CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 98

2009-10-21T00:35:42Z

Fathima Shaikh:

{{UnderConstruction}}
* [[Author]]: ^^^Fathima Shaikh^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|Inverting
|-
|'''Active site residues'''
|Known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH98.html
|}
</div>


== Substrate specificities ==
The glycoside hydrolases of this family are endo-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of A and B trisaccharides from glycoconjugates <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The presence of a L-fucose residue on the substrate is essential for activity of some members of this family (EABase, Sp4GH98) <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The crystal structure of Sp3GH98 suggests that the fucose residue is not required as a specificity determinant in this enzyme <cite>Higgins2009</cite>.

== Kinetics and Mechanism ==

Family GH98 galactosidases are inverting enzymes, as first shown by NMR monitoring of the Sp4GH98 catalyzed hydrolysis of the LewisY tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.

== Catalytic Residues ==

The catalytic base, an aspartate and glutamate diad, and the catalytic acid, glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical proof for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the pKa of the leaving group of the substrate <cite>Shaikh2009</cite>.

== Three-dimensional structures ==

The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub> 8</sub> barrel in the catalytic domain <cite>Higgins2009</cite>

== Family Firsts ==

;First sterochemistry determination:

''Streptococcus pneumoniae'' TIGR4 endo-b-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.
;First catalytic base identification:

Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.
;First catalytic acid identification:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

;First 3-D structure:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

== References ==
<biblio>
# Ashida2005 pmid=15618227
# Higgins2009 pmid=19608744
# Shaikh2009 pmid=19630404
# Rigden2005 pmid=16212961

</biblio>


<nowiki>[[Category:Glycoside Hydrolase Families|GH98]]</nowiki>

Glycoside Hydrolase Family 98

2009-10-21T00:34:09Z

Fathima Shaikh:

Glycoside Hydrolase Family 98

2009-10-21T00:32:22Z

Fathima Shaikh:

{{UnderConstruction}}
* [[Author]]: ^^^Fathima Shaikh^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|Inverting
|-
|'''Active site residues'''
|Known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH98.html
|}
</div>


== Substrate specificities ==
The glycoside hydrolases of this family are endo-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of A and B trisaccharides from glycoconjugates <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The presence of a L-fucose residue on the substrate is essential for activity of some members of this family (EABase, Sp4GH98) <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The crystal structure of Sp3GH98 suggests that the fucose residue is not required as a specificity determinant in this enzyme <cite>Higgins2009</cite>.

== Kinetics and Mechanism ==

Family GH98 galactosidases are inverting enzymes, as first shown by NMR monitoring of the Sp4GH98 catalyzed hydrolysis of the LewisY tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.

== Catalytic Residues ==

The catalytic base, an aspartate and glutamate diad, and the catalytic acid, glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical proof for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the pKa of the leaving group of the substrate <cite>Shaikh2009</cite>.

== Three-dimensional structures ==

The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub> 8</sub> barrel in the catalytic domain <cite>Higgins2009</cite>

== Family Firsts ==

;First sterochemistry determination:

''Streptococcus pneumoniae'' TIGR4 endo-b-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.
;First catalytic base identification:

Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.
;First catalytic acid identification:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

;First 3-D structure:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

== References ==
<biblio>
#1Ashida2005 pmid=15618227
#2Higgins2009 pmid=19608744
#3Shaikh2009 pmid=19630404
#4Rigden2005 pmid=16212961

</biblio>


<nowiki>[[Category:Glycoside Hydrolase Families|GHnnn]]</nowiki>

Glycoside Hydrolase Family 98

2009-10-21T00:30:29Z

Fathima Shaikh:

{{UnderConstruction}}
* [[Author]]: ^^^Fathima Shaikh^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|Inverting
|-
|'''Active site residues'''
|Known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GHnn.html
|}
</div>


== Substrate specificities ==
The glycoside hydrolases of this family are endo-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of A and B trisaccharides from glycoconjugates <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The presence of a L-fucose residue on the substrate is essential for activity of some members of this family (EABase, Sp4GH98) <cite> Ashida2005 Higgins2009 Shaikh2009</cite>. The crystal structure of Sp3GH98 suggests that the fucose residue is not required as a specificity determinant in this enzyme <cite>Higgins2009</cite>.

== Kinetics and Mechanism ==

Family GH98 galactosidases are inverting enzymes, as first shown by NMR monitoring of the Sp4GH98 catalyzed hydrolysis of the LewisY tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.

== Catalytic Residues ==

The catalytic base, an aspartate and glutamate diad, and the catalytic acid, glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical proof for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the pKa of the leaving group of the substrate <cite>Shaikh2009</cite>.

== Three-dimensional structures ==

The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub> 8</sub> barrel in the catalytic domain <cite>Higgins2009</cite>

== Family Firsts ==

;First sterochemistry determination:

''Streptococcus pneumoniae'' TIGR4 endo-b-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.
;First catalytic base identification:

Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.
;First catalytic acid identification:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

;First 3-D structure:
Streptococcus pneumoniae SP3-BS71 endo-b-galactosidase Sp3GH98 <cite>Higgins2009</cite>.

Streptococcus pneumoniae TIGR4 endo-b-galactosidase Sp4GH98 <cite>Higgins2009</cite>.

== References ==
<biblio>
#Ashida2005 pmid=15618227
#Higgins2009 pmid=19608744
#Shaikh2009 pmid=19630404
#Rigden2005 pmid=16212961

</biblio>


<nowiki>[[Category:Glycoside Hydrolase Families|GHnnn]]</nowiki>

User:Fathima Shaikh

2009-10-21T00:11:36Z

Fathima Shaikh: Created page with ' Fathima Aidha Shaikh received her Bachelors of Science (Combined Honours in Chemistry and Biochemistry) from the University of British Columbia in 2005 and is currently a doctor…'

Fathima Aidha Shaikh received her Bachelors of Science (Combined Honours in Chemistry and Biochemistry) from the University of British Columbia in 2005 and is currently a doctoral student in the laboratory of Dr. Stephen G. Withers. Her graduate work focuses on the mechanism and engineering of enzymes involved in blood-antigen modification and cleavage. Fathima was funded by a UGF and currently holds a senior graduate fellowship from the Michael Smith Foundation for Health Research.