Glycoside Hydrolase Family 53 - Revision history

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

2021-12-18T21:16:41Z

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

Harry Brumer: Text replacement - "Leila Lo Leggio" to "Leila LoLeggio"

2021-12-18T20:59:45Z

Text replacement - "Leila Lo Leggio" to "Leila LoLeggio"

Leila LoLeggio: /* Function and Substrate specificities */

2015-05-29T16:41:29Z

Function and Substrate specificities

Leila LoLeggio: /* Substrate specificities */

2015-05-29T16:33:37Z

Substrate specificities

Harry Brumer: updated CAZyDBlink

2012-09-10T16:39:16Z

updated CAZyDBlink

Spencer Williams at 03:11, 14 June 2011

2011-06-14T03:11:33Z

Spencer Williams at 04:19, 13 June 2010

2010-06-13T04:19:06Z

Harry Gilbert: /* Catalytic Residues */

2010-02-21T23:56:29Z

Catalytic Residues

Harry Brumer: /* Catalytic Residues */

2010-02-10T14:06:56Z

Catalytic Residues

Harry Brumer: /* Substrate specificities */

2010-02-10T14:05:16Z

Substrate specificities

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

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Leila Lo Leggio^^^
+* [[Author]]: ^^^Leila LoLeggio^^^
-* [[Responsible Curator]]:  ^^^Leila Lo Leggio^^^
+* [[Responsible Curator]]:  ^^^Leila LoLeggio^^^
 ----

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 == Function and Substrate specificities ==
-The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.In a number of bacteria, GH53 &beta;-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 &beta;-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.
+The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed. In a number of bacteria, GH53 &beta;-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 &beta;-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.
 == Kinetics and Mechanism ==

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-== Substrate specificities ==
+== Function and Substrate specificities ==
-The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.
+The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.In a number of bacteria, GH53 &beta;-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 &beta;-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.
 == Kinetics and Mechanism ==

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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH53.html
+| colspan="2" |{{CAZyDBlink}}GH53.html
 |}
 </div>

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 == Substrate specificities ==
-The only known specificity for [[glycoside hydrolase]]s of this family is beta-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.
+The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.
 == Kinetics and Mechanism ==
-GH53 beta-1,4-galactanases follow a [[retaining]] mechanism as first demonstrated by following the stereochemical course of rection for the endo-beta-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' (at that time referred to as ''Pseudomonas fluorescens'' subspecies ''cellulosa'') <cite>Braithwaite1997</cite>. Most characterized members have been reported to be [[endo]]-acting, although processivity has been suggested in one case <cite>Hinz2005</cite>.
+GH53 &beta;-1,4-galactanases follow a [[retaining]] mechanism as first demonstrated by following the stereochemical course of rection for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' (at that time referred to as ''Pseudomonas fluorescens'' subspecies ''cellulosa'') <cite>Braithwaite1997</cite>. Most characterized members have been reported to be [[endo]]-acting, although processivity has been suggested in one case <cite>Hinz2005</cite>.
 == Catalytic Residues ==
-The catalytic residues were first identified for the [[endo]]-beta-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as a [[general acid/base]] (E161) and the other as a [[catalytic nucleophile]] (E270).
+The catalytic residues were first identified for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as a [[general acid/base]] (E161) and the other as a [[catalytic nucleophile]] (E270).
 == Three-dimensional structures ==
-As for all members of Clan GH-A <cite>Jenkins1995, Henrissat1995</cite>, structurally characterized GH53 enzymes <cite>Ryttersgaard2002,LeNours2003,Ryttersgaard2004</cite> display a (beta/alpha)8 barrel structure for the catalytic domain, usually with fairly compact loop structure and a sequence under 400 residues in length. The catalytic residues are typically positioned at the C-terminal ends of beta strands 4 and 7 in the barrel. Somewhat unusually, none of the four structurally characterized GH53 catalytic domains was accompanied by other catalytic domains or accessory modules, but modularity can be inferred by sequence in other members of the family. A disulphide bridging two loops (beta/alpha loops 7 and 8) in 3 known fungal structures <cite>Ryttersgaard2002,LeNours2003</cite>, is replaced functionally by a calcium ion in one bacterial structure <cite>Ryttersgaard2004</cite>.  For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 <cite>Ryttersgaard2004,LeNours2009</cite>. Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled <cite>LeNours2009</cite>.
+As for all members of Clan GH-A <cite>Jenkins1995, Henrissat1995</cite>, structurally characterized GH53 enzymes <cite>Ryttersgaard2002,LeNours2003,Ryttersgaard2004</cite> display a (&beta;/&alpha;)<sub>8</sub> barrel structure for the catalytic domain, usually with fairly compact loop structure and a sequence under 400 residues in length. The catalytic residues are typically positioned at the C-terminal ends of &beta;strands 4 and 7 in the barrel. Somewhat unusually, none of the four structurally characterized GH53 catalytic domains was accompanied by other catalytic domains or accessory modules, but modularity can be inferred by sequence in other members of the family. A disulphide bridging two loops (&beta;/&alpha; loops 7 and 8) in 3 known fungal structures <cite>Ryttersgaard2002,LeNours2003</cite>, is replaced functionally by a calcium ion in one bacterial structure <cite>Ryttersgaard2004</cite>.  For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 <cite>Ryttersgaard2004,LeNours2009</cite>. Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled <cite>LeNours2009</cite>.
 == Family Firsts ==
-;First stereochemistry determination: ''Cellvibrio japonicus'' endo-beta-1,4-galactanase <cite>Braithwaite1997</cite>.
+;First stereochemistry determination: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.
-;First [[catalytic nucleophile]] identification: ''Cellvibrio japonicus'' endo-beta-1,4-galactanase <cite>Braithwaite1997</cite>.
+;First [[catalytic nucleophile]] identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.
-;First [[general acid/base]] residue identification: ''Cellvibrio japonicus'' endo-beta-1,4-galactanase <cite>Braithwaite1997</cite>.
+;First [[general acid/base]] residue identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.
-;First 3-D structure: ''Aspergillus aculeatus'' endo-beta-1,4-galactanase <cite>Ryttersgaard2002</cite>.
+;First 3-D structure: ''Aspergillus aculeatus'' endo-&beta;-1,4-galactanase <cite>Ryttersgaard2002</cite>.
 == References ==

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 == Catalytic Residues ==
-The catalytic residues were first identified for the endo-beta-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). As expected for a member for clan GH-A, the two catalytic residues were, by a combination of mutagenesis and kinetic analysis, identified to be two glutamates, one acting as an acid-base (E161) and the other as a nucleophile (E270).
+The catalytic residues were first identified for the endo-beta-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as an acid-base (E161) and the other as a nucleophile (E270).
 == Three-dimensional structures ==