https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Zui+FujimotoCAZypedia - User contributions [en-ca]2026-05-04T16:24:03ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=11776User:Zui Fujimoto2017-10-31T00:28:44Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.naro.affrc.go.jp/english/index.html National Agriculture and Food Research Organization](NARO), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH31]] α-1,6-glucosyltransferase <cite>Fujimoto2017b</cite><br />
<br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH62]] α-L-arabinofuranosidase <cite>Maehara2014</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<cite>Suzuki2014 Fujimoto2017a</cite><br />
* [[GH78]] α-L-rhamnosidase <cite>Fujimoto2013</cite><br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Fujimoto2013 pmid=23486481<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
#Suzuki2014 pmid=24616103<br />
#Maehara2014 pmid=24482228<br />
#Fujimoto2017a pmid=28385816<br />
#Fujimoto2017b pmid=28698247<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=11775User:Zui Fujimoto2017-10-31T00:28:19Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.naro.affrc.go.jp/english/index.html National Agriculture and Food Research Organization](NARO), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH31]] α-1,6-glucosyltransferase <cite>Fujimoto2017b</cite><br />
<br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH62]] α-L-arabinofuranosidase <cite>Maehara2014</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<cite>Suzuki2014</cite>,<cite>Fujimoto2017a</cite><br />
* [[GH78]] α-L-rhamnosidase <cite>Fujimoto2013</cite><br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Fujimoto2013 pmid=23486481<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
#Suzuki2014 pmid=24616103<br />
#Maehara2014 pmid=24482228<br />
#Fujimoto2017a pmid=28385816<br />
#Fujimoto2017b pmid=28698247<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=10631Glycoside Hydrolase Family 782015-05-22T05:57:38Z<p>Zui Fujimoto: /* Substrate specificities */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Zui Fujimoto^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Genes encoding family GH78 [[glycoside hydrolases]] are found in bacteria and fungi. The sole identified activity of enzymes of this family is hydrolysis of α-L-rhamnosides (EC 3.2.1.40). The GH78 α-L-rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnosides, including: flavonoid glycosides such as naringin, hesperidin and rutin; polysaccharides such as rhamnogalacturonan and arabinogalactan-protein and glycolipids. α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an [[inverting]] mechanism as elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>. Typical GH78 α-L-rhamnosidases have molecular masses in the range 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
Crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), notably including an enzyme-product complex structure, suggested that Glu895 is the catalytic [[general base]] responsible for activating a water molecule, and that Glu636 is the catalytic [[general acid]], assisting leaving-group departure <cite>Fujimoto2013</cite>. All characterized α-L-rhamnosidases appear to contain a glutamate as the catalytic general base.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure of a GH78 member was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>. Subsequently, the crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by a structural genomics project (PDB ID [{{PDBlink}}3cih 3cih]) <cite>Bonanno2005</cite>. The crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with the product L-rhamnose has revealed key active-site details (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n]) <cite>Fujimoto2013</cite>. More recently, the crystal structure of a ''Klebsiella oxytoca'' α-rhamnosidase (KoRha) has been solved in complex L-rhamnose.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic domain of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type-3 fold β-domain often appears at the N-terminus, and a C-terminal Greek key β-domain exists just after the catalytic domain. Several β-domains are also inserted between the N-terminal domain and the catalytic domain. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module ([[CBM67]]), which binds terminal L-rhamnose sugars in the presence of a calcium ion <cite>Fujimoto2013</cite>. On the other hand, KoRha has only two structual domains, one β-domain and one catalytic domain, forming a homodimer <cite>ONeill2015</cite>. These two domains are common among all structure-determined enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First [[general base]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First [[general acid]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Young1989 Young, NM, Johnston RAZ, and Richards, JC. ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 1989 Aug;191(1):53-62. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
#ONeill2015 pmid=25846411 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=10629Glycoside Hydrolase Family 782015-05-19T10:07:57Z<p>Zui Fujimoto: /* References */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Zui Fujimoto^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Genes encoding family GH78 [[glycoside hydrolases]] are found in bacteria and fungi. The sole identified activity of enzymes of this family is hydrolysis of α-L-rhamnosides (EC 3.2.1.40). The GH76 α-L-rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnosides, including: flavonoid glycosides such as naringin, hesperidin and rutin; polysaccharides such as rhamnogalacturonan and arabinogalactan-protein and glycolipids. α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an [[inverting]] mechanism as elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>. Typical GH78 α-L-rhamnosidases have molecular masses in the range 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
Crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), notably including an enzyme-product complex structure, suggested that Glu895 is the catalytic [[general base]] responsible for activating a water molecule, and that Glu636 is the catalytic [[general acid]], assisting leaving-group departure <cite>Fujimoto2013</cite>. All characterized α-L-rhamnosidases appear to contain a glutamate as the catalytic general base.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure of a GH78 member was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>. Subsequently, the crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by a structural genomics project (PDB ID [{{PDBlink}}3cih 3cih]) <cite>Bonanno2005</cite>. The crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with the product L-rhamnose has revealed key active-site details (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n]) <cite>Fujimoto2013</cite>. More recently, the crystal structure ofα-rhamnosidase from ''Klebsiella oxytoca'' α-rhamnosidase (KoRha) in complex L-rhamnose.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic domain of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type-3 fold β-domain often appears at the N-terminus, and a C-terminal Greek key β-domain exists just after the catalytic domain. Several β-domains are also inserted between the N-terminal domain and the catalytic domain. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module ([[CBM67]]), which binds terminal L-rhamnose sugars in the presence of a calcium ion <cite>Fujimoto2013</cite>. On the other hand, KoRha has only two structual domains, one β-domain and one catalytic domain, forming a homodimer <cite>ONeill2015</cite>. These two domains are common among all structure-determined enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First [[general base]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First [[general acid]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Young1989 Young, NM, Johnston RAZ, and Richards, JC. ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 1989 Aug;191(1):53-62. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
#ONeill2015 pmid=25846411 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=10628Glycoside Hydrolase Family 782015-05-19T10:07:08Z<p>Zui Fujimoto: /* Three-dimensional structures */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Zui Fujimoto^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Genes encoding family GH78 [[glycoside hydrolases]] are found in bacteria and fungi. The sole identified activity of enzymes of this family is hydrolysis of α-L-rhamnosides (EC 3.2.1.40). The GH76 α-L-rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnosides, including: flavonoid glycosides such as naringin, hesperidin and rutin; polysaccharides such as rhamnogalacturonan and arabinogalactan-protein and glycolipids. α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an [[inverting]] mechanism as elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>. Typical GH78 α-L-rhamnosidases have molecular masses in the range 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
Crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), notably including an enzyme-product complex structure, suggested that Glu895 is the catalytic [[general base]] responsible for activating a water molecule, and that Glu636 is the catalytic [[general acid]], assisting leaving-group departure <cite>Fujimoto2013</cite>. All characterized α-L-rhamnosidases appear to contain a glutamate as the catalytic general base.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure of a GH78 member was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>. Subsequently, the crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by a structural genomics project (PDB ID [{{PDBlink}}3cih 3cih]) <cite>Bonanno2005</cite>. The crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with the product L-rhamnose has revealed key active-site details (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n]) <cite>Fujimoto2013</cite>. More recently, the crystal structure ofα-rhamnosidase from ''Klebsiella oxytoca'' α-rhamnosidase (KoRha) in complex L-rhamnose.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic domain of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type-3 fold β-domain often appears at the N-terminus, and a C-terminal Greek key β-domain exists just after the catalytic domain. Several β-domains are also inserted between the N-terminal domain and the catalytic domain. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module ([[CBM67]]), which binds terminal L-rhamnose sugars in the presence of a calcium ion <cite>Fujimoto2013</cite>. On the other hand, KoRha has only two structual domains, one β-domain and one catalytic domain, forming a homodimer <cite>ONeill2015</cite>. These two domains are common among all structure-determined enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First [[general base]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First [[general acid]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Young1989 Young, NM, Johnston RAZ, and Richards, JC. ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 1989 Aug;191(1):53-62. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=10476Glycoside Hydrolase Family 782015-01-20T02:01:01Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Zui Fujimoto^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project (PDB ID [{{PDBlink}}3cih 3cih])<cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose has been reported (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n])<cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, NM, Johnston RAZ, and Richards, JC. ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 1989 Aug;191(1):53-62. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=9943User:Zui Fujimoto2014-05-21T01:25:29Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH62]] α-L-arabinofuranosidase <cite>Maehara2014</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<cite>Suzuki2014</cite><br />
* [[GH78]] α-L-rhamnosidase <cite>Fujimoto2013</cite><br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Fujimoto2013 pmid=23486481<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
#Suzuki2014 pmid=24616103<br />
#Maehara2014 pmid=24482228<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=9942Glycoside Hydrolase Family 662014-05-21T01:15:11Z<p>Zui Fujimoto: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH66 contains [[endo]]-acting dextranase (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).<br />
Dex enzymes hydrolyze α-1,6 linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into [[GH49]] and GH66. In contrast to inverting [[GH49]] enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]].The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
The second structure for GH66 has been reported for CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno])<cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of SmDex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First [[catalytic nucleophile]] identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First [[general acid/base]] residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
#Nsuzu2014 pmid=24616103<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=9941Glycoside Hydrolase Family 662014-05-21T01:12:43Z<p>Zui Fujimoto: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH66 contains [[endo]]-acting dextranase (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).<br />
Dex enzymes hydrolyze α-1,6 linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into [[GH49]] and GH66. In contrast to inverting [[GH49]] enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]].The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
The second structure for GH66 has been reported for CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno])<cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of SmDex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First [[catalytic nucleophile]] identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First [[general acid/base]] residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
#Nsuzu2014 pmid=24616103<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=9940Glycoside Hydrolase Family 662014-05-21T01:06:14Z<p>Zui Fujimoto: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH66 contains [[endo]]-acting dextranase (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).<br />
Dex enzymes hydrolyze α-1,6 linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into [[GH49]] and GH66. In contrast to inverting [[GH49]] enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]].The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
The second structure for GH66 has been reported for CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk, -[{{PDBlink}}3wno 3wno])<cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of SmDex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First [[catalytic nucleophile]] identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First [[general acid/base]] residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
#Nsuzu2014 pmid=24616103<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9939Glycoside Hydrolase Family 782014-05-21T00:56:14Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project (PDB ID [{{PDBlink}}3cih 3cih])<cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose has been reported (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n])<cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, NM, Johnston RAZ, and Richards, JC. ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 1989 Aug;191(1):53-62. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9938Glycoside Hydrolase Family 782014-05-21T00:54:28Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project (PDB ID [{{PDBlink}}3cih 3cih])<cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose has been reported (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n])<cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, NM, Johnston RAZ and Richards, JC. (1989) ''Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components.'' Carbohydr. Res. 191(1) 53-62 [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9937Glycoside Hydrolase Family 782014-05-21T00:48:49Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB ID [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project (PDB ID [{{PDBlink}}3cih 3cih])<cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose has been reported (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n])<cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx])<cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, N.M., Johnston R.A.Z. and Richards, J.C. (1989) Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components. Carbohydr. Res. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9936Glycoside Hydrolase Family 782014-05-20T09:26:59Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one components of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, N.M., Johnston R.A.Z. and Richards, J.C. (1989) Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components. Carbohydr. Res. [http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9935Glycoside Hydrolase Family 782014-05-20T09:23:47Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one components of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, N.M., Johnston R.A.Z. and Richards, J.C. (1989) Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components. Carbohydr. Res. [<br />
http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9934Glycoside Hydrolase Family 782014-05-20T09:23:04Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one components of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase [Young1989].<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Young1989 Young, N.M., Johnston R.A.Z. and Richards, J.C. (1989) Purification of the α-L-rhamnosidase of ''Penicillium decumbens'' and characterisation of two glycopeptide components. Carbohydr. Res. [<br />
http://dx.doi.org/10.1016/0008-6215(89)85045-1 DOI: 10.1016/0008-6215(89)85045-1]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9933Glycoside Hydrolase Family 782014-05-20T08:58:48Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.<br />
<br />
α-L-Rhamnosidases have been found to be one components of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase [].<br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.<br />
<br />
α-L-rhamnosidases have molecular masses of 80-120 kDa, and are most active at pH 4.0 to 8 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Mutter1994, Hashimoto1999, Manzanares2000, Koseki2008, Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Mutter1994 pmid=7972516<br />
#Pitson1998 pmid=9464254<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=9932Glycoside Hydrolase Family 662014-05-20T06:54:01Z<p>Zui Fujimoto: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH66 contains [[endo]]-acting dextranase (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).<br />
Dex enzymes hydrolyze α-1,6 linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into [[GH49]] and GH66. In contrast to inverting [[GH49]] enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]].The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes. The second structure has been reported for CITase-T3040 <cite>Nsuzu2014</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First [[catalytic nucleophile]] identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First [[general acid/base]] residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
#Nsuzu2014 pmid=24616103<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9931Glycoside Hydrolase Family 782014-05-20T06:49:44Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>.<br />
<br />
''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) was a monomer with a molecular mass of about 100 kDa and was most active at pH 7.0 and 50°C against the gellan-degrading product (rhamnosyl-glucose) <cite>Hashimoto1999</cite>.<br />
''Aspergillus aculeatus'' two α-L-rhamnosidases (RhaA and RhaB) had molecular masses of 92 and 85 kDa, and were most active at pH 4.5 to 5, showed Km and Vmax values of 2.8 mM and 24 U/mg (RhaA) and 0.30 mM and 14 U/mg (RhaB) against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Manzanares2000</cite>. <br />
''Aspergillus kawachii'' α-L-rhamnosidase had a molecular mass of 90 kDa and exhibited optimal activity at pH 4.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Koseki2008</cite>.<br />
''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) had a molecular mass of 113 kDa and exhibited optimal activity at pH 6.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase (RamA), by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Hashimoto1999 pmid=10415111<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9930Glycoside Hydrolase Family 782014-05-20T06:47:07Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>.<br />
<br />
''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) was a monomer with a molecular mass of about 100 kDa and was most active at pH 7.0 and 50°C against the gellan-degrading product (rhamnosyl-glucose) <cite>Hashimoto1999</cite>.<br />
''Aspergillus aculeatus'' two α-L-rhamnosidases (RhaA and RhaB) had molecular masses of 92 and 85 kDa, and were most active at pH 4.5 to 5, showed Km and Vmax values of 2.8 mM and 24 U/mg (RhaA) and 0.30 mM and 14 U/mg (RhaB) against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Manzanares2000</cite>. <br />
''Aspergillus kawachii'' α-L-rhamnosidase had a molecular mass of 90 kDa and exhibited optimal activity at pH 4.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Koseki2008</cite>.<br />
''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) had a molecular mass of 113 kDa and exhibited optimal activity at pH 6.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase (RamA), by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Manzanares2000 pmid=11319105<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9929Glycoside Hydrolase Family 782014-05-20T06:11:28Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, or polysaccharides such as rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>.<br />
<br />
''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) was a monomer with a molecular mass of about 100 kDa and was most active at pH 7.0 and 50°C against the gellan-degrading product (rhamnosyl-glucose) <cite>Hashimoto1999</cite>.<br />
''Aspergillus kawachii'' α-L-rhamnosidase had a molecular mass of 90 kDa and exhibited optimal activity at pH 4.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Koseki2008</cite>.<br />
''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) had a molecular mass of 113 kDa and exhibited optimal activity at pH 6.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase (RamA), by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=9928User:Zui Fujimoto2014-05-20T06:03:17Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH62]] α-L-arabinofuranosidase <cite>Maehara2014</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<cite>Suzuki2014</cite><br />
* [[GH78]] α-L-rhamnosidase <cite>Fujimoto2013</cite><br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Fujimoto2013 pmid=23486481<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
#Suzuki2012 pmid=24616103<br />
#Maehara2014 pmid=24482228<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9927Glycoside Hydrolase Family 782014-05-20T05:54:34Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, or polysaccharides such as rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>.<br />
<br />
''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) was a monomer with a molecular mass of about 100 kDa and was most active at pH 7.0 and 50°C against the gellan-degrading product (rhamnosyl-glucose) <cite>Hashimoto1999</cite>.<br />
''Aspergillus kawachii'' α-L-rhamnosidase had a molecular mass of 90 kDa and exhibited optimal activity at pH 4.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Koseki2008</cite>.<br />
''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) had a molecular mass of 113 kDa and exhibited optimal activity at pH 6.0 and temperature of 50°C against ''p''-nitrophenyl-α-L-rhamnopyranoside <cite>Ichinose2013</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) indicated that Glu895 appeared to be the catalytic general base, and Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule <cite>Fujimoto2013</cite>.<br />
Glutamate is conserved for the catalytic general base in all characterized α-L-rhamnosidases.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
α-L-Rhamnosidases have a modular structure. BsRhaB, BT1001, and SaRha78A show five-, four and six-module structures. The catalytic module of GH78 enzymes is an (α/α)<sub>6</sub>-barrel. A fibronectin type 3 fold β-domain often appears in the N-terminus, and the Greek key β-domain exist just after the catalytic module comprising the C-terminus. Several β-domains are inserted between the N-terminal domain and the catalytic module. ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) possesses one carbohydrate binding module (CBM67), which binds terminal L-rhamnose sugars in the presence of calcium ion <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase (RamA), by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
#Koseki2008 pmid=18633609<br />
#Ichinose2013 pmid=23291751<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9926Glycoside Hydrolase Family 782014-05-20T04:41:16Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, or polysaccharides such as rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>.<br />
<br />
== Catalytic Residues ==<br />
The crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) indicated that Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule, and Glu895 appeared to be the catalytic general base <cite>Fujimoto2013</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>.<br />
Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase RamA, by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
#Bonanno2005 pmid=16211523<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9925Glycoside Hydrolase Family 782014-05-20T03:01:41Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|GH-M<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, such as naringin and rutin, or rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>..<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase RamA, by <sup>1</sup>H-NMR <cite>Zverlov2000</cite>.<br />
;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.<br />
;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
#Fujimoto2013 pmid=23486481<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9924Glycoside Hydrolase Family 782014-05-20T02:20:30Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, such as naringin and rutin, or rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR [Zverlov2000].<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase RamA by <sup>1</sup>H-NMR.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: α-L-rhamnosidase B (BsRhaB) from ''Bacillus'' sp. GL1 [Cui2007].<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_78&diff=9923Glycoside Hydrolase Family 782014-05-20T02:10:47Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: <br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH78'''<br />
|-<br />
|'''Clan''' <br />
|<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH78.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, such as naringin and rutin, or rhamnogalacturonan and arabinogalactan-protein. <br />
<br />
== Kinetics and Mechanism ==<br />
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR [Zverlov2000].<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Clostridium stercorarium'' α-L-rhamnosidase RamA by <sup>1</sup>H-NMR.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: α-L-rhamnosidase B (BsRhaB) from ''Bacillus'' sp. GL1 [Cui2007].<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
#Zverlov2000 pmid=10632887<br />
#Cui2007 pmid=17936784<br />
<br />
[[Category:Glycoside Hydrolase Families|GH078]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=9365User:Zui Fujimoto2013-10-07T05:16:21Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH78]] α-L-rhamnosidase <cite>Fujimoto2013</cite><br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Fujimoto2013 pmid=23486481<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=9364Glycoside Hydrolase Family 662013-10-07T05:03:58Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module (CBM35) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7753Glycoside Hydrolase Family 662012-11-12T08:01:41Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module (CBM35) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. [http://dx.doi.org/10.1271/bbb.57.1225 DOI:10.1271/bbb.57.1225]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7749User:Zui Fujimoto2012-11-08T09:14:13Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66|Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7748User:Zui Fujimoto2012-11-08T09:11:05Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66 Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7747User:Zui Fujimoto2012-11-08T09:08:21Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[Glycoside Hydrolase Family 66 (GH66)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7746User:Zui Fujimoto2012-11-08T09:07:58Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|150px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[Glycoside Hydrolase Family 36 (GH36)]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio><br />
<br />
[[Category:Contributors|Fujimoto,Zui]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7745Glycoside Hydrolase Family 662012-11-08T08:21:43Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7744Glycoside Hydrolase Family 662012-11-08T08:19:50Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like>-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7743Glycoside Hydrolase Family 662012-11-08T08:04:17Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_79&diff=7742Glycoside Hydrolase Family 792012-11-08T06:53:10Z<p>Zui Fujimoto: /* References */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^<br />
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH79'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH79.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC 3.2.1.166) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.<br />
<br />
Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite>. Heparanase is an endo-β-glucuronidase that degrades the heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').<br />
<br />
== Kinetics and Mechanism ==<br />
GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and site-directed mutagenesis studies <cite> Michikawa2012 </cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.<br />
;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.<br />
;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.<br />
;First 3-D structure: ''A. capsulatum'' β-glucuronidase (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Eudes2008 pmid=18667448<br />
#Kuroyama2001 pmid=11423108<br />
#Konishi2008 pmid=18377882<br />
#Sasaki2000 pmid=10858442<br />
#Michikawa2012 pmid=22367201 <br />
#Vlodavsky1999 pmid=10395325<br />
#Toyoshima1999 pmid=10446189<br />
#Kussie1999 pmid=10405343<br />
#Hulett1999 pmid=10395326<br />
#Fairbanks1999 pmid=10514423<br />
#Nardella2004 pmid=14967027<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH079]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_79&diff=7741Glycoside Hydrolase Family 792012-11-08T06:51:51Z<p>Zui Fujimoto: /* References */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^<br />
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH79'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH79.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (EC [{{EClink}}3.2.1.31 3.2.1.31]) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (EC 3.2.1.-) <cite>Kuroyama2001</cite>, baicalin β-glucuronidase (EC [{{EClink}}3.2.1.167 3.2.1.167]) <cite> Sasaki2000 </cite>, heparanase (EC 3.2.1.166) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (EC 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.<br />
<br />
Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite>. Heparanase is an endo-β-glucuronidase that degrades the heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').<br />
<br />
== Kinetics and Mechanism ==<br />
GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and site-directed mutagenesis studies <cite> Michikawa2012 </cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.<br />
;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.<br />
;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.<br />
;First 3-D structure: ''A. capsulatum'' β-glucuronidase (PDB IDs [{{PDBlink}}3vny 3vny], [{{PDBlink}}3vnz 3vnz], [{{PDBlink}}3vo0 3vo0]) <cite> Michikawa2012 </cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Eudes2008 pmid=18667448<br />
#Kuroyama2001 pmid=11423108<br />
#Konishi2008 pmid=18377882<br />
#Sasaki2000 pmid=10858442<br />
#Michikawa2012 pmid=22878205<br />
#Vlodavsky1999 pmid=10395325<br />
#Toyoshima1999 pmid=10446189<br />
#Kussie1999 pmid=10405343<br />
#Hulett1999 pmid=10395326<br />
#Fairbanks1999 pmid=10514423<br />
#Nardella2004 pmid=14967027<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH079]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7738Glycoside Hydrolase Family 662012-11-08T04:18:28Z<p>Zui Fujimoto: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7737User:Zui Fujimoto2012-11-08T02:48:29Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|200px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences](NIAS), Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He acts as a [[Responsible Curator]] for the [[GH66]] page.<br />
He has determined the crystal structures of<br />
<br />
* [[GH10]] endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* [[GH13]] α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* [[GH27]] α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* [[GH43]] exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* [[GH79]] β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio></div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7736User:Zui Fujimoto2012-11-08T02:35:32Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|200px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He has determined the crystal structures of<br />
<br />
* GH10 endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* GH13 α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* GH27 α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* GH43 exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* [[GH66]] dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* GH79 β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio></div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7735User:Zui Fujimoto2012-11-08T02:22:27Z<p>Zui Fujimoto: </p>
<hr />
<div>[[Image:ZuiC2.jpg|200px|right]]<br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He has determined the crystal structures of<br />
<br />
* GH10 endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* GH13 α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* GH27 α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* GH43 exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* GH66 dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* GH79 β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio></div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=File:ZuiC2.jpg&diff=7734File:ZuiC2.jpg2012-11-08T02:21:09Z<p>Zui Fujimoto: </p>
<hr />
<div></div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7732User:Zui Fujimoto2012-11-08T01:54:42Z<p>Zui Fujimoto: </p>
<hr />
<div><br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He has determined the crystal structures of<br />
<br />
* GH10 endo-1,4-β-xylanase <cite>Fujimoto2000</cite><br />
* GH13 α-amylase <cite>Fujimoto1998 Suvd2001</cite><br />
* GH27 α-galactosidase <cite>Fujimoto2003 Fujimoto2009</cite> and β-L-arabinopyranosidase <cite>Ichinose2009</cite><br />
* GH43 exo-1,5-α-L-arabinofuranosidase <cite>Fujimoto2010</cite><br />
* GH66 dextranase <cite>Suzuki2012</cite> and cycloisomaltooligosaccharide glucanotransferase<br />
* GH79 β-glucuronidase <cite>Michikawa2012</cite><br />
* GT5 starch synthase <cite>Momma2012</cite><br />
<br />
<br />
----<br />
<biblio><br />
#Fujimoto2000 pmid=10884353<br />
#Fujimoto1998 pmid=9514750<br />
#Suvd2001 pmid=11226887<br />
#Fujimoto2003 pmid=12657636<br />
#Fujimoto2009 pmid=19809163<br />
#Ichinose2009 pmid=19608743<br />
#Fujimoto2010 pmid=20739278<br />
#Suzuki2012 pmid=22337884<br />
#Michikawa2012 pmid=22367201<br />
#Momma2012 pmid=22878205<br />
</biblio></div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7708User:Zui Fujimoto2012-11-07T09:30:48Z<p>Zui Fujimoto: </p>
<hr />
<div><br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He has determined the crystal structures of<br />
<br />
* GH10 endo-1,4-β-xylanase [1]<br />
* GH13 α-amylase [2] [3]<br />
* GH27 α-galactosidase [4] [5] and β-L-arabinopyranosidase [6]<br />
* GH43 exo-1,5-α-L-arabinofuranosidase [7]<br />
* GH66 dextranase [8] and cycloisomaltooligosaccharide glucanotransferase<br />
* GH79 β-glucuronidase [9]<br />
* GT5 starch synthase [10]<br />
<br />
<br />
# Fujimoto Z, Kuno A, Kaneko S, Yoshida S, Kobayashi H, Kusakabe I, Mizuno H. Crystal structure of ''Streptomyces olivaceoviridis'' E-86 β-xylanase containing xylan-binding domain. ''J Mol Biol'' 2000 '''300'''(3):575-585. PMID:10884353<br />
# Fujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H. Crystal structure of a catalytic-site mutant α-amylase from ''Bacillus subtilis'' complexed with maltopentaose. ''J Mol Biol'' 1998 '''277'''(2):393-407. PMID:9514750<br />
# Suvd D, Fujimoto Z, Takase K, Matsumura M, Mizuno H. Crystal structure of ''Bacillus stearothermophilus'' α-amylase: possible factors determining the thermostability. ''J Biochem'' 2001 '''129'''(3):461-468. PMID:11226887<br />
# Fujimoto Z, Kaneko S, Momma M, Kobayashi H, Mizuno H. Crystal structure of rice α-galactosidase complexed with D-galactose. ''J Biol Chem'' 2003 '''278'''(22):20313-20318. PMID:12657636<br />
# Fujimoto Z, Kaneko S, Kim WD, Park GG, Momma M, Kobayashi H. The tetramer structure of the glycoside hydrolase family 27α-galactosidase I from ''Umbelopsis vinacea''. ''Biosci Biotechnol Biochem'' 2009 '''73'''(10):2360-2364. PMID:19809163<br />
# Ichinose H, Fujimoto Z, Honda M, Harazono K, Nishimoto Y, Uzura A, Kaneko S. A β-L-arabinopyranosidase from ''Streptomyces avermitilis'' is a novel member of glycoside hydrolase family 27. ''J Biol Chem'' 2009 '''284'''(37):25097-25106. PMID:19608743<br />
# Fujimoto Z, Ichinose H, Maehara T, Honda M, Kitaoka M, Kaneko S. Crystal structure of an exo-1,5-α-L-arabinofuranosidase from ''Streptomyces avermitilis'' provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43. ''J Biol Chem'' 2010 '''285'''(44):34134-34143. PMID:20739278<br />
# Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A. Structural elucidation of dextran degradation mechanism by ''streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J Biol Chem'' 2012 '''287'''(24):19916-19926. PMID:22337884<br />
# Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers SG, Fujimoto Z, Kaneko S. Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from ''Acidobacterium capsulatum''. ''J Biol Chem'' 2012 '''287'''(17):14069-14077. PMID:22367201<br />
# Momma M, Fujimoto Z. Interdomain disulfide bridge in the rice granule bound starch synthase I catalytic domain as elucidated by x-ray structure analysis. ''Biosci Biotechnol Biochem'' 2012 '''76'''(8):1591-1595. PMID:22878205</div>Zui Fujimotohttps://www.cazypedia.org/index.php?title=User:Zui_Fujimoto&diff=7707User:Zui Fujimoto2012-11-07T09:28:54Z<p>Zui Fujimoto: Created page with " '''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the..."</p>
<hr />
<div><br />
<br />
'''Zui FUJIMOTO''' is a research scientist in [http://www.nias.affrc.go.jp/index_e.html National Institute of Agrobiological Sciences], Japan. He received his Ph.D. from the Graduate School of Agricultural and Life Sciences, The University of Tokyo. His research interests are the structural insights into protein functions of agricultural and food chemical use. He has determined the crystal structures of<br />
<br />
GH10 endo-1,4-β-xylanase [1]<br />
GH13 α-amylase [2] [3]<br />
GH27 α-galactosidase [4] [5] and β-L-arabinopyranosidase [6]<br />
GH43 exo-1,5-α-L-arabinofuranosidase [7]<br />
GH66 dextranase [8] and cycloisomaltooligosaccharide glucanotransferase<br />
GH79 β-glucuronidase [9]<br />
GT5 starch synthase [10]<br />
<br />
# Fujimoto Z, Kuno A, Kaneko S, Yoshida S, Kobayashi H, Kusakabe I, Mizuno H. Crystal structure of ''Streptomyces olivaceoviridis'' E-86 β-xylanase containing xylan-binding domain. ''J Mol Biol'' 2000 '''300'''(3):575-585. PMID:10884353<br />
# Fujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H. Crystal structure of a catalytic-site mutant α-amylase from ''Bacillus subtilis'' complexed with maltopentaose. ''J Mol Biol'' 1998 '''277'''(2):393-407. PMID:9514750<br />
# Suvd D, Fujimoto Z, Takase K, Matsumura M, Mizuno H. Crystal structure of ''Bacillus stearothermophilus'' α-amylase: possible factors determining the thermostability. ''J Biochem'' 2001 '''129'''(3):461-468. PMID:11226887<br />
# Fujimoto Z, Kaneko S, Momma M, Kobayashi H, Mizuno H. Crystal structure of rice α-galactosidase complexed with D-galactose. ''J Biol Chem'' 2003 '''278'''(22):20313-20318. PMID:12657636<br />
# Fujimoto Z, Kaneko S, Kim WD, Park GG, Momma M, Kobayashi H. The tetramer structure of the glycoside hydrolase family 27α-galactosidase I from ''Umbelopsis vinacea''. ''Biosci Biotechnol Biochem'' 2009 '''73'''(10):2360-2364. PMID:19809163<br />
# Ichinose H, Fujimoto Z, Honda M, Harazono K, Nishimoto Y, Uzura A, Kaneko S. A β-L-arabinopyranosidase from ''Streptomyces avermitilis'' is a novel member of glycoside hydrolase family 27. ''J Biol Chem'' 2009 '''284'''(37):25097-25106. PMID:19608743<br />
# Fujimoto Z, Ichinose H, Maehara T, Honda M, Kitaoka M, Kaneko S. Crystal structure of an exo-1,5-α-L-arabinofuranosidase from ''Streptomyces avermitilis'' provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43. ''J Biol Chem'' 2010 '''285'''(44):34134-34143. PMID:20739278<br />
# Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A. Structural elucidation of dextran degradation mechanism by ''streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J Biol Chem'' 2012 '''287'''(24):19916-19926. PMID:22337884<br />
# Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers SG, Fujimoto Z, Kaneko S. Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from ''Acidobacterium capsulatum''. ''J Biol Chem'' 2012 '''287'''(17):14069-14077. PMID:22367201<br />
# Momma M, Fujimoto Z. Interdomain disulfide bridge in the rice granule bound starch synthase I catalytic domain as elucidated by x-ray structure analysis. ''Biosci Biotechnol Biochem'' 2012 '''76'''(8):1591-1595. PMID:22878205</div>Zui Fujimoto