
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.
−
* '''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 ==  
 
== Functionalities ==  
−
''Content in this section should include, in paragraph form, a description of:''
+
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.
−
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
+
''Paenibacillus xylaniclastuicus'' was isolated from anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source <cite>Tachaapaikoon2012 Ratanakhanockchai2012</cite>.
−
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
+
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.
−
* '''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 ==
 
== Family Firsts ==
−
;First Identified
+
;First Identified:''Px''CBM91 from ''Px''Xyl43A of ''Paenibacillus xynaniclasticus'' strain TW1 <cite>Ito2022</cite>.
−
:Insert archetype here, possibly including ''very brief'' synopsis.
+
;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
 
−
:Insert archetype here, possibly including ''very brief'' synopsis.
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
−
#Cantarel2009 pmid=18838391
+
#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]
−
#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. [https://doi.org/10.1042/BIO03004026 Download PDF version].
+
#Ito2022 pmid=36312872
−
#Boraston2004 pmid=15214846
+
#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
−
#Hashimoto2006 pmid=17131061
+
#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]
−
#Shoseyov2006 pmid=16760304
 
−
#Guillen2010 pmid=19908036
 
−
#Armenta2017 pmid=28547780
 
 
</biblio>
 
</biblio>
  
 
<!-- Do not delete this Category tag -->
 
<!-- Do not delete this Category tag -->
 
[[Category:Carbohydrate Binding Module Families|CBM091]]
 
[[Category:Carbohydrate Binding Module Families|CBM091]]

Latest revision as of 10:35, 31 August 2024

Under construction icon-blue-48px.png

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

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

Ligand specificities

CBM91 from Paenibacillus xynaniclasticus bound to oat spelt xylan with Ka 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

  1. 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]

  2. 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]

  3. 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]

  4. 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]
Retrieved from "http://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_91&oldid=18363"