CAZypedia - User contributions [en-ca]

User:Didier Ndeh

2019-03-03T14:56:27Z

Didier Ndeh:

[[Image:DidierNdeh.png|200px|right]]

Didier Ndeh is a postdoctoral research associate at the Institute for Cell and Molecular Biosciences (ICAMB), Newcastle University, UK. Didier completed his PhD at Newcastle University in the year 2013. Since then, Didier’s research has focused on the understanding of host-microbial interactions involving the human gut microbiota. Prior to his PhD, Didier obtained a BSc in Biochemistry from the University of Buea in Cameroon in 2007. He was later offered a UK Commonwealth Scholarship to study for his MSc in Biotechnology at Nottingham Trent University, which he completed in 2009. Didier later worked as a research assistant on an Onchocerciasis Drug Research programme at the Biotechnology Unit of the University of Buea before obtaining another UK Commonwealth Scholarship to study for his PhD at Newcastle University. Didier’s work on complex glycan metabolism by the human gut microbiota has led to the discovery of several novel carbohydrate-acting enzyme families including [[GH137]], [[GH138]], [[GH139]], [[GH140]], [[GH141]], [[GH142]], and [[GH143]] <cite>Ndeh2017</cite>. Didier (in collaboration with Arnaud Basle and ^^^Harry Gilbert^^^) determined the first crystal structure of a [[GH141]] enzyme, specifically the pectin degrading BT1002 fucosidase encoded by the human gut bacterium Bacteroides thetaiotaomicron <cite>Ndeh2017</cite>.

----

References
<biblio>
#Ndeh2017 pmid=28329766

</biblio>


[[Category:Contributors|Ndeh,Didier]]

Glycoside Hydrolase Family 138

2018-02-01T23:16:23Z

Didier Ndeh:

{{UnderConstruction}}
* [[Author]]: ^^^Didier Ndeh^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH138'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|unknown
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH138.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of family 138 (GH138) exhibit α-D-galacturonidase activity. This is based on data from the characterisation of the founding member of the family BT0997 encoded by the prominent human gut bacterium ''B. thetaiotaomicron'' <cite>Ndeh2017</cite>. BT0997 hydrolyses a derivative fragment (GalAα1-2(GalAβ1-3)(2MeXylα1-3Fucα1-4)Rhaα1-3Api) of Chain A from the pectic polysaccharide Rhamnogalacturonan II, producing D-galacturonic acid and the resulting fragment GalAβ1-3(2MeXylα1-3Fucα1-4)Rhaα1-3Api <cite>Ndeh2017</cite>. Several members of this family have been identified in gut and environmental bacteria with a majority of the encoding microbes belonging to the Bacteroidetes phylum <cite>Lombard2014 Cantarel2009</cite>. This phylum is highly represented in human gut microbial populations <cite>Qin2010</cite>.

== Kinetics and Mechanism ==
The kinetic mechanism for this family has not been reported

== Catalytic Residues ==
The catalytic residues for this family have not yet been identified.

== Three-dimensional structures ==
No 3D structure for a member of this family has been currently reported

== Family Firsts ==
;First stereochemistry determination:Currently unknown.
;First catalytic nucleophile identification:Currently unknown.
;First general acid/base residue identification:Currently unknown.
;First 3-D structure:Currently unknown.
== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Ndeh2017 pmid=28329766
#Qin2010 pmid=20203603
#Lombard2014 pmid=24270786

</biblio>

[[Category:Glycoside Hydrolase Families|GH138]]

File:Blank user-200px.png

2018-02-01T23:08:50Z

Didier Ndeh: Didier Ndeh uploaded a new version of File:Blank user-200px.png

From http://commons.wikimedia.org/wiki/File:Blank_user.svg

Glycoside Hydrolase Family 138

2018-01-20T18:31:26Z

Didier Ndeh:

{{UnderConstruction}}
* [[Author]]: ^^^Didier Ndeh^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH138'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|unknown
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH138.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of family 138 (GH138) exhibit α-D-galacturonidase activity. This is based on data from the characterisation of the founding member of the family BT0997 encoded by the prominent human gut bacterium ''B. thetaiotaomicron'' <cite>Ndeh2017</cite>. BT0997 hydrolyses a derivative fragment (GalAα1-2(GalAβ1-3)(2MeXylα1-3Fucα1-4)Rhaα1-3Api) of Chain A from the pectic polysaccharide Rhamnogalacturonan II, producing D-galacturonic acid and the resulting fragment GalAβ1-3(2MeXylα1-3Fucα1-4)Rhaα1-3Api <cite>Ndeh2017</cite>. To date, over 33 members of this family have been identified in gut and environmental bacteria and a majority of the encoding microbes (over 80%) belong to the Bacteroidetes phylum <cite>Lombard2014 Cantarel2009</cite>. This phylum is highly represented in human gut microbial populations <cite>Qin2010</cite>.

== Kinetics and Mechanism ==
The kinetic mechanism for this family has not been reported

== Catalytic Residues ==
The catalytic residues for this family have not yet been identified.

== Three-dimensional structures ==
No 3D structure for a member of this family has been currently reported

== Family Firsts ==
;First stereochemistry determination:Currently unknown.
;First catalytic nucleophile identification:Currently unknown.
;First general acid/base residue identification:Currently unknown.
;First 3-D structure:Currently unknown.
== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Ndeh2017 pmid=28329766
#Qin2010 pmid=20203603
#Lombard2014 pmid=24270786

</biblio>

[[Category:Glycoside Hydrolase Families|GH138]]

User:Didier Ndeh

2018-01-20T18:30:37Z

Didier Ndeh:

[[Image:Blank_user-200px.png|200px|right]]

Didier Ndeh is a postdoctoral research associate at the Institute for Cell and Molecular Biosciences (ICAMB), Newcastle University, UK. Didier completed his PhD at Newcastle University in the year 2013. Since then, Didier’s research has focused on the understanding of host-microbial interactions involving the human gut microbiota. Prior to his PhD, Didier obtained a BSc in Biochemistry from the University of Buea in Cameroon in 2007. He was later offered a UK Commonwealth Scholarship to study for his MSc in Biotechnology at Nottingham Trent University, which he completed in 2009. Didier later worked as a research assistant on an Onchocerciasis Drug Research programme at the Biotechnology Unit of the University of Buea before obtaining another UK Commonwealth Scholarship to study for his PhD at Newcastle University. Didier’s work on complex glycan metabolism by the human gut microbiota has led to the discovery of several novel carbohydrate-acting enzyme families including [[GH137]], [[GH138]], [[GH139]], [[GH140]], [[GH141]], [[GH142]], and [[GH143]] <cite>Ndeh2017</cite>. Didier (in collaboration with Arnaud Basle and ^^^Harry Gilbert^^^) determined the first crystal structure of a [[GH137]] enzyme, specifically the pectin degrading BT1002 fucosidase encoded by the human gut bacterium Bacteroides thetaiotaomicron <cite>Ndeh2017</cite>.

----

References
<biblio>
#Ndeh2017 pmid=28329766

</biblio>


[[Category:Contributors|Ndeh,Didier]]

Glycoside Hydrolase Family 138

2018-01-18T09:43:16Z

Didier Ndeh:

{{UnderConstruction}}
* [[Author]]: ^^^Didier Ndeh^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH138'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|unknown
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH138.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of family 138 (GH138) exhibit α-D-galacturonidase activity. This is based on data from the characterisation of the founding member of the family BT0997 encoded by the prominent human gut bacterium ''B. thetaiotaomicron'' <cite>Ndeh2017</cite>. BT0997 hydrolyses a derivative fragment (GalAα1-2(GalAβ1-3)(2MeXylα1-3Fucα1-4)Rhaα1-3Api) of Chain A from the pectic polysaccharide Rhamnogalacturonan II, producing D-galacturonic acid and the resulting fragment GalAβ1-3(2MeXylα1-3Fucα1-4)Rhaα1-3Api <cite>Ndeh2017</cite>. To date, over 33 members of this family have been identified in gut and environmental bacteria and a majority of the encoding microbes (over 80%) belong to the Bacteroidetes phylum <cite>Lombard2014</cite><cite>Cantarel2009</cite>. This phylum is highly represented in human gut microbial populations <cite>Qin2010</cite>.

== Kinetics and Mechanism ==
The kinetic mechanism for this family has not been reported

== Catalytic Residues ==
The catalytic residues for this family have not yet been identified.

== Three-dimensional structures ==
No 3D structure for a member of this family has been currently reported

== Family Firsts ==
;First stereochemistry determination:Currently unknown.
;First catalytic nucleophile identification:Currently unknown.
;First general acid/base residue identification:Currently unknown.
;First 3-D structure:Currently unknown.
== References ==
<biblio>
#Cantarel2009 pmid=18838391
#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].
#Ndeh2017 pmid=28329766
#Qin2010 pmid=20203603
#Lombard2014 pmid=24270786

</biblio>

[[Category:Glycoside Hydrolase Families|GH138]]

Glycoside Hydrolase Family 138

2018-01-18T09:27:06Z

Didier Ndeh:

{{UnderConstruction}}
* [[Author]]: ^^^Didier Ndeh^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH138'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|unknown
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH138.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of family 138 (GH138) exhibit α-D-galacturonidase activity. This is based on data from the characterisation of the founding member of the family BT0997 encoded by the prominent human gut bacterium ''B. thetaiotaomicron'' <cite>Ndeh2017</cite>. BT0997 hydrolyses a derivative fragment (GalAα1-2(GalAβ1-3)(2MeXylα1-3Fucα1-4)Rhaα1-3Api) of Chain A from the pectic polysaccharide Rhamnogalacturonan II, producing D-galacturonic acid and the resulting fragment GalAβ1-3(2MeXylα1-3Fucα1-4)Rhaα1-3Api <cite>Ndeh2017</cite>. To date, over 33 members of this family have been identified in gut and environmental bacteria and a majority of the encoding microbes (over 80%) belong to the Bacteroidetes phylum <cite>Lombard2014</cite><cite>Cantarel2009</cite>. This phylum is highly represented in human gut microbial populations <cite>Qin2010</cite>.

== Kinetics and Mechanism ==
The kinetic mechanism for this family has not been reported

== Catalytic Residues ==
The catalytic residues for this family have not yet been identified.

== Three-dimensional structures ==
No 3D structure for a member of this family has been currently reported

== Family Firsts ==
;First stereochemistry determination:Currently unknown.
;First catalytic nucleophile identification:Currently unknown.
;First general acid/base residue identification:Currently unknown.
;First 3-D structure:Currently unknown.
== References ==
<biblio>
#Cantarel2009 pmid=18838391
#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].
#Ndeh2017 pmid=28329766
#Qin2010 pmid=20203603
#Lombard2014 pmid=24270786

</biblio>

[[Category:Glycoside Hydrolase Families|GH138]]

Glycoside Hydrolase Family 138

2018-01-18T09:24:47Z

Didier Ndeh:

{{UnderConstruction}}
* [[Author]]: ^^^Didier Ndeh^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH138'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|unknown
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH138.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of family 138 (GH138) exhibit α-D-galacturonidase activity. This is based on data from the characterisation of the founding member of the family BT0997 encoded by the prominent human gut bacterium B. thetaiotaomicron <cite>Ndeh2017</cite>. BT0997 hydrolyses a derivative fragment (GalAα1-2(GalAβ1-3)(2MeXylα1-3Fucα1-4)Rhaα1-3Api) of Chain A from the pectic polysaccharide Rhamnogalacturonan II, producing D-galacturonic acid and the resulting fragment GalAβ1-3(2MeXylα1-3Fucα1-4)Rhaα1-3Api <cite>Ndeh2017</cite>. To date, over 33 members of this family have been identified in gut and environmental bacteria and a majority of the encoding microbes (over 80%) belong to the Bacteroidetes phylum <cite>Lombard2014</cite><cite>Cantarel2009</cite>. This phylum is highly represented in human gut microbial populations <cite>Qin2010</cite>.

== Kinetics and Mechanism ==
The kinetic mechanism for this family has not been reported

== Catalytic Residues ==
The catalytic residues for this family have not yet been identified.

== Three-dimensional structures ==
No 3D structure for a member of this family has been currently reported

== Family Firsts ==
;First stereochemistry determination:Currently unknown.
;First catalytic nucleophile identification:Currently unknown.
;First general acid/base residue identification:Currently unknown.
;First 3-D structure:Currently unknown.
== References ==
<biblio>
#Cantarel2009 pmid=18838391
#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].
#Ndeh2017 pmid=28329766
#Qin2010 pmid=20203603
#Lombard2014 pmid=24270786

</biblio>

[[Category:Glycoside Hydrolase Families|GH138]]

User:Didier Ndeh

2018-01-18T09:04:11Z

Didier Ndeh:

[[Image:Blank_user-200px.png|200px|right]]

Didier Ndeh is a postdoctoral research associate at the Institute for Cell and Molecular Biosciences (ICAMB), Newcastle University, UK. Didier completed his PhD at Newcastle University in the year 2013. Since then, Didier’s research has focused on the understanding of host-microbial interactions involving the human gut microbiota. Prior to his PhD, Didier obtained a BSc in Biochemistry from the University of Buea in Cameroon in 2007. He was later offered a UK Commonwealth Scholarship to study for his MSc in Biotechnology at Nottingham Trent University, which he completed in 2009. Didier later worked as a research assistant on an Onchocerciasis Drug Research programme at the Biotechnology Unit of the University of Buea before obtaining another UK Commonwealth Scholarship to study for his PhD at Newcastle University. Didier’s work on complex glycan metabolism by the human gut microbiota has led to the discovery of several novel carbohydrate-acting enzyme families including GH137, GH138, GH139, GH140, GH141, GH142, and GH143 <cite>Ndeh2017</cite>. Didier (in collaboration with Arnaud Basle and Harry J Gilbert) determined the first crystal structure of a GH137 enzyme, specifically the pectin degrading BT1002 fucosidase encoded by the human gut bacterium Bacteroides thetaiotaomicron <cite>Ndeh2017</cite>.

----

References
<biblio>
#Gilbert2008 pmid=18430603
#Ndeh2017 pmid=28329766

</biblio>


[[Category:Contributors|Ndeh,Didier]]