Polysaccharide Lyase Family 9 - Revision history

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

2021-12-18T21:19:31Z

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

Wade Abbott at 22:55, 16 June 2020

2020-06-16T22:55:34Z

Wade Abbott at 22:54, 16 June 2020

2020-06-16T22:54:09Z

Ana Luis at 14:02, 15 June 2020

2020-06-15T14:02:09Z

Ana Luis at 13:59, 15 June 2020

2020-06-15T13:59:07Z

Ana Luis at 20:47, 14 June 2020

2020-06-14T20:47:10Z

Ana Luis at 20:18, 14 June 2020

2020-06-14T20:18:19Z

Harry Brumer: fixed line spacing

2017-09-15T17:40:13Z

fixed line spacing

Harry Brumer at 21:32, 14 September 2017

2017-09-14T21:32:53Z

Harry Brumer: fixed EC links

2017-09-14T21:32:27Z

fixed EC links

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-* [[Author]]: ^^^Ana Luis^^^
+* [[Author]]: [[User:Ana Luis|Ana Luis]]
-* [[Responsible Curator]]:  ^^^Wade Abbott^^^
+* [[Responsible Curator]]:  [[User:Wade Abbott|Wade Abbott]]
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 * [[Author]]: ^^^Ana Luis^^^
 * [[Responsible Curator]]:  ^^^Wade Abbott^^^

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 <!-- This is the end of the table -->
 == Substrate specificities ==
-Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan)by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two characterized PL9 rhamnogalacturonan endolyase  are active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([{{EClink}}4.2.2.- EC 4.2.2.-])  <cite>Brooks1990 Kondo2011</cite>.
+Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyase. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan) by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two PL9 endo-acting lyases have been shown to be active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([{{EClink}}4.2.2.- EC 4.2.2.-])  <cite>Brooks1990 Kondo2011</cite>.
 == Kinetics and Mechanism ==

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 == Catalytic Residues ==
-[[File:Active site PL9.png|thumb|300px|right|'''Figure 1.''' '''BT4170 ([{{PDBlink}}5OLR PDB ID 5OLR]) and Pel9A ([{{PDBlink}}1RU4 PDB ID 1RU4]) active site'''.  Superimposed active residues of BT4170  (cyan) and Pel9A (green). The calcium ions are represented as spheres (gray). The first calcium is found in both structures. However, Ca<sup>2+</sup>_2 is only present in BT4170 struture.]]
+[[File:Active site PL9 1.png|thumb|300px|right|'''Figure 1.''' '''BT4170 ([{{PDBlink}}5OLR PDB ID 5OLR]) and Pel9A ([{{PDBlink}}1RU4 PDB ID 1RU4]) active site'''.  Superimposed active residues of BT4170  (cyan) and Pel9A (green). The calcium ions are represented as spheres (gray). The first calcium is found in both structures. However, Ca<sup>2+</sup>_2 is only present in BT4170 struture.]]
 In Pel9A the lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family (Figure 1) <cite>Luis2018</cite>. In BT4170 rhamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases (Figure 1) <cite>Luis2018</cite>.
 == Three-dimensional structures ==

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 <!-- This is the end of the table -->
 == Substrate specificities ==
-Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan)by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two characterized PL9 rhamnogalacturonan endolyase  are active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase (EC 4.2.2.-) <cite>Brooks1990 Kondo2011</cite>.
+Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan)by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two characterized PL9 rhamnogalacturonan endolyase  are active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([{{EClink}}4.2.2.- EC 4.2.2.-])  <cite>Brooks1990 Kondo2011</cite>.
 == Kinetics and Mechanism ==
-PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. The characterization of the ''Bacteroides thetaiotaomicron'' rhamnogalacturonan lyase (BT4170) revealed an additional calcium ion also interacting with the substrate (Figure 1) <cite>Luis2018</cite>. Mutagenesis studies suggest that this second calcium ion also plays a role in catalysis in rhamnogalacturonan lyases <cite>Luis2018</cite>.
+PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. The characterization of the ''Bacteroides thetaiotaomicron'' rhamnogalacturonan lyase (BT4170) revealed an additional calcium ion also interacting with the substrate and playing a role in catalysis (Figure 1) <cite>Luis2018</cite>.
 == Catalytic Residues ==
 [[File:Active site PL9.png|thumb|300px|right|'''Figure 1.''' '''BT4170 ([{{PDBlink}}5OLR PDB ID 5OLR]) and Pel9A ([{{PDBlink}}1RU4 PDB ID 1RU4]) active site'''.  Superimposed active residues of BT4170  (cyan) and Pel9A (green). The calcium ions are represented as spheres (gray). The first calcium is found in both structures. However, Ca<sup>2+</sup>_2 is only present in BT4170 struture.]]
-The lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family <cite>Luis2018</cite>. In BT4170, rhamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases (Figure 1) <cite>Luis2018</cite>.
+In Pel9A the lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family (Figure 1) <cite>Luis2018</cite>. In BT4170 rhamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases (Figure 1) <cite>Luis2018</cite>.
 == Three-dimensional structures ==
 [[File:PL9.png|thumb|300px|right|'''Figure 2.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([{{PDBlink}}1RU4 PDB ID 1RU4]) '''A.''' Schematic representation of Pel9A parallel β-helix fold colour ramped from blue (N-terminal) to red (C-terminal). The active site is represented as sticks and highlighted inside the black box. The calcium is represented as sphere (gray) '''B.''' Blow up of the active site. The residues interacting with calcium and the proposed catalytic base (K237) are represented as stick in green and yellow, respectively.]]
 PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([{{PDBlink}}1RU4 PDB ID 1RU4]) and displays a right-handed parallel β-helix fold (Figure 2A). The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft (Figure 2B) <cite>Jenkins2004</cite>. The structure of the rhamnogalacturonan lyase (BT4170) in complex with the enzyme product showed that apart from the catalytic apparatus, there is little conservation of substrate binding residues between this enzyme and the pectate lyase Pel9A <cite>Luis2018</cite>.
 == Family Firsts ==

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 <!-- This is the end of the table -->
 == Substrate specificities ==
-Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan,a pectin component present in the plant cell walls. An enzyme in PL9 was described as active on sheath, a thioloic glycoconjugate secreted by ''Sphaerotilus natans'' <cite>Takeda2000</cite>. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase (EC 4.2.2.-) <cite>Brooks1990 Kondo2011</cite>.
+Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan)by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two characterized PL9 rhamnogalacturonan endolyase  are active on rhamnogalacturonan-I [https://www.enzyme-database.org/query.php?ec=4.2.2.23  (EC 4.2.2.23)] <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase (EC 4.2.2.-) <cite>Brooks1990 Kondo2011</cite>.
 == Kinetics and Mechanism ==
-PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>.
+PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. The characterization of the ''Bacteroides thetaiotaomicron'' rhamnogalacturonan lyase (BT4170) revealed an additional calcium ion also interacting with the substrate <cite>Luis2018</cite>. Mutagenesis studies suggest that this second calcium ion also plays a role in catalysis in rhamnogalacturonan lyases <cite>Luis2018</cite>.
 == Catalytic Residues ==
-The lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>.
+The lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family <cite>Luis2018</cite>. In BT4170, rahamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases <cite>Luis2018</cite>.
 == Three-dimensional structures ==
 [[File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([{{PDBlink}}1RU4 PDB ID 1RU4]) '''A.''' Schematic representation of Pel9A parallel β-helix fold colour ramped from blue (N-terminal) to red (C-terminal). The active site is represented as sticks and highlighted inside the black box. The calcium is represented as sphere (gray) '''B.''' Blow up of the active site. The residues interacting with calcium and the proposed catalytic base (K237) are represented as stick in green and yellow, respectively.]]
-PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([{{PDBlink}}1RU4 PDB ID 1RU4]) and displays a right-handed parallel β-helix fold (Figure 1A). The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft (Figure 1B) <cite>Jenkins2004</cite>.
+PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([{{PDBlink}}1RU4 PDB ID 1RU4]) and displays a right-handed parallel β-helix fold (Figure 1A). The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft (Figure 1B) <cite>Jenkins2004</cite>. The structure of the rhamnogalacturonan lyase (BT4170) in complex with the enzyme product showed that apart from the catalytic apparatus, there is little conservation of substrate binding residues between this enzyme and the pectate lyase Pel9A <cite>Luis2018</cite>.
 == Family Firsts ==
@@ Line 51: / Line 51: @@
 <biblio>
 #Jenkins2004 pmid=14670977
-#Takeda2000 pmid=11055955
+#Luis2018 pmid=29255254
 #Kondo2011 pmid=21095202
 #Seyedarabi2010 pmid=20000851