Polysaccharide Lyase Family 17 - Revision history

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

2021-12-18T21:14:12Z

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

Birte Svensson at 12:01, 19 June 2020

2020-06-19T12:01:43Z

Emil Stender at 08:49, 15 June 2020

2020-06-15T08:49:54Z

Emil Stender at 12:39, 26 February 2020

2020-02-26T12:39:33Z

Harry Brumer at 15:49, 8 July 2019

2019-07-08T15:49:46Z

Emil Stender at 07:42, 8 July 2019

2019-07-08T07:42:34Z

Emil Stender at 07:36, 8 July 2019

2019-07-08T07:36:35Z

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

2019-07-04T15:13:13Z

Added DOI links to Acta Chem. Scand., Korean J. Chem. references

Emil Stender at 11:20, 4 July 2019

2019-07-04T11:20:58Z

Emil Stender at 11:19, 4 July 2019

2019-07-04T11:19:08Z

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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]]: ^^^Emil Stender^^^
+* [[Author]]: [[User:Emil Stender|Emil Stender]]
-* [[Responsible Curator]]:  ^^^Birte Svensson^^^
+* [[Responsible Curator]]:  [[User:Birte Svensson|Birte Svensson]]
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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]]: ^^^Emil Stender^^^
 * [[Responsible Curator]]:  ^^^Birte Svensson^^^

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 == Substrate specificities ==
-PL17 contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins currently not assigned to any subfamily. Subfamily 2 has been shown to be exolytic alginate lyases <cite>Jagtap2014,Park2014,Shin2015,Wang2015</cite> with activity for all tree block structures observed <cite>Mathieu2018</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>. Subfamily 1 has been found to be hyaluroran endo-lyases or poly-glucuronic acid lyases <cite>Mathieu2018</cite>. Hyaluronan consisting of ''N''-acetyl-D-glucoamine and 1,4 linked D-glucoronic acid <cite>Meyer1940</cite>.
+PL17 contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins currently not assigned to any subfamily. Subfamily 2 has been shown to be exolytic alginate lyases <cite>Jagtap2014,Park2014,Shin2015,Wang2015</cite> with activity for all three block structures observed <cite>Mathieu2018</cite>. Alginate consisting of 1,4 linked β-{{Smallcaps|D}}-mannuronic acid and α-{{Smallcaps|L}}-guluronic acid arranged in poly-mannuronic acid , poly-guluronic acid  or poly-mannuronic/guluronic acid blocks <cite>Haug1967,Haug1966</cite>. Subfamily 1 has been found to be hyaluroran endo-lyases or poly-glucuronic acid lyases <cite>Mathieu2018</cite>. Hyaluronan consisting of ''N''-acetyl-{{Smallcaps|D}}-glucoamine and 1,4 linked {{Smallcaps|D}}-glucoronic acid <cite>Meyer1940</cite>.
 == Kinetics and Mechanism ==
-[[Image:Cat_res_PL17.png|thumb|400px|'''Figure 1.''' +1 subsite of the alginate lyase Alg17c]]
+[[Image:Cat_res_PL17.png|thumb|400px|'''Figure 1.''' +1 subsite of the alginate lyase Alg17c (PDB: 4OJZ)]]
 The β-elimination catalyzed by the PL17 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 histidine and asparagine. 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 <cite>Park2014</cite>.
 == Catalytic Residues ==
-After charge neutralization a tyrosine functions as the catalytic base and another tyrosine the acid. They were originally identified as Y456 and Y258 in Alg17c from ''Saccharophagus degradans'' <cite>Park2014</cite>.
+After charge neutralization a tyrosine functions as the catalytic base and another tyrosine as the acid. These were originally identified as Y456 and Y258 in Alg17c from ''Saccharophagus degradans'' <cite>Park2014</cite>.
 == Three-dimensional structures ==
@@ Line 48: / Line 48: @@
 == Family Firsts ==
 ;First catalytic activity: MJ-3 alginate lyase assayed by monitoring the absorbance at 235 nm  and characterizing the degradation products by TLC and <sup>1</sup>H-NMR <cite>Park2012</cite>.
-;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (Y258A and Y450A inactive) <cite>Park2014</cite>
+;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis of mutants (Y258A and Y450A inactive) <cite>Park2014</cite>
 ;First charge neutralizer: N201 and H202 in the Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (N201A inactive and H202L 4.6 % activity remaining) <cite>Park2014</cite>
 ;First 3-D structure: Alg17c crystal structure <cite>Park2014</cite>

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 |-
 |'''Mechanism'''
-|β-eliminationg
+|β-elimination
 |-|-
 |'''Charge neutralizer'''
@@ Line 48: / Line 48: @@
 == Family Firsts ==
 ;First catalytic activity: MJ-3 alginate lyase assayed by monitoring the absorbance at 235 nm  and characterizing the degradation products by TLC and <sup>1</sup>H-NMR <cite>Park2012</cite>.
-;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (Y258 and Y450A inactive) <cite>Park2014</cite>
+;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (Y258A and Y450A inactive) <cite>Park2014</cite>
 ;First charge neutralizer: N201 and H202 in the Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (N201A inactive and H202L 4.6 % activity remaining) <cite>Park2014</cite>
 ;First 3-D structure: Alg17c crystal structure <cite>Park2014</cite>

@@ Line 48: / Line 48: @@
 == Family Firsts ==
 ;First catalytic activity: MJ-3 alginate lyase assayed by monitoring the absorbance at 235 nm  and characterizing the degradation products by TLC and <sup>1</sup>H-NMR <cite>Park2012</cite>.
-;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their concervation in PL17, mutagenesis and kinetic analysis (Y258 and Y450A inactive) <cite>Park2014</cite>
+;First catalytic base/acid: Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (Y258 and Y450A inactive) <cite>Park2014</cite>
-;First charge neutralizer: N201 and H202 in the Alg17c crystal structure identified by their concervation in PL17, mutagenesis and kinetic analysis (N201A inactive and H202L 4.6 % activity remaining) <cite>Park2014</cite>
+;First charge neutralizer: N201 and H202 in the Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (N201A inactive and H202L 4.6 % activity remaining) <cite>Park2014</cite>
 ;First 3-D structure: Alg17c crystal structure <cite>Park2014</cite>
 == References ==

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 One crystal structure is available in PL17, that of Alg17c from Saccharophagus degradans belonging to subfamily 2 <cite>Park2014</cite>. It is an (α/α)6 barrel + anti-parallel β-sheet with the catalytic machinery located in the (α/α)<sub>6</sub> barrel (Figure 2). Alg17c is a homodimer, though that does not appear to be a general feature of PL17 <cite>Jagtap2014,Park2014,Shin2015,Wang2015</cite>.
 == Family Firsts ==
-;First catalytic activity: MJ-3 alginate lyase <cite>park2012</cite>.
+;First catalytic activity: MJ-3 alginate lyase assayed by monitoring the absorbance at 235 nm  and characterizing the degradation products by TLC and <sup>1</sup>H-NMR <cite>Park2012</cite>.
 ;First catalytic base/acid: Alg17c crystal structure <cite>Park2014</cite>
 ;First charge neutralizer: Alg17c crystal structure <cite>Park2014</cite>

@@ Line 56: / Line 56: @@
 #Jagtap2014 pmid=24795372
 #Park2014 pmid=24478312
-#Shin2015 Shin, J. W., Lee, O. K., Park, H. H., Kim, H. S., and Lee, E. Y. (2015) Molecular characterization of a novel oligoalginate lyase consisting of AlgL- and heparinase II/III-like domains from Stenotrophomonas maltophilia KJ-2 and its application to alginate saccharification. Korean J. Chem. Eng. 32, 917–924
+#Shin2015 Shin, J. W., Lee, O. K., Park, H. H., Kim, H. S., and Lee, E. Y. (2015) Molecular characterization of a novel oligoalginate lyase consisting of AlgL- and heparinase II/III-like domains from Stenotrophomonas maltophilia KJ-2 and its application to alginate saccharification. Korean J. Chem. Eng. 32, 917–924 [http://dx.doi.org/10.1007/s11814-014-0282-1 DOI:10.1007/s11814-014-0282-1]
 #Wang2015 pmid=25335746
 #Mathieu2018 pmid=29795267
-#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]
 #Meyer1940 pmid=19870951
 #Park2012 pmid=21826589

@@ Line 13: / Line 13: @@
 |-
 |'''3D structure'''
-|(α/α)6 barrel + anti-parallel β-sheet
+|(α/α)<sub>6</sub> barrel + anti-parallel β-sheet
 |-
 |'''Mechanism'''
@@ Line 45: / Line 45: @@
 [[Image:PL17_structure.png|thumb|400px|'''Figure 2.''' Crystal structures of the substrate complex of the homo-dimeric Alg17c (PDB: 4OJZ) with the substrate in blue.]]
-One crystal structure is available in PL17, that of Alg17c from Saccharophagus degradans belonging to subfamily 2 <cite>Park2014</cite>. It is an (α/α)6 barrel + anti-parallel β-sheet with the catalytic machinery located in the (α/α)6 barrel (Figure 2). Alg17c is a homodimer, though that does not eppear to be a general feature of PL17 <cite>Jagtap2014,Park2014,Shin2015,Wang2015</cite>.
+One crystal structure is available in PL17, that of Alg17c from Saccharophagus degradans belonging to subfamily 2 <cite>Park2014</cite>. It is an (α/α)6 barrel + anti-parallel β-sheet with the catalytic machinery located in the (α/α)<sub>6</sub> barrel (Figure 2). Alg17c is a homodimer, though that does not appear to be a general feature of PL17 <cite>Jagtap2014,Park2014,Shin2015,Wang2015</cite>.
 == Family Firsts ==
 ;First catalytic activity: MJ-3 alginate lyase <cite>park2012</cite>.