Polysaccharide Lyase Family 2 - Revision history

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

2021-12-18T21:17:27Z

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

Wade Abbott: /* References */

2015-08-06T11:16:34Z

References

Wade Abbott: /* Kinetics and Mechanism */

2015-08-06T11:14:43Z

Kinetics and Mechanism

Wade Abbott: /* Kinetics and Mechanism */

2015-08-06T11:14:22Z

Kinetics and Mechanism

Wade Abbott: /* Three-dimensional structures */

2014-09-10T15:05:53Z

Three-dimensional structures

Wade Abbott at 15:04, 10 September 2014

2014-09-10T15:04:26Z

Wade Abbott at 15:04, 10 September 2014

2014-09-10T15:04:01Z

Wade Abbott at 15:00, 10 September 2014

2014-09-10T15:00:39Z

Wade Abbott: /* Three-dimensional structures */

2014-09-10T14:58:46Z

Three-dimensional structures

Wade Abbott: /* Three-dimensional structures */

2014-09-10T14:54:57Z

Three-dimensional structures

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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]]: ^^^Wade Abbott^^^
+* [[Author]]: [[User:Wade Abbott|Wade Abbott]]
-* [[Responsible Curator]]:  ^^^Wade Abbott^^^
+* [[Responsible Curator]]:  [[User:Wade Abbott|Wade Abbott]]
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 #Abbott2013 pmid=24013861
 #Lombard2010 pmid=20925655
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL002]]

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 == Kinetics and Mechanism ==
-Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticty in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.
+Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticity in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.
 == Catalytic Residues ==

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 == Kinetics and Mechanism ==
-Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite).
+Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticty in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.
 == Catalytic Residues ==

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 == Three-dimensional structures ==
-[[Image:PL2A.png|thumb|350px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k],  2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.
+[[Image:PL2A.png|thumb|350px|[{{PDBlink}}2v8j YePL2A] in complex with Mn<sup>2+</sup>]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k],  2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.
 == Family Firsts ==