CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 81

2018-06-01T14:34:53Z

Marcelo Liberato:

{{CuratorApproved}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to [http://www.cazy.org/CBM81_characterized.html CAZy], other members were found exclusively in gammaproteobacteria <cite>Weiner2008</cite>. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1) <cite>Campos2016</cite>. The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs <cite>Campos2016</cite>. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

The first crystallographic structures from CBM81 family were deposited in the Protein Data Bank in 2016. Two structures from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), were obtained independent of the catalytic module <cite>Campos2016</cite>. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|Type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction <cite>Campos2016</cite>. This observation explains the enthalpically driven binding between the CBM and the ligand. In conclusion, CBM_E1 is classified as [[Carbohydrate-binding_modules#Types|type B]], due to its affinity for soluble glycan chains instead of crystalline polysaccharides, but presents the [[Carbohydrate-binding_modules#Types|type A]] flat binding-site.

== Functionalities ==
CBM_E1 demonstrated binding to amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides <cite>Campos2016</cite>. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. CBM81 may enhance endoglucanase activity by bringing the enzyme module into proximity of the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Weiner2008 pmid=18516288
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-25T16:15:22Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>, and it is the unique member characterized so far. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members are indicated as characterized, based on work from Weiner ''et al'' <cite>Weiner2008</cite>, but no structural or functional properties were described by the authors. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand. In conclusion, CBM_E1 may be classified as [[Carbohydrate-binding_modules#Types|type B]], due to its affinity for soluble glycan chains instead of crystalline polysaccharides, but presents the [[Carbohydrate-binding_modules#Types|type A]] flat binding-site.

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by bringing the enzyme module into proximity of the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Weiner2008 pmid=18516288
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-25T10:51:15Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>, and it is the unique member characterized so far. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members are indicated as characterized. However, no structural or functional properties were described <cite>Weiner2008</cite>.The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand. In conclusion, CBM_E1 may be classified as [[Carbohydrate-binding_modules#Types|type B]], due to its affinity for soluble glycan chains instead of crystalline polysaccharides, but presents the [[Carbohydrate-binding_modules#Types|type A]] flat binding-site.

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by bringing the enzyme module into proximity of the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Weiner2008 pmid=18516288
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-24T16:03:55Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members have been characterized in the literature since then. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|Type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand, and the preference for glycan chains instead of crystalline polysaccharides. Consequently, defining the classification of CBM_E1 as a [[Carbohydrate-binding_modules#Types|type B]].

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by bringing the enzyme module into proximity of the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-24T15:59:04Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members have been characterized in the literature since then. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|Type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand, and the preference for glycan chains instead of crystalline polysaccharides. Consequently, defining the classification of CBM_E1 as a [[Carbohydrate-binding_modules#Types|type B]].

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by approximating the catalytic domain to the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-24T15:57:55Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members have been characterized in the literature since then. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|Type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand, and the preference for glycan chains instead of cristalline plyssacharides. Consequently, defining the classification of CBM_E1 as a [[Carbohydrate-binding_modules#Types|type B]].

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by approximating the catalytic domain to the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

Carbohydrate Binding Module Family 81

2018-05-24T15:56:44Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to [http://www.cazy.org/CBM81_characterized.html CAZy], another two members have been characterized in the literature since then. The founding CBM81 (named CBM_E1) was identified from a sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (''K''A of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of [[Carbohydrate-binding_modules#Types|type B]] CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of [[Carbohydrate-binding_modules#Types|type A]] CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide are the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich fold with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved independent of the catalytic module. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which coordinates ligand binding. No differences were observed between apo and ligand complexed structures.

The CBM81 is the first CBM family to exhibit mixed characteristics from [[Carbohydrate-binding_modules#Types|type A]] and [[Carbohydrate-binding_modules#Types|type B]] CBM binding sites. [[Carbohydrate-binding_modules#Types|Type A]] CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the surface aromatic residues and the monosaccharide units <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to [[Carbohydrate-binding_modules#Types|type A]] CBMs, in the crystal structure of the complex one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand and the preference for glycan chains instead of cristalline plyssacharides, defining the classification of CBM_E1 as a [[Carbohydrate-binding_modules#Types|type B]].

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members so far deposited in CAZy. The CBM81 may enhance endoglucanase activity by approximating the catalytic domain to the substrate <cite>Herve2010</cite>; however, this effect has not been experimentally demonstrated for this family.

== Family Firsts ==
;First Identified: The CBM81 CBM_E1 was identified as part of a GH5 endoglucanase, originating from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.

;First Structural Characterization: The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the ligand cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

User:Marcelo Liberato

2018-05-19T23:45:30Z

Marcelo Liberato:

[[Image:marcelo liberato.jpg|200px|right]]
Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* [[GH5]] ''Bacillus licheniformis'' endoglucanase <cite>Liberato2016</cite>

* [[GH12]] ''Trichoderma harzianum'' endoglucanase <cite>Prates2013</cite>

* [[GH62]] ''Aspergillus nidulans'' arabinofuranosidase <cite>Contesini2017</cite>

'''Carbohydrate-binding modules:'''

* [[CBM46]] ''Bacillus licheniformis'' <cite>Liberato2016</cite>

* [[CBM81]] from sugar cane soil metagenome <cite>Campos2016</cite>

'''References'''
<biblio>
#Liberato2016 pmid=27032335
#Prates2013 pmid=23516599
#Contesini2017 pmid=28890404
#Campos2016 pmid=27621314
</biblio>


[[Category:Contributors|Liberato,Marcelo]]

File:Marcelo liberato.jpg

2018-05-19T23:43:49Z

Marcelo Liberato: Marcelo Liberato

Marcelo Liberato

Carbohydrate Binding Module Family 81

2018-05-19T23:25:50Z

Marcelo Liberato:

{{UnderConstruction}}
* [[Author]]: ^^^Marcelo Liberato^^^
* [[Responsible Curator]]: ^^^Fabio Squina^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM81.html
|}
</div>


== Ligand specificities ==
The family CBM81 was first described on September 12, 2016 <cite>Campos2016</cite>. According to CAZy, another two members were characterized in literature since then. The first CBM81 (named CBM_E1) was identified from sugar cane soil metagenome library <cite>Alvarez2013</cite>, as part of a GH5 endoglucanase, where the catalytic module and the CBM are connected by a 32 amino acids (serine-rich) linker. The CBM_E1 interaction with soluble ligands was determined by Isothermal Titration Calorimetry, resulting in the highest affinity with barley β-glucan (Ka of 1.4 x 10-4 M-1), followed by cellohexaose (1.2 x 10-4 M-1), xyloglucan (0.5 x 10-4 M-1) and cellopentaose (0.4 x 10-4 M-1). The protein did not show any affinity for xylan and oligosaccharides such as cellotetraose, mannohexaose, and xylohexaose. The thermodynamic parameters indicated that the CBM_E1 binding to ligands is enthalpically driven, which is a typical characteristic of Type B CBMs <cite>Georgelis2012</cite>. On the other hand, based on pull-down assays with insoluble carbohydrates, the CBM_E1 was able to bind to Avicel, but not to Bacterial Microcrystalline Cellulose (BMCC), which is characteristic of Type A CBMs. The Avicel is composed of about 40% of amorphous regions <cite>Hall2010</cite>, these disordered regions of the polysaccharide should be the probable CBM_E1 binding region.

== Structural Features ==
[[Image:Figure1_CBM81.png|thumb|300px|right|'''Figure 1. Cartoon structure representation of CBM_E1 complexed with cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]), the first member of family CBM81.''' CBM_E1 presents a beta sandwich folding with a flat binding site composed of three tryptophans and one lysine. The ligand is coordinated by CH-pi interactions with W375 and W427, and hydrogen bonds with W398 and K423. The N-terminal and C-terminal regions are coloured in blue and red, respectively.]]

Two structures of CBM81 are deposited in the Protein Data Bank so far. Both from CBM_E1, in the absence (PDB ID [{{PDBlink}}5klc 5KLC]) and presence of cellopentaose (PDB ID [{{PDBlink}}5kle 5KLE]) <cite>Campos2016</cite>. The structures were solved separately from the catalytic domain. CBM_E1 is composed of a beta sandwich with four and five beta-strands connected by loops (Figure 1). Parallel to the beta-strands, three tryptophan are exposed to solvent forming a planar surface, which was demonstrated to coordinate the ligand binding. No differences were observed between apo and ligand complexed structures.
The CBM81 is the first CBM family to exhibit mixing characteristics from Type A and Type B. The Type A CBMs bind to the surface of crystalline polysaccharides (such as cellulose and chitin) through CH-pi interactions between the aromatic residues and the monosaccharide’s units from carbohydrates <cite>Gilbert2013</cite>. Although the planar surface of this CBM81 member is composed of aromatic residues, similar to Type A CBMs, one of the tryptophans has the indole ring perpendicular to the oligosaccharide chain, leading to a hydrogen bond instead of a hydrophobic interaction. This observation explains the enthalpically driven binding between the CBM and the ligand, defining the classification of CBM_E1 as a Type B.

== Functionalities ==
The CBM_E1 was demonstrated to bind amorphous regions of cellulose, as well as beta-glucan, xyloglucan and cello-oligosaccharides. All these ligands are typical substrates of endoglucanases, which are the enzymes linked to the CBM81 members deposited so far. The CBM81 can enhance endoglucanases activity by approximating the catalytic domain to the substrate <cite>Herve2010</cite>. However, this effect was not experimentally demonstrated for this family.

== Family Firsts ==
;First Identified
:The CBM81 was identified as part of a GH5 endoglucanase, originated from an uncultured microorganism (metagenomics) <cite>Campos2016</cite>.
;First Structural Characterization
:The first crystal structures of the family CBM81 were from CBM_E1, in absence and presence of the substrate cellopentaose <cite>Campos2016</cite>.

== References ==
<biblio>
#Campos2016 pmid=27621314
#Alvarez2013 pmid=24358302
#Georgelis2012 pmid=22927418
#Hall2010 pmid=20148968
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM081]]

File:Figure1 CBM81.png

2018-05-19T22:53:11Z

Marcelo Liberato: Figure for CBM81 family. Created by Marcelo Liberato

Figure for CBM81 family. Created by Marcelo Liberato

Carbohydrate Binding Module Family 81

2018-05-17T23:53:11Z

Marcelo Liberato:

Carbohydrate Binding Module Family 81

2018-05-17T23:38:35Z

Marcelo Liberato:

User:Marcelo Liberato

2017-11-25T00:47:34Z

Marcelo Liberato:

[[Image:Blank_user-200px.png|200px|right]]
Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* [[GH5]] ''Bacillus licheniformis'' endoglucanase <cite>Liberato2016</cite>

* GH12 ''Trichoderma harzianum'' endoglucanase <cite>Prates2013</cite>

* GH62 ''Aspergillus nidulans'' arabinofuranosidase <cite>Contesini2017</cite>

'''Carbohydrate-binding modules:'''

* CBM46 ''Bacillus licheniformis'' <cite>Liberato2016</cite>

* CBM81 from sugar cane soil metagenome <cite>Campos2016</cite>

'''References'''
<biblio>
Liberato2016 pmid=27032335
</biblio>

<biblio>
Prates2013 pmid=23516599
</biblio>

<biblio>
Contesini2017 pmid=28890404
</biblio>

<biblio>
Campos2016 pmid=27621314
</biblio>


[[Category:Contributors|Liberato,Marcelo]]

User:Marcelo Liberato

2017-11-19T17:45:31Z

Marcelo Liberato:

Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* GH5 ''Bacillus licheniformis'' endoglucanase [1]

* GH12 ''Trichoderma harzianum'' endoglucanase [2]

* GH62 ''Aspergillus nidulans'' arabinofuranosidase [3]

'''Carbohydrate-binding modules:'''

* CBM46 ''Bacillus licheniformis'' [1]

* CBM81 from sugar cane soil metagenome [4]

'''References'''

1. Liberato MV, Silveira RL, Prates ÉT, De Araujo EA, Pellegrini VOA, Camilo CM, Kadowaki MA, Neto MO, Popov A, Skaf MS and Polikarpov I. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep. 2016 Apr 1; 6:23473. DOI:10.1038/srep23473 | PubMed ID:27032335 | HubMed [Liberato2016].

2. Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I and Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. Plos One. 2013 Mar;8(3):e59069. DOI:10.1371/journal.pone.0059069 | PubMed ID:23516599 | HubMed [Prates2013].

3. Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS and Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochim Biophys Acta. 2017 Dec;1865(12):1758-1769. DOI: 10.1016/j.bbapap.2017.09.001 | PubMed ID:28890404 | HubMed [Contesini2017].

4. Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC and Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem. 2016 Nov 4;291(45):23734-23743. DOI:10.1074/jbc.M116.744383 | PubMed ID:27621314 | HubMed [Campos2017].

User:Marcelo Liberato

2017-11-19T17:44:48Z

Marcelo Liberato:

Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* GH5 ''Bacillus licheniformis'' endoglucanase [1]

* GH12 ''Trichoderma harzianum'' endoglucanase [2]

* GH62 ''Aspergillus nidulans'' arabinofuranosidase [3]

'''Carbohydrate-binding modules:'''

* CBM46 ''Bacillus licheniformis'' [1]

* CBM81 from sugar cane soil metagenome [4]

'''References'''

## Liberato MV, Silveira RL, Prates ÉT, De Araujo EA, Pellegrini VOA, Camilo CM, Kadowaki MA, Neto MO, Popov A, Skaf MS and Polikarpov I. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep. 2016 Apr 1; 6:23473. DOI:10.1038/srep23473 | PubMed ID:27032335 | HubMed [Liberato2016].

# Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I and Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. Plos One. 2013 Mar;8(3):e59069. DOI:10.1371/journal.pone.0059069 | PubMed ID:23516599 | HubMed [Prates2013].

# Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS and Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochim Biophys Acta. 2017 Dec;1865(12):1758-1769. DOI: 10.1016/j.bbapap.2017.09.001 | PubMed ID:28890404 | HubMed [Contesini2017].

# Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC and Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem. 2016 Nov 4;291(45):23734-23743. DOI:10.1074/jbc.M116.744383 | PubMed ID:27621314 | HubMed [Campos2017].

User:Marcelo Liberato

2017-11-19T17:44:02Z

Marcelo Liberato:

Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* GH5 ''Bacillus licheniformis'' endoglucanase [1]

* GH12 ''Trichoderma harzianum'' endoglucanase [2]

* GH62 ''Aspergillus nidulans'' arabinofuranosidase [3]

'''Carbohydrate-binding modules:'''

* CBM46 ''Bacillus licheniformis'' [1]

* CBM81 from sugar cane soil metagenome [4]

'''References'''

# Liberato MV, Silveira RL, Prates ÉT, De Araujo EA, Pellegrini VOA, Camilo CM, Kadowaki MA, Neto MO, Popov A, Skaf MS and Polikarpov I. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep. 2016 Apr 1; 6:23473. DOI:10.1038/srep23473 | PubMed ID:27032335 | HubMed [Liberato2016].

# Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I and Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. Plos One. 2013 Mar;8(3):e59069. DOI:10.1371/journal.pone.0059069 | PubMed ID:23516599 | HubMed [Prates2013].

# Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS and Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochim Biophys Acta. 2017 Dec;1865(12):1758-1769. DOI: 10.1016/j.bbapap.2017.09.001 | PubMed ID:28890404 | HubMed [Contesini2017].

# Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC and Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem. 2016 Nov 4;291(45):23734-23743. DOI:10.1074/jbc.M116.744383 | PubMed ID:27621314 | HubMed [Campos2017].

User:Marcelo Liberato

2017-11-19T17:43:33Z

Marcelo Liberato:

Marcelo Liberato is a postdoctoral fellow in the Brazilian Bioethanol Science and Technology Laboratory (CTBE). He obtained his B. Sc. in Biology from the Federal University of São Carlos and his master and PhD were obtained in Biomolecular Physics at University of São Paulo, under the supervision of Prof. Igor Polikarpov. His work is focused on multimodular enzymes, trying to comprehend the influences of accessory modules on catalytic domains. He has determined the crystal structures of

'''Glycoside Hydrolases:'''

* GH5 ''Bacillus licheniformis'' endoglucanase [1]

* GH12 ''Trichoderma harzianum'' endoglucanase [2]

* GH62 ''Aspergillus nidulans'' arabinofuranosidase [3]

'''Carbohydrate-binding modules:'''

* CBM46 ''Bacillus licheniformis'' [1]

* CBM81 from sugar cane soil metagenome [4]

'''References'''

# Liberato MV, Silveira RL, Prates ÉT, De Araujo EA, Pellegrini VOA, Camilo CM, Kadowaki MA, Neto MO, Popov A, Skaf MS and Polikarpov I. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep. 2016 Apr 1; 6:23473. DOI:10.1038/srep23473 | PubMed ID:27032335 | HubMed [Liberato2016].

## Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I and Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. Plos One. 2013 Mar;8(3):e59069. DOI:10.1371/journal.pone.0059069 | PubMed ID:23516599 | HubMed [Prates2013].

### Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS and Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochim Biophys Acta. 2017 Dec;1865(12):1758-1769. DOI: 10.1016/j.bbapap.2017.09.001 | PubMed ID:28890404 | HubMed [Contesini2017].

#### Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC and Squina FM. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J Biol Chem. 2016 Nov 4;291(45):23734-23743. DOI:10.1074/jbc.M116.744383 | PubMed ID:27621314 | HubMed [Campos2017].

User:Marcelo Liberato

2017-11-19T01:12:26Z

Marcelo Liberato: