CAZypedia - User contributions [en-ca]

User:Alex Anderson

2024-04-23T20:18:44Z

Alex Anderson:

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

Dr. Anderson recieved his BSc (2017) and MSc (2019) from Wilfrid Laurier University (Canada) in the lab of Dr. [[User:Joel Weadge|Joel Weadge]], alongside [[User:Michael Suits|Michael Suits]], at WLU where he studied the structure and function of the cellulose phosphoethanolamine transferase BcsG in ''E. coli''. Dr. Anderson received his Ph.D. from the University of Guelph in 2024 under the supervision of Dr. [[User:Anthony Clarke|Anthony Clarke]] where he worked on the mechanism of peptidoglycan ''O''-acetyltransferases. Dr. Anderson is presently a postdoctoral fellow at McMaster University in the lab of Dr. John Whitney where he studies Type VI-secreted polymorphic toxins that target carbohydrate structures.

Dr. Anderson and colleagues have demonstrated the structures of:

CAZy-unclassified ''Escherichia coli'' phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH5]] ''Clostridioides difficile'' endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2020</cite>

CAZy-unclassified ''Campylobacter jejuni'' peptidoglycan O-acetyltransferase PatB (8TLB)

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2020 pmid=33264329
</biblio>


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2020-12-04T03:29:51Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University (Canada) in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex completed his MSc in 2019 the lab of Dr. ^^^Joel Weadge^^^, alongside ^^^Michael Suits^^^, at WLU where he studied the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. Alex is currently a PhD candidate in the lab of Dr. ^^^Anthony Clarke^^^ at the University of Guelph where he studies the mechanism of peptidoglycan O-acetylation in Gram-negative bacteria.

Alex and colleagues have demonstrated the structures of:

CAZy-unclassified ''Escherichia coli'' phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH5]] ''Clostridioides difficile'' endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2020</cite>

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2020 pmid=33264329
</biblio>


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2020-10-30T19:58:48Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University (Canada) in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex completed his MSc in 2019 the lab of Dr. ^^^Joel Weadge^^^, alongside ^^^Michael Suits^^^, at WLU where he studied the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. Alex is currently a PhD candidate in the lab of Dr. ^^^Anthony Clarke^^^ at the University of Guelph where he studies the mechanism of peptidoglycan O-acetylation in Gram-negative bacteria.

Alex and colleagues have demonstrated the structures of:

CAZy-unclassified ''Escherichia coli'' phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH5]] ''Clostridioides difficile'' endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2019</cite>

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2019 Scott W, Lowrance B, Anderson AC, Weadge JT. Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ. bioRxiv837344; https://doi.org/10.1101/837344
</biblio>


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2020-05-21T17:39:27Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University (Canada) in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex completed his MSc in 2019 the lab of Dr. ^^^Joel Weadge^^^, alongside ^^^Michael Suits^^^, at WLU where he studied the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. Alex is currently a PhD student in the lab of Dr. ^^^Anthony Clarke^^^ at the University of Guelph where he studies the mechanism of peptidoglycan O-acetylation in Gram-negative bacteria.

Alex and colleagues have demonstrated the structures of:

CAZy-unclassified ''Escherichia coli'' phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH5]] ''Clostridioides difficile'' endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2019</cite>

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2019 Scott W, Lowrance B, Anderson AC, Weadge JT. Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ. bioRxiv837344; https://doi.org/10.1101/837344
</biblio>


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2020-05-21T16:49:18Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University (Canada) in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex completed his MSc in 2019 the lab of Dr. ^^^Joel Weadge^^^, alongside ^^^Michael Suits^^^, at WLU where he studied the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. Alex is currently a PhD student in the lab of Anthony Clarke at the University of Guelph where he studies the mechanism of peptidoglycan O-acetylation in Gram-negative bacteria.

Alex and colleagues have demonstrated the structures of:

CAZy-unclassified ''Escherichia coli'' phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH5]] ''Clostridioides difficile'' endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2019</cite>

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2019 Scott W, Lowrance B, Anderson AC, Weadge JT. Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ. bioRxiv837344; https://doi.org/10.1101/837344
</biblio>


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2020-05-21T16:47:53Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University (Canada) in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex completed his MSc in 2019 the lab of Dr. ^^^Joel Weadge^^^, alongside ^^^Michael Suits^^^, at WLU where he studied the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. Alex is currently a PhD student in the lab of Anthony Clarke at the University of Guelph where he studies the mechanism of peptidoglycan O-acetylation in Gram-negative bacteria.

Alex and colleagues have demonstrated the structures of:

CAZy-unclassified Escherichia coli phosphoethanolamine transferase BcsG (6PCZ/6PD0) <cite>Anderson2020</cite>

[[GH8]] Clostridoides difficile endo-β-glucanase CcsZ (6UJE/6UJF) <cite>Scott2019</cite>

----

<biblio>
#Anderson2020 pmid=32152228
#Scott2019 Scott W, Lowrance B, Anderson AC, Weadge JT. Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ. bioRxiv837344; https://doi.org/10.1101/837344
</biblio>


[[Category:Contributors|Anderson,Alex]]

Carbohydrate Esterase Family 9

2019-02-28T17:21:49Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 9'''
|-
|'''Acid/alcohol sugar substrate'''
|Alcohol
|-
|'''Metal-dependent'''
|Yes
|-
|'''Active site residues'''
|Known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE9.html
|}
</div>


== Substrate specificities ==
CE family 9 esterases catalyze the deacetylation of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate. This reaction has been demonstrated to be important for both amino sugar metabolism and peptidoglycan cell wall recycling in bacteria <cite>#Park2001</cite>. Experimental substrate specificity profiles for two CE9 enzymes demonstrated that they are active on other structurally similar amino sugar phosphates, such as N-acetyl- galactosamine-6-phosphate and N-acetyl-mannosamine-6-phosphate, although their reported affinities are 40-fold and 6-fold lower, respectively <cite>#Ahangar2018</cite>.

== Kinetics and Mechanism ==
Removal of the acetate group by CE9 enzymes is proposed to be carried out by nucleophilic attack of the acetate carbon by a metal-bound hydroxide ion <cite>#Vincent2004</cite>. A proton is donated to the amine leaving group by a catalytic acid residue, and the tetrahedral transition state is stabilized either by the interaction of a second metal ion with the polarized carbonyl oxygen <cite>#Vincent2004</cite>, or by a catalytic base residue where a second metal ion is absent from the active site, although the latter has not been experimentally demonstrated.

== Catalytic Residues ==
The precise mechanism of catalysis has yet to be elucidated for CE9, although several conserved features in the active sites of resolved CE9 members suggest they play an important role in their function. In ''Bacillus subtilis'' NagA, ''Thermotoga maritima'' NagA, and ''Mycobacterium smegmatis'' NagA, four histidine residues are responsible for coordination of the metal cofactor(s), along with a glutamate in ''B. subtilis'' and ''T. maritima'', and an aspartic acid in ''M. smegmatis'' <cite>#Vincent2004,#Osipiuk2002,#Ferreira2006</cite>. The ''Escherichia coli'' NagA appears to have a glutamine, gluatamate, asparagine and an aspartate as the coordination enviroment, although this structure crystallized as the apoenzyme, and so this configuration is uncertain <cite>#Ferreira2006</cite>. In all structures, a strictly conserved aspartic acid residue is then thought to serve as a base to activate a water molecule, and then as an acid to protonate the leaving amine <cite>#Vincent2004</cite>.

== Three-dimensional structures ==
The resolved structures of CE9 enzymes demonstrate variability in their organization and metal binding. For example, ''Vibrio cholerae'' NagA and ''B. subtilis'' NagA form dimers in their biologically relevant assemblies <cite>#Osipiuk2002, #Vincent2004</cite>, while ''E. coli'' NagA forms a tetramer <cite>#Ferreira2006</cite>. Additionally, these same enzymes appear to contain a Ni2+ ion <cite>#Osipiuk2002</cite>, two Fe2+ ions <cite>#Vincent2004</cite>, and a Zn2+ ion <cite>#Ferreira2006</cite> in their active sites, respectively. All resolved CE9 enzymes contain a distorted (β/α)8 fold containing the active site, and a small β-sheet domain comprising residues from both the N- and C-termini.

== Family Firsts ==
;First characterized: The ''E. coli'' N-acetylglucosamine-6-phosphate deacetylase NagA was the first CE9 enzyme to have its activity demonstrated <cite>#White1967</cite>.
;First 3-D structure: The first structure of a CE9 enzyme published was the ''B. subtilis'' NagA, containing a two-Fe2+ catalytic center <cite>#Vincent2004</cite>.
;First mechanistic insight: The structure of the ''B. subtilis'' NagA enzyme was reported with a bound N-acetylglucosamine-6-phosphate molecule and provided evidence for the proposed metal-dependent catalytic mechanism <cite>#Vincent2004</cite>.

== References ==
<biblio>
#Park2001 pmid=11395446
#Osipiuk2002 PDB entry [{{PDBlink}}3EGJ 3egj], unpublished.
#Vincent2004 pmid=14557261
#Ferreira2006 pmid=16630633
#Ahangar2018 pmid=29728457
#White1967 pmid=4861885
</biblio>

[[Category:Carbohydrate Esterase Families|CE009]]

Carbohydrate Esterase Family 4

2019-01-16T20:57:09Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 4'''
|-
|'''Acid/alcohol sugar substrate'''
|Alcohol
|-
|'''Metal-dependent'''
|Yes (with exception)
|-
|'''Active site residues'''
|Known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE4.html
|}
</div>


== Substrate specificities ==
CE family 4 esterases catalyze the de-acylation of polysaccharides. Known activities of CE family 4 members include acetylxylan esterases, chitin deacetylases, chitooligosaccharide deacetylases, and peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, PdaA from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.

== Kinetics and Mechanism ==
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn2+, but Co2+ is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.

== Catalytic Residues ==
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn2+ ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co2+ in place of Zn2+'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co2+ in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.

== Three-dimensional structures ==
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)7 fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).

== Family Firsts ==
;First characterized: TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.
;First mechanistic insight: The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>.
;First 3-D structure: The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)7 fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.

== References ==
<biblio>
#Hayhurst2008 pmid=18784364
#Fukushima2005 pmid=15687192
#Blair2005 pmid=16221761
#Taylor2006 pmid=16431911
#Andres2014 pmid=24810719
#Arnaouteli2015 pmid=25825488
#Deng2009 pmid=18978064
#Nishiyama2013 pmid=23275162
#John1993 pmid=8421697
#Blair2004 pmid=15251431

</biblio>

[[Category:Carbohydrate Esterase Families|CE004]]

User:Alex Anderson

2018-08-31T18:06:32Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex is currently a Masters candidate in the lab of Dr. Joel Weadge, alongside ^^^Michael Suits^^^, at WLU where he studies the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens. His most recent work includes the structure of the cellulose phosphoethanolamine transferase BcsG, essential for extracellular matrix assembly in ''E.coli'' K-12 and ''S. enterica''.


[[Category:Contributors|Anderson,Alex]]

Carbohydrate Esterase Family 4

2018-08-31T18:04:01Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 4'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE4.html
|}
</div>


== Substrate specificities ==
CE family 4 esterases catalyze the de-acylation of polysaccharides. Known activities of CE family 4 members include acetylxylan esterases, chitin deacetylases, chitooligosaccharide deacetylases, and peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, PdaA from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.

== Kinetics and Mechanism ==
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn2+, but Co2+ is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.

== Catalytic Residues ==
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn2+ ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co2+ in place of Zn2+'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co2+ in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.

== Three-dimensional structures ==
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)7 fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).

== Family Firsts ==
;First characterized
TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.
;First mechanistic insight
The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>.
;First 3-D structure
The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)7 fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.

== References ==
<biblio>
#Hayhurst2008 pmid=18784364
#Fukushima2005 pmid=15687192
#Blair2005 pmid=16221761
#Taylor2006 pmid=16431911
#Andres2014 pmid=24810719
#Arnaouteli2015 pmid=25825488
#Deng2009 pmid=18978064
#Nishiyama2013 pmid=23275162
#John1993 pmid=8421697
#Blair2004 pmid=15251431

</biblio>

[[Category:Carbohydrate Esterase Families|CE004]]

Carbohydrate Esterase Family 9

2018-08-27T17:51:01Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 9'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE9.html
|}
</div>


== Substrate specificities ==
CE family 9 esterases catalyze the deacetylation of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate. This reaction has been demonstrated to be important for both amino sugar metabolism and peptidoglycan cell wall recycling in bacteria <cite>#Park2001</cite>. Experimental substrate specificity profiles for two CE9 enzymes demonstrated that they are active on other structurally similar amino sugar phosphates, such as N-acetyl- galactosamine-6-phosphate and N-acetyl-mannosamine-6-phosphate, although their reported affinities are 40-fold and 6-fold lower, respectively <cite>#Ahangar2018</cite>.

== Kinetics and Mechanism ==
Removal of the acetate group by CE9 enzymes is proposed to be carried out by nucleophilic attack of the acetate carbon by a metal-bound hydroxide ion <cite>#Vincent2004</cite>. A proton is donated to the amine leaving group by a catalytic acid residue, and the tetrahedral transition state is stabilized either by the interaction of a second metal ion with the polarized carbonyl oxygen <cite>#Vincent2004</cite>, or by a catalytic base residue where a second metal ion is absent from the active site, although the latter has not been experimentally demonstrated.

== Catalytic Residues ==
The precise mechanism of catalysis has yet to be elucidated for CE9, although several conserved features in the active sites of resolved CE9 members suggest they play an important role in their function. In ''Bacillus subtilis'' NagA, ''Thermotoga maritima'' NagA, and ''Mycobacterium smegmatis'' NagA, four histidine residues are responsible for coordination of the metal cofactor(s), along with a glutamate in ''B. subtilis'' and ''T. maritima'', and an aspartic acid in ''M. smegmatis'' <cite>#Vincent2004,#Osipiuk2002,#Ferreira2006</cite>. The ''Escherichia coli'' NagA appears to have a glutamine, gluatamate, asparagine and an aspartate as the coordination enviroment, although this structure crystallized as the apoenzyme, and so this configuration is uncertain <cite>#Ferreira2006</cite>. In all structures, a strictly conserved aspartic acid residue is then thought to serve as a base to activate a water molecule, and then as an acid to protonate the leaving amine <cite>#Vincent2004</cite>.

== Three-dimensional structures ==
The resolved structures of CE9 enzymes demonstrate variability in their organization and metal binding. For example, ''Vibrio cholerae'' NagA and ''B. subtilis'' NagA form dimers in their biologically relevant assemblies <cite>#Osipiuk2002, #Vincent2004</cite>, while ''E. coli'' NagA forms a tetramer <cite>#Ferreira2006</cite>. Additionally, these same enzymes appear to contain a Ni2+ ion <cite>#Osipiuk2002</cite>, two Fe2+ ions <cite>#Vincent2004</cite>, and a Zn2+ ion <cite>#Ferreira2006</cite> in their active sites, respectively. All resolved CE9 enzymes contain a distorted (β/α)8 fold containing the active site, and a small β-sheet domain comprising residues from both the N- and C-termini.

== Family Firsts ==
;First characterized
The ''E. coli'' N-acetylglucosamine-6-phosphate deacetylase NagA was the first CE9 enzyme to have its activity demonstrated <cite>#White1967</cite>.
;First 3-D structure
The first structure of a CE9 enzyme published was the ''B. subtilis'' NagA, containing a two-Fe2+ catalytic center <cite>#Vincent2004</cite>.
;First mechanistic insight
The structure of the ''B. subtilis'' NagA enzyme was reported with a bound N-acetylglucosamine-6-phosphate molecule and provided evidence for the proposed metal-dependent catalytic mechanism <cite>#Vincent2004</cite>.
== References ==
<biblio>
#Park2001 pmid=11395446

#Osipiuk2002 https://www.rcsb.org/structure/3EGJ

#Vincent2004 pmid=14557261

#Ferreira2006 pmid=16630633

#Ahangar2018 pmid=29728457

#White1967 pmid=4861885

</biblio>

[[Category:Carbohydrate Esterase Families|CE009]]

Carbohydrate Esterase Family 9

2018-08-27T17:14:18Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 9'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE9.html
|}
</div>


== Substrate specificities ==
CE family 9 esterases catalyze the deacetylation of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate. This reaction has been demonstrated to be important for both amino sugar metabolism and peptidoglycan cell wall recycling in bacteria <cite>#Park2001</cite>. Experimental substrate specificity profiles for two CE9 enzymes demonstrated that they are active on other structurally similar amino sugar phosphates, such as N-acetyl- galactosamine-6-phosphate and N-acetyl-mannosamine-6-phosphate, although their reported affinities are 40-fold and 6-fold lower, respectively <cite>#Ahangar2018</cite>.

== Kinetics and Mechanism ==
Removal of the acetate group by CE9 enzymes is proposed to be carried out by nucleophilic attack of the acetate carbon by a metal-bound hydroxide ion <cite>#Vincent2004</cite>. A proton is donated to the amine leaving group by a catalytic acid residue, and the tetrahedral transition state is stabilized either by the interaction of a second metal ion with the polarized carbonyl oxygen <cite>#Vincent2004</cite>, or by a catalytic base residue where a second metal ion is absent from the active site, although the latter has not been experimentally demonstrated.

== Catalytic Residues ==
The precise mechanism of catalysis has yet to be elucidated for CE9, although several conserved features in the active sites of resolved CE9 members suggest they play an important role in their function. In ''Bacillus subtilis'' NagA, ''Thermotoga maritima'' NagA, and ''Mycobacterium smegmatis'' NagA, four histidine residues are responsible for coordination of the metal cofactor(s), along with a glutamate in ''B. subtilis'' and ''T. maritima'', and an aspartic acid in ''M. smegmatis'' <cite>#Vincent2004,#Osipiuk2002,#Ferreira2006</cite>. The ''Escherichia coli'' NagA appears to have a glutamine, gluatamate, asparagine and an aspartate as the coordination enviroment, although this structure crystallized as the apoenzyme, and so this configuration is uncertain <cite>#Ferreira2006</cite>. In all structures, a strictly conserved aspartic acid residue is then thought to serve as a base to activate a water molecule, and then as an acid to protonate the leaving amine <cite>#Vincent2004</cite>.

== Three-dimensional structures ==
The resolved structures of CE9 enzymes demonstrate variability in their organization and metal binding. For example, ''Vibrio cholerae'' NagA and ''B. subtilis'' NagA form dimers in their biologically relevant assemblies <cite>#Osipiuk2002, #Vincent2004</cite>, while ''E. coli'' NagA forms a tetramer <cite>#Ferreira2006</cite>. Additionally, these same enzymes appear to contain a Ni2+ ion <cite>#Osipiuk2002</cite>, two Fe2+ ions <cite>#Vincent2004</cite>, and a Zn2+ ion <cite>#Ferreira2006</cite> in their active sites, respectively. All resolved CE9 enzymes contain a distorted (β/α)8 fold containing the active site, and a small β-sheet domain comprising residues from both the N- and C-termini.

== Family Firsts ==
;First characterized
The ''E. coli'' N-acetylglucosamine-6-phosphate deacetylase NagA was the first CE9 enzyme to have its activity demonstrated <cite>#White1967</cite>.
;First 3-D structure
The first structure of a CE9 enzyme published was the ''B. subtilis'' NagA, containing a two-Fe2+ catalytic center <cite>#Vincent2004</cite>.
;First mechanistic insight
The structure of the ''B. subtilis'' NagA enzyme was reported with a bound N-acetylglucosamine-6-phosphate molecule and provided evidence for the proposed metal-dependent catalytic mechanism <cite>#Vincent2004</cite>.
== References ==
<biblio>
#Park2001 pmid=11395446

#Osipiuk2002 https://www.rcsb.org/structure/3EGJ

#Vincent2004 pmid=14557261

#Ferreira2006 pmid=16630633

#Ahangar2018 pmid= 29728457

#White1967 pmid=4861885

</biblio>

[[Category:Carbohydrate Esterase Families|CE009]]

Carbohydrate Esterase Family 4

2018-08-02T21:53:17Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 4'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE4.html
|}
</div>


== Substrate specificities ==
CE family 4 esterases catalyze the de-acylation of polysaccharides. Known activities of CE family 4 members include acetylxylan esterases, chitin deacetylases, chitooligosaccharide deacetylases, and peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, YfjS from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.

== Kinetics and Mechanism ==
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn2+, but Co2+ is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.

== Catalytic Residues ==
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn2+ ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co2+ in place of Zn2+'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co2+ in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.

== Three-dimensional structures ==
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)7 fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).

== Family Firsts ==
;First characterized
TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.
;First mechanistic insight
The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>.
;First 3-D structure
The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)7 fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.

== References ==
<biblio>
#Hayhurst2008 pmid=18784364
#Fukushima2005 pmid=15687192
#Blair2005 pmid=16221761
#Taylor2006 pmid=16431911
#Andres2014 pmid=24810719
#Arnaouteli2015 pmid=25825488
#Deng2009 pmid=18978064
#Nishiyama2013 pmid=23275162
#John1993 pmid=8421697
#Blair2004 pmid=15251431

</biblio>

[[Category:Carbohydrate Esterase Families|CE004]]

Carbohydrate Esterase Family 4

2018-07-20T17:26:18Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 4'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE4.html
|}
</div>


== Substrate specificities ==
CE family 4 esterases catalyze the de-acylation of polysaccharides. As of June 2018, there are 60 characterized CE4 enzymes, 18 of which are acetylxylan esterases, 15 are chitin deacetylases, 14 are chitooligosaccharide deacetylases, and 13 are peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, YfjS from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.

== Kinetics and Mechanism ==
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn2+, but Co2+ is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.

== Catalytic Residues ==
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn2+ ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co2+ in place of Zn2+'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co2+ in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.

== Three-dimensional structures ==
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)7 fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).

== Family Firsts ==
;First characterized
TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.
;First mechanistic insight
The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>.
;First 3-D structure
The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)7 fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.

== References ==
<biblio>
#Hayhurst2008 pmid=18784364
#Fukushima2005 pmid=15687192
#Blair2005 pmid=16221761
#Taylor2006 pmid=16431911
#Andres2014 pmid=24810719
#Arnaouteli2015 pmid=25825488
#Deng2009 pmid=18978064
#Nishiyama2013 pmid=23275162
#John1993 pmid=8421697
#Blair2004 pmid=15251431

</biblio>

[[Category:Carbohydrate Esterase Families|CE004]]

Carbohydrate Esterase Family 4

2018-07-18T17:34:41Z

Alex Anderson:

{{UnderConstruction}}
* [[Author]]: ^^^Alex Anderson^^^
* [[Responsible Curator]]: ^^^Michael Suits^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Carbohydrate Esterase Family 4'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CE4.html
|}
</div>


== Substrate specificities ==
CE family 4 esterases catalyze the de-acylation of polysaccharides. As of June 2018, there are 60 characterized CE4 enzymes, 18 of which are acetylxylan esterases, 15 are chitin deacetylases, 14 are chitooligosaccharide deacetylases, and 13 are peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, YfjS from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.

== Kinetics and Mechanism ==
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn2+, but Co2+ is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.

== Catalytic Residues ==
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn2+ ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co2+ in place of Zn2+'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co2+ in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.

== Three-dimensional structures ==
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)8 fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).

== Family Firsts ==
;First characterized
TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.
;First mechanistic insight
The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>.
;First 3-D structure
The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)8 fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.

== References ==
<biblio>
#Hayhurst2008 pmid=18784364
#Fukushima2005 pmid=15687192
#Blair2005 pmid=16221761
#Taylor2006 pmid=16431911
#Andres2014 pmid=24810719
#Arnaouteli2015 pmid=25825488
#Deng2009 pmid=18978064
#Nishiyama2013 pmid=23275162
#John1993 pmid=8421697
#Blair2004 pmid=15251431

</biblio>

[[Category:Carbohydrate Esterase Families|CE004]]

User:Alex Anderson

2018-05-31T14:03:52Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex is currently a Masters candidate in the lab of Dr. Joel Weadge, alongside ^^^Michael Suits^^^, at WLU where he studies the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens.


[[Category:Contributors|Anderson,Alex]]

User:Alex Anderson

2018-05-31T14:00:05Z

Alex Anderson:

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

Alex Anderson recieved his BScH from Wilfrid Laurier University in 2017, and began his foray into microbiology as a diagnostic laboratory technician at the Public Health Ontario Laboratories where he became fascinated with microbial cell surface structure and function. Alex is currently a Masters candidate in the lab of Dr. Joel Weadge at WLU where he studies the structure and function of CAZymes responsible for the biosynthesis, modification and export of cellulosic materials involved in biofilm formation in Gram-negative pathogens.


[[Category:Contributors|Anderson,Alex]]

File:Aa.jpg

2018-05-31T13:49:54Z

Alex Anderson: User photo for Alex Anderson

User photo for Alex Anderson