CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 86

2020-02-13T08:25:26Z

Maria Louise Leth:

{{CuratorApproved}}
* [[Author]]: ^^^Maria Louise Leth^^^
* [[Responsible Curator]]: ^^^Maher Abou Hachem^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM86.html
|}
</div>


== Ligand specificities ==
[[File:cbm86 fig1.png|thumb|300px|right| '''Figure 1''' A) Domain organization of the xylanase ''Ri''Xyn10A from ''R. intestinalis''. Grey module: signal peptide, light green module: BIG2, bacterial immunoglobulin-like domain group 2, dark green domain: LBR, Listeria-Bacteriodes repeat domain, and AA: amino acids. B) Architecture of the shallow binding site. C) Crystal structure of ''Ri''CBM86 ([{{PDBlink}}6SGF PDB: 6SGF]) with the four visible xylosyl residues of the xylohexaose ligand. The aromatic residues and the residues contributing to direct hydrogen bonding are shown as sticks in green.]]
The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82 <cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''D=479 µM), followed by xylopentaose (''K''D=490 µM), xylotetraose (''K''D=998 µM), and xylotriose (''K''D=1900 µM) <cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''D=0.02 mg ml-1) compared to birch glucuronoxylan (''K''D=0.6 mg ml-1) <cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides <cite>Leth2019</cite>.

== Structural Features ==
The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([{{PDBlink}}6SGF PDB: 6SGF]) <cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent. The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding <cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand <cite>Szabo</cite> or employ Ca2+ to mediate ligand binding <cite>Jamal</cite>.

== Functionalities ==
Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides<cite>Leth2018 Leth2019</cite>. The truncation of this module from ''Ri''Xyn10A resulted in about two fold higher ''K''m and a similar increase in ''k''cat, suggesting that this module contributes to xylan affinity and xylan capture <cite>Leth2018</cite>.

== Family Firsts ==
;First Identified
Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82 <cite>Leth2018</cite>.
;First Structural Characterization
The first crystal structure of the family CBM86 is ''Ri''CBM86 ([{{PDBlink}}6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A <cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.

== References ==
<biblio>
#Leth2018 pmid=29610517
#Leth2019 pmid=31693302
#Szabo pmid=11598143
#Jamal pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM086]]

Carbohydrate Binding Module Family 86

2020-02-06T13:38:52Z

Maria Louise Leth:

{{UnderConstruction}}
* [[Author]]: ^^^Maria Louise Leth^^^
* [[Responsible Curator]]: ^^^Maher Abou Hachem^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM86.html
|}
</div>


== Ligand specificities ==
The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82<cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''D=479 µM), followed by xylopentaose (''K''D=490 µM), xylotetraose (''K''D=998 µM), and xylotriose (''K''D=1900 µM)<cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''D=0.02 mg ml-1) compared to birch glucuronoxylan (''K''D=0.6 mg ml-1)<cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides<cite>Leth2019</cite>.

[[File:cbm86 fig1.png|thumb|300px|right| '''Figure 1''' A) Domain organization of the xylanase ''Ri''Xyn10A from ''R. intestinalis''. Grey module: signal peptide, light green module: BIG2, bacterial immunoglobulin-like domain group 2, dark green domain: LBR, Listeria-Bacteriodes repeat domain, and AA: amino acids. B) Architecture of the shallow binding site. C) Crystal structure of ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) with the four visible xylosyl residues of the xylohexaose ligand. The aromatic residues and the residues contributing to direct hydrogen bonding are shown as sticks in green.]]

== Structural Features ==
The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF])<cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent. The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding<cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand<cite>Szabo</cite> or employ Ca2+ to mediate ligand binding<cite>Jamal</cite>.

== Functionalities ==
Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides<cite>Leth2018 Leth2019</cite>. The truncation of this module from ''Ri''Xyn10A resulted in about two fold higher ''K''m and a similar increase in ''k''cat, suggesting that this module contributes to xylan affinity and xylan capture<cite>Leth2018</cite>.

== Family Firsts ==
;First Identified
Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82<cite>Leth2018</cite>.

;First Structural Characterization
The first crystal structure of the family CBM86 is ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A<cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.

== References ==
<biblio>
#Leth2018 pmid=29610517

#Leth2019 pmid=31693302

#Szabo pmid=11598143

#Jamal pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM086]]

File:Cbm86 fig1.png

2020-02-06T13:32:26Z

Maria Louise Leth:

Carbohydrate Binding Module Family 86

2020-02-06T12:54:32Z

Maria Louise Leth:

{{UnderConstruction}}
* [[Author]]: ^^^Maria Louise Leth^^^
* [[Responsible Curator]]: ^^^Maher Abou Hachem^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM86.html
|}
</div>


== Ligand specificities ==
The CBM86 family was first described in 2018. The founding member, ''Ri''CBM86, was identified in a modular GH10 xylanase from the human gut bacteria ''Roseburia intestinalis'' L1-82<cite>Leth2018</cite>. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (''K''D=479 µM), followed by xylopentaose (''K''D=490 µM), xylotetraose (''K''D=998 µM), and xylotriose (''K''D=1900 µM)<cite>Leth2018</cite>. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (''K''D=0.02 mg ml-1) compared to birch glucuronoxylan (''K''D=0.6 mg ml-1)<cite>Leth2018</cite>. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides<cite>Leth2019</cite>.

== Structural Features ==
The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF])<cite>Leth2019</cite>. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan<cite>Leth2018</cite>. W42 contribute in addition to affinity, but to a less extent. The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding<cite>Leth2018</cite>. ''Ri''CBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand or employ Ca2+ to mediate ligand binding<cite>Jamal</cite>.

== Functionalities ==
Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides<cite>Leth2018 Leth2019</cite>. The truncation of this module from ''Ri''Xyn10A resulted in about two fold higher ''K''m and a similar increase in ''k''cat, suggesting that this module contributes to xylan affinity and xylan capture<cite>Leth2018</cite>.

== Family Firsts ==
;First Identified
Family CBM86 was first identified as part of the modular xylanase ''Ri''Xyn10A from ''R. intestinalis'' L1-82<cite>Leth2018</cite>.

;First Structural Characterization
The first crystal structure of the family CBM86 is ''Ri''CBM86 ([https://www.rcsb.org/structure/6SGF PDB: 6SGF]) originating from ''Ri''Xyn10A<cite>Leth2019</cite>. The structure was determined in the presence of the ligand xylohexaose.

== References ==
<biblio>
#Leth2018 pmid=29610517

#Leth2019 pmid=31693302

#Jamal pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM086]]

User:Maria Louise Leth

2020-02-06T09:06:52Z

Maria Louise Leth:

[[Image:Mleth.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment], Technical University of Denmark.

I have contributed to the structure determination and biochemical characterization of:

* [[CBM86]] ''Roseburia intestinalis'' L1-82 xylan binding module, ''Ri''CBM86, from the modular xylanase ''Ri''Xyn10A <cite>Leth2019</cite> '''Family First'''.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T09:18:13Z

Maria Louise Leth:

[[Image:Mleth.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment], Technical University of Denmark.

I have contributed to the structure determination and biochemical characterization of:

* [[CBM86]] ''Roseburia intestinalis'' L1-82 xylan binding module, ''Ri''CBM86, from the modular xylanase ''Ri''Xyn10A <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T09:06:45Z

Maria Louise Leth:

[[Image:Mleth.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment], Technical University of Denmark.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]] <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T09:04:57Z

Maria Louise Leth:

[[Image:mleth-200px.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment], Technical University of Denmark.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]] <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

File:Mleth.png

2020-02-05T09:04:08Z

Maria Louise Leth:

User:Maria Louise Leth

2020-02-05T09:00:22Z

Maria Louise Leth:

[[Image:Blank_user-200px.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment], Technical University of Denmark.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]] <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T08:54:51Z

Maria Louise Leth:

[[Image:Blank_user-200px.png|200px|right]]
I am a post doc at [https://www.bioengineering.dtu.dk/english The Department of Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>. My research currently focuses on enzyme discovery for degradation and/or detoxification of pharmaceutical contaminants in waste water in collaboration with [https://www.env.dtu.dk/english The Department of Environment,] Technical University of Denmark.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]] <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T08:48:19Z

Maria Louise Leth:

[[Image:Blank_user-200px.png|200px|right]]
I am a post doc at The Department of [https://www.bioengineering.dtu.dk/english Biotechnology and Biomedicine], Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of [https://www.cazypedia.org/index.php/User:Maher_Abou_Hachem Maher Abou Hachem] at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis'' <cite>Leth2018</cite> <cite>LaRosa2019</cite>.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]] <cite>Leth2019</cite>.

----

<biblio>
#Leth2018 pmid=29610517
#LaRosa2019 pmid=30796211
#Leth2019 pmid=31693302

</biblio>


[[Category:Contributors|Leth,Maria Louise]]

User:Maria Louise Leth

2020-02-05T07:59:58Z

Maria Louise Leth:

[[Image:Blank_user-200px.png|200px|right]]
I am a post doc at The Department of Biotechnology and Biomedicine, Technical University of Denmark. I obtained my PhD degree in 2019 under the supervision of Maher Abou Hachem at the Technical University of Denmark. My PhD studies focused on the enzymatic degradation of xylan and mannan by the human gut symbiont ''Roseburia intestinalis''.

* I have contributed to the structure determination and biochemical characterization of the xylan binding [[CBM86]].

----

<biblio>
#Gilbert2008 pmid=18430603

</biblio>


[[Category:Contributors|Leth,Maria Louise]]