Polysaccharide Lyase Family 15 - Revision history

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

2021-12-18T21:17:04Z

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

Birte Svensson at 12:01, 19 June 2020

2020-06-19T12:01:01Z

Harry Brumer: resized figure 2

2020-06-15T21:29:46Z

resized figure 2

Emil Stender at 08:34, 15 June 2020

2020-06-15T08:34:44Z

Emil Stender at 08:34, 15 June 2020

2020-06-15T08:34:23Z

Emil Stender at 08:22, 5 July 2019

2019-07-05T08:22:38Z

Emil Stender at 08:12, 5 July 2019

2019-07-05T08:12:00Z

Emil Stender at 11:24, 4 July 2019

2019-07-04T11:24:14Z

Harry Brumer: Added PDB link

2019-07-03T15:19:50Z

Added PDB link

Harry Brumer: Added DOI links to Acta Chem. Scand. references, minor grammatical correction

2019-07-03T15:17:28Z

Added DOI links to Acta Chem. Scand. references, minor grammatical correction

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Emil Stender^^^
+* [[Author]]: [[User:Emil Stender|Emil Stender]]
-* [[Responsible Curator]]:  ^^^Birte Svensson^^^
+* [[Responsible Curator]]:  [[User:Birte Svensson|Birte Svensson]]
 ----

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Emil Stender^^^
 * [[Responsible Curator]]:  ^^^Birte Svensson^^^

@@ Line 42: / Line 42: @@
 == Three-dimensional structures ==
-[[Image:Atu3025_structure.png|thumb|500px|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB ID [{{PDBlink}}3AFL 3AFL]) with the MGG substrate in blue.]]
+[[Image:Atu3025_structure.png|thumb|400px|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB ID [{{PDBlink}}3AFL 3AFL]) with the MGG substrate in blue.]]
 The first crystal structure available for a PL15 member was that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)<sub>6</sub> barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.

@@ Line 35: / Line 35: @@
 == Kinetics and Mechanism ==
-[[Image:Catalytic_PL15.png|thumb|400px|'''Figure 1''' +1 subsite of the alginate lyase Atu3025 with the MGG substrate]]
+[[Image:Catalytic_PL15.png|thumb|400px|'''Figure 1''' +1 subsite of the alginate lyase Atu3025 with the MGG substrate.]]
 The β-elimination catalyzed by the PL15 enzymes results in the formation of a C4-C5 unsaturated sugar residue at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by the conserved H531 and R314 (Atu3025 numbering)<cite>Ochiai2010</cite>. This lowers the pKa value of the C5-proton allowing for abstraction by the catalytic base (Figure 1). A catalytic acid then donates a proton to the glycosidic linkage resulting in the β-elimination.

@@ Line 32: / Line 32: @@
 == Substrate specificities ==
-PL15 contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins not assigned to any subfamily. Subfamily 1 has been shown to only degrade alginate <cite>Miyake2003,Ochiai2010,Jagtap2014,Hashimoto20005</cite> while subfamily 2 has been found to be heparin and heparan sulfate lyases <cite>Cartmell2017,Helbert2019</cite>. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks <cite>Haug1967, Haug1966</cite>. Heparin consisting of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-L-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-D-glucuronic acid with a considerably more variable sulfation and acetylation pattern <cite>Garron2010</cite>.
+PL15 contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins not assigned to any subfamily. Subfamily 1 has been shown to only degrade alginate <cite>Miyake2003,Ochiai2010,Jagtap2014,Hashimoto20005</cite> while subfamily 2 has been found to be heparin and heparan sulfate lyases <cite>Cartmell2017,Helbert2019</cite>. Alginate consist of 1,4 linked β-{{Smallcaps|D}}-mannuronic acid and α-{{Smallcaps|L}}-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks <cite>Haug1967, Haug1966</cite>. Heparin consist of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-{{Smallcaps|L}}-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-{{Smallcaps|D}}-glucuronic acid with a considerably more variable sulfation and acetylation pattern <cite>Garron2010</cite>.
 == Kinetics and Mechanism ==
-[[Image:Catalytic_PL15.png|thumb|400px|'''Figure 1''' +1 subsite of the alginate lyase Atu3025]]
+[[Image:Catalytic_PL15.png|thumb|400px|'''Figure 1''' +1 subsite of the alginate lyase Atu3025 with the MGG substrate]]
-The β-elimination catalyzed by the PL15 enzymes results in the formation of a C4-C5 unsaturated sugar at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by the conserved H531 and R314 (Atu3025 numbering)<cite>Ochiai2010</cite>. This lowers the pKa value of the C5-proton allowing for abstraction by the catalytic base (Figure 1). A catalytic acid then donates a proton to the glycosidic linkage resulting in the β-elimination.
+The β-elimination catalyzed by the PL15 enzymes results in the formation of a C4-C5 unsaturated sugar residue at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by the conserved H531 and R314 (Atu3025 numbering)<cite>Ochiai2010</cite>. This lowers the pKa value of the C5-proton allowing for abstraction by the catalytic base (Figure 1). A catalytic acid then donates a proton to the glycosidic linkage resulting in the β-elimination.
 == Catalytic Residues ==
-After charge neutralization a histidine functions as the catalytic base and a tyrosine the acid. They were originally identified as H311 and Y365 in Atu3025 from ''Agrobacterium fabrum'' <cite>Ochiai2010</cite>.
+After charge neutralization a histidine functions as the catalytic base and a tyrosine as the acid. They were originally identified as H311 and Y365 in Atu3025 from ''Agrobacterium fabrum'' <cite>Ochiai2010</cite>.
 == Three-dimensional structures ==
-[[Image:Atu3025_structure.png|thumb|500px|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB ID [{{PDBlink}}3AFL 3AFL]) with the substrate in blue.]]
+[[Image:Atu3025_structure.png|thumb|500px|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB ID [{{PDBlink}}3AFL 3AFL]) with the MGG substrate in blue.]]
-The first crystal structure available for a PL15 memberwas that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)<sub>6</sub> barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
+The first crystal structure available for a PL15 member was that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)<sub>6</sub> barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
 == Family Firsts ==
 ;First catalytic activity: Alginate lyase IV from ''Sphingomonas sp'' activity shown against alginate di- and trisaccharides by TLC from purified protein  <cite>Miyake2003</cite>.
-;First catalytic base/acid: Atu3025 from ''Agrobacterium fabrum''. H311 and Y365 was suggested as Acid/base based upon the crystal structure of the substrate complex, residue conservation, mutagenesis and activity analysis (H311A: inactive and Y365A: 0.3 % activity remaining)<cite>Ochiai2010</cite>.
+;First catalytic base/acid: Atu3025 from ''Agrobacterium fabrum''. H311 and Y365 was suggested as acid/base based upon the crystal structure of the substrate complex, residue conservation, mutagenesis and activity analysis (H311A: inactive and Y365A: 0.3 % activity remaining)<cite>Ochiai2010</cite>.
 ;First charge neutralizer: Atu3025 from ''Agrobacterium fabrum'' H531 was suggested based on the crystal structure, its conservation, mutagenesis and activity analysis (H531A 0.45 % activity). R314 is proposed based on its proximity to the carboxylate group in the +1 subsite and its conservation <cite>Ochiai2010</cite>.
 ;First 3-D structure: Atu3025 from ''Agrobacterium fabrum'' an exo alginate lyase from subfamily 1 <cite>Ochiai2010</cite>.

@@ Line 32: / Line 32: @@
 == Substrate specificities ==
-PL15 currently contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins currently not assigned to any subfamily. Subfamily one has been shown to only degrade alginate <cite>Miyake2003,Ochiai2010,Jagtap2014,Hashimoto20005</cite> while subfamily 2 has been found to be heparin and heparan sulfate lyases <cite>Cartmell2017,Helbert2019</cite>. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks <cite>Haug1967, Haug1966</cite>. Heparin consisting of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-L-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-D-glucuronic acid with a considerably more variable sulfation and acetylation pattern <cite>Garron2010</cite>.
+PL15 currently contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins not assigned to any subfamily. Subfamily 1 has been shown to only degrade alginate <cite>Miyake2003,Ochiai2010,Jagtap2014,Hashimoto20005</cite> while subfamily 2 has been found to be heparin and heparan sulfate lyases <cite>Cartmell2017,Helbert2019</cite>. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks <cite>Haug1967, Haug1966</cite>. Heparin consisting of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-L-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-D-glucuronic acid with a considerably more variable sulfation and acetylation pattern <cite>Garron2010</cite>.
 == Kinetics and Mechanism ==
@@ Line 43: / Line 43: @@
 == Three-dimensional structures ==
 [[Image:Atu3025_structure.png|thumb|1000|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB ID [{{PDBlink}}3AFL 3AFL]) with the substrate in blue.]]
-As of 2019, there is only a single crystal structure available for a PL15 member, that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)6 barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
+As of 2019, there is only a single crystal structure available for a PL15 member, that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)<sub>6</sub> barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
 == Family Firsts ==

@@ Line 43: / Line 43: @@
 == Three-dimensional structures ==
 [[Image:Atu3025_structure.png|thumb|1000|'''Figure 2''' Crystal structures of the substrate complex of the monomeric Atu3025 (PDB: 3AFL) with the substrate in blue.]]
-There is only a single crystal structure available in PL15. That of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)6 barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
+As of 2019, there is only a single crystal structure available for a PL15 member, that of the alginate lyase Atu3025 from ''Agrobacterium fabrum'' (Figure 2) <cite>Ochiai2010</cite>. The catalytic domains consists of an N-terminal (α/α)6 barrel domain  and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)<sub>6</sub> barrel  and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain <cite>Ochiai2010</cite>.
 == Family Firsts ==
@@ Line 60: / Line 60: @@
 #Cartmell2017 pmid=28630303
 #Helbert2019 pmid=30850540
-#Haug1967 Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704
+#Haug1967 Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704. [http://dx.doi.org/10.3891/acta.chem.scand.21-0691 DOI:10.3891/acta.chem.scand.21-0691]
-#Haug1966 Haug, A., Larsen, B., and Smidsrod, O. (1966) A study of constitution of alginic acid by partial acid hydrolysis. Acta Chem. Scand. 20, 183–190
+#Haug1966 Haug, A., Larsen, B., and Smidsrod, O. (1966) A study of constitution of alginic acid by partial acid hydrolysis. Acta Chem. Scand. 20, 183–190. [http://dx.doi.org/10.3891/acta.chem.scand.20-0183 DOI:10.3891/acta.chem.scand.20-0183]
 #Garron2010 pmid=20805221