Polysaccharide Lyase Family 22 - Revision history

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

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

Harry Brumer: /* Family Firsts */

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Family Firsts

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Harry Brumer: /* Substrate specificities */

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Substrate specificities

Harry Brumer: /* Substrate specificities */

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Substrate specificities

Harry Brumer at 18:10, 15 September 2014

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Wade Abbott at 04:01, 12 September 2014

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Wade Abbott at 03:56, 12 September 2014

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Wade Abbott at 03:55, 12 September 2014

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Wade Abbott at 03:55, 12 September 2014

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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]]: ^^^Richard McLean^^^ and ^^^Wade Abbott^^^
+* [[Author]]: [[User:Richard McLean|Richard McLean]] and [[User:Wade Abbott|Wade Abbott]]
-* [[Responsible Curator]]:  ^^^Wade Abbott^^^
+* [[Responsible Curator]]:  [[User:Wade Abbott|Wade Abbott]]
 ----

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 ;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 <cite>Abbott2010</cite>.
 ;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937) <cite>Shevchik1989</cite>.
-;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]).
+;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633 (''Unpublished:'' [{{PDBlink}}3c5m PDB 3C5M]).
 == References ==

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 == Three-dimensional structures ==
-[[Image:3pe7.png|thumb|230px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The first structure of a PL22 determined was from ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]) in 2008 by x-ray diffraction to 2.60 Å ([http://www.nesg.org/ Northeast Structural Genomics Consortium]). This was followed in 2010 by YePL2A from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 ([{{PDBlink}}3pe7 PDB 3PE7]), which was solved in complex with Mn<sup>2+</sup> and acetate by x-ray diffraction to 1.65 Å <cite>Abbott2010</cite>. The two proteins share ~69% sequence identity and highly similar 3D structures. The PL22 fold is a &beta;<sub>7</sub> propeller with the catalytic machinery and metal coordination pocket housed at the center of the enzyme.
+[[Image:3pe7.png|thumb|400px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The first structure of a PL22 determined was from ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]) in 2008 by x-ray diffraction to 2.60 Å ([http://www.nesg.org/ Northeast Structural Genomics Consortium]). This was followed in 2010 by YePL2A from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 ([{{PDBlink}}3pe7 PDB 3PE7]), which was solved in complex with Mn<sup>2+</sup> and acetate by x-ray diffraction to 1.65 Å <cite>Abbott2010</cite>. The two proteins share ~69% sequence identity and highly similar 3D structures. The PL22 fold is a &beta;<sub>7</sub> propeller with the catalytic machinery and metal coordination pocket housed at the center of the enzyme.
 == Family Firsts ==

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 == Substrate specificities ==
-Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally known as oligogalacturonide transeliminases (OGTE) <cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs). This enzyme family is found primarily in phytopathogenic or intestinal bacteria where it plays a role in the metabolism of pectic fibres.
+Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally known as oligogalacturonide transeliminases (OGTE) <cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs). This enzyme family is found primarily in phytopathogenic or intestinal bacteria where it plays a role in the metabolism of pectin.
 PL22s remove 5-keto-4-deoxyuronate (4-deoxy-{{smallcaps|l}}-threo-5-hexosulose uronic acid, DKI) from short chain oligalacturonides and display preferential activity on digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010 Kester1999</cite>. Activity on trigalacturonate is significantly lower and PL22s appear to completely lack activity on long chain polymers of α-(1,4)-linked polygalacturonate <cite>Abbott2010 Kester1999</cite>. Differing levels of activity has been reported on methylated short chain oligogalacturonides depending on the location of methylation <cite>Kester1999</cite>.

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 == Substrate specificities ==
-Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally known as oligogalacturonide transeliminases (OGTE)<cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs). This enzyme family is found primarily in phytopathogenic or intestinal bacteria where it plays a role in the metabolism of pectic fibres.
+Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally known as oligogalacturonide transeliminases (OGTE) <cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs). This enzyme family is found primarily in phytopathogenic or intestinal bacteria where it plays a role in the metabolism of pectic fibres.
 PL22s remove 5-keto-4-deoxyuronate (4-deoxy-{{smallcaps|l}}-threo-5-hexosulose uronic acid, DKI) from short chain oligalacturonides and display preferential activity on digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010 Kester1999</cite>. Activity on trigalacturonate is significantly lower and PL22s appear to completely lack activity on long chain polymers of α-(1,4)-linked polygalacturonate <cite>Abbott2010 Kester1999</cite>. Differing levels of activity has been reported on methylated short chain oligogalacturonides depending on the location of methylation <cite>Kester1999</cite>.
-−
 == Kinetics and Mechanism ==
 PL22s harness a β-elimination mechanism to cleave the glycosidic bonds in oligogalacturonides. This process 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 &alpha;-proton and charge neutralization of the oxyanion intermediate. YePL22 (YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081; [http://www.ncbi.nlm.nih.gov/protein/123442156 gi|123442156|]) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) <cite>Abbott2010</cite>, which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate.

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 == Kinetics and Mechanism ==
-PL22s harness a β-elimination reaction to cleave the glycosidic bonds in oligogalacturonides. This process 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 &alpha;-proton and charge neutralization of the oxyanion intermediate. YePL22 (YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081; [http://www.ncbi.nlm.nih.gov/protein/123442156 gi|123442156|]) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) <cite>Abbott2010</cite>, which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate.
+PL22s harness a β-elimination mechanism to cleave the glycosidic bonds in oligogalacturonides. This process 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 &alpha;-proton and charge neutralization of the oxyanion intermediate. YePL22 (YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081; [http://www.ncbi.nlm.nih.gov/protein/123442156 gi|123442156|]) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) <cite>Abbott2010</cite>, which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate.
 == Catalytic Residues ==
-Within the structure of YePL22, H242 is the only basic residue that is in proximity to the &alpha;-proton of a modelled galacturonate <cite>Abbott2010</cite>. This histidine is highly conserved within PL22s with only ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) displaying an alternative residue (T236); however, whether this gene product is a lyase has yet to be determined. The 'stabilizing arginine' <cite>Abbott2010</cite> (YE1876: R217) is completely conserved across the PL22 family.
+Within the structure of YePL22, H242 is the only basic residue that is in proximity to the &alpha;-proton of a modelled galacturonate <cite>Abbott2010</cite>. This histidine is highly conserved within PL22s with only ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) displaying an alternative residue (T236); however, whether this protein is a lyase has yet to be determined. The 'stabilizing arginine' <cite>Abbott2010</cite> (YE1876: R217) is completely conserved across the PL22 family.
-The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088: H287, H353, H355; YE1876: H287, H353, H355) and one glutamine (VPA0088: Q350; YeOGL: Q350). It is of note however that although these residues are perfectly conserved in all reported subfamily 1 sequences and several outlier sequences, there are minor differences in subfamily 2 <cite>Lombard2010</cite>: H287 is invariant; however, Q350 is not conserved, and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may alter the chemistry of metal coordination selectivity. Further experimentation will be required to define this relationship.
+The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088: H287, H353, H355; YE1876: H287, H353, H355) and one glutamine (VPA0088: Q350; YeOGL: Q350). It is of note however that although these residues are perfectly conserved in all reported subfamily 1 sequences and several outlier sequences, there are minor differences in subfamily 2 <cite>Lombard2010</cite>: H287 is invariant, Q350 is not conserved, and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may alter the chemistry of metal coordination selectivity. Further experimentation will be required to define this relationship.
 == Three-dimensional structures ==