Polysaccharide Lyase Family 6 - Revision history

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

2021-12-18T21:16:52Z

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

Emil Stender at 13:21, 17 November 2020

2020-11-17T13:21:06Z

Harry Brumer at 18:24, 5 August 2020

2020-08-05T18:24:20Z

Birte Svensson at 11:57, 19 June 2020

2020-06-19T11:57:42Z

Emil Stender at 08:21, 15 June 2020

2020-06-15T08:21:58Z

Emil Stender at 11:34, 12 March 2020

2020-03-12T11:34:44Z

Emil Stender at 12:06, 26 February 2020

2020-02-26T12:06:37Z

Emil Stender at 12:04, 26 February 2020

2020-02-26T12:04:05Z

Emil Stender at 13:03, 21 February 2020

2020-02-21T13:03:57Z

Harry Brumer: Added DOI links to Acta Chem. Scand. references

2019-07-05T15:38:33Z

Added DOI links to Acta Chem. Scand. references

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 {{CuratorApproved}}
 * [[Author]]: [[User:Emil Stender|Emil G.P. Stender]]
-* [[Responsible Curator]]:  ^^^Birte Svensson^^^
+* [[Responsible Curator]]:  [[User:Birte Svensson|Birte Svensson]]
 ----

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 == Three-dimensional structures ==
 [[Image:PL6_structures.png|thumb|600px|'''Figure 2.''' Crystal structures of the monomeric chrondroitinase B and AlyF as well as the dimeric AlyGC. Catalytic residues and substrates are in green, the neutralizing calcium is the red sphere.]]
-PL6 catalytic domain adopts a parallel β-helix fold with the activesite located on the surface of one of the β-sheets (Figure 2). The first PL6 structure solved was the chrondoitinase B from ''Pedobacter heparinus'' (1.7 Å) <cite>Huang1999</cite> later it was shown that this enzyme is calcium dependent <cite>Michel2004</cite>. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) <cite>Xu2017</cite>. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) <cite>Lyu2019</cite>. The first mannuronic acid specific alginate lyase structure was ''Bcel''PL6 (1.3Å) from human gut ''Bacteroides cellulosilyticus'' <cite>Stender2019</cite>. All four structure belong to subfamily 1. There are no available crystal structures from subfamilies 2 and 3.
+PL6 catalytic domain adopts a parallel β-helix fold with the active site located on the surface of one of the β-sheets (Figure 2). The first PL6 structure solved was the chrondoitinase B from ''Pedobacter heparinus'' (1.7 Å) <cite>Huang1999</cite> later it was shown that this enzyme is calcium dependent <cite>Michel2004</cite>. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) <cite>Xu2017</cite>. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) <cite>Lyu2019</cite>. The first mannuronic acid specific alginate lyase structure was ''Bcel''PL6 (1.3Å) from human gut ''Bacteroides cellulosilyticus'' <cite>Stender2019</cite>. All four structures belong to subfamily 1. There are no available crystal structures from subfamilies 2 and 3.
 == Family Firsts ==

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 == Substrate specificities ==
-PL6 contains 3 subfamilies <cite>Lombard2010</cite> all of which contain members catalyzing the depolymerisation of alginate <cite>Mathieu2016</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>Haug1966 Haug1967</cite>. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks <cite>Mathieu2016</cite>, while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid <cite>Lyu2019 Xu2017</cite>, poly-mannuronic acid <cite>Maki1993 Stender2019</cite>, poly-mannuronic/guluronic acid <cite>Mathieu2016</cite> as well as dermatan sulfate (formerly chrondroitin B) <cite>Mathieu2016 #Huang1999 #Michel2004</cite>. Dermatan sulfate consist of N-acetyl galactosamine (GalNAc) and glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern <cite>Trowbridge2002</cite>.
+PL6 contains 3 subfamilies <cite>Lombard2010 Mathieu2016</cite> all of which contain members catalyzing the depolymerisation of alginate <cite>Mathieu2016</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>Haug1966 Haug1967</cite>. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks <cite>Mathieu2016</cite>, while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid <cite>Lyu2019 Xu2017</cite>, poly-mannuronic acid <cite>Maki1993 Stender2019</cite>, poly-mannuronic/guluronic acid <cite>Mathieu2016</cite> as well as dermatan sulfate (formerly chrondroitin B) <cite>Mathieu2016 #Huang1999 #Michel2004</cite>. Dermatan sulfate consist of N-acetyl galactosamine (GalNAc) and glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern <cite>Trowbridge2002</cite>.
 == Kinetics and Mechanism ==

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

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 == Substrate specificities ==
-PL6 contains 3 subfamilies <cite>Lombard2010</cite> all of which contain members catalyzing the depolymerisation of alginate <cite>Mathieu2016</cite>. Alginate consist 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>Haug1966 Haug1967</cite>. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks <cite>Mathieu2016</cite>, while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid <cite>Lyu2019 Xu2017</cite>, poly-mannuronic acid <cite>Maki1993 Stender2019</cite>, poly-mannuronic/guluronic acid <cite>Mathieu2016</cite> as well as dermatan sulfate (formerly chrondroitin B) <cite>Mathieu2016 #Huang1999 #Michel2004</cite>. Dermatan sulfate consist of N-acetyl galactosamine (GalNAc) and glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern <cite>Trowbridge2002</cite>.
+PL6 contains 3 subfamilies <cite>Lombard2010</cite> all of which contain members catalyzing the depolymerisation of alginate <cite>Mathieu2016</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>Haug1966 Haug1967</cite>. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks <cite>Mathieu2016</cite>, while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid <cite>Lyu2019 Xu2017</cite>, poly-mannuronic acid <cite>Maki1993 Stender2019</cite>, poly-mannuronic/guluronic acid <cite>Mathieu2016</cite> as well as dermatan sulfate (formerly chrondroitin B) <cite>Mathieu2016 #Huang1999 #Michel2004</cite>. Dermatan sulfate consist of N-acetyl galactosamine (GalNAc) and glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern <cite>Trowbridge2002</cite>.
 == Kinetics and Mechanism ==
 [[Image:PL6_lyase_mechanism.png|thumb|600px| '''Figure 1.''' ''Syn'' – or ''anti'' – β-elimination catalyzed by PL6 enzymes acting on alginate. M represents mannuronic acid and G guluronic acid. n represents the continued sugar chain. In both cases the catalytic base abstracts the C5 proton and an acid donates one resulting in the β-elimination of the 1,4 glycosidic linkage.]]
-The β-elimination catalyzed by the PL6 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 a calcium <cite>Xu2017 Michel2004</cite> or by water <cite>Lyu2019</cite>. This lowers the p''K''<sub>a</sub> 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. This can be done in ''syn'' with the acid and base on the same side of the sugar ring in the transition state (the case for D-mannuronic acid) or ''anti'' where they are on opposite sides of the sugar ring (the case for L-guluronic acid) <cite>Garron2010 Xu2018</cite>.
+The β-elimination catalyzed by the PL6 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 a calcium <cite>Xu2017 Michel2004</cite> or by water <cite>Lyu2019</cite>. This lowers the p''K''<sub>a</sub> 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. This can be done in ''syn'' with the acid and base on the same side of the sugar ring in the transition state (the case for {{Smallcaps|D}}-mannuronic acid) or ''anti'' where they are on opposite sides of the sugar ring (the case for {{Smallcaps|L}}-guluronic acid) <cite>Garron2010 Xu2018</cite>.
 == Catalytic Residues ==

@@ Line 35: / Line 35: @@
 == Kinetics and Mechanism ==
-[[Image:PL6_lyase_mechanism.png|thumb|600px| '''Figure 1.''' ''Syn'' – or ''anti'' – β-elimination catalyzed by PL6 enzymes acting on alginate. M represents mannuronic acid and G guluronic acid. n represents the continued sugar chain.]]
+[[Image:PL6_lyase_mechanism.png|thumb|600px| '''Figure 1.''' ''Syn'' – or ''anti'' – β-elimination catalyzed by PL6 enzymes acting on alginate. M represents mannuronic acid and G guluronic acid. n represents the continued sugar chain. In both cases the catalytic base abstracts the C5 proton and an acid donates one resulting in the β-elimination of the 1,4 glycosidic linkage.]]
-The β-elimination catalyzed by the PL6 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 a calcium <cite>Xu2017 Michel2004</cite> or by water <cite>Lyu2019</cite>. This lowers the pK<sub>a</sub> 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. This can be done in ''syn'' with the acid and base on the same side of the sugar ring in the transition state (the case for D-mannuronic acid) or ''anti'' where they are on opposite sides of the sugar ring (the case for L-guluronic acid) <cite>Garron2010 Xu2018</cite>.
+The β-elimination catalyzed by the PL6 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 a calcium <cite>Xu2017 Michel2004</cite> or by water <cite>Lyu2019</cite>. This lowers the p''K''<sub>a</sub> 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. This can be done in ''syn'' with the acid and base on the same side of the sugar ring in the transition state (the case for D-mannuronic acid) or ''anti'' where they are on opposite sides of the sugar ring (the case for L-guluronic acid) <cite>Garron2010 Xu2018</cite>.
 == Catalytic Residues ==
-After charge neutralization a lysine functions as the catalytic base and an arginine the acid. They were originally identified as K253 and R273 in chondroitinase B from ''Pedobacter Heparinus'' <cite>Huang1999</cite>. PL6 is the only discovered alginate lyase family that uses K/R as a catalytic base/acid pair <cite>Xu2018</cite>.
+After charge neutralization a lysine functions as the catalytic base and an arginine as the acid. They were originally identified as K253 and R273 in chondroitinase B from ''Pedobacter heparinus'' <cite>Huang1999</cite>. PL6 is so far the only discovered alginate lyase family that uses K/R as a catalytic base/acid pair <cite>Xu2018</cite>.
 == Three-dimensional structures ==
-[[Image:PL6_structures.png|thumb|600px|'''Figure 2.''' Crystal structures of the monomeric chrondroitinase B and AlyF aswell as the dimeric AlyGC. Catalytic residues and substrates are in green the neutralizing calcium is the red sphere.]]
+[[Image:PL6_structures.png|thumb|600px|'''Figure 2.''' Crystal structures of the monomeric chrondroitinase B and AlyF as well as the dimeric AlyGC. Catalytic residues and substrates are in green, the neutralizing calcium is the red sphere.]]
-PL6 catalytic domain adopts a parallel β-helix fold with the activesite located on the surface of one of the β-sheets (Figure 2). The first PL6 structure solved was the chrondoitinase B from ''Pedobacter Heparinus'' (1.7 Å) <cite>Huang1999</cite> later it was shown that this enzyme is calcium dependent <cite>Michel2004</cite>. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) <cite>Xu2017</cite>. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) <cite>Lyu2019</cite>. The first mannuronic acid specific alginate lyase structure was ''Bcel''PL6 (1.3Å) from human gut ''Bacteroides cellulosilyticus'' <cite>Stender2019</cite>. All four structure belong to subfamily 1. There are no available crystal structures from subfamilies 2 and 3.
+PL6 catalytic domain adopts a parallel β-helix fold with the activesite located on the surface of one of the β-sheets (Figure 2). The first PL6 structure solved was the chrondoitinase B from ''Pedobacter heparinus'' (1.7 Å) <cite>Huang1999</cite> later it was shown that this enzyme is calcium dependent <cite>Michel2004</cite>. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) <cite>Xu2017</cite>. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) <cite>Lyu2019</cite>. The first mannuronic acid specific alginate lyase structure was ''Bcel''PL6 (1.3Å) from human gut ''Bacteroides cellulosilyticus'' <cite>Stender2019</cite>. All four structure belong to subfamily 1. There are no available crystal structures from subfamilies 2 and 3.
 == Family Firsts ==
 ;First catalytic activity: OS-ALG-9 from ''Pseudomonas'' sp. on non-purified recombinant enzyme by the thiobarbituric acid method <cite>Maki1993</cite>
-;First catalytic base/acid: The catalytic arginine was originally identified in  Chondroitinase B from ''Pedobacter Heparinus'' based on the crystal structure, concervation, mutagenesis and activity analysis (R271E no activity, R271K 0.09 % activity) <cite>Michel2004</cite>. The catalytic lysine was identified later by conservation, mutagenesis and activity analysis  <cite>Xu2017</cite>
+;First catalytic base/acid: The catalytic arginine was originally identified in  Chondroitinase B from ''Pedobacter heparinus'' based on the crystal structure, concervation, mutagenesis and activity analysis (R271E no activity, R271K 0.09 % activity) <cite>Michel2004</cite>. The catalytic lysine was identified later based on  conservation, mutagenesis and activity analysis  <cite>Xu2017</cite>
 ;First charge neutralizer: Calcium in Chondroitinase B from ''Pedobacter Heparinus'' by by crystallography and assaying the effect of calcium on enzyme activity <cite>Michel2004</cite>.
 ;First 3-D structure: Chondroitinase B from ''Pedobacter Heparinus'' <cite>Huang1999</cite>.

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 #Lombard2010 pmid=20925655
 #Mathieu2016 pmid=27438604
-#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]
 #Lyu2019 pmid=31004719
 #Xu2017 pmid=28154171