Difference between revisions of "Carbohydrate Binding Module Family 16"

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

All Medline abstracts: PubMed

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-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Maria_Matard-Mann|Maria Matard-Mann]]
-* [[Responsible Curator]]:  ^^^Elizabeth Ficko-Blean^^^
+* [[Responsible Curator]]:  [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]
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 == Ligand specificities ==
-Family 16 CBMs ([http://www.cazy.org/CBM16.html CAZy - CBM16])  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 mean of ITC (isothermal titration calorimetry) analysis 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>.
+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>.
 == 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. ]]
+[[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 substrate 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 <cite>Bae2008</cite>. Affinity studies of targeted mutants for the predicted key resides 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 [[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).
 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>.
@@ Line 32: / Line 32: @@
 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 <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>.
+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>.
 == Family Firsts ==
-;First Identified: Cloning of Man5A GH5 by Cann ''et al''. in 1999 reaveled the presence of two tandem CBM16 on the C-terminal end. Their deletion resulted in failure of the catalytic module to bind to cellulose column, and significant loss of both mannanase and carboxy methylcellulase activities <cite>Cann1999</cite>.
+;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>.
-;First Structural Characterization: Bae ''et al''. solved in 2008 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>.
+;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>.
 == References ==