Glycoside Hydrolase Family 86 - Revision history

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

2021-12-18T21:14:36Z

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

Mirjam Czjzek: /* Substrate specificities */

2014-01-06T08:27:02Z

Substrate specificities

Mirjam Czjzek: /* Substrate specificities */

2014-01-06T08:18:08Z

Substrate specificities

Mirjam Czjzek: /* Substrate specificities */

2014-01-06T08:07:48Z

Substrate specificities

Mirjam Czjzek: /* Substrate specificities */

2014-01-06T08:06:35Z

Substrate specificities

Mirjam Czjzek at 17:22, 18 December 2013

2013-12-18T17:22:08Z

Mirjam Czjzek: /* Family Firsts */

2013-12-18T17:17:51Z

Family Firsts

Mirjam Czjzek at 16:48, 18 December 2013

2013-12-18T16:48:12Z

Mirjam Czjzek: /* Kinetics and Mechanism */

2013-12-18T16:23:36Z

Kinetics and Mechanism

Mirjam Czjzek: /* Substrate specificities */

2013-12-18T16:20:11Z

Substrate specificities

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 {{CuratorApproved}}
-* [[Author]]: ^^^Mirjam Czjzek^^^
+* [[Author]]: [[User:Mirjam Czjzek|Mirjam Czjzek]]
-* [[Responsible Curator]]:  ^^^Mirjam Czjzek^^^
+* [[Responsible Curator]]:  [[User:Mirjam Czjzek|Mirjam Czjzek]]
 ----

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating α-1,3-linked 3,6-anhydro-L-galactose (LA) and β-1,4-linked D-galactose (G) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysaccharide chain is ideally made of alternating 1,3-linked β-D-galactose (G) and 1,4-linked 3,6-anhydro-α-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating α-1,3-linked D-galactose (G) and β-1,4-linked 3,6-anhydro-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating α-1,3-linked 3,6-anhydro-L-galactose (LA) and β-1,4-linked D-galactose (G) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating β-1,3-linked D-galactose (G) and α-1,4-linked 3,6-anhydro-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating α-1,3-linked D-galactose (G) and β-1,4-linked 3,6-anhydro-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  This polysacchride chain is ideally made of alternating β-1,3-linked D-galactose (G) and α-1,4-linked 3,6-anhydro-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Osamu2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Ariga2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==
@@ Line 52: / Line 52: @@
 #Ekborg2006 pmid=16672483
 #Hehemann2012 pmid=23150581
+#Ariga2012 pmid=22814498
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH086]]

@@ Line 44: / Line 44: @@
 ;First catalytic nucleophile identification: Glu279 in BpGH86A from ''B.plebeius''.
 ;First general acid/base residue identification: Glu152 in BpGH86A from ''B.plebeius''.
-;First 3-D structure: BpGH86A from ''B.plebeius'', 4AW7.
+;First 3-D structure: The crystal structure of BpGH86A from ''B.plebeius'', ([{{PDBlink}}4aw7 PDB 4aw7]).
 == References ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Osamu2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The main products released by the endo-acting enzyme that cleaves &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
+[[Glycoside hydrolases]] of family 86 have first been identified to be &beta;-agarases (EC [{{EClink}}3.2.1.81 3.2.1.81]) that cleave &beta;-1,4 glycosidic bonds of agarose.  Four agarolytic enzymes have been characterized: AgrA from ''Pseudoalteromonas atlantica'', AgaO from ''Microbulbifer thermotolerans JAMB-A94'', Aga86E from ''Saccharophagus degradans 2-40'' <cite>Belas1989,Ohta2004,Ekborg2006</cite> and more recently a GH86 &beta;-agarase from a non marine ''Vibrio'' species (sp. OA-2007)<cite>Osamu2012</cite>. AgaO from ''M. thermotolerans'' was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product <cite>Ohta2004</cite>, while the recombinant Aga86E from ''S. degradans'' released only neoagarobiose in an exo-acting manner <cite>Ekborg2006</cite>. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes ''B. plebeius'' that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of &beta;-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ <cite>Hehemann2012</cite>.
 == Kinetics and Mechanism ==
-A potential retaining mechanism of this glycoside hydrolase family can be inferred from analogy to clan [{{CAZyDBlink}}Glycoside-Hydrolases.html GH-A enzymes] and is confirmed by structural analyses of a product complex that shows an arrangement of the putative catalytic residues in agreement with the double displacement mechanism . No mechanistic or kinetic analysis demonstrating the stereochemical outcome of the reaction have been reported for this family to date.
+A potential retaining mechanism of this glycoside hydrolase family can be inferred from analogy to clan [{{CAZyDBlink}}Glycoside-Hydrolases.html GH-A enzymes], and is confirmed by structural analyses of a product complex showing an arrangement of the putative catalytic residues that is in agreement with the double displacement mechanism <cite>Hehemann2012</cite>. However, no mechanistic or kinetic analysis demonstrating the stereochemical outcome of the reaction have been reported for this family to date.
 == Catalytic Residues ==
-Actually, the catalytic residues can only be inferred from analogy to clan GH-A enzymes as two glutamate residues.
+The catalytic residues can be inferred from the crystal structure and by analogy to clan GH-A enzymes as two glutamate residues, which are Glu152 (acid/base) and Glu279 (nucleophile) in BpGH86A from ''B. plebeius'' <cite>Hehemann2012</cite>.
 == Three-dimensional structures ==
-No 3D structure is available to date.
+The first 3D structure was determined in 2012 by <cite>Hehemann2012</cite> et al. In agreement with distant sequence homology to clan [{{CAZyDBlink}}Glycoside-Hydrolases.html GH-A enzymes], the overall topology contains an N-terminal (β/α)<sub>8</sub> barrel. However the enzyme architecture is more complex and contains two additional Cterminal β-sandwich domains, which align via their convex faces to the exterior of the (β/α)<sub>8</sub> barrel and connect with two N-terminal β-strands that become part of these C-terminal β-sandwich domains.
 == Family Firsts ==
 ;Identification of first family member: The first member of this family, AgrA, was identified in ''Pseudoalteromonas atlantica'' <cite>Belas1989</cite>.
-;First stereochemistry determination: not determined yet.
+;First stereochemistry determination: the retaining mechanism is inferred from the arrangement of the most probable catalytic residues in the crystal structure of a product complex <cite>Hehemann2012</cite>.
-;First catalytic nucleophile identification: not determined yet.
+;First catalytic nucleophile identification: Glu279 in BpGH86A from ''B.plebeius''.
-;First general acid/base residue identification: not determined yet.
+;First general acid/base residue identification: Glu152 in BpGH86A from ''B.plebeius''.
-;First 3-D structure: not determined yet.
+;First 3-D structure: BpGH86A from ''B.plebeius'', 4AW7.
 == References ==