CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 87

2021-02-24T18:02:17Z

Natalie Bamford:

{{UnderConstruction}}
* [[Author]]: ^^^Natalie Bamford^^^
* [[Responsible Curator]]: ^^^Lynne Howell^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM087.html
|}
</div>

[[File:CBM87 figures-01.png|thumb|550px|right|'''Figure 1. Agd3CBM87 from ''A. fumigatus'' adopts a Rossman-like fold.
A.''' The structure of Agd3CBM87 (PDB 6NWZ) consists of three ⍺-helices (H1-H3) and a central β-sheet (indicated with a grey box and numbered from N-terminus to C-terminus). A secondary β-sheet (indicated with a grey line) involves the N-terminus of the sixth and C-terminus of the fifth β-strands of the central sheet. '''B.''' Cartoon representation of the central β-sheet showing the arrangement of strands. Numbering is based on location in the primary sequences from N-terminus to C-terminus. Other secondary structure elements are not shown. '''C.''' The side view of the structure with partial transparency reveals the secondary β-sheet. The strands from the central sheet are numbered. Structure images were created in PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC).]]

== Ligand specificities ==
The CBM87 family was formed in 2020 after the structural and functional characterization of Agd3, a galactosaminogalactan deacetylase involved in ''Aspergillus fumigatus'' biofilm formation <cite>Bamford2020</cite>. This study also resulted in the creation of a novel carbohydrate esterase superfamily, the CE18 family. Functional characterization has focused on the CBM87 module Agd3CBM87. Binding of Agd3CBM87 to soluble galactosaminogalactan from culture supernatants of ''A. fumigatus'' was demonstrated using an ELISA based assay <cite>Bamford2020</cite>. Galactosaminogalactan is a linear heteropolymer of ⍺-1,4-linked D-galactose (Gal) and partially deacetylated N-acetyl-D-galactosamine (GalNAc and GalN) <cite>Fontaine2011 Lee2016</cite>. Using electrospray ionization mass spectrometry (ESI-MS) and synthesized oligosaccharides Agd3CBM87 was found to have higher affinity for ⍺-1,4-(GalN-⍺-1,4-GalNAc)3 as compared to Gal, GalNAc, or GalN homopolymers of the same linkage <cite>Bamford2020</cite>.

== Structural Features ==
CBM87 members are roughly 220 residues in length and are found N-terminal to CE18 domains. The structure of ''A. fumigatus'' Agd3CBM87, was determined using X-ray crystallography to 2.6 Å resolution (PDB 6NWZ) <cite>Bamford2020</cite>. The structure contains a Rossman-like fold (Figure 1A). The central β-sheet consists of seven strands, with the sixth stand running anti-parallel to the other stands (Figure 1B). The fifth and sixth strands rotate at one end to lie almost perpendicular to the primary central sheet and form the centre of a smaller secondary sheet (Figure 1C). The loops at the C-terminal end of the central β-sheet form a cleft that is predicted to be the location of GAG binding (Figure 2A). Surface exposed conserved aromatic residues (W292 and W344 in ''A. fumigatus'' Agd3) were found to contribute to GAG binding (Figure 2B). Binding studies of site directed alanine mutants of W292 and W344 had reduced affinity for GAG produced by ''A. fumigatus'' cultures, supporting this hypothesis <cite>Bamford2020</cite>. The presence of an open binding cleft suggests that CBM87s can bind within a polysaccharide chain and thus may be Type B CBMs.

== Functionalities ==
All CBM87 members, to date, are found N-terminal to CE18 domains (CAZy Database, Feb, 1 2021). The first characterized CE18, Agd3, was found to be important for exopolysaccharide processing and biofilm formation in the fungus ''A. fumigatus'' <cite>Lee2016</cite>. The structure of Agd3 revealed that the CBM87 domain extends the CE18 active site cleft (Figure 2C). When the CBM87 domain was removed from Agd3, the constructs could not be successfully expressed or purified suggesting that the CBM was required for stability of the catalytic domain <cite>Bamford2020</cite>. Due to this, the levels of deacetylation activity could not be compared between the CE18 alone and in the presence of the CBM. Therefore, mutations were made in the CBM to disrupt predicted carbohydrate binding sites. Mutation of the conserved surface exposed aromatics, W292 or W344, to alanine led to decreased activity in a GAG deacetylation assay <cite>Bamford2020</cite>. The CBM87 domain is proposed to contribute important substrate binding sites leading to increase substrate affinity. This was confirmed using mass spectrometry of synthesized hepta-saccharide substrates which revealed a decreased rate of primary deacetylation by the W344A variant. Wild-type Agd3 is capable of deacetylating GAG polymers on multiple subsites <cite>Bamford2020</cite>. Whether other CBM87 members have similar roles in their cognate systems is still to be determined.
[[File:CBM87 figures-02.png|thumb|750px|'''Figure 2. Proposed carbohydrate binding site contains two conserved aromatic residues. A.''' Surface representation of the X-ray crystal structure of Agd3CBM87 with W292 and W344 shown in orange. Dotted line represents the proposed binding site for GAG. '''B.''' Sequence logo representation of a sequence alignment of the 24 family members (as of February 1, 2021). Aromatic residues are coloured in orange and all other amino acids are in black. ''A. fumigatus'' Agd3 W292 aligns with aromatic residues (71% W, 25% Y, and 4% F). Logo was created using WebLogo v3 <cite>Crooks2004</cite>. '''C.''' The CBM87 domain (orange) is C-terminal to the CE18 domain (purple) and contributes to an elongated substrate binding cleft. The CBM binding subsites are coloured as in panel A, and the active site of the CE18 is coloured dark blue. The active site zinc ion is coloured grey.]]

== Family Firsts ==
;First Identified
:The first CBM87 member (Agd3CBM87) to be identified was from ''A. fumigatus'' Agd3 <cite>Bamford2020</cite>.
;First Structural Characterization
:The first crystal structure of a CBM87 was Agd3CBM87 <cite>Bamford2020</cite>.

== References ==
<biblio>
#Bamford2020 pmid=32415073
#Fontaine2011 pmid=22102815
#Lee2016 pmid=27048799
#Crooks2004 pmid=15173120
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM087]]

Carbohydrate Binding Module Family 87

2021-02-24T16:54:08Z

Natalie Bamford:

{{UnderConstruction}}
* [[Author]]: ^^^Natalie Bamford^^^
* [[Responsible Curator]]: ^^^Lynne Howell^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM087.html
|}
</div>

[[File:CBM87 figures-01.png|thumb|550px|right|'''Figure 1. Agd3CBM87 from ''A. fumigatus'' adopts a Rossman-like fold.
A.''' The structure of Agd3CBM87 (PDB 6NWZ) consists of three ⍺-helices (H1-H3) and a central β-sheet (indicated with a grey box and numbered from N-terminus to C-terminus). A secondary β-sheet (indicated with a grey line) involves the N-terminus of the sixth and C-terminus of the fifth β-strands of the central sheet. '''B.''' Cartoon representation of the central β-sheet showing the arrangement of strands. Numbering is based on location in the primary sequences from N-terminus to C-terminus. Other secondary structure elements are not shown. '''C.''' The side view of the structure with partial transparency reveals the secondary β-sheet. The strands from the central sheet are numbered. Structure images were created in PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC).]]

== Ligand specificities ==
The CBM87 family was formed in 2020 after the structural and functional characterization of Agd3, a galactosaminogalactan deacetylase involved in ''Aspergillus fumigatus'' biofilm formation <cite>Bamford2020</cite>. This study also resulted in the creation of a novel carbohydrate esterase superfamily, the CE18 family. Thus, function characterization has focused on the CBM87 module Agd3CBM87. Binding of Agd3CBM87 to soluble galactosaminogalactan from culture supernatants of ''A. fumigatus'' was demonstrated using an ELISA based assay <cite>Bamford2020</cite>. Galactosaminogalactan is a linear heteropolymer of ⍺-1,4-linked D-galactose (Gal) and partially deacetylated N-acetyl-D-galactosamine (GalNAc and GalN) <cite>Fontaine2011 Lee2016</cite>. Using electrospray ionization mass spectrometry (ESI-MS) and synthesized oligosaccharides Agd3CBM87 was found to have higher affinity for ⍺-1,4-(GalN-⍺-1,4-GalNAc)3 as compared to Gal, GalNAc, or GalN homopolymers of the same linkage <cite>Bamford2020</cite>.

== Structural Features ==
CBM87 members are roughly 220 residues in length and are found N-terminal to CE18 domains. The structure of ''A. fumigatus'' Agd3CBM87, was determined using X-ray crystallography to 2.6 Å resolution (PDB 6NWZ) <cite>Bamford2020</cite>. The structure contains a Rossman-like fold (Figure 1A). The central β-sheet consists of seven strands, with the sixth stand running anti-parallel to the other stands (Figure 1B). The fifth and sixth strands rotate at one end to lie almost perpendicular to the primary central sheet and form the centre of a smaller secondary sheet (Figure 1C). The loops at the C-terminal end of the central β-sheet form a cleft that is predicted to be the location of GAG binding (Figure 2A). Surface exposed conserved aromatic residues (W292 and W344 in ''A. fumigatus'' Agd3) were found to contribute to GAG binding (Figure 2B). Binding studies of site directed alanine mutants of W292 and W344 had reduced affinity for GAG produced by ''A. fumigatus'' cultures, supporting this hypothesis <cite>Bamford2020</cite>. The presence of an open binding cleft suggests that CBM87s can bind within a polysaccharide chain and thus may be Type B CBMs.

== Functionalities ==
All CBM87 members, to date, are found N-terminal to CE18 domains (CAZy Database, Feb, 1 2021). The first characterized CE18, Agd3, was found to be important for exopolysaccharide processing and biofilm formation in the fungus ''A. fumigatus'' <cite>Lee2016</cite>. The structure of Agd3 revealed that the CBM87 domain extends the CE18 active site cleft (Figure 2C). When the CBM87 domain was removed from Agd3, the constructs could not be successfully expressed or purified suggesting that the CBM was required for stability of the catalytic domain <cite>Bamford2020</cite>. Due to this, the levels of deacetylation activity could not be compared between the CE18 alone and in the presence of the CBM. Therefore, mutations were made in the CBM to disrupt predicted carbohydrate binding sites. Mutation of the conserved surface exposed aromatics, W292 or W344, to alanine led to decreased activity in a GAG deacetylation assay <cite>Bamford2020</cite>. The CBM87 domain is proposed to contribute important substrate binding sites leading to increase substrate affinity. This was confirmed using mass spectrometry of synthesized hepta-saccharide substrates which revealed a decreased rate of primary deacetylation by the W344A variant. Wild-type Agd3 is capable of deacetylating GAG polymers on multiple subsites <cite>Bamford2020</cite>. Whether other CBM87 members have similar roles in their cognate systems is still to be determined.
[[File:CBM87 figures-02.png|thumb|750px|'''Figure 2. Proposed carbohydrate binding site contains two conserved aromatic residues. A.''' Surface representation of the X-ray crystal structure of Agd3CBM87 with W292 and W344 shown in orange. Dotted line represents the proposed binding site for GAG. '''B.''' Sequence logo representation of a sequence alignment of the 24 family members (as of February 1, 2021). Aromatic residues are coloured in orange and all other amino acids are in black. ''A. fumigatus'' Agd3 W292 aligns with aromatic residues (71% W, 25% Y, and 4% F). Logo was created using WebLogo v3 <cite>Crooks2004</cite>. '''C.''' The CBM87 domain (orange) is C-terminal to the CE18 domain (purple) and contributes to an elongated substrate binding cleft. The CBM binding subsites are coloured as in panel A, and the active site of the CE18 is coloured dark blue. The active site zinc ion is coloured grey.]]

== Family Firsts ==
;First Identified
:The first CBM87 member (Agd3CBM87) to be identified was from ''A. fumigatus'' Agd3 <cite>Bamford2020</cite>.
;First Structural Characterization
:The first crystal structure of a CBM87 was Agd3CBM87 <cite>Bamford2020</cite>.

== References ==
<biblio>
#Bamford2020 pmid=32415073
#Fontaine2011 pmid=22102815
#Lee2016 pmid=27048799
#Crooks2004 pmid=15173120
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM087]]

Carbohydrate Binding Module Family 87

2021-02-24T10:45:37Z

Natalie Bamford:

{{UnderConstruction}}
* [[Author]]: ^^^Natalie Bamford^^^
* [[Responsible Curator]]: ^^^Lynne Howell^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM087.html
|}
</div>

[[File:CBM87 figures-01.png|thumb|550px|right|'''Figure 1. Agd3CBM87 from ''A. fumigatus'' adopts a Rossman-like fold.
A.''' The structure of Agd3CBM87 (PDB 6NWZ) consists of three ⍺-helices (H1-H3) and a central β-sheet (indicated with a grey box and numbered from N-terminus to C-terminus). A secondary β-sheet (indicated with a grey line) involves the N-terminus of the sixth and C-terminus of the fifth β-strands of the central sheet. '''B.''' Cartoon representation of the central β-sheet showing the arrangement of strands. Numbering is based on location in the primary sequences from N-terminus to C-terminus. Other secondary structure elements are not shown. '''C.''' The side view of the structure with partial transparency reveals the secondary β-sheet. The strands from the central sheet are numbered. Structure images were created in PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC).]]

== Ligand specificities ==
The CBM87 family was formed in 2020 after the structural and functional characterization of Agd3, a galactosaminogalactan deacetylase involved in ''Aspergillus fumigatus'' biofilm formation <cite>Bamford2020</cite>. This study also resulted in the creation of a novel carbohydrate esterase superfamily, the CE18 family. Thus, function characterization has focused on the CBM87 module Agd3CBM87. Binding of Agd3CBM87 to soluble galactosaminogalactan from culture supernatants of ''A. fumigatus'' was demonstrated using an ELISA based assay <cite>Bamford2020</cite>. Galactosaminogalactan is a linear heteropolymer of ⍺-1,4-linked D-galactose (Gal) and partially deacetylated N-acetyl-D-galactosamine (GalNAc and GalN) <cite>Fontaine2011 Lee2016</cite>. Using electrospray ionization mass spectrometry (ESI-MS) and synthesized oligosaccharides Agd3CBM87 was found to have higher affinity for ⍺-1,4-(GalN-⍺-1,4-GalNAc)3 as compared to Gal, GalNAc, or GalN homopolymers of the same linkage <cite>Bamford2020</cite>.

== Structural Features ==
CBM87 members are roughly 220 residues in length and are found N-terminal to CE18 domains. The structure of ''A. fumigatus'' Agd3CBM87, was determined using X-ray crystallography to 2.6 Å resolution (PDB 6NWZ) <cite>Bamford2020</cite>. The structure contains a Rossman-like fold (Figure 1A). The central β-sheet consists of seven strands, with the sixth stand running anti-parallel to the other stands (Figure 1B). The fifth and sixth strands rotate at one end to lie almost perpendicular to the primary central sheet and form the centre of a smaller secondary sheet (Figure 1C). The loops at the C-terminal end of the central β-sheet form a cleft that is predicted to be the location of GAG binding (Figure 2A). Surface exposed conserved aromatic residues (W292 and W344 in ''A. fumigatus'' Agd3) were found to contribute to GAG binding (Figure 2B). Binding studies of site directed alanine mutants of W292 and W344 had reduced affinity for GAG produced by ''A. fumigatus'' cultures, supporting this hypothesis <cite>Bamford2020</cite>.

== Functionalities ==
All CBM87 members, to date, are found N-terminal to CE18 domains (CAZy Database, Feb, 1 2021). The first characterized CE18, Agd3, was found to be important for exopolysaccharide processing and biofilm formation in the fungus ''A. fumigatus'' <cite>Lee2016</cite>. The structure of Agd3 revealed that the CBM87 domain extends the CE18 active site cleft (Figure 2C). When the CBM87 domain was removed from Agd3, the constructs could not be successfully expressed or purified suggesting that the CBM was required for stability of the catalytic domain <cite>Bamford2020</cite>. Due to this, the levels of deacetylation activity could not be compared between the CE18 alone and in the presence of the CBM. Therefore, mutations were made in the CBM to disrupt predicted carbohydrate binding sites. Mutation of the conserved surface exposed aromatics, W292 or W344, to alanine led to decreased activity in a GAG deacetylation assay <cite>Bamford2020</cite>. The CBM87 domain is proposed to contribute important substrate binding sites leading to increase substrate affinity. This was confirmed using mass spectrometry of synthesized hepta-saccharide substrates which revealed a decreased rate of primary deacetylation by the W344A variant. Wild-type Agd3 is capable of deacetylating GAG polymers on multiple subsites <cite>Bamford2020</cite>. Whether other CBM87 members have similar roles in their cognate systems is still to be determined.
[[File:CBM87 figures-02.png|thumb|750px|'''Figure 2. Proposed carbohydrate binding site contains two conserved aromatic residues. A.''' Surface representation of the X-ray crystal structure of Agd3CBM87 with W292 and W344 shown in orange. Dotted line represents the proposed binding site for GAG. '''B.''' Sequence logo representation of a sequence alignment of the 24 family members (as of February 1, 2021). Aromatic residues are coloured in orange and all other amino acids are in black. ''A. fumigatus'' Agd3 W292 aligns with aromatic residues (71% W, 25% Y, and 4% F). Logo was created using WebLogo v3 <cite>Crooks2004</cite>. '''C.''' The CBM87 domain (orange) is C-terminal to the CE18 domain (purple) and contributes to an elongated substrate binding cleft. The CBM binding subsites are coloured as in panel A, and the active site of the CE18 is coloured dark blue. The active site zinc ion is coloured grey.]]

== Family Firsts ==
;First Identified
:The first CBM87 member (Agd3CBM87) to be identified was from ''A. fumigatus'' Agd3 <cite>Bamford2020</cite>.
;First Structural Characterization
:The first crystal structure of a CBM87 was Agd3CBM87 <cite>Bamford2020</cite>.

== References ==
<biblio>
#Bamford pmid=32415073
#Fontaine pmid=22102815
#Lee pmid=27048799
#Crooks pmid=15173120
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM087]]

File:CBM87 figures-02.png

2021-02-24T10:22:15Z

Natalie Bamford: Figure 2 for the CBM87 page.

Figure 2 for the CBM87 page.

File:CBM87 figures-01.png

2021-02-24T10:20:08Z

Natalie Bamford: Figure 1 for CBM87 page

Figure 1 for CBM87 page

User:Lynne Howell

2020-09-15T15:53:27Z

Natalie Bamford:

[[Image:Howell_Lynne_new.jpeg|200px|right]]

'''Lynne Howell''' obtained an undergraduate degree in Biophysics from the [https://www.leeds.ac.uk/ University of Leeds] in 1983 and a Ph.D. in Crystallography from the [https://london.ac.uk/ University of London] under the guidance of Prof. Dame Jane Goodfellow. She spent three years as a postdoctoral fellow with [https://petskolab.bwh.harvard.edu/ Professor Gregory Petsko] at the [https://www.mit.edu/ Massachusetts Institute of Technology] before moving to Paris to study with Dr. Roberto Poljak and Dr. André Menez at the [https://www.pasteur.fr/en Institut Pasteur]. After a year as a staff scientist in Paris, Dr. Howell joined [https://www.sickkids.ca/Research/Molecular-Medicine/index.html The Hospital of Sick Children] in Toronto in late 1991 and was cross appointed to the [https://www.utoronto.ca/ University of Toronto] shortly thereafter. She’s a recipient of a Canada Research Chair in Structural Biology and her research is focused on microbial biofilm formation, specifically understanding at the molecular level the exopolysaccharide biosynthetic systems of various bacteria and fungi (more information can be found on the [https://lab.research.sickkids.ca/howell/ laboratory webpage]). This work has involved collaborations with [[User: Anthony Clarke|Prof. Anthony Clarke]], [https://sites.chem.utoronto.ca/nitz/ Prof. Mark Nitz], [https://www.universiteitleiden.nl/en/staffmembers/jeroen-codee#tab-1 Prof. Jeroen Codée], [http://klassengroup.ca/ Prof. John Klassen], [https://www.mcgill.ca/microimm/donald-sheppard Prof. Don Sheppard] and [[User: Joel Weadge|Prof. Joel Weadge]], among others.

Her lab has determined the crystal structures of multiple carbohydrate active enzymes including (but not limited to):

*[[Glycoside Hydrolase Family 39|GH39]] ''Pseudomonas aeruginosa'' PslG, PSL polysaccharide hydrolase <cite>Baker2015</cite>
*[[Glycoside Hydrolase Family 47|GH47]] ''Penicillium citrinum'' α-1,2-mannosidase <cite>Lobsanov2002</cite>
*[[Glycoside Hydrolase Family 114|GH114]] ''Aspergillus fumigatus'' Ega3, an α-1,4-galactosaminidase <cite>Bamford2019</cite>
*[[Glycoside Hydrolase Family 135|GH135]] ''Aspergillus clavatus'' Sph3, an α-1,4-N-acetylgalactosaminidase  <cite>Bamford2015</cite>
*[[Glycoside Hydrolase Family 153|GH153]] ''Bordetella bronchiseptica'' PgaB (C-terminal domain), a poly-β-1,6-D-glucosamine hydrolase <cite>Little2018</cite>
*[[Glycoside Hydrolase Family 166|GH166]] ''Pseudomonas aeruginosa'' PelA (N-terminal domain), α-1,4-N-acetylgalactosaminidase <cite>LeMauff2019</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Ammonifex degensii'' IcaB, a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2014</cite> 
*[[Carbohydrate Esterase Family 4|CE4]] ''Bordetella bronchiseptica'' PgaB (N-terminal domain), a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2015</cite>
*[[Carbohydrate Esterase Family 4|CE4]]/[[Glycoside Hydrolase Family 153|GH153]] ''Escherichia coli'' PgaB, a poly-β-1,6-D-glucosamine deacetylase and hydrolase <cite>Little2014b</cite>
*[[CE18]] and [[Carbohydrate Binding Module Family 87|CBM87]] ''Aspergillus fumigatus'' Agd3, an α-1,4-N-acetylgalactosaminidase deacetylase <cite>Bamford2020</cite> 
*PL5 ''Pseudomonas aeruginosa'' AlgL, (no associated paper)
*[[Polysaccharide Lyase Family 7|PL7]] ''Klebsiella pneumoniae'' Alginate lyase, (no associated paper)
*GT15 ''Saccharomyces cerevisiae'' ⍺-1,2-monnosyltransferase complex Kre2p/Mnt1p <cite>Lobsanov2004</cite>
*''Pseudomonas syringae'' AlgG, β-D-mannuronate (alginate) C5-epimerase <cite>Wolfram2014</cite>
*''Pseudomonas putida'' AlgJ, involved in alginate O-acetylation <cite>Baker2014</cite>
*''Pseudomonas aeruginosa'' AlgX, alginate O-acetylase <cite>Riley2013</cite>
*''Pseudomonas protegens'' PelX, a C-4 epimerase that interconverts UDP-GalNAc and UDP-GlcNAc <cite>Marmont2020</cite>
*''Bacillus cereus'' PatB1, peptidoglycan O-acetylase <cite>Sychantha2018</cite>
*''Streptococcus pneumoniae'' OatA, peptidoglycan O-acetylase <cite>Sychantha2017</cite>
*''Staphylococcus aureus'' OatA, peptidoglycan O-acetylase <cite>Jones2020</cite>

----

<biblio>
#Baker2015 pmid=26424791
#Lobsanov2002 pmid=11714724
#Bamford2019 pmid=31416836
#Bamford2015 pmid=26342082
#Little2018 pmid=29684093
#LeMauff2019 pmid=31167793
#Little2014 pmid=25359777
#Little2015 pmid=26203190
#Little2014b pmid=24994902
#Bamford2020 pmid=32415073
#Lobsanov2004 pmid=14752117
#Wolfram2014 pmid=24398681
#Baker2014 pmid=25165982
#Riley2013 pmid=23779107
#Marmont2020 pmid=32601062
#Sychantha2018 pmid=29083419
#Sychantha2018 pmid=29077761
#Jones2020 pmid=32350117

</biblio>


[[Category:Contributors|Howell,Lynne]]

File:Howell Lynne new.jpeg

2020-09-15T15:52:08Z

Natalie Bamford:

User:Lynne Howell

2020-09-15T10:03:04Z

Natalie Bamford:

[[Image:LynneHowell.jpg|200px|right]]

'''Lynne Howell''' obtained an undergraduate degree in Biophysics from the [https://www.leeds.ac.uk/ University of Leeds] in 1983 and a Ph.D. in Crystallography from the [https://london.ac.uk/ University of London] under the guidance of Prof. Dame Jane Goodfellow. She spent three years as a postdoctoral fellow with [https://petskolab.bwh.harvard.edu/ Professor Gregory Petsko] at the [https://www.mit.edu/ Massachusetts Institute of Technology] before moving to Paris to study with Dr. Roberto Poljak and Dr. André Menez at the [https://www.pasteur.fr/en Institut Pasteur]. After a year as a staff scientist in Paris, Dr. Howell joined [https://www.sickkids.ca/Research/Molecular-Medicine/index.html The Hospital of Sick Children] in Toronto in late 1991 and was cross appointed to the [https://www.utoronto.ca/ University of Toronto] shortly thereafter. She’s a recipient of a Canada Research Chair in Structural Biology and her research is focused on microbial biofilm formation, specifically understanding at the molecular level the exopolysaccharide biosynthetic systems of various bacteria and fungi (more information can be found on the [https://lab.research.sickkids.ca/howell/ laboratory webpage]). This work has involved collaborations with [[User: Anthony Clarke|Prof. Anthony Clarke]], [https://sites.chem.utoronto.ca/nitz/ Prof. Mark Nitz], [https://www.universiteitleiden.nl/en/staffmembers/jeroen-codee#tab-1 Prof. Jeroen Codée], [http://klassengroup.ca/ Prof. John Klassen], [https://www.mcgill.ca/microimm/donald-sheppard Prof. Don Sheppard] and [[User: Joel Weadge|Prof. Joel Weadge]], among others.

Her lab has determined the crystal structures of multiple carbohydrate active enzymes including (but not limited to):

*[[Glycoside Hydrolase Family 39|GH39]] ''Pseudomonas aeruginosa'' PslG, PSL polysaccharide hydrolase <cite>Baker2015</cite>
*[[Glycoside Hydrolase Family 47|GH47]] ''Penicillium citrinum'' α-1,2-mannosidase <cite>Lobsanov2002</cite>
*[[Glycoside Hydrolase Family 114|GH114]] ''Aspergillus fumigatus'' Ega3, an α-1,4-galactosaminidase <cite>Bamford2019</cite>
*[[Glycoside Hydrolase Family 135|GH135]] ''Aspergillus clavatus'' Sph3, an α-1,4-N-acetylgalactosaminidase <cite>Bamford2015</cite>
*[[Glycoside Hydrolase Family 153|GH153]] ''Bordetella bronchiseptica'' PgaB (C-terminal domain), a poly-β-1,6-D-glucosamine hydrolase <cite>Little2018</cite>
*[[Glycoside Hydrolase Family 166|GH166]] ''Pseudomonas aeruginosa'' PelA (N-terminal domain), α-1,4-N-acetylgalactosaminidase <cite>LeMauff2019</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Ammonifex degensii'' IcaB, a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2014</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Bordetella bronchiseptica'' PgaB (N-terminal domain), a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2015</cite>
*[[Carbohydrate Esterase Family 4|CE4]]/[[Glycoside Hydrolase Family 153|GH153]] ''Escherichia coli'' PgaB, a poly-β-1,6-D-glucosamine deacetylase and hydrolase <cite>Little2014b</cite>
*[[CE18]] and [[Carbohydrate Binding Module Family 87|CBM87]] ''Aspergillus fumigatus'' Agd3, an α-1,4-N-acetylgalactosaminidase deacetylase <cite>Bamford2020</cite>
*PL5 ''Pseudomonas aeruginosa'' AlgL, (no associated paper)
*[[Polysaccharide Lyase Family 7|PL7]] ''Klebsiella pneumoniae'' Alginate lyase, (no associated paper)
*GT15 ''Saccharomyces cerevisiae'' ⍺-1,2-monnosyltransferase complex Kre2p/Mnt1p <cite>Lobsanov2004</cite>
*''Pseudomonas syringae'' AlgG, β-D-mannuronate (alginate) C5-epimerase <cite>Wolfram2014</cite>
*''Pseudomonas putida'' AlgJ, involved in alginate O-acetylation <cite>Baker2014</cite>
*''Pseudomonas aeruginosa'' AlgX, alginate O-acetylase <cite>Riley2013</cite>
*''Pseudomonas protegens'' PelX, a C-4 epimerase that interconverts UDP-GalNAc and UDP-GlcNAc <cite>Marmont2020</cite>
*''Bacillus cereus'' PatB1, peptidoglycan O-acetylase <cite>Sychantha2018</cite>
*''Streptococcus pneumoniae'' OatA, peptidoglycan O-acetylase <cite>Sychantha2017</cite>
*''Staphylococcus aureus'' OatA, peptidoglycan O-acetylase <cite>Jones2020</cite>

----

<biblio>
#Baker2015 pmid=26424791
#Lobsanov2002 pmid=11714724
#Bamford2019 pmid=31416836
#Bamford2015 pmid=26342082
#Little2018 pmid=29684093
#LeMauff2019 pmid=31167793
#Little2014 pmid=25359777
#Little2015 pmid=26203190
#Little2014b pmid=24994902
#Bamford2020 pmid=32415073
#Lobsanov2004 pmid=14752117
#Wolfram2014 pmid=24398681
#Baker2014 pmid=25165982
#Riley2013 pmid=23779107
#Marmont2020 pmid=32601062
#Sychantha2018 pmid=29083419
#Sychantha2018 pmid=29077761
#Jones2020 pmid=32350117

</biblio>


[[Category:Contributors|Howell,Lynne]]

User:Lynne Howell

2020-09-15T09:11:29Z

Natalie Bamford:

[[Image:LynneHowell.jpg|200px|right]]

'''Lynne Howell''' obtained an undergraduate degree in Biophysics from the [https://www.leeds.ac.uk/ University of Leeds] in 1983 and a Ph.D. in Crystallography from the [https://london.ac.uk/ University of London] under the guidance of Prof. Dame Jane Goodfellow. She spent three years as a postdoctoral fellow with [https://petskolab.bwh.harvard.edu/ Professor Gregory Petsko] at the [https://www.mit.edu/ Massachusetts Institute of Technology] before moving to Paris to study with Dr. Roberto Poljak and Dr. André Menez at the [https://www.pasteur.fr/en Institut Pasteur]. After a year as a staff scientist in Paris, Dr. Howell joined [https://www.sickkids.ca/Research/Molecular-Medicine/index.html The Hospital of Sick Children] in Toronto in late 1991 and was cross appointed to the [https://www.utoronto.ca/ University of Toronto] shortly thereafter. She’s a recipient of a Canada Research Chair in Structural Biology and her research is focused on microbial biofilm formation, specifically understanding at the molecular level the exopolysaccharide biosynthetic systems of various bacteria and fungi (more information can be found on the [https://lab.research.sickkids.ca/howell/ laboratory webpage]). This work has involved collaborations with [[User: Anthony Clarke|Prof. Anthony Clarke]], [https://sites.chem.utoronto.ca/nitz/ Prof. Mark Nitz], [https://www.universiteitleiden.nl/en/staffmembers/jeroen-codee#tab-1 Prof. Jeroen Codée], [http://klassengroup.ca/ Prof. John Klassen], [https://www.mcgill.ca/microimm/donald-sheppard Prof. Don Sheppard] and [[User: Joel Weadge|Prof. Joel Weadge]], among others.

Her lab has determined the crystal structures of multiple carbohydrate active enzymes including (but not limited to):

*[[Glycoside Hydrolase Family 39|GH39]] ''Pseudomonas aeruginosa'' PslG, PSL polysaccharide hydrolase <cite>Baker2015</cite>
*[[Glycoside Hydrolase Family 47|GH47]] ''Penicillium citrinum'' α-1,2-mannosidase <cite>Lobsanov2002</cite>
*[[Glycoside Hydrolase Family 114|GH114]] ''Aspergillus fumigatus'' Ega3, an α-1,4-galactosaminidase <cite>Bamford2019</cite>
*[[Glycoside Hydrolase Family 135|GH135]] ''Aspergillus clavatus'' Sph3, an α-1,4-N-acetylgalactosaminidase <cite>Bamford2015</cite>
*[[Glycoside Hydrolase Family 153|GH153]] ''Bordetella bronchiseptica'' PgaB (C-terminal domain), a poly-β-1,6-D-glucosamine hydrolase <cite>Little2018</cite>
*[[Glycoside Hydrolase Family 166|GH166]] ''Pseudomonas aeruginosa'' PelA (N-terminal domain), α-1,4-N-acetylgalactosaminidase <cite>LeMauff2019</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Ammonifex degensii'' IcaB, a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2014</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Bordetella bronchiseptica'' PgaB (N-terminal domain), a poly-β-1,6-N-acetyl-D-glucosamine deacetylase <cite>Little2018</cite>
*[[Carbohydrate Esterase Family 4|CE4]]/[[Glycoside Hydrolase Family 153|GH153]] ''Escherichia coli'' PgaB, a poly-β-1,6-D-glucosamine deacetylase and hydrolase <cite>Little2014b</cite>
*[[CE18]] and [[Carbohydrate Binding Module Family 87|CBM87]] ''Aspergillus fumigatus'' Agd3, an α-1,4-N-acetylgalactosaminidase deacetylase <cite>Bamford2020</cite>
*PL5 ''Pseudomonas aeruginosa'' AlgL, (no associated paper)
*[[Polysaccharide Lyase Family 7|PL7]] ''Klebsiella pneumoniae'' Alginate lyase, (no associated paper)
*GT15 ''Saccharomyces cerevisiae'' ⍺-1,2-monnosyltransferase complex Kre2p/Mnt1p <cite>Lobsanov2004</cite>
*''Pseudomonas syringae'' AlgG, β-D-mannuronate (alginate) C5-epimerase <cite>Wolfram2014</cite>
*''Pseudomonas putida'' AlgJ, involved in alginate O-acetylation <cite>Baker2014</cite>
*''Pseudomonas aeruginosa'' AlgX, alginate O-acetylase <cite>Riley2013</cite>
*''Pseudomonas protegens'' PelX, a C-4 epimerase that interconverts UDP-GalNAc and UDP-GlcNAc <cite>Marmont2020</cite>
*''Bacillus cereus'' PatB1, peptidoglycan O-acetylase <cite>Sychantha2018</cite>
*''Streptococcus pneumoniae'' OatA, peptidoglycan O-acetylase <cite>Sychantha2017</cite>
*''Staphylococcus aureus'' OatA, peptidoglycan O-acetylase <cite>Jones2020</cite>

----

<biblio>
#Baker2015 pmid=26424791
#Lobsanov2002 pmid=11714724
#Bamford2019 pmid=31416836
#Bamford2015 pmid=26342082
#Little2018 pmid=29684093
#LeMauff2019 pmid=31167793
#Little2014 pmid=25359777
#Little2018 pmid=29684093
#Little2014b pmid=24994902
#Bamford2020 pmid=32415073
#Lobsanov2004 pmid=14752117
#Wolfram2014 pmid=24398681
#Baker2014 pmid=25165982
#Riley2013 pmid=23779107
#Marmont2020 pmid=32601062
#Sychantha2018 pmid=29083419
#Sychantha2018 pmid=29077761
#Jones2020 pmid=32350117

</biblio>


[[Category:Contributors|Howell,Lynne]]

File:LynneHowell.jpg

2020-09-15T09:10:58Z

Natalie Bamford:

User:Natalie Bamford

2020-05-29T12:43:59Z

Natalie Bamford:

[[File:NatalieBamford.png|200px|right]]

'''Natalie Bamford''' did her undergraduate degree at the [http://biochemistry.utoronto.ca/ University of Toronto in Biochemistry]. She then completed her graduate work supervised by [[User: Lynne Howell|Lynne Howell]] conducting research out of the Hospital for Sick Children. This led to her obtaining her PhD in Biochemistry from the University of Toronto in 2019. Her research focused on the carbohydrate active enzymes involved in exopolysaccharide production used by microbes in biofilm formation. This included structural and biochemical characterization of glycoside hydrolases <cite>Bamford2015 Snarr2017 Little2018 LeMauff2019 Bamford2019</cite>, carbohydrate esterases <cite>Little2014 Little2014b Little2015 Bamford2020</cite>, and a carbohydrate binding module <cite>Bamford2020</cite>. Natalie's studies helped in the creation of three GH families ([[Glycoside Hydrolase Family 135|GH135]], [[Glycoside Hydrolase Family 153|GH153]], [http://www.cazy.org/GH166.html GH166]), one CE family (CE18) and one CBM family ([[Carbohydrate Binding Module Family 87|CBM87]]). She is now a postdoctoral fellow at the University of Dundee with [https://www.lifesci.dundee.ac.uk/people/nicola-stanley-wall Nicola Stanley-Wall].

She has aided in the determination of crystal structures including:
*[[Glycoside Hydrolase Family 114|GH114]] ''Aspergillus fumigatus'' Ega3, an α-1,4-galactosaminidase <cite>Bamford2019</cite>
*[[Glycoside Hydrolase Family 135|GH135]] ''Aspergillus clavatus'' Sph3, an α-1,4-''N''-acetylgalactosaminidase <cite>Bamford2015</cite>
*[[Glycoside Hydrolase Family 153|GH153]] ''Bordetella bronchiseptica'' PgaB, a poly-β-1,6-D-glucosamine hydrolase <cite>Little2018</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Ammonifex degensii'' IcaB, a poly-β-1,6-''N''-acetyl-D-glucosamine deacetylase <cite>Little2014b</cite>
*[http://www.cazy.org/CE18.html CE18] and [[Carbohydrate Binding Module Family 87|CBM87]] ''Aspergillus fumigatus'' Agd3, an α-1,4-''N''-acetylgalactosaminidase deacetylase <cite>Bamford2020</cite>

----

<biblio>
#Bamford2015 pmid:26342082
#Snarr2017 pmid:28634301
#Little2018 pmid:29684093
#LeMauff2019 pmid:31167793
#Bamford2019 pmid:31416836
#Little2014 pmid:24994902
#Little2014b pmid:25359777
#Little2015 pmid:26203190
#Bamford2020 pmid:32415073
</biblio>


[[Category:Contributors|Bamford,Natalie]]

User:Natalie Bamford

2020-05-29T12:13:36Z

Natalie Bamford:

[[File:NatalieBamford.png|200px|right]]

'''Natalie Bamford''' did her undergraduate degree at the [http://biochemistry.utoronto.ca/ University of Toronto in Biochemistry]. She then completed her graduate work supervised by [[User: Lynne Howell|Lynne Howell]] conducting research out of the Hospital for Sick Children. This led to her obtaining her PhD in Biochemistry from the University of Toronto in 2019. Her research focused on the carbohydrate active enzymes involved in exopolysaccharide production used by microbes in biofilm formation. This included structural and biochemical characterization of glycoside hydrolases <cite>Bamford2015 Snarr2017 Little2018 LeMauff2019 Bamford2019</cite>, carbohydrate esterase <cite>Little2014 Little2014b Little2015 Bamford2020</cite>, and a carbohydrate binding module <cite>Bamford2020</cite>. Natalie's studies helped in the creation of three GH families ([[Glycoside Hydrolase Family 135|GH135]], [[Glycoside Hydrolase Family 153|GH153]], [http://www.cazy.org/GH166.html GH166]), one CE family (CE18) and one CBM family ([[Carbohydrate Binding Module Family 87|CBM87]]). She is now a postdoctoral fellow at the University of Dundee with [https://www.lifesci.dundee.ac.uk/people/nicola-stanley-wall Nicola Stanley-Wall].

She has aided in the determination of crystal structures including:
*[[Glycoside Hydrolase Family 114|GH114]] ''Aspergillus fumigatus'' Ega3, an α-1,4-galactosaminidase <cite>Bamford2019</cite>
*[[Glycoside Hydrolase Family 135|GH135]] ''Aspergillus clavatus'' Sph3, an α-1,4-''N''-acetylgalactosaminidase <cite>Bamford2015</cite>
*[[Glycoside Hydrolase Family 153|GH153]] ''Bordetella bronchiseptica'' PgaB, a poly-β-1,6-D-glucosamine hydrolase <cite>Little2018</cite>
*[[Carbohydrate Esterase Family 4|CE4]] ''Ammonifex degensii'' IcaB, a poly-β-1,6-''N''-acetyl-D-glucosamine deacetylase <cite>Little2014b</cite>
*[http://www.cazy.org/CE18.html CE18] and [[Carbohydrate Binding Module Family 87|CBM87]] ''Aspergillus fumigatus'' Agd3, an α-1,4-''N''-acetylgalactosaminidase deacetylase <cite>Bamford2020</cite>

----

<biblio>
#Bamford2015 pmid:26342082
#Snarr2017 pmid:28634301
#Little2018 pmid:29684093
#LeMauff2019 pmid:31167793
#Bamford2019 pmid:31416836
#Little2014 pmid:24994902
#Little2014b pmid:25359777
#Little2015 pmid:26203190
#Bamford2020 pmid:32415073
</biblio>


[[Category:Contributors|Bamford,Natalie]]

File:NatalieBamford.png

2020-05-29T09:33:41Z

Natalie Bamford: