https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Ana+LuisCAZypedia - User contributions [en-ca]2026-05-03T02:26:17ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15329Polysaccharide Lyase Family 92020-06-15T14:02:09Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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>. <br />
<br />
== Kinetics and Mechanism ==<br />
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>. <br />
<br />
== Catalytic Residues ==<br />
[[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.]]<br />
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>.<br />
== Three-dimensional structures ==<br />
[[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.]]<br />
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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:Active_site_PL9_1.png&diff=15328File:Active site PL9 1.png2020-06-15T14:00:41Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15327Polysaccharide Lyase Family 92020-06-15T13:59:07Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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>. <br />
<br />
== Kinetics and Mechanism ==<br />
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>. <br />
<br />
== Catalytic Residues ==<br />
[[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.]]<br />
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>.<br />
== Three-dimensional structures ==<br />
[[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.]]<br />
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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15322Polysaccharide Lyase Family 92020-06-14T20:47:10Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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>. <br />
<br />
== Kinetics and Mechanism ==<br />
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>. <br />
<br />
== Catalytic Residues ==<br />
[[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.]]<br />
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>.<br />
== Three-dimensional structures ==<br />
[[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.]]<br />
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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:Active_site_PL9.png&diff=15321File:Active site PL9.png2020-06-14T20:30:00Z<p>Ana Luis: Ana Luis uploaded a new version of File:Active site PL9.png</p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=File:Active_site_PL9.png&diff=15320File:Active site PL9.png2020-06-14T20:20:15Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15319Polysaccharide Lyase Family 92020-06-14T20:18:19Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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>. <br />
<br />
== Kinetics and Mechanism ==<br />
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>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
[[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.]]<br />
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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_77&diff=13003Carbohydrate Binding Module Family 772018-05-13T22:22:22Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM77.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM77 is a bacterial family of binding modules that comprises around 110 amino acids. Only the founding member of this family, CBM77<sub>RfPL1/9</sub> has been characterized. This binding module found in ''Ruminococcus flavefaciens'' binds exclusively to homogalacturonan (pectin) with low degrees of methyl esterification (DE) <cite>Venditto2016</cite>. By isothermal titration calorimetry, CBM77<sub>RfPL1/9</sub> displays high affinity for low DE pectins such as, lime DE 11% and citrus pectin DE 30% (K<sub>A</sub> 1.8 x 10<sup>5</sup> M<sup>-1</sup> and 1.1 x 10<sup>4</sup> M<sup>-1</sup>, respectively). This binding module displays a reduction in affinity as the DE of the ligand increase. Indeed CBM77<sub>RfPL1/9</sub> exhibits no binding to polygalacturonic acid with a DE ≥80%. This binding module displays optimum binding to oligosaccharides of α1,4-D-Galacturonic acid (GalA) with a degree of polymerization of 7 to 8. Additionally, the presence of a chelating agent (EDTA) did not influence CBM77<sub>RfPL1/9</sub> affinity indicating a metal independent binding mechanism <cite>Venditto2016</cite>. The only other example of a CBM that binds to homogalacturonan backbone is [[CBM32]] from ''Yersinia enterolitica'' (YeCBM32) (which is not a component of an enzyme) <cite>Abbott2007</cite>.<br />
<br />
== Structural Features ==<br />
[[File:CBM77.jpg|thumb|300px|right|'''Figure 1. CBM77<sub>RfPL1/9</sub>.''' Schematic representation of CBM77<sub>RfPL1/9</sub> β-sandwich fold colour ramped from blue (N-terminal) to red (C-terminal), embedded in the surface representation of the protein. The residues that contribute to ligand recognition are shown in stick format.]]<br />
<br />
The three-dimensional structure of ''Ruminoccocus'' CBM77<sub>RfPL1/9</sub> ([{{PDBlink}}5FU5 5FU5]) solved using X-ray displays a beta-sandwich fold in which the 13 antiparallel β-strands are organized in two β-sheets <cite>Venditto2016</cite>.<br />
<br />
The key residues implicated in substrate binding were identified by site-direct mutagenesis. The canonical ligand binding site of a endo-active [[Carbohydrate-binding_modules#Types|type B]] CBM adopts a cleft-like structure. However, in CBM77<sub>RfPL1/9</sub>, the alanine mutation of aromatic or basic amino acids in the concave surface had no effect on ligand binding. Only the alanine mutation of three invariant basic residues (Lys1092, Lys1107, and Lys1162) located at the convex surface of CBM77<sub>RfPL1/9</sub> abrogated binding to polygalacturonic acid (PGA), showing the location of the binding site. The single alanine mutants of two distal basic residues (Lys1136 and Lys1141) displayed only a modest reduction in affinity for PGA when compared with the wild-type protein. However, the double mutation Lys1136A/Lys1141A resulted in complete loss of binding indicating that these lysines display functional redundancy. Additionally, based on the mutant binding data, the CBM77<sub>RfPL1/9</sub> ligand recognition surface is ~ 25 Å suggesting that the binding site can accommodate a hexasaccharide <cite>Venditto2016</cite>.<br />
<br />
The CBM77<sub>RfPL1/9</sub> ligand recognition mediated by basic polar residues is distinct from other CBMs where aromatic residues play a central role in glycan recognition, but resembles glycosaminoglycan binding proteins, where ligand recognition is also mediated by basic residues (arginine and lysines) <cite>Hileman1998</cite>.<br />
<br />
== Functionalities == <br />
''Ruminoccocus flavefaciens'' CBM77<sub>RfPL1/9</sub> is a component of an enzyme that contains two catalytic modules, belonging to polysaccharide lyase families 1 ([[PL1]]) and 9 ([[PL9]]) and a C-terminal dockerin module. Consistent with the CBM77<sub>RfPL1/9</sub>, both PL enzymes display pectate lyase activity <cite>Venditto2016</cite>.<br />
<br />
This CBM family contains 26 members from a range of bacteria suggesting a general role in pectin degradation that is not specific to the cellulosome organization or the rumen environment. In the majority of the proteins, the CBM77 is appended to PL1 catalytic modules although PL9 sequences are also present <cite>Venditto2016</cite>.<br />
<br />
Additionally, the binding of CBM77<sub>RfPL1/9</sub> was also tested in the context of plant cell wall. This binding module specifically labelled homogalacturonan in ''Tobacco'' stem sections <cite>Venditto2016</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified: CBM77<sub>RfPL1/9</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.<br />
;First Structural Characterization: The first available crystal was CBM77<sub>RfPL1/9</sub> <cite>Venditto2016</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Venditto2016 pmid=27298375<br />
#Abbott2007 pmid=17292916<br />
#Hileman1998 pmid=9631661<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM077]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:CBM77.jpg&diff=13002File:CBM77.jpg2018-05-13T22:06:24Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_76&diff=13001Carbohydrate Binding Module Family 762018-05-13T19:54:16Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM76.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM76 is a small family containing only five members found exclusively in Ruminococci. The founding member of this family is CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' that recognizes different β-1,4-glucans <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity of this binding module to xyloglucan (K<sub>A</sub> 1.1 x 10<sup>6</sup> M<sup>-1</sup>) is 100-fold higher than to glucomannan, barley β-glucan, hydroxyethylcellulose and XXXG (the repeating unit of xyloglucan, where X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) <cite>Venditto2016</cite>.<br />
<br />
== Structural Features ==<br />
No three-dimensional structure has been solved for this CBM family.<br />
<br />
== Functionalities == <br />
The founding member of this family, CBM76<sub>RfGH44</sub>, is appended to a glycoside hydrolase family 44 ([[GH44]]) and a C-terminal dockerin. The binding module specificity to β-1,4-glucans is consistent with the previously reported activity for [[GH44]] enzymes (endoglucanase or xyloglucanase) <cite>Venditto2016</cite>. However, the impact of CBM76<sub>RfGH44</sub> binding module on [[GH44]] substrate recognition and catalysis it is not known.<br />
<br />
== Family Firsts ==<br />
;First Identified:CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.<br />
;First Structural Characterization: No three-dimensional structure has been solved for this CBM family.<br />
<br />
== References ==<br />
<biblio><br />
#Venditto2016 pmid=27298375<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM076]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_76&diff=13000Carbohydrate Binding Module Family 762018-05-13T19:50:21Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM76.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM76 is a small family containing only five members found exclusively in Ruminococci. The founding member of this family is CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' that recognizes different β-1,4-glucans <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity of this binding module to xyloglucan (K<sub>A</sub> 1.1 x 10<sup>6</sup>) is 100-fold higher than to glucomannan, barley β-glucan, hydroxyethylcellulose and XXXG (the repeating unit of xyloglucan, where X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) <cite>Venditto2016</cite>.<br />
<br />
== Structural Features ==<br />
No three-dimensional structure has been solved for this CBM family.<br />
<br />
== Functionalities == <br />
The founding member of this family, CBM76<sub>RfGH44</sub>, is appended to a glycoside hydrolase family 44 ([[GH44]]) and a C-terminal dockerin. The binding module specificity to β-1,4-glucans is consistent with the previously reported activity for [[GH44]] enzymes (endoglucanase or xyloglucanase) <cite>Venditto2016</cite>. However, the impact of CBM76<sub>RfGH44</sub> binding module on [[GH44]] substrate recognition and catalysis it is not known.<br />
<br />
== Family Firsts ==<br />
;First Identified:CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.<br />
;First Structural Characterization: No three-dimensional structure has been solved for this CBM family.<br />
<br />
== References ==<br />
<biblio><br />
#Venditto2016 pmid=27298375<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM076]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_76&diff=12999Carbohydrate Binding Module Family 762018-05-13T19:50:01Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM76.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM76 is a small family containing only five members found exclusively in Ruminococci. The founding member of this family is CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' that recognizes different β-1,4-glucans <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity of this binding module to xyloglucan (K<sub>A</sub> 1.1 x 10<sup>6</sup>) is 100-fold higher than to glucomannan, barley β-glucan, hydroxyethylcellulose and XXXG (the repeating unit of xyloglucan, where X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) <cite>Venditto2016</cite>.<br />
<br />
== Structural Features ==<br />
No three-dimensional structure has been solved for this CBM family.<br />
<br />
== Functionalities == <br />
The founding member of this family, CBM76<sub>RfGH44</sub>, is appended to a glycoside hydrolase family 44 ([[GH44]]) and a C-terminal dockerin. The binding module specificity to β-1,4-glucans is consistent with the previously reported activity for [[GH44]] enzymes (endoglucanase or xyloglucanase) <cite>Venditto2016</cite>. However, the impact of CBM76<sub>RfGH44</sub> binding module on [[GH44]] substrate recognition and catalysis it is not known.<br />
<br />
<br />
== Family Firsts ==<br />
;First Identified:CBM76<sub>RfGH44</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.<br />
;First Structural Characterization: No three-dimensional structure has been solved for this CBM family.<br />
<br />
== References ==<br />
<biblio><br />
#Venditto2016 pmid=27298375<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM076]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_75&diff=12995Carbohydrate Binding Module Family 752018-05-08T21:52:16Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM75.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</cite>.<br />
<br />
== Structural Features ==<br />
No three-dimensional structure has been solved for this CBM family.<br />
<br />
== Functionalities == <br />
''Ruminococcus flavefaciens'' CBM75<sub>RfGH43</sub>, is a biding module of a protein containing a glycoside hydrolase family 43 ([[GH43]]) and a C-terminal dockerin module <cite>Venditto2016</cite>. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases <cite>Mewis2016</cite>. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but do not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is usually consistent with the activity of the appended enzyme. Since CBM75<sub>RfGH43</sub> binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato <cite>Venditto2016</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified: CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.<br />
;First Structural Characterization: No three-dimensional structure has been solved for this family.<br />
<br />
== References ==<br />
<biblio><br />
#Venditto2016 pmid=27298375<br />
#Mewis2016 pmid=26729713<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM075]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=User:Ana_Luis&diff=12820User:Ana Luis2018-04-29T19:50:18Z<p>Ana Luis: </p>
<hr />
<div>[[Image:ALfoto.jpg|200px|right]]<br />
I obtained a M.Sc in Pharmaceutical Sciences at [http://http://www.ulisboa.pt/en/ Universtiy of Lisbon] in 2009. After I worked with Dr. Carlos Fontes at [http://www.fmv.ulisboa.pt/_ingles/ Technical University of Lisbon], studying the mechanisms of protein-carbohydrate interactions. Between 2013 and 2017 I moved to [http://www.ncl.ac.uk/ Newcastle University] (UK) to do my PhD under the supervision of Prof. ^^^Harry Gilbert^^^. During this time I studied the mechanisms behind pectin degradation and utilization by the gut bacterium ''Bacteroides thetaiotaomicron''. I’m currently a PostDoc mentored by Prof. [http://www.medkem.gu.se/mucinbiology/biblio2015.html Gunnar C. Hansson] ([https://www.gu.se/English University of Gothenburg], Sweden) and [http://microbe.med.umich.edu/people/eric-martens-phd Eric C. Martens] ([http://umich.edu/ University of Michigan], USA). My research is focused on functional and structural characterization of enzymes and carbohydrate-binding modules. I'm currently interested in understanding the mechanisms behind mucin degradation by gut bacteria and its implications in inflammatory bowel disease.<br />
<br />
I contributed to structural-functional characterization of:<br />
* [[CBM65]] from ''Eubacterium cellulosolvens'' ('''Family First''' structure and description of substrate recognition) <cite>Luis2013</cite><br />
* [[CBM77]] from ''Ruminococcus flavefaciens'' ('''Family First''') <cite>Venditto2016</cite><br />
* [[GH106]] BT0986 and BT4145 from ''Bacteorides thetaiotaomicron'' ('''Family First''' structure and mechanism of catalysis description) <cite>Ndeh2017, Luis2018 </cite><br />
* [[GH103]] BT1003 from ''Bacteorides thetaiotaomicron'' (first report of an aceric acidase enzyme) <cite>Ndeh2017</cite>;<br />
* [[PL9]] BT4170 ''Bacteroides thetaiotaomicron'' (first rhamnogalacturonan lyase inside PL9 family) <cite>Luis2018</cite>;<br />
<br />
----<br />
<br />
<biblio><br />
#Luis2013 pmid=23229556<br />
#Venditto2016 pmid=27298375<br />
#Ndeh2017 pmid=28329766<br />
#Luis2018 pmid=29255254<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Luis,Ana]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_65&diff=12819Carbohydrate Binding Module Family 652018-04-29T19:36:11Z<p>Ana Luis: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM65.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
The founding members of family CBM65 (CBM65A and CBM65B) were identified in ''Eubacterium cellulosolvens'' endoglucanase ''Ec''Cel5A <cite>Yoda2005</cite>. This bacterial CBM family displays affinity to plant cell wall polysaccharides. Both modules CBM65A and CBM65B bind to acid swollen cellulose, β1,3/1,4 mixed linked glucans (lichenan and barley β-glucan) and decorated β1,4-glucans such as xyloglucan, hydroxyethylcellulose (HEC) and carboxymethylcellulose (CMC) <cite>Yoda2005 Luis2013</cite>. Both CBM65 modules also have weak affinity for glucomannan but there is no reports of binding to additional alfa or beta-glucans <cite>Luis2013</cite>. By isothermal titration calorimetry (ITC), CBM65A displays higher affinity for xyloglucan comparative to β1,3/1,4 mixed linked glucans and HEC. Additionally, this CBM binds with similar affinity to the oligosaccharides cellopentaose and XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose), the repeating unit of xyloglucan. Binding to shorter cellooligosacharides was too week to be quantified (cellotetraose) or not detectable (cellotriose) <cite>Luis2013</cite>.<br />
<br />
<br />
== Structural Features ==<br />
[[File:CBM65.png|thumb|300px|right|'''Figure 1. CBM65B in complex with XXXG.''' Schematic representation of CBM65B β-shandwich fold colour ramped from blue (N-terminal) to red (C-terminal), embedded in the surface representation of the protein. XXXG is shown in stick format with glucose and sylose carbons colored yellow and magenta, respectively.]]<br />
The three-dimensional structures of ''Eubacterium cellulosolvens'' CBM65A ([{{PDBlink}}4AFM 4AFM]) and CBM65B ([{{PDBlink}}2YPJ 2YPJ]) solved using X-ray display a beta-sandwich fold (Figure 1) <cite>Luis2013</cite>. The ligand binding site located at the concave surface of the protein adopts a cleft-like structure typical of a [https://www.cazypedia.org/index.php/Carbohydrate-binding_modules type B] CBM <cite>Luis2013</cite>.<br />
<br />
The CBM65B structure was obtained in complex with XXXG (Figure 1). Four tryptophans (W602, W607, W651, and W646) make extensive hydrophobic contacs with the backbone and the xylose side chains. Alanine substitution of these tryptophans abrogated cellohexaose and β-glucan recognition, confirming the important role of these aromatic residues in backbone recognition. The mutagenesis of W607, W646 also caused a substantial reduction in affinity to xyloglucan. However, only the mutation W651A abrogated binding to all ligand (xyloglucan, β-glucan and cellohexaose), confirming the key role of this residue in subtract backbone and side chains recognition <cite>Luis2013</cite>. An additional aromatic amino acid (Y685) also makes hydrophobic interactions with xylose side chains. The mechanism of ligand recognition by CBM65A and CBM65A is driven by apolar interactions with the surface of these conserved five aromatic residues (W602, W607, W651, W646 and Tyr685), where the hydrophobic interactions with the xylose side chains make a significant contribution to CBM65 binding. Indeed, this recognition of xylose side chains explains the higher affinity to xyloglucan and XXXG comparatively to undecorated β-glucans and cellotetraose, respectively <cite>Luis2013</cite>.<br />
<br />
The structure in complex revealed that the ligand biding is also driven by polar interactions between Q110 and the glucose backbone, since the alanine substitution of this residue significantly reduce binding to β-glucan and cellohexaose <cite>Luis2013</cite>. A second polar residue (Q106), only present in CBM65A, also plays an important role in ligand recognition. The alanine mutation of Q106 abrogated cellohexaose recognition but has no impact on binding to mixed linked β1,3/1,4-glucans (by ITC and plant cell wall labelling assays), suggesting that this residue has a key role only in cellulose recognition and CBM65A binding site is capable of specifically recognise both linear β1,4-glucans and β1,3-b-1,4 mixed linked glucans <cite>Luis2013</cite>.<br />
<br />
== Functionalities == <br />
CBM65s were first identified in the ''Eubacterium cellulosolvens'' ''Ec''Cel5A endoglucanse. The molecular architecture of ''Ec''Cel5A shows two CBM65 modules (denominated A and B) appended to two glycoside hydrolases family 5 ([https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_5 GH5]) <cite>Yoda2005</cite>. The CBM65A and CBM65B specificity for β-glucans (β1,4 and β1,3/14-mixed linked) is consistent with the reported activity of the appended enzymes <cite>Yoda2005</cite>. Indeed, both GH5s catalytic modules are more active on lichenan (β1,3-b-1,4 mixed linked glucan) and carboxymethylcellulose (β1,4-glucan) than in xylan. The removal of the CBM65s modules associated with the GH5 catalytic domains resulted in a significant decrease of the enzymatic activity against all tested substrates, suggesting that both binding modules have an important role on catalysis enhancing the enzyme activity <cite>Yoda2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:CBM65A and CBM65B from the ''Eubacterium cellulosolvens'' ''Ec''Cel5A endoglucanse <cite>Yoda2005</cite>.<br />
;First Structural Characterization<br />
:The first available crystal structure and the first complex structure of a CBM65 were CBM65A ([{{PDBlink}}4AFM 4AFM]) and CBM65B ([{{PDBlink}}2YPJ 2YPJ]), respectively <cite>Luis2013</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Yoda2005 pmid=16204489<br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM065]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:CBM65.png&diff=12818File:CBM65.png2018-04-29T19:34:25Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_65&diff=12817Carbohydrate Binding Module Family 652018-04-29T18:52:54Z<p>Ana Luis: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM65.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
The founding members of family CBM65 (CBM65A and CBM65B) were identified in ''Eubacterium cellulosolvens'' endoglucanase ''Ec''Cel5A <cite>Yoda2005</cite>. This bacterial CBM family displays affinity to plant cell wall polysaccharides. Both modules CBM65A and CBM65B bind to acid swollen cellulose, β1,3/1,4 mixed linked glucans (lichenan and barley β-glucan) and decorated β1,4-glucans such as xyloglucan, hydroxyethylcellulose (HEC) and carboxymethylcellulose (CMC) <cite>Yoda2005 Luis2013</cite>. Both CBM65 modules also have weak affinity for glucomannan but there is no reports of binding to additional alfa or beta-glucans <cite>Luis2013</cite>. By isothermal titration calorimetry (ITC), CBM65A displays higher affinity for xyloglucan comparative to β1,3/1,4 mixed linked glucans and HEC. Additionally, this CBM binds with similar affinity to the oligosaccharides cellopentaose and XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose), the repeating unit of xyloglucan. Binding to shorter cellooligosacharides was too week to be quantified (cellotetraose) or not detectable (cellotriose) <cite>Luis2013</cite>.<br />
<br />
<br />
== Structural Features ==<br />
The three-dimensional structures of ''Eubacterium cellulosolvens'' CBM65A ([{{PDBlink}}4AFM 4AFM]) and CBM65B ([{{PDBlink}}2YPJ 2YPJ]) solved using X-ray display a beta-sandwich fold <cite>Luis2013</cite>. The ligand binding site located at the concave surface of the protein adopts a cleft-like structure typical of a [https://www.cazypedia.org/index.php/Carbohydrate-binding_modules type B] CBM <cite>Luis2013</cite>.<br />
<br />
The CBM65B structure was obtained in complex with XXXG. Four tryptophans (W602, W607, W651, and W646) make extensive hydrophobic contacs with the backbone and the xylose side chains. Alanine substitution of these tryptophans abrogated cellohexaose and β-glucan recognition, confirming the important role of these aromatic residues in backbone recognition. The mutagenesis of W607, W646 also caused a substantial reduction in affinity to xyloglucan. However, only the mutation W651A abrogated binding to all ligand (xyloglucan, β-glucan and cellohexaose), confirming the key role of this residue in subtract backbone and side chains recognition <cite>Luis2013</cite>. An additional aromatic amino acid (Y685) also makes hydrophobic interactions with xylose side chains. The mechanism of ligand recognition by CBM65A and CBM65A is driven by apolar interactions with the surface of these conserved five aromatic residues (W602, W607, W651, W646 and Tyr685), where the hydrophobic interactions with the xylose side chains make a significant contribution to CBM65 binding. Indeed, this recognition of xylose side chains explains the higher affinity to xyloglucan and XXXG comparatively to undecorated β-glucans and cellotetraose, respectively <cite>Luis2013</cite>.<br />
<br />
The structure in complex revealed that the ligand biding is also driven by polar interactions between Q110 and the glucose backbone, since the alanine substitution of this residue significantly reduce binding to β-glucan and cellohexaose <cite>Luis2013</cite>. A second polar residue (Q106), only present in CBM65A, also plays an important role in ligand recognition. The alanine mutation of Q106 abrogated cellohexaose recognition but has no impact on binding to mixed linked β1,3/1,4-glucans (by ITC and plant cell wall labelling assays), suggesting that this residue has a key role only in cellulose recognition and CBM65A binding site is capable of specifically recognise both linear β1,4-glucans and β1,3-b-1,4 mixed linked glucans <cite>Luis2013</cite>.<br />
<br />
== Functionalities == <br />
CBM65s were first identified in the ''Eubacterium cellulosolvens'' ''Ec''Cel5A endoglucanse. The molecular architecture of ''Ec''Cel5A shows two CBM65 modules (denominated A and B) appended to two glycoside hydrolases family 5 ([https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_5 GH5]) <cite>Yoda2005</cite>. The CBM65A and CBM65B specificity for β-glucans (β1,4 and β1,3/14-mixed linked) is consistent with the reported activity of the appended enzymes <cite>Yoda2005</cite>. Indeed, both GH5s catalytic modules are more active on lichenan (β1,3-b-1,4 mixed linked glucan) and carboxymethylcellulose (β1,4-glucan) than in xylan. The removal of the CBM65s modules associated with the GH5 catalytic domains resulted in a significant decrease of the enzymatic activity against all tested substrates, suggesting that both binding modules have an important role on catalysis enhancing the enzyme activity <cite>Yoda2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:CBM65A and CBM65B from the ''Eubacterium cellulosolvens'' ''Ec''Cel5A endoglucanse <cite>Yoda2005</cite>.<br />
;First Structural Characterization<br />
:The first available crystal structure and the first complex structure of a CBM65 were CBM65A ([{{PDBlink}}4AFM 4AFM]) and CBM65B ([{{PDBlink}}2YPJ 2YPJ]), respectively <cite>Luis2013</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Yoda2005 pmid=16204489<br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM065]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_65&diff=12816Carbohydrate Binding Module Family 652018-04-29T18:32:40Z<p>Ana Luis: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM65.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
The founding members of family CBM65 (CBM65A and CBM65B) were identified in ''Eubacterium cellulosolvens'' endoglucanase ''Ec''Cel5A <cite>Yoda2005</cite>. This bacterial CBM family displays affinity to plant cell wall polysaccharides. Both modules CBM65A and CBM65B bind to acid swollen cellulose, β1,3/1,4 mixed linked glucans (lichenan and barley β-glucan) and decorated β1,4-glucans such as xyloglucan, hydroxyethylcellulose (HEC) and carboxymethylcellulose (CMC) <cite>Yoda2005 Luis2013</cite>. Both CBM65 modules also have weak affinity for glucomannan but there is no reports of binding to additional alfa or beta-glucans <cite>Luis2013</cite>. By isothermal titration calorimetry (ITC), CBM65A displays higher affinity for xyloglucan comparative to β1,3/1,4 mixed linked glucans and HEC. Additionally, this CBM binds with similar affinity to the oligosaccharides cellopentaose and XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose), the repeating unit of xyloglucan. Binding to shorter cellooligosacharides was too week to be quantified (cellotetraose) or not detectable (cellotriose) <cite>Luis2013</cite>.<br />
<br />
<br />
== Structural Features ==<br />
The three-dimensional structures of ''Eubacterium cellulosolvens'' CBM65A ([{{PDBlink}}4AFM 4AFM]) and CBM65B ([{{PDBlink}}2YPJ 2YPJ]) solved using X-ray display a beta-sandwich fold <cite>Luis2013</cite>. The ligand binding site located at the concave surface of the protein adopts a cleft-like structure typical of a type B CBM <cite>Luis2013</cite>.<br />
<br />
The CBM65B structure was obtained in complex with XXXG. Four tryptophans (W602, W607, W651, and W646) make extensive hydrophobic contacs with the backbone and the xylose side chains. Alanine substitution of these tryptophans abrogated cellohexaose and b-glucan recognition, confirming the important role of these aromatic residues in backbone recognition. The mutagenesis of W607, W646 also caused a substantial reduction in affinity to xyloglucan, However, only the mutation W651A abrogated binding to all ligand (xyloglucan, b-glucan and cellohexaose), confirming the key role of this residue in subtract backbone and side chains recognition. An additional aromatic amino acid (Y685) also makes hydrophobic interactions with xylose side chains. The mechanism of ligand recognition by CBM65A and CBM65A is driven by apolar interactions with the surface of these conserved five aromatic residues (W602, W607, W651, W646 and Tyr685), where the hydrophobic interactions with the xylose side chains make a significant contribution to CBM65 binding. Indeed, this recognition of xylose side chains explains the higher affinity to xyloglucan and XXXG comparatively to undecorated b-glucans and cellotetraose, respectively.<br />
<br />
The structure in complex revealed that the ligand biding is also driven by polar interactions between Q110 and the glucose backbone, since the alanine substitution of this residue significantly reduce binding to b-glucan and cellohexaose. A second polar residue (Q106), only present in CBM65A, also plays an important role in ligand recognition. The alanine mutation of Q106 abrogated cellohexaose recognition but has no impact on binding to mixed linked b1,3-1,4-glucans (by ITC and plant cell wall labelling assays), suggesting that this residue has a key role only in cellulose recognition and CBM65A binding site is capable of specifically recognise both linear b1,4-glucans and b1,3-b-1,4 mixed linked glucans.<br />
== Functionalities == <br />
CBM65s were first identified in the Eubacterium cellulosolvens EcCel5A endoglucanse. The molecular architecture of EcCel5A shows two CBM65 modules (denominated A and B) appended to two glycoside hydrolases family 5 (GH5 page). The CBM65A and CBM65B specificity for b-glucans (b1,4 and b1,3/14-mixed linked) is consistent with the reported activity of the appended enzymes. Indeed, both GH5s catalytic modules are more active on lichenan (b1,3-b-1,4 mixed linked glucan) and carboxymethylcellulose (b1,4-glucan) than in xylan. The removal of the CBM65s modules associated with the GH5 catalytic domains resulted in a significant decrease of the enzymatic activity against all tested substrates, suggesting that both binding modules have an important role on catalysis enhancing the enzyme activity.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Insert archetype here, possibly including ''very brief'' synopsis.<br />
;First Structural Characterization<br />
:Insert archetype here, possibly including ''very brief'' synopsis.<br />
<br />
== References ==<br />
<biblio><br />
#Yoda2005 pmid=16204489<br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM065]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_65&diff=12815Carbohydrate Binding Module Family 652018-04-29T18:26:21Z<p>Ana Luis: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM65.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
The founding members of family CBM65 (CBM65A and CBM65B) were identified in ''Eubacterium cellulosolvens'' endoglucanase ''Ec''Cel5A <cite>Yoda2005</cite>. This bacterial CBM family displays affinity to plant cell wall polysaccharides. Both modules CBM65A and CBM65B bind to acid swollen cellulose, β1,3/1,4 mixed linked glucans (lichenan and barley β-glucan) and decorated β1,4-glucans such as xyloglucan, hydroxyethylcellulose (HEC) and carboxymethylcellulose (CMC)<cite>Yoda2005 Luis2013</cite>. Both CBM65 modules also have weak affinity for glucomannan but there is no reports of binding to additional alfa or beta-glucans <cite>Luis2013</cite>. By isothermal titration calorimetry (ITC), CBM65A displays higher affinity for xyloglucan comparative to β1,3/1,4 mixed linked glucans and HEC. Additionally, this CBM binds with similar affinity to the oligosaccharides cellopentaose and XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose), the repeating unit of xyloglucan. Binding to shorter cellooligosacharides was too week to be quantified (cellotetraose) or not detectable (cellotriose) <cite>Luis2013</cite>.<br />
<br />
<br />
== Structural Features ==<br />
The three-dimensional structures of Eubacterium cellulosolvens CBM65A (4afm) and CBM65B (2ypj) solved using X-ray display a beta-sandwich fold. The ligand binding site located at the concave surface of the protein adopts a cleft-like structure typical of a type B CBM (link to CBM page).<br />
<br />
The CBM65B structure was obtained in complex with XXXG. Four tryptophans (W602, W607, W651, and W646) make extensive hydrophobic contacs with the backbone and the xylose side chains. Alanine substitution of these tryptophans abrogated cellohexaose and b-glucan recognition, confirming the important role of these aromatic residues in backbone recognition. The mutagenesis of W607, W646 also caused a substantial reduction in affinity to xyloglucan, However, only the mutation W651A abrogated binding to all ligand (xyloglucan, b-glucan and cellohexaose), confirming the key role of this residue in subtract backbone and side chains recognition. An additional aromatic amino acid (Y685) also makes hydrophobic interactions with xylose side chains. The mechanism of ligand recognition by CBM65A and CBM65A is driven by apolar interactions with the surface of these conserved five aromatic residues (W602, W607, W651, W646 and Tyr685), where the hydrophobic interactions with the xylose side chains make a significant contribution to CBM65 binding. Indeed, this recognition of xylose side chains explains the higher affinity to xyloglucan and XXXG comparatively to undecorated b-glucans and cellotetraose, respectively.<br />
<br />
The structure in complex revealed that the ligand biding is also driven by polar interactions between Q110 and the glucose backbone, since the alanine substitution of this residue significantly reduce binding to b-glucan and cellohexaose. A second polar residue (Q106), only present in CBM65A, also plays an important role in ligand recognition. The alanine mutation of Q106 abrogated cellohexaose recognition but has no impact on binding to mixed linked b1,3-1,4-glucans (by ITC and plant cell wall labelling assays), suggesting that this residue has a key role only in cellulose recognition and CBM65A binding site is capable of specifically recognise both linear b1,4-glucans and b1,3-b-1,4 mixed linked glucans.<br />
== Functionalities == <br />
CBM65s were first identified in the Eubacterium cellulosolvens EcCel5A endoglucanse. The molecular architecture of EcCel5A shows two CBM65 modules (denominated A and B) appended to two glycoside hydrolases family 5 (GH5 page). The CBM65A and CBM65B specificity for b-glucans (b1,4 and b1,3/14-mixed linked) is consistent with the reported activity of the appended enzymes. Indeed, both GH5s catalytic modules are more active on lichenan (b1,3-b-1,4 mixed linked glucan) and carboxymethylcellulose (b1,4-glucan) than in xylan. The removal of the CBM65s modules associated with the GH5 catalytic domains resulted in a significant decrease of the enzymatic activity against all tested substrates, suggesting that both binding modules have an important role on catalysis enhancing the enzyme activity.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Insert archetype here, possibly including ''very brief'' synopsis.<br />
;First Structural Characterization<br />
:Insert archetype here, possibly including ''very brief'' synopsis.<br />
<br />
== References ==<br />
<biblio><br />
#Yoda2005 pmid=16204489<br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM065]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=User:Ana_Luis&diff=12401User:Ana Luis2018-02-11T23:56:52Z<p>Ana Luis: </p>
<hr />
<div>[[<br />
Image:ALfoto.jpg|200px|right]]<br />
<br />
<br />
<br />
<br />
I obtained a M.Sc in Pharmaceutical Sciences at [http://http://www.ulisboa.pt/en/ Universtiy of Lisbon] in 2009. After I worked with Dr. Carlos Fontes at [http://www.fmv.ulisboa.pt/_ingles/ Technical University of Lisbon], studying the mechanisms of protein-carbohydrate interactions. Between 2013 and 2017 I moved to [http://www.ncl.ac.uk/ Newcastle University] (UK) to do my PhD under the supervision of Prof. ^^^Harry Gilbert^^^. During this time I studied the mechanisms behind pectin degradation and utilization by the gut bacterium ''Bacteroides thetaiotaomicron''. I’m currently a PostDoc mentored by Prof. [http://www.medkem.gu.se/mucinbiology/biblio2015.html Gunnar C. Hansson] ([https://www.gu.se/English University of Gothenburg], Sweden) and [http://microbe.med.umich.edu/people/eric-martens-phd Eric C. Martens] ([http://umich.edu/ University of Michigan], USA). My research is focused on functional and structural characterization of enzymes and carbohydrate-binding modules. I'm currently interested in understanding the mechanisms behind mucin degradation by gut bacteria and its implications in inflammatory bowel disease.<br />
<br />
<br />
I contributed to structural-functional characterization of:<br />
<br />
[http://www.cazy.org/CBM65.html CBM65] from ''Eubacterium cellulosolvens'' ('''Family First''') <cite>Luis2013</cite>;<br />
<br />
[http://www.cazy.org/CBM77.html CBM77] from ''Ruminococcus flavefaciens'' ('''Family First''') <cite>Venditto2016</cite>;<br />
<br />
[http://www.cazy.org/GH106.html GH106] BT0986 and BT4145 from ''Bacteorides thetaiotaomicron'' ('''Family First''' structure and mechanism of catalysis description) <cite>Ndeh2017, Luis2018 </cite>;<br />
<br />
[http://www.cazy.org/GH103.html GH103] BT1003 from ''Bacteorides thetaiotaomicron'' (first report of an aceric acidase enzyme) <cite>Ndeh2017</cite>;<br />
<br />
[http://www.cazy.org/PL9.html PL9] BT4170 ''Bacteroides thetaiotaomicron'' (first rhamnogalacturonan lyase inside PL9 family) <cite>Luis2018</cite>;<br />
<br />
----<br />
<br />
<biblio><br />
#Luis2013 pmid=23229556<br />
#Venditto2016 pmid=27298375<br />
#Ndeh2017 pmid=28329766<br />
#Luis2018 pmid=29255254<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Luis,Ana]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=User:Ana_Luis&diff=12400User:Ana Luis2018-02-11T23:54:40Z<p>Ana Luis: </p>
<hr />
<div>[[Image:ALfoto.jpg|200px|right]]<br />
<br />
<br />
I obtained a M.Sc in Pharmaceutical Sciences at [http://http://www.ulisboa.pt/en/ Universtiy of Lisbon] in 2009. After I worked with Dr. Carlos Fontes at [http://www.fmv.ulisboa.pt/_ingles/ Technical University of Lisbon], studying the mechanisms of protein-carbohydrate interactions. Between 2013 and 2017 I moved to [http://www.ncl.ac.uk/ Newcastle University] (UK) to do my PhD under the supervision of Prof. ^^^Harry Gilbert^^^. During this time I studied the mechanisms behind pectin degradation and utilization by the gut bacterium ''Bacteroides thetaiotaomicron''. I’m currently a PostDoc mentored by Prof. [http://www.medkem.gu.se/mucinbiology/biblio2015.html Gunnar C. Hansson] ([https://www.gu.se/English University of Gothenburg], Sweden) and [http://microbe.med.umich.edu/people/eric-martens-phd Eric C. Martens] ([http://umich.edu/ University of Michigan], USA). My research is focused on functional and structural characterization of enzymes and carbohydrate-binding modules. I'm currently interested in understanding the mechanisms behind mucin degradation by gut bacteria and its implications in inflammatory bowel disease.<br />
<br />
<br />
I contributed to structural-functional characterization of:<br />
<br />
[http://www.cazy.org/CBM65.html CBM65] from ''Eubacterium cellulosolvens'' ('''Family First''') <cite>Luis2013</cite>;<br />
<br />
[http://www.cazy.org/CBM77.html CBM77] from ''Ruminococcus flavefaciens'' ('''Family First''') <cite>Venditto</cite>;<br />
<br />
[http://www.cazy.org/GH106.html GH106] BT0986 and BT4145 from ''Bacteorides thetaiotaomicron'' ('''Family First''' structure and mechanism of catalysis description) <cite>Ndeh2017, Luis2018 </cite>;<br />
<br />
[http://www.cazy.org/GH103.html GH103] BT1003 from ''Bacteorides thetaiotaomicron'' (first report of an aceric acidase enzyme) <cite>Ndeh2017</cite>;<br />
<br />
[http://www.cazy.org/PL9.html PL9] BT4170 ''Bacteroides thetaiotaomicron'' (first rhamnogalacturonan lyase inside PL9 family) <cite>Luis2018</cite>;<br />
<br />
----<br />
<br />
<biblio><br />
#Luis2013 pmid=23229556<br />
#Venditto2016 pmid=27298375<br />
#Ndeh2017 pmid=28329766<br />
#Luis2018 pmid=29255254<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Luis,Ana]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_106&diff=12399Glycoside Hydrolase Family 1062018-02-11T23:13:11Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH106'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH106.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The glycoside hydrolases of this family are alfa L-rhamnosidases ([http://www.enzyme-database.org/query.php?ec=3.2.1.40 EC 3.2.1.40]). The first GH106 characterized was Rham from ''Sphingomonas paucimobilis'' FP2001. This enzyme showed activity against p-nitrophenyl α-L-rhamnopyranoside <cite>Miyata2005</cite>. More recently, two ''Bacteroides thetaiotaomicron'' enzymes (BT0986 and BT4145) have been characterized. These enzymes are exo active against linkages present in pectin polysaccharides. BT0986 cleaves the L-Rha-α-1,2-L-Arap linkage in the terminal region of Chain B of rhamnogalacturonan II <cite>Ndeh2017</cite>. The enzyme BT4145 targets the L-Rha-α-1,4-D-GalA linkage in the backbone of rhamnogalacturonan I <cite>Luis2018</cite>. All of genes encoding family 106 members are found in bacteria ([http://www.cazy.org/GH106.html CAZy]).<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH106 members act by inverting the anomeric configuration of the glycone sugar participating in the scissle glycosidic linkage (inverting mechanism), and thus mediate bond cleave through a single displacement mechanism <cite>Luis2018</cite>. Additionally, GH106 enzymes are Ca 2+ dependent <cite>Ndeh2017</cite>. The only other ion dependent enzyme families are the exo-α-mannosidases [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_38 GH38], [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_47 GH47] and [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_92 GH92]. The structure of BT0986 in complex with D-rhamnopyranose tetrazole indicates that catalysis is proceeds via a B<sub>2,5</sub> transition state <cite>Ndeh2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
[[File:BT0986_2.png|thumb|300px|right|'''Figure 1.''' '''BT0986 active site.''' The catalytic amino acids are shown in orange and yellow are the remaining key residues present in the active site. The calcium ion in the active site is shown as a cyan sphere and its polar contacts indicated by black dashed lines. D-rhamnopyranose tetrazole is represented in green.]]<br />
Structural characterization of ''B. thetaiotaomicron'' BT0986 identified two highly conserved carboxylate amino acids (E461 and E593) that were essential for activity (Figure 1). These glutamates are separated by 8.0 Å, a distance between catalytic residues consistent with an inverting mechanism. Additionally, E593, which is 5.8 Å from the anomeric carbon is ideally positioned to act as general base and E461 is the general acid <cite>Ndeh2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:BT0986_1.png|thumb|300px|right|'''Figure 2.''' '''BT0986 structure'''([https://www.rcsb.org/structure/5MQN 5MQN]). The figure shows the (β/α)<sub>8</sub>-barrel domain (1, yellow) and the additional two b-stranded domains (2 to 6). The D-rhamnopyranose tetrazole represented as sticks with carbon in green and the calcium ion (cyan sphere) are shown at the centre of the (β/α)<sub>8</sub>-barrel.]]<br />
The three-dimensional structure of ''B. thetaiotaomicron'' BT0986 solved using X-ray crystallography represents the first structure of an GH106 enzyme ([https://www.rcsb.org/structure/5MQN 5MQN]). BT0986 displays a N-terminal catalytic domain that presents an (β/α)<sub>8</sub>-barrel fold with several appended several β-stranded domains (C-terminal) (Figure 2) <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: BT4145 from ''Bacteroides thetaiotaomicron'' <cite>Luis2018</cite>.<br />
;First catalytic nucleophile identification: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First 3-D structure: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Miyata2005 Miyata T, Kashige N, Satho T, Yamaguchi T, Aso Y and Miake F.Cloning (2005) Sequence analysis, and expression of the gene encoding ''Sphingomonas paucimobilis'' FP2001 alpha-L-rhamnosidase. ''Curr Microbiol'', vol 51, no. 2., pp. 105-109. <br />
#Ndeh2017 pmid=28329766 <br />
#Luis2018 pmid=29255254 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH106]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:BT0986_2.png&diff=12398File:BT0986 2.png2018-02-11T23:04:26Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=File:BT0986_1.png&diff=12397File:BT0986 1.png2018-02-11T23:04:08Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_141&diff=12396Glycoside Hydrolase Family 1412018-02-11T23:02:31Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH141'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH141.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of family 141 ([http://www.cazy.org/GH141.html CAZy]) display α-L-fucosidase ([http://www.enzyme-database.org/query.php?ec=3.2.1.51 EC 3.2.1.51]) or xylanase ([http://www.enzyme-database.org/query.php?ec=3.2.1.8 EC 3.2.1.8]) activities. The ''Bacteroides thetaiotaomicron'' enzyme BT1002 was the founding member of this family. The enzyme cleaves 2-O-methyl-D-xylose-α-1,3-L-fucose from rhamnogalacturonan II, a complex pectin conserved in the primary cell walls <cite>Ndeh2017</cite>. Recently, an endo-xylanase from ''Clostridium thermocellum'' (Xyn141E) was also described. Xyn141E is most active against arabinoxylan. However, this enzyme also displays side activities against carboxymethyl cellulose, barley beta glucan and mannan from ivory nut <cite>Heinze2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Very little is known about the kinetics or mechanism of GH141 enzymes. However, in BT1002 crystal structure, the distance of 6.1 Å between the catalytic residues suggests that members of this family may be retaining enzymes and follow a double displacement mechanism <cite>Ndeh2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
In BT1002 structure, two aspartates (Asp 523 and Asp564) located within the active site pocket are the catalytic residues. Site directed mutagenesis of these residues abolished the catalytic activity of BT1002 indicating the essential role in catalysis. Additionally, the structural location of the catalytic residues suggests that Asp523 (at the base of the pocket) acts as catalytic nucleophile and Asp564 (at the lip of the active site) is the general acid-base residue <cite>Ndeh2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:BT1002.png|thumb|300px|right|'''Figure 1.''' '''BT1002 strucutre'''. ([https://www.rcsb.org/structure/5MQP PDB ID 5PDB]) The figure shows the β-parallel catalytic domain (purple) and the additional β-sandwich domain (yellow)]]<br />
The three-dimensional structure has been solved for ''B. thetaiotaomicron'' BT1002 at 2 Å ([https://www.rcsb.org/structure/5MQP PDB ID 5PDB]). The protein has two domains: a N-terminal β-sandwich and a C-terminal β-parallel catalytic domain (Figure 1) <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Currently unknown.<br />
;First catalytic nucleophile identification: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First 3-D structure: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Heinze2017 pmid=28894250<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH141]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:BT0986.png&diff=12395File:BT0986.png2018-02-11T23:01:49Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=File:BT1002.png&diff=12394File:BT1002.png2018-02-11T22:48:26Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_106&diff=12393Glycoside Hydrolase Family 1062018-02-11T22:29:44Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH106'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH106.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The glycoside hydrolases of this family are alfa L-rhamnosidases ([http://www.enzyme-database.org/query.php?ec=3.2.1.40 EC 3.2.1.40]). The first GH106 characterized was Rham from ''Sphingomonas paucimobilis'' FP2001. This enzyme showed activity against p-nitrophenyl α-L-rhamnopyranoside <cite>Miyata2005</cite>. More recently, two ''Bacteroides thetaiotaomicron'' enzymes (BT0986 and BT4145) have been characterized. These enzymes are exo active against linkages present in pectin polysaccharides. BT0986 cleaves the L-Rha-α-1,2-L-Arap linkage in the terminal region of Chain B of rhamnogalacturonan II <cite>Ndeh2017</cite>. The enzyme BT4145 targets the L-Rha-α-1,4-D-GalA linkage in the backbone of rhamnogalacturonan I <cite>Luis2018</cite>. All of genes encoding family 106 members are found in bacteria ([http://www.cazy.org/GH106.html CAZy]).<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH106 members act by inverting the anomeric configuration of the glycone sugar participating in the scissle glycosidic linkage (inverting mechanism), and thus mediate bond cleave through a single displacement mechanism <cite>Luis2018</cite>. Additionally, GH106 enzymes are Ca 2+ dependent <cite>Ndeh2017</cite>. The only other ion dependent enzyme families are the exo-α-mannosidases [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_38 GH38], [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_47 GH47] and [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_92 GH92]. The structure of BT0986 in complex with D-rhamnopyranose tetrazole indicates that catalysis is proceeds via a B<sub>2,5</sub> transition state <cite>Ndeh2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
Structural characterization of ''B. thetaiotaomicron'' BT0986 identified two highly conserved carboxylate amino acids (E461 and E593) that were essential for activity. These glutamates are separated by 8.0 Å, a distance between catalytic residues consistent with an inverting mechanism. Additionally, E593, which is 5.8 Å from the anomeric carbon is ideally positioned to act as general base and E461 is the general acid <cite>Ndeh2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of ''B. thetaiotaomicron'' BT0986 solved using X-ray crystallography represents the first structure of an GH106 enzyme ([https://www.rcsb.org/structure/5MQN 5MQN]). BT0986 displays a N-terminal catalytic domain that presents an (α/α)<sub>8</sub>-barrel fold with several appended several β-stranded domains (C-terminal) <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: BT4145 from ''Bacteroides thetaiotaomicron'' <cite>Luis2018</cite>.<br />
;First catalytic nucleophile identification: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First 3-D structure: BT0986 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Miyata2005 Miyata T, Kashige N, Satho T, Yamaguchi T, Aso Y and Miake F.Cloning (2005) Sequence analysis, and expression of the gene encoding ''Sphingomonas paucimobilis'' FP2001 alpha-L-rhamnosidase. ''Curr Microbiol'', vol 51, no. 2., pp. 105-109. <br />
#Ndeh2017 pmid=28329766 <br />
#Luis2018 pmid=29255254 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH106]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_106&diff=12392Glycoside Hydrolase Family 1062018-02-11T22:07:12Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH106'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH106.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The glycoside hydrolases of this family are alfa L-rhamnosidases ([http://www.enzyme-database.org/query.php?ec=3.2.1.40 EC 3.2.1.40]). The first GH106 characterized was Rham from ''Sphingomonas paucimobilis'' FP2001. This enzyme showed activity against p-nitrophenyl α-L-rhamnopyranoside. More recently, two Bacteroides thetaiotaomicron enzymes (BT0986 and BT4145) have been characterized. These enzymes are exo active against linkages present in pectin polysaccharides. BT0986 cleaves the L-Rha-a-1,2-L-Arap linkage in the terminal region of Chain B of rhamnogalacturonan II. The enzyme BT4145 targets the L-Rha-a-1,4-D-GalA linkage in the backbone of rhamnogalacturonan I. All of genes encoding family 106 members are found in bacteria.<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
# Miyata2005 Miyata T, Kashige N, Satho T, Yamaguchi T, Aso Y and Miake F.Cloning (2005) Sequence analysis, and expression of the gene encoding ''Sphingomonas paucimobilis'' FP2001 alpha-L-rhamnosidase. ''Curr Microbiol'', vol 51, no. 2., pp. 105-109. <br />
#Ndeh2017 pmid=28329766 <br />
#Luis2018 pmid=29255254 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH106]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_141&diff=12391Glycoside Hydrolase Family 1412018-02-11T21:15:10Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH141'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH141.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of family 141 ([http://www.cazy.org/GH141.html CAZy]) display α-L-fucosidase ([http://www.enzyme-database.org/query.php?ec=3.2.1.51 EC 3.2.1.51]) or xylanase ([http://www.enzyme-database.org/query.php?ec=3.2.1.8 EC 3.2.1.8]) activities. The ''Bacteroides thetaiotaomicron'' enzyme BT1002 was the founding member of this family. The enzyme cleaves 2-O-methyl-D-xylose-α-1,3-L-fucose from rhamnogalacturonan II, a complex pectin conserved in the primary cell walls <cite>Ndeh2017</cite>. Recently, an endo-xylanase from ''Clostridium thermocellum'' (Xyn141E) was also described. Xyn141E is most active against arabinoxylan. However, this enzyme also displays side activities against carboxymethyl cellulose, barley beta glucan and mannan from ivory nut <cite>Heinze2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Very little is known about the kinetics or mechanism of GH141 enzymes. However, in BT1002 crystal structure, the distance of 6.1 Å between the catalytic residues suggests that members of this family may be retaining enzymes and follow a double displacement mechanism <cite>Ndeh2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
In BT1002 structure, two aspartates (Asp 523 and Asp564) located within the active site pocket are the catalytic residues. Site directed mutagenesis of these residues abolished the catalytic activity of BT1002 indicating the essential role in catalysis. Additionally, the structural location of the catalytic residues suggests that Asp523 (at the base of the pocket) acts as catalytic nucleophile and Asp564 (at the lip of the active site) is the general acid-base residue <cite>Ndeh2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure has been solved for ''B. thetaiotaomicron'' BT1002 at 2 Å ([https://www.rcsb.org/structure/5MQP PDB ID 5PDB]). The protein has two domains: an N-terminal β-sandwich and a C-terminal β-parallel catalytic domain <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Currently unknown.<br />
;First catalytic nucleophile identification: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
;First 3-D structure: BT1002 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Heinze2017 pmid=28894250<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH141]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_139&diff=12390Glycoside Hydrolase Family 1392018-02-11T20:41:16Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH139'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|unknown<br />
|-<br />
|'''Active site residues'''<br />
|not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH139.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH139 family ([http://www.cazy.org/GH139.html CAZy]) display the novel α-2-O-methyl-L-fucosidase activity. The enzyme BT0984 from ''Bacteroides thetaiotaomicron'' is the only member of this family that has been characterized. This exo-enzyme targets the α-2-O-methyl-L-fucose at chain B of the complex pectin rhamnogalacturonan-II <cite>Ndeh2017</cite>. All of genes encoding family 139 members are found in bacteria.<br />
<br />
== Kinetics and Mechanism ==<br />
The stereochemistry of the reaction catalyzed by GH129 members has not yet been studied.<br />
<br />
== Catalytic Residues ==<br />
Not known.<br />
<br />
== Three-dimensional structures ==<br />
No three-dimensional structure has been solved for this family.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Unknown.<br />
;First catalytic nucleophile identification: Unknown.<br />
;First general acid/base residue identification: Unknown.<br />
;First 3-D structure: Unknown.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH139]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_139&diff=12389Glycoside Hydrolase Family 1392018-02-11T20:27:47Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH139'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|unknown<br />
|-<br />
|'''Active site residues'''<br />
|not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH139.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH139 family ([www.cazy.org/GH139.html CAZy]) display the novel a-2-O-methyl-L-fucosidase activity (EC…….). The enzyme BT0984 from Bacteroides thetaiotaomicron is the only member of this family that has been characterized. This exo-enzyme targets the a-2-O-methyl-L-fucose at chain B of the complex rhamnogalacturonan-II present in the plants cell wall. All of genes encoding family 139 members are found in bacteria.<br />
<br />
Content is to be added here.<br />
<br />
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH139]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_139&diff=12388Glycoside Hydrolase Family 1392018-02-11T20:23:44Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH139'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|unknown<br />
|-<br />
|'''Active site residues'''<br />
|not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH139.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH139]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11738Polysaccharide Lyase Family 92017-09-14T20:14:02Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.* EC 4.2.2.-]) <cite>Brooks1990 Kondo2011</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11737Polysaccharide Lyase Family 92017-09-14T20:10:04Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.* EC 4.2.2.-]) <cite>Brooks1990 Kondo2011</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11736Polysaccharide Lyase Family 92017-09-14T20:06:47Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.* EC 4.2.2.-]) <cite>Brooks1990 Kondo2011</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11735Polysaccharide Lyase Family 92017-09-14T20:04:29Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2])<cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.* EC 4.2.2.-]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>Brooks1990 Kondo2011</cite>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11734Polysaccharide Lyase Family 92017-09-14T20:02:42Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2])<cite>Jenkins2004</cite>. Additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyases ([http://www.enzyme-database.org/query.php?ec=4.2.2.* EC 4.2.2.-]) <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11733Polysaccharide Lyase Family 92017-09-14T20:00:49Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
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 ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2])<cite>Jenkins2004</cite>. Other additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11732Polysaccharide Lyase Family 92017-09-14T19:43:56Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan or sheath, a thioloic glycoconjugate secreted by ''Sphaerotilus natans'' <cite>Jenkins2004</cite>. <br />
<br />
<br />
a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11731Polysaccharide Lyase Family 92017-09-14T19:43:09Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan or sheath, a thioloic glycoconjugate secreted by ''Sphaerotilus natans'' <cite>Jenkins2004</cite>. <br />
<br />
<br />
a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
<br />
[[<br />
<br />
File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
<br />
<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Takeda2000 pmid=11055955<br />
#Kondo2011 pmid=121095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11730Polysaccharide Lyase Family 92017-09-14T15:58:10Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
[[File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11729Polysaccharide Lyase Family 92017-09-14T15:51:59Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
[[File:PL9.png|thumb|300px|right|'''Figure 1.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 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.]]<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 1RU4]) and displays a right-handed parallel β-helix fold. 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 <cite>Jenkins2004</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:PL9.png&diff=11728File:PL9.png2017-09-14T15:32:48Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11015Polysaccharide Lyase Family 92015-11-21T22:52:28Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 1RU4]) and displays a right-handed parallel β-helix fold. 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 <cite>Jenkins2004</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11014Polysaccharide Lyase Family 92015-11-21T22:49:51Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrades homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 [https://www.cazypedia.org/index.php/Polysaccharide_Lyase_Family_1 PL1] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 1RU4]) and displays a right-handed parallel β-helix fold. 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 <cite>Jenkins2004</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=11013Polysaccharide Lyase Family 92015-11-21T22:43:47Z<p>Ana Luis: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrades homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
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 PL1 family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. <br />
<br />
== Catalytic Residues ==<br />
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>. <br />
<br />
== Three-dimensional structures ==<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 1RU4]) and displays a right-handed parallel β-helix fold. 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 <cite>Jenkins2004</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=User:Ana_Luis&diff=10985User:Ana Luis2015-10-04T20:14:40Z<p>Ana Luis: </p>
<hr />
<div>[[Image:ALfoto.jpg|200px|right]]<br />
<br />
I obtained a M.Sc in Pharmaceutical Sciences at [http://http://www.ulisboa.pt/en/ Universtiy of Lisbon] in 2009. After I worked with Dr. Carlos Fontes at [http://www.fmv.ulisboa.pt/_ingles/ Technical University of Lisbon], studying the mechanisms of protein-carbohydrate interactions. Currently, I'm doing the PhD under the supervision of Prof. [https://www.cazypedia.org/index.php/User:Harry_Gilbert Harry Gilbert] at [http://www.ncl.ac.uk/ Newcastle University]. My research has focus on functional and structural characterization of enzymes and carbohydrate binding modules. I'm also interested in understanding the mechanisms behind pectin degradation and utilization by intestinal bacteria.<br/>I contributed to structural-functional characterization of [http://www.cazy.org/CBM65.html CBM65 ] ('''Family First''') <cite>Luis2013</cite> <br />
<br />
<br />
----<br />
<br />
<biblio><br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Luis,Ana]]</div>Ana Luishttps://www.cazypedia.org/index.php?title=File:ALfoto.jpg&diff=10984File:ALfoto.jpg2015-10-04T19:16:55Z<p>Ana Luis: </p>
<hr />
<div></div>Ana Luishttps://www.cazypedia.org/index.php?title=User:Ana_Luis&diff=10983User:Ana Luis2015-10-04T19:02:23Z<p>Ana Luis: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
<br />
I obtained a M.Sc in Pharmaceutical Sciences at University of Lisbon in 2009. After I worked with Dr. Carlos Fontes at Technical University of Lisbon, studying the mechanisms of protein-carbohydrate interactions. Currently, I'm doing the PhD under the supervision of Prof. Harry Gilbert at Newcastle University. My research has focus on functional and structural characterization of enzymes and carbohydrate binding modules. I'm also interested in understanding the mechanisms behind the pectins degradation and utilization by intestinal bacteria.<br />
I contributed to structural-functional characterization of CBM65 ('''Family first''') <cite>Luis2013</cite> <br />
<br />
<br />
----<br />
<br />
<biblio><br />
#Luis2013 pmid=23229556<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Luis,Ana]]</div>Ana Luis