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Difference between revisions of "Carbohydrate Binding Module Family 16"

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* [[Author]]: [[User:Maria_Matard-Mann|Maria Matard-Mann]]
 
* [[Author]]: [[User:Maria_Matard-Mann|Maria Matard-Mann]]
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== Ligand specificities ==
 
== Ligand specificities ==
Family 16 CBMs are found essentially in bacteria (only 4 are in archaea compared to 494 bacteria inventoried in CAZY). They are also found associated with catalytic modules belonging mainly to 4 families of CAZymes:  GH5 mannanase (Bae 2008, Su 2010), GH16 kappa carrageenase (Barbeyron 1998, Matard-Mann 2017, Salmean 2017), GH18 chitinase (Barabote 2009) and PL18 alginate lyase (Dong, 2014; Sim 2017). Binding to glucomannan and kappa-carrageenan has been demonstrated. CBM16 binding to glucomannan (mixed β-1,4-linked polymer contains both glucose and mannose) has been studied by mean of ITC analysis and crystallography of complex with pentomannan and pentoglucan (Bae et al., 2008; Su 2010 ). Conversely, binding to kappa-carrageenan has been shown by a double-blind approach on polysaccharide microarray (Salmean 2017).
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Family 16 CBMs are found essentially in bacteria (with the exception of some CBM16 members in archaea). They are also found associated with catalytic modules belonging mainly to 4 families of CAZymes:  [[GH5]] mannanases <cite>Bae2008 Su2010</cite>, [[GH16]] kappa carrageenases <cite>Barbeyron1998 Matard-Mann2017 Salmean2018</cite>, [[GH18]] chitinases <cite>Barabote2009</cite> and [[PL18]] alginate lyases <cite>Dong2014 Sim2017</cite>. Binding to glucomannan and kappa-carrageenan has been demonstrated <cite>Bae2008 Su2010 Salmean2018</cite>. CBM16 binding to glucomannan (mixed β-1,4-linked polymer contains both glucose and mannose) has been studied by ITC (isothermal titration calorimetry) analyses and X-ray crystallography of complexes with pentomannan and pentoglucan <cite>Bae2008 Su2010</cite>. Conversely, binding to kappa-carrageenan has been shown by a double-blind approach using polysaccharide microarrays <cite>Salmean2018</cite>.
 
 
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.
 
''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 ==
 +
[[File:CBM16-1.png|thumb|300px|right|'''Figure 1.''' The structure of CBM16-1 of ''Caldanaerobius polysaccharolyticus'' ManA, in complex with cellopentaose, [{{PDBlink}}2zex PDB ID  2zex]. Four key residues of the binding cleft are highlighted. ]]
 +
CBM16 is a [[Carbohydrate-binding_modules#Types|type B]]  CBM family, with a characteristic concave cleft, allowing the binding of ligand longer than triose. The ligand binding cleft shows some promiscuity as it can accommodate pentoses containing glucose and mannose, but only in the context of planar polymers like β-1,4-glucans and not helical β-1,3-glucans <cite>Bae2008</cite>. The crystallographic structure determination of both CBMs from ''Caldanaerobius polysaccharolyticus'' (formerly ''Thermoanaerobacterium polysaccharolyticum'') ManA revealed the importance of two aromatic residues in the binding cleft as well as two stretches of polar residues on both sides of the cleft,  [{{PDBlink}}2zew PDB ID  2zew] <cite>Bae2008</cite>. Affinity studies of targeted mutants for the predicted key residues confirmed the importance of two tryptophans (Trp-20 and Trp-125), and two glutamines (Gln-81 and Gln-93) <cite>Su2010</cite> (see Figure 1). 
  
CBM16 is a type B CBM family, with a characteristic concave cleft, allowing the binding of substrate longer than triose. The ligand binding cleft shows some promiscuity as it can accommodate both pentoses (glucose and mannose), but only in the context of planar polymer like β-1,4-glucans, and not helical β-1,3-glucans (Bae 2008). The crystallographic structure determination of both CBM of Caldanaerobius polysaccharolyticus (formerly Thermoanaerobacterium polysaccharolyticum) ManA revealed the importance of two aromatic residues in the binding cleft, as long as two stretches of polar residues on both sides of the cleft (Bae 2008). Study of affinity of targeted mutant for the predicted key resides confirmed the importance of two tryptophanes (Trp-20 and Trp-125), and two glutamines (Gln-81 and Gln-93) (Su 2010).
+
Based on sequence similarity and conservation of secondary structure elements it has been proposed that, along with the [[CBM4]], [[CBM17]], [[CBM22]] and [[CBM27]] families, they form a superfamily <cite>Sunna2001</cite>.
 
 
Based on sequence similarity and conservation of secondary structure element, it has been proposed that along with the CBM-4, 17, 22 and 27 families, they form a superfamily (Sunna, 2001).
 
 
 
 
 
''Content in this section should include, in paragraph form, a description of:''
 
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
 
* '''Type:''' Include here Type A, B, or C and properties
 
* '''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 ==
  
In the Man5A of Caldanaerobius polysaccharolyticus, the deletion of its both CBM16 severely impaired the ability of the catalytic module (GH5) to bind cellulose (Cann 1999).
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In the Man5A of ''Caldanaerobius polysaccharolyticus'', the deletion of both its CBM16s severely impairs the ability of the catalytic module ([[GH5]]) to bind cellulose <cite>Cann1999</cite>.
  
In the case of CgkA from Zobellia galactanivorans, the presence of the CBM16 is not required for the enzymatic activity on kappa-carrageenan, but has been shown to take part in  the processive mechanism of the catalytic module (GH16) (Matard-Mann 2017).
+
In the case of CgkA from ''Zobellia galactanivorans'', the presence of the CBM16 is not required for the enzymatic activity on kappa-carrageenan, but has been shown to take part in  the processive mechanism of the catalytic module ([[GH16]]) <cite>Matard-Mann2017</cite>.
  
Even if frequently found within the gene coding for alginate lyase from family PL18, it is absent in the mature form of the enzyme, and no role in alginate degradation has been found up to now (Sim 2017). A chaperon function of this N-terminal module has been proposed after observation that its deletion hindered the correct folding and activity of the catalytic module (Dong 2014).
+
Even if frequently encoded within the gene for alginate lyase from family [[PL18]], it is absent in the mature form of the enzyme, and no role in alginate degradation has been found up to now <cite>Sim2017</cite>. A chaperone function of this N-terminal module has been proposed after observation that its deletion hindered the correct folding and activity of the catalytic module <cite>Dong2014</cite>.
''Content in this section should include, in paragraph form, a description of:''
 
* '''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
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;First Identified: Cloning of Man5A GH5 by Cann ''et al''. in 1999 reaveled the presence of two tandem CBM16s on the C-terminal end. Their deletion resulted in failure of the catalytic module to bind to a cellulose column, and significant loss of both mannanase and carboxy methylcellulase activities <cite>Cann1999</cite>.
Cann 1999: two CBM16 tandem associated, in C-terminal side of the Man5A GH5
+
 
;First Structural Characterization
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;First Structural Characterization: In 2008 Bae ''et al''. solved  the first structures of the CBM16 family: both modules of ''Caldanaerobius polysaccharolyticus''  Man5A,  [{{PDBlink}}2zew PDB ID  2zew], and two complexes of CBM16-1, one with cellopentaose [{{PDBlink}}2zex PDB ID  2zex] and one with mannopentaose [{{PDBlink}}2zey PDB ID  2zey]<cite>Bae2008</cite>.
Bae 2008
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#Cantarel2009 pmid=18838391
+
#Bae2008 pmid=18025086
#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].
+
#Su2010 pmid=20739280
#Boraston2004 pmid=15214846
+
#Barbeyron1998 pmid=9580981
#Hashimoto2006 pmid=17131061
+
#Matard-Mann2017 pmid=29030427
#Shoseyov2006 pmid=16760304
+
#Salmean2018 pmid=29410423
#Guillen2010 pmid=19908036
+
#Barabote2009 pmid=19270083
#Armenta2017 pmid=28547780
+
#Dong2014 pmid=25210041
 +
#Sim2017 pmid=29057942
 +
#Sunna2001 pmid=11389686
 +
#Cann1999 pmid=10049399
 +
 
 
</biblio>
 
</biblio>
  
 
[[Category:Carbohydrate Binding Module Families|CBM016]] <!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. -->
 
[[Category:Carbohydrate Binding Module Families|CBM016]] <!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. -->

Latest revision as of 13:16, 18 December 2021

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CAZy DB link
https://www.cazy.org/CBM16.html

Ligand specificities

Family 16 CBMs are found essentially in bacteria (with the exception of some CBM16 members in archaea). They are also found associated with catalytic modules belonging mainly to 4 families of CAZymes: GH5 mannanases [1, 2], GH16 kappa carrageenases [3, 4, 5], GH18 chitinases [6] and PL18 alginate lyases [7, 8]. Binding to glucomannan and kappa-carrageenan has been demonstrated [1, 2, 5]. CBM16 binding to glucomannan (mixed β-1,4-linked polymer contains both glucose and mannose) has been studied by ITC (isothermal titration calorimetry) analyses and X-ray crystallography of complexes with pentomannan and pentoglucan [1, 2]. Conversely, binding to kappa-carrageenan has been shown by a double-blind approach using polysaccharide microarrays [5].

Structural Features

Figure 1. The structure of CBM16-1 of Caldanaerobius polysaccharolyticus ManA, in complex with cellopentaose, PDB ID 2zex. Four key residues of the binding cleft are highlighted.

CBM16 is a type B CBM family, with a characteristic concave cleft, allowing the binding of ligand longer than triose. The ligand binding cleft shows some promiscuity as it can accommodate pentoses containing glucose and mannose, but only in the context of planar polymers like β-1,4-glucans and not helical β-1,3-glucans [1]. The crystallographic structure determination of both CBMs from Caldanaerobius polysaccharolyticus (formerly Thermoanaerobacterium polysaccharolyticum) ManA revealed the importance of two aromatic residues in the binding cleft as well as two stretches of polar residues on both sides of the cleft, PDB ID 2zew [1]. Affinity studies of targeted mutants for the predicted key residues confirmed the importance of two tryptophans (Trp-20 and Trp-125), and two glutamines (Gln-81 and Gln-93) [2] (see Figure 1).

Based on sequence similarity and conservation of secondary structure elements it has been proposed that, along with the CBM4, CBM17, CBM22 and CBM27 families, they form a superfamily [9].

Functionalities

In the Man5A of Caldanaerobius polysaccharolyticus, the deletion of both its CBM16s severely impairs the ability of the catalytic module (GH5) to bind cellulose [10].

In the case of CgkA from Zobellia galactanivorans, the presence of the CBM16 is not required for the enzymatic activity on kappa-carrageenan, but has been shown to take part in the processive mechanism of the catalytic module (GH16) [4].

Even if frequently encoded within the gene for alginate lyase from family PL18, it is absent in the mature form of the enzyme, and no role in alginate degradation has been found up to now [8]. A chaperone function of this N-terminal module has been proposed after observation that its deletion hindered the correct folding and activity of the catalytic module [7].

Family Firsts

First Identified
Cloning of Man5A GH5 by Cann et al. in 1999 reaveled the presence of two tandem CBM16s on the C-terminal end. Their deletion resulted in failure of the catalytic module to bind to a cellulose column, and significant loss of both mannanase and carboxy methylcellulase activities [10].
First Structural Characterization
In 2008 Bae et al. solved the first structures of the CBM16 family: both modules of Caldanaerobius polysaccharolyticus Man5A, PDB ID 2zew, and two complexes of CBM16-1, one with cellopentaose PDB ID 2zex and one with mannopentaose PDB ID 2zey[1].

References

  1. Bae B, Ohene-Adjei S, Kocherginskaya S, Mackie RI, Spies MA, Cann IK, and Nair SK. (2008). Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA. J Biol Chem. 2008;283(18):12415-25. DOI:10.1074/jbc.M706513200 | PubMed ID:18025086 [Bae2008]
  2. Su X, Agarwal V, Dodd D, Bae B, Mackie RI, Nair SK, and Cann IK. (2010). Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules. J Biol Chem. 2010;285(45):34665-76. DOI:10.1074/jbc.M110.168302 | PubMed ID:20739280 [Su2010]
  3. Barbeyron T, Gerard A, Potin P, Henrissat B, and Kloareg B. (1998). The kappa-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases. Mol Biol Evol. 1998;15(5):528-37. DOI:10.1093/oxfordjournals.molbev.a025952 | PubMed ID:9580981 [Barbeyron1998]
  4. Matard-Mann M, Bernard T, Leroux C, Barbeyron T, Larocque R, Préchoux A, Jeudy A, Jam M, Nyvall Collén P, Michel G, and Czjzek M. (2017). Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases. J Biol Chem. 2017;292(48):19919-19934. DOI:10.1074/jbc.M117.808279 | PubMed ID:29030427 [Matard-Mann2017]
  5. Salmeán AA, Guillouzo A, Duffieux D, Jam M, Matard-Mann M, Larocque R, Pedersen HL, Michel G, Czjzek M, Willats WGT, and Hervé C. (2018). Double blind microarray-based polysaccharide profiling enables parallel identification of uncharacterized polysaccharides and carbohydrate-binding proteins with unknown specificities. Sci Rep. 2018;8(1):2500. DOI:10.1038/s41598-018-20605-9 | PubMed ID:29410423 [Salmean2018]
  6. Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, and Berry AM. (2009). Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res. 2009;19(6):1033-43. DOI:10.1101/gr.084848.108 | PubMed ID:19270083 [Barabote2009]
  7. Dong S, Wei TD, Chen XL, Li CY, Wang P, Xie BB, Qin QL, Zhang XY, Pang XH, Zhou BC, and Zhang YZ. (2014). Molecular insight into the role of the N-terminal extension in the maturation, substrate recognition, and catalysis of a bacterial alginate lyase from polysaccharide lyase family 18. J Biol Chem. 2014;289(43):29558-69. DOI:10.1074/jbc.M114.584573 | PubMed ID:25210041 [Dong2014]
  8. Sim PF, Furusawa G, and Teh AH. (2017). Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2. Sci Rep. 2017;7(1):13656. DOI:10.1038/s41598-017-13288-1 | PubMed ID:29057942 [Sim2017]
  9. Sunna A, Gibbs MD, and Bergquist PL. (2001). Identification of novel beta-mannan- and beta-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules. Biochem J. 2001;356(Pt 3):791-8. DOI:10.1042/0264-6021:3560791 | PubMed ID:11389686 [Sunna2001]
  10. Cann IK, Kocherginskaya S, King MR, White BA, and Mackie RI. (1999). Molecular cloning, sequencing, and expression of a novel multidomain mannanase gene from Thermoanaerobacterium polysaccharolyticum. J Bacteriol. 1999;181(5):1643-51. DOI:10.1128/JB.181.5.1643-1651.1999 | PubMed ID:10049399 [Cann1999]

All Medline abstracts: PubMed