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Difference between revisions of "Carbohydrate Binding Module Family 49"

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== 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.
+
Plant endoglucanases belong to glycosyl hydrolase family 9 (GH9), which contains enzymes capable of breaking β-1,4 glycosidic bonds within a glycan chain [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_9/Plant_endoglucanases]. The GH9 family in plants has been divided into three sub-families on the basis of variations in protein sequences <cite>Urbanowicz2007b  Libertini2004  </cite>. The GH9C sub-family proteins are comprised of a single N-terminal transmembrane helix, a GH9 catalytic domain, and a a C-terminal carbohydrate binding module (CBM49). Urbanowicz et al. showed that the CBM49 module of SlCel9C1 binds crystalline cellulose <cite>Urbanowicz2007a</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</cite>.
 
  
 
== Structural Features ==
 
== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
+
CBM49 domains are about  100–110 amino acids long. BLAST searches and predictive protein modeling indicate that these domains are most similar to CBM2. A refined model of the SlCel9C1 CBM domain, based on the template from CBM2 of C. fimi xylanase 10A (1EXG), closely matched the features of the β-barrel fold of the parent structure (i.e. only a few short insertions/deletions are present in the final alignment).     
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
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* '''Fold:''' Predicted β-barrel fold  
* '''Type:''' Include here Type A, B, or C and properties
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* '''Type:''' Predicted Type A  
* '''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.
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* '''Features of ligand binding:''' No structural information is available. However, site-directed mutagenesis of SlCel9C1-CBM49 showed that Trp522, Trp559, and Trp573 contribute to the interaction of CBM49 with crystalline cellulose.  
  
 
== Functionalities ==  
 
== Functionalities ==  
''Content in this section should include, in paragraph form, a description of:''
+
CBM49 modules are found appended to plant GH9 endoglucanases, and are currently thought to be unique to plants <cite>Urbanowicz2007</cite>. The three members of plant GH9 class C have not been well studied in Arabidopsis, however, the tomato and rice orthologs of At1g64390 (AtGH9C2) have been examined. For example, Urbanowicz et al. provided evidence for the binding of the tomato SlCel9C1 CBM to crystalline cellulose, as well as hydrolysis of artificial cellulosic polymers, and a variety of plant cell wall polysaccharides by the catalytic domain <cite>Urbanowicz2007a</cite>. A similar study was performed on the orthologous rice endoglucanase, further confirming that the catalytic domain is capable of hydrolyzing a suite of polysaccharides <cite>Yoshida2006b</cite>. Yoshida and Komae also provided evidence that the CBM49 module is post-translationally cleaved in the apoplast <cite>Yoshida2006a</cite>. Glass et al. have shown that over-expression of PtGH9C2 and down-regulation of AtGH9C2 results in plants with modified degrees of cell wall crystallinity, which was inversely correlated with changes in plant height and rosette diameter <cite>Glass2015</cite>. Genetic modification of GH9C enzymes in planta suggest that CBM49s function to target plant GH9 enzymes to crystalline cellulose prior to proteolytic cleavage, thereby regulating cross-linking with hemicellulosic polysaccharides, and preserving the crystallinity of the newly synthesized cellulose microfibrils, limiting cell expansion <cite>Glass2015</cite>.
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
 
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
 
* '''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
:Insert archetype here, possibly including ''very brief'' synopsis.
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:The cellulose binding function of CBM49 was first demonstrated in Solanum lycopersicum SlCel9C in 2007 <cite>Urbanowicz2007a</cite>.  
 
;First Structural Characterization
 
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.
+
:There is no available structure for CBM49 at this time.
 
+
   
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#Cantarel2009 pmid=18838391
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#Urbanowicz2007a pmid=17322304
#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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+
#Urbanowicz2007b pmid=17687051
#Boraston2004 pmid=15214846
+
#Libertini2004 pmid=15170254
#Hashimoto2006 pmid=17131061
+
#Yoshida2006a    pmid=17056619   
#Shoseyov2006 pmid=16760304
+
    #Yoshida2006b pmid=17056618   
#Guillen2010 pmid=19908036
+
      #Glass2015 pmid=25756224   
 
</biblio>
 
</biblio>
  
 
[[Category:Carbohydrate Binding Module Families|CBM049]]
 
[[Category:Carbohydrate Binding Module Families|CBM049]]

Revision as of 12:59, 19 July 2017

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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
http://www.cazy.org/CBM49.html

Ligand specificities

Plant endoglucanases belong to glycosyl hydrolase family 9 (GH9), which contains enzymes capable of breaking β-1,4 glycosidic bonds within a glycan chain [1]. The GH9 family in plants has been divided into three sub-families on the basis of variations in protein sequences [1, 2]. The GH9C sub-family proteins are comprised of a single N-terminal transmembrane helix, a GH9 catalytic domain, and a a C-terminal carbohydrate binding module (CBM49). Urbanowicz et al. showed that the CBM49 module of SlCel9C1 binds crystalline cellulose [3].

Structural Features

CBM49 domains are about 100–110 amino acids long. BLAST searches and predictive protein modeling indicate that these domains are most similar to CBM2. A refined model of the SlCel9C1 CBM domain, based on the template from CBM2 of C. fimi xylanase 10A (1EXG), closely matched the features of the β-barrel fold of the parent structure (i.e. only a few short insertions/deletions are present in the final alignment).

  • Fold: Predicted β-barrel fold
  • Type: Predicted Type A
  • Features of ligand binding: No structural information is available. However, site-directed mutagenesis of SlCel9C1-CBM49 showed that Trp522, Trp559, and Trp573 contribute to the interaction of CBM49 with crystalline cellulose.

Functionalities

CBM49 modules are found appended to plant GH9 endoglucanases, and are currently thought to be unique to plants [4]. The three members of plant GH9 class C have not been well studied in Arabidopsis, however, the tomato and rice orthologs of At1g64390 (AtGH9C2) have been examined. For example, Urbanowicz et al. provided evidence for the binding of the tomato SlCel9C1 CBM to crystalline cellulose, as well as hydrolysis of artificial cellulosic polymers, and a variety of plant cell wall polysaccharides by the catalytic domain [3]. A similar study was performed on the orthologous rice endoglucanase, further confirming that the catalytic domain is capable of hydrolyzing a suite of polysaccharides [5]. Yoshida and Komae also provided evidence that the CBM49 module is post-translationally cleaved in the apoplast [6]. Glass et al. have shown that over-expression of PtGH9C2 and down-regulation of AtGH9C2 results in plants with modified degrees of cell wall crystallinity, which was inversely correlated with changes in plant height and rosette diameter [7]. Genetic modification of GH9C enzymes in planta suggest that CBM49s function to target plant GH9 enzymes to crystalline cellulose prior to proteolytic cleavage, thereby regulating cross-linking with hemicellulosic polysaccharides, and preserving the crystallinity of the newly synthesized cellulose microfibrils, limiting cell expansion [7].

Family Firsts

First Identified
The cellulose binding function of CBM49 was first demonstrated in Solanum lycopersicum SlCel9C in 2007 [3].
First Structural Characterization
There is no available structure for CBM49 at this time.

References

  1. Urbanowicz BR, Bennett AB, Del Campillo E, Catalá C, Hayashi T, Henrissat B, Höfte H, McQueen-Mason SJ, Patterson SE, Shoseyov O, Teeri TT, and Rose JK. (2007) Structural organization and a standardized nomenclature for plant endo-1,4-beta-glucanases (cellulases) of glycosyl hydrolase family 9. Plant Physiol. 144, 1693-6. DOI:10.1104/pp.107.102574 | PubMed ID:17687051 | HubMed [Urbanowicz2007b]
  2. Libertini E, Li Y, and McQueen-Mason SJ. (2004) Phylogenetic analysis of the plant endo-beta-1,4-glucanase gene family. J Mol Evol. 58, 506-15. DOI:10.1007/s00239-003-2571-x | PubMed ID:15170254 | HubMed [Libertini2004]
  3. Urbanowicz BR, Catalá C, Irwin D, Wilson DB, Ripoll DR, and Rose JK. (2007) A tomato endo-beta-1,4-glucanase, SlCel9C1, represents a distinct subclass with a new family of carbohydrate binding modules (CBM49). J Biol Chem. 282, 12066-74. DOI:10.1074/jbc.M607925200 | PubMed ID:17322304 | HubMed [Urbanowicz2007a]
  4. Yoshida K and Komae K. (2006) A rice family 9 glycoside hydrolase isozyme with broad substrate specificity for hemicelluloses in type II cell walls. Plant Cell Physiol. 47, 1541-54. DOI:10.1093/pcp/pcl020 | PubMed ID:17056618 | HubMed [Yoshida2006b]
  5. Yoshida K, Imaizumi N, Kaneko S, Kawagoe Y, Tagiri A, Tanaka H, Nishitani K, and Komae K. (2006) Carbohydrate-binding module of a rice endo-beta-1,4-glycanase, OsCel9A, expressed in auxin-induced lateral root primordia, is post-translationally truncated. Plant Cell Physiol. 47, 1555-71. DOI:10.1093/pcp/pcl021 | PubMed ID:17056619 | HubMed [Yoshida2006a]
  6. Glass M, Barkwill S, Unda F, and Mansfield SD. (2015) Endo-β-1,4-glucanases impact plant cell wall development by influencing cellulose crystallization. J Integr Plant Biol. 57, 396-410. DOI:10.1111/jipb.12353 | PubMed ID:25756224 | HubMed [Glass2015]
All Medline abstracts: PubMed | HubMed