Glycoside Hydrolase Family 78 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:14:59Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Zui Fujimoto: /* Substrate specificities */

2015-05-22T05:57:38Z

Substrate specificities

Harry Brumer: /* Three-dimensional structures */

2015-05-19T17:32:25Z

Three-dimensional structures

Zui Fujimoto: /* References */

2015-05-19T10:07:57Z

References

Zui Fujimoto: /* Three-dimensional structures */

2015-05-19T10:07:08Z

Three-dimensional structures

Spencer Williams at 03:07, 6 February 2015

2015-02-06T03:07:17Z

Spencer Williams at 04:07, 31 January 2015

2015-01-31T04:07:55Z

Spencer Williams at 03:59, 31 January 2015

2015-01-31T03:59:17Z

Harry Brumer: /* References */

2015-01-23T23:37:00Z

References

Harry Brumer: /* Family Firsts */

2015-01-23T23:36:38Z

Family Firsts

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Zui Fujimoto^^^
+* [[Author]]: [[User:Zui Fujimoto|Zui Fujimoto]]
-* [[Responsible Curator]]:  ^^^Zui Fujimoto^^^
+* [[Responsible Curator]]:  [[User:Zui Fujimoto|Zui Fujimoto]]
 ----

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 == Substrate specificities ==
-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>.
+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>.
 == Kinetics and Mechanism ==

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 == Three-dimensional structures ==
-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.
+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.
 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.

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 #Koseki2008 pmid=18633609
 #Ichinose2013 pmid=23291751
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH078]]

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 == Three-dimensional structures ==
-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>.  More recently, the crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with the product L-rhamnose has been reported, revealing key active-site details (PDB IDs [{{PDBlink}}3w5m 3w5m], [{{PDBlink}}3w5n 3w5n]) <cite>Fujimoto2013</cite>.
+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.
-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>.
+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.
 == Family Firsts ==

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 == Catalytic Residues ==
-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 proton donor (acid), responsible for assisting leaving-group departure, in the [[inverting]] mechanism used by the enzyme <cite>Fujimoto2013</cite>.  All characterized α-L-rhamnosidases appear to contain a corresponding glutamate as the catalytic general base.
+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 proton donor (acid), responsible for assisting leaving-group departure, in the [[inverting]] mechanism used by the enzyme <cite>Fujimoto2013</cite>.  All characterized α-L-rhamnosidases appear to contain a corresponding glutamate as the catalytic general base.
 == Three-dimensional structures ==

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 == Substrate specificities ==
-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.  α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.
+Family GH78 genes are found in bacteria and fungi. The characterized activity of this family is hydrolysis of α-L-rhamnosides (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, including: flavonoid glycosides such as naringin, hesperidin and rutin, polysaccharides such as rhamnogalacturonan and arabinogalactan-protein, or glycolipids.  α-L-Rhamnosidases have been found to be one component of rhamnogalacturonan hydrolase <cite>Mutter1994</cite>, or naringinase <cite>Young1989</cite>.
 == Kinetics and Mechanism ==
-GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.  A number of 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>.
+GH78 enzymes hydrolyze glycosidic bonds through an [[inverting]] mechanism as elucidated by proton NMR <cite>Pitson1998, Zverlov2000</cite>.  A number of 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>.
 == Catalytic Residues ==
-The 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 proton donor (acid), responsible for assisting leaving-group departure, in the [[inverting]] mechanism used by the enzyme <cite>Fujimoto2013</cite>.  All characterized α-L-rhamnosidases appear to contain a corresponding glutamate as the catalytic general base.
+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 proton donor (acid), responsible for assisting leaving-group departure, in the [[inverting]] mechanism used by the enzyme <cite>Fujimoto2013</cite>.  All characterized α-L-rhamnosidases appear to contain a corresponding glutamate as the catalytic general base.
 == Three-dimensional structures ==
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 == Family Firsts ==
 ;First stereochemistry determination: ''Aspergillus aculeatus'' α-L-rhamnosidase (RhaA), by <sup>1</sup>H-NMR <cite>Pitson1998</cite>.
-;First general base residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.
+;First [[general base]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.
-;First general acid residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.
+;First [[general acid]] residue identification: ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data <cite>Fujimoto2013</cite>.
 ;First 3-D structure: ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) (PDB IDs [{{PDBlink}}2okx 2okx]) <cite>Cui2007</cite>.

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 == References ==
 <biblio>
 #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]
 #Mutter1994 pmid=7972516