https://www.cazypedia.org/api.php?action=feedcontributions&user=Michael+Suits&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-28T16:19:37ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_7&diff=15644Carbohydrate Esterase Family 72020-07-23T02:51:30Z<p>Michael Suits: maritima</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]]: ^^^Emily Rodriguez^^^<br />
* [[Responsible Curator]]s: ^^^Michael Suits^^^ and ^^^Joel Weadge^^^<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" |'''Carbohydrate Esterase Family CE7'''<br />
|-<br />
|'''Clan''' <br />
|(α/β/α)-Sandwich<br />
|-<br />
|'''Mechanism'''<br />
|Serine Hydrolase<br />
|-<br />
|'''Active site residues'''<br />
|Known, Catalytic Triad<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE7.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Carbohydrate Esterase Family 7 currently contains enzymes classified as acetyl xylan esterases (AXEs) and cephalosporin-C deacetylases<cite>Nakamura2017</cite>. One exception is the AXE from ''Thermotoga martitima'' that lacks detectable activity towards acetylated xylan, but rather, shorter acetylated xylo-oligomers<cite>Levisson2012</cite>. A common feature of the oligomeric enzymes belonging to this family is that they usually serve as multifunctional deacetylases and are active on a broad range of small substrates with relatively low acetyl-positional specificity<cite>Levisson2012,Krastanova2005,Lorenz1997,Vincent2003</cite>. Some examples include xylose tetraacetate, glucose pentaacetate, α-napthyl acetate, 4-methylumbelliferyl acetate and ''p''-nitrophenyl acetate (''p''NP-acetate)<cite>Degrassi2000</cite>. Substrate binding is proposed to be largely mediated through non-specific hydrophobic interactions with surface amino acid residues<cite>Vincent2003</cite>. <br />
== Catalytic Residues ==<br />
Members of this family use the catalytic triad of serine, histidine and aspartate<cite>Biely2012</cite>. The aspartate promotes the amphoteric nature of the histidine residue so that it can abstract a proton from the serine residue to render the serine nucleophilic<cite>Levisson2012</cite>. The Gly-X-Ser-X-Gly motif, containing the nucleophilic serine, is common amongst the broad α/β-hydrolase family to which the CE7 enzymes belong<cite>Mitsushima1995</cite>. The glycine residues near the catalytic serine are important to prevent any steric hindrance that may occur from amino acids with larger side chains and form the basis for the nucleophilic “elbow” turn motif that is present in these enzymes<cite>Levisson2012</cite>. [[Image:CAH Bsubtilis CE7.jpg|thumb|300px|Figure 1: CAH from B. subtilis ([{{PDBlink}}1ODS PDB ID 1ODS]). A) An individual monomer from the overall CAH structure showing the α/β-hydrolase fold formed by each subunit and the β-strand-like interface domain needed for association of the monomers. The catalytic triad of Ser181, Asp 269 and His 298 are highlighted in cyan. B) Characteristic donut-shaped quaternary structure of the CAH hexamer. Each monomer is represented in a different colour.]]<br />
== Kinetics and Mechanism ==<br />
The CE7 family of esterases catalyze the removal of O-acetyl groups from cephalosporin-C, xylan and xylo-oligosaccharides<cite>Vincent2003,Biely2012</cite>. Members of this family present their active site residues in typical positions observed for α/β-hydrolases<cite>Sista_Kameshwar2018</cite>. The catalytic triad residues responsible for de-O-acetylation are found on loops near the C-terminus of the β-strands 5, 7 and 8 for the catalytic serine, aspartate and histidine, respectively<cite>Ollis1992</cite>. Similar to other α/β-hydrolases, the CE7 enzymes follow a mechanism where the serine is deprotonated by the histidine imidazole side chain; thereby allowing for nucleophilic attack of the serine on the incoming carbonyl of the substrate’s acetyl group<cite>Sista_Kameshwar2018</cite>. The result is a transient tetrahedral oxyanion intermediate, which is stabilized by the backbone amide group of a highly conserved glutamate residue (found in a signature RGQ motif adjacent to the nucleophilic serine at the end of β-strand 4) and a less conserved tyrosine that together form the oxyanion hole of the enzyme<cite>Levisson2012,<cite>Vincent2003</cite>. The tetrahedral intermediate then collapses resulting in an acetyl-enzyme intermediate and release of the de-O-acetylated product. A water molecule entering the active site is deprotonated by histidine and then nucleophilic attack by water on the acetyl-enzyme takes place to liberate acetate and the free enzyme<cite>Sista_Kameshwar2018</cite>. A recent study on the CE7 AXE (TM0077) from ''T. martitima'' provided further support into the catalytic mechanism<cite>Levisson2012</cite>. TM0077 was co-crystallized with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, that led to a 110° rotation of the catalytic serine and the formation of a covalent tetrahedral intermediate that was unable to collapse back to the starting materials (TM0077 and PMSF/paraoxan)<cite>Levisson2012</cite>. Trapping the tetrahedral intermediate is strong evidence that CE7 enzymes proceed by the proposed mechanism. <br />
<br />
Kinetic parameters and specific activities have been determined for some members of CE7. CAH from ''Bacillus subtilis'', AXE from ''Paenibacillus'' sp. R4 and AXE (TM0077) from ''T. maritima'' were assayed for their activity against ''p''NP-acetate and were found to have ''K''<sub>M</sub> values of 0.29 +/- 0.01, 0.15 +/- 0.01 and 0.19 +/- 0.03 mM, respectively, and ''k''<sub>cat</sub>/''K''<sub>M</sub> values of 260, 360 and 310 s<sup>-1</sup>mM<sup>-1</sup>, respectively<cite>Levisson2012,Vincent2003,Takimoto1994,Park2018</cite>. There has been discrepancy regarding the ability of these CE7 enzymes to utilize acetylated xylan as a substrate. While a ''Bacillus pumilus'' AXE has demonstrated a specific activity against acetylated xylan of 41 +/- 8 U/mg, ''T. maritima'''s AXE had no demonstrated activity and the acetyl xylan esterase, Axe1, from ''Thermoanerobacterium saccharolyticum'' strain JW/SL-YS485 had no activity in one study and 5.2 U/mg (8-fold lower than the ''B. pumilus'' enzyme) in another study<cite>Levisson2012,Lorenz1997,Degrassi1998,Shao1995</cite>. In light of the apparent low/no activity against acetylated xylan, the enzymes from ''T. maritima'' and ''T. saccharolyticum'' were assayed against smaller substrates, where the ''T. maritima'' AXE (TM0077) had high activity against glucose pentaacetate with a ''k''<sub>cat</sub> of 2900 s<sup>-1</sup> and Axe1 from ''T. saccharolyticum'' had high activity against xylose tetraacetate with separately reported specific activities of 210 and 740 U/mg<cite>Levisson2012,Lorenz1997,Shao1995</cite>. Lastly, CAH from ''B. subtilis'' has been kinetically characterized with regards to activity towards cephalosporin-C with a ''K''<sub>M</sub> of 24 mM and a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 7.0 s<sup>-1</sup>mM<sup>-1</sup>, which has supported its naming as a cephalosporin-C deacetylase<cite>Takimoto1994</cite>.<br />
== Three-dimensional structures ==<br />
There are six resolved structures currently reported for the CE7 family. These include the AXE from ''B. pumilus'' ([{{PDBlink}}2XLB PDB ID 2XLB]), cephalosporin-C deacetylase (CAH) from ''B. subtilis'' strain 168 ([{{PDBlink}}1ODS PDB ID 1ODS]), the AXE from ''Paenibacillus'' sp. R4 ([{{PDBlink}}6AGQ PDB ID 6AGQ]), acetyl xylan esterase 1 (Axe1) from ''T. saccharolyticum'' strain JW/SL-YS485 ([{{PDBlink}}3FCY PDB ID 3FCY]), the AXE (TM0077) from ''T. maritima'' ([{{PDBlink}}1VLQ PDB ID 1VLQ]) and, lastly, an unclassified protein named Axe1-NaM1 ([{{PDBlink}}6FKX PDB ID 6FKX]).<br />
<br />
Enzymes in the CE7 family contain high levels of multimerization, with quaternary structures containing 4, 5, 6 and 8 subunits described<cite>Vincent2003</cite>. For each of the six resolved structures from the CE7 family, individual subunits adopt a classic α/β-hydrolase fold that consists of a central eight-stranded β-sheet surrounded by α-helices on both sides (See Fig. 1A)<cite>Levisson2012</cite>. Together, the multimerized subunits adopt a donut-like shape that results in the formation of a tunnel leading to the centre of the protein (See Fig. 1B). Each of the active sites from the individual multimers are arranged so that they face into the centre of the tunnel<cite>Vincent2003</cite>.<br />
<br />
== Family Firsts ==<br />
;First Characterized:The first cephalosporin-C deacetylase (CAH) of this family to be characterized was from ''B. subtilis'' strain 168 in 1975<cite>Abbot1975</cite>. CAH is able to deacetylate cephalosporin-C, as well as cephalosporin-C derivatives (eg., cephalosporanic acid and cephalothin) at the 3’ position<cite>Abbot1975</cite>. The first acetyl xylan esterase to be characterized was Axe1, from the anaerobic thermophilic bacterium ''T. saccharolyticum'' strain JW/SL-YS485 in 1995<cite>Shao1995</cite>. When in the presence of acetylated xylan, Axe1 showed esterase activity that liberated acetate, leading to its name<cite>Shao1995</cite>. However, Axe1 has also demonstrated active against other acetylated sugars<cite>Shao1995</cite>. <br />
;First Mechanistic Insight: The first mechanistic insight into the CE7 family came from the CAH enzyme from ''B. subtilis'' in 1994 when Takimoto and coworkers tested the effects of various chemicals (''eg.'', EDTA, PMSF, diisopropyl flurophosphate) on CAH activity and concluded that serine is likely important for catalysis<cite>Takimoto1994</cite>. Almost 10 years later in 2003, Vincent and colleagues resolved the crystal structure of CAH, confirming that serine was present in the active site and that an aspartate and histidine completed the catalytic triad<cite>Vincent2003</cite>. More recently, co-crystallization of the AXE (TM0077) from ''T. martitima'' with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, led to trapping of the tetrahedral intermediate; thereby providing further support for the serine-histidine-aspartate mediated mechanism described for this family. <br />
;First 3-D Structure:The first resolved structure in this family was the cephalosporin-C deacetylase, CAH ([{{PDBlink}}1ODS PDB ID 1ODS]) from ''B. subtilis'' strain 168 in 2003<cite>Vincent2003</cite>. The quaternary structure consisted of a trimer of dimers to make up a donut-shaped homohexamer with 32kDa subunits that each adopt the α/β hydrolase fold (See Fig. 1A)<cite>Vincent2003</cite>. The hydrophobic core containing the six active site centers is thought to help exclude large substrates and is shielded from solvents through a lid-like domain<cite>Vincent2003</cite>. In order for the hexamer to form, there are α-helix interactions as well as a β-strand-like interface associating between monomers (See Fig. 1A)<cite>Vincent2003,Sista_Kameshwar2018</cite>.<br />
== References ==<br />
<biblio><br />
#Nakamura2017 Nakamura, AM, Nascimento, AS and Polikarpov, I. (2017) Structural diversity of carbohydrate esterases. ''Biotechnol. Res. Innov.'', vol. 1, pp. 35-51. [https://doi.org/10.1016/j.biori.2017.02.001].<br />
#Levisson2012 pmid=22411095<br />
#Krastanova2005 pmid=15769599<br />
#Lorenz1997 pmid=9286998<br />
#Vincent2003 pmid=12842474<br />
#Degrassi2000 pmid=10878123<br />
#Biely2012 pmid=22580218<br />
#Mitsushima1995 pmid=7793942<br />
#Sista_Kameshwar2018 pmid=30533253<br />
#Ollis1992 pmid=1409539<br />
#Takimoto1994 Takimoto, A, Mitsushima, K, Yagi, S. and Sonoyama, T. (1994) Purification, Characterization and Partial Amino Acid Sequences of a Novel Cephalosporin-C Deacetylase from ''Bacillus subtilis''. ''J. Fermentation Bioeng.'', vol. 77, no. 1, pp. 17-22.<br />
#Park2018 pmid=30379876<br />
#Degrassi1998 pmid=10215579<br />
#Shao1995 pmid=7574610<br />
#Abbot1975 pmid=241292<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE007]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_7&diff=15643Carbohydrate Esterase Family 72020-07-23T02:48:21Z<p>Michael Suits: </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]]: ^^^Emily Rodriguez^^^<br />
* [[Responsible Curator]]s: ^^^Michael Suits^^^ and ^^^Joel Weadge^^^<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" |'''Carbohydrate Esterase Family CE7'''<br />
|-<br />
|'''Clan''' <br />
|(α/β/α)-Sandwich<br />
|-<br />
|'''Mechanism'''<br />
|Serine Hydrolase<br />
|-<br />
|'''Active site residues'''<br />
|Known, Catalytic Triad<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE7.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Carbohydrate Esterase Family 7 currently contains enzymes classified as acetyl xylan esterases (AXEs) and cephalosporin-C deacetylases<cite>Nakamura2017</cite>. One exception is the AXE from ''Thermotoga martitima'' that lacks detectable activity towards acetylated xylan, but rather, shorter acetylated xylo-oligomers<cite>Levisson2012</cite>. A common feature of the oligomeric enzymes belonging to this family is that they usually serve as multifunctional deacetylases and are active on a broad range of small substrates with relatively low acetyl-positional specificity<cite>Levisson2012,Krastanova2005,Lorenz1997,Vincent2003</cite>. Some examples include xylose tetraacetate, glucose pentaacetate, α-napthyl acetate, 4-methylumbelliferyl acetate and ''p''-nitrophenyl acetate (''p''NP-acetate)<cite>Degrassi2000</cite>. Substrate binding is proposed to be largely mediated through non-specific hydrophobic interactions with surface amino acid residues<cite>Vincent2003</cite>. <br />
== Catalytic Residues ==<br />
Members of this family use the catalytic triad of serine, histidine and aspartate<cite>Biely2012</cite>. The aspartate promotes the amphoteric nature of the histidine residue so that it can abstract a proton from the serine residue to render the serine nucleophilic<cite>Levisson2012</cite>. The Gly-X-Ser-X-Gly motif, containing the nucleophilic serine, is common amongst the broad α/β-hydrolase family to which the CE7 enzymes belong<cite>Mitsushima1995</cite>. The glycine residues near the catalytic serine are important to prevent any steric hindrance that may occur from amino acids with larger side chains and form the basis for the nucleophilic “elbow” turn motif that is present in these enzymes<cite>Levisson2012</cite>. [[Image:CAH Bsubtilis CE7.jpg|thumb|300px|Figure 1: CAH from B. subtilis ([{{PDBlink}}1ODS PDB ID 1ODS]). A) An individual monomer from the overall CAH structure showing the α/β-hydrolase fold formed by each subunit and the β-strand-like interface domain needed for association of the monomers. The catalytic triad of Ser181, Asp 269 and His 298 are highlighted in cyan. B) Characteristic donut-shaped quaternary structure of the CAH hexamer. Each monomer is represented in a different colour.]]<br />
== Kinetics and Mechanism ==<br />
The CE7 family of esterases catalyze the removal of O-acetyl groups from cephalosporin C, xylan and xylo-oligosaccharides<cite>Vincent2003,Biely2012</cite>. Members of this family present their active site residues in typical positions observed for α/β-hydrolases<cite>Sista_Kameshwar2018</cite>. The catalytic triad residues responsible for de-O-acetylation are found on loops near the C-terminus of the β-strands 5, 7 and 8 for the catalytic serine, aspartate and histidine, respectively<cite>Ollis1992</cite>. Similar to other α/β-hydrolases, the CE7 enzymes follow a mechanism where the serine is deprotonated by the histidine imidazole side chain; thereby allowing for nucleophilic attack of the serine on the incoming carbonyl of the substrate’s acetyl group<cite>Sista_Kameshwar2018</cite>. The result is a transient tetrahedral oxyanion intermediate, which is stabilized by the backbone amide group of a highly conserved glutamate residue (found in a signature RGQ motif adjacent to the nucleophilic serine at the end of β-strand 4) and a less conserved tyrosine that together form the oxyanion hole of the enzyme<cite>Levisson2012,<cite>Vincent2003</cite>. The tetrahedral intermediate then collapses resulting in an acetyl-enzyme intermediate and release of the de-O-acetylated product. A water molecule entering the active site is deprotonated by histidine and then nucleophilic attack by water on the acetyl-enzyme takes place to liberate acetate and the free enzyme<cite>Sista_Kameshwar2018</cite>. A recent study on the CE7 AXE (TM0077) from ''T. martitima'' provided further support into the catalytic mechanism<cite>Levisson2012</cite>. TM0077 was co-crystallized with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, that led to a 110° rotation of the catalytic serine and the formation of a covalent tetrahedral intermediate that was unable to collapse back to the starting materials (TM0077 and PMSF/paraoxan)<cite>Levisson2012</cite>. Trapping the tetrahedral intermediate is strong evidence that CE7 enzymes proceed by the proposed mechanism. <br />
<br />
Kinetic parameters and specific activities have been determined for some members of CE7. CAH from ''Bacillus subtilis'', AXE from ''Paenibacillus'' sp. R4 and AXE (TM0077) from ''T. maritima'' were assayed for their activity against ''p''NP-acetate and were found to have ''K''<sub>M</sub> values of 0.29 +/- 0.01, 0.15 +/- 0.01 and 0.19 +/- 0.03 mM, respectively, and ''k''<sub>cat</sub>/''K''<sub>M</sub> values of 260, 360 and 310 s<sup>-1</sup>mM<sup>-1</sup>, respectively<cite>Levisson2012,Vincent2003,Takimoto1994,Park2018</cite>. There has been discrepancy regarding the ability of these CE7 enzymes to utilize acetylated xylan as a substrate. While a ''Bacillus pumilus'' AXE has demonstrated a specific activity against acetylated xylan of 41 +/- 8 U/mg, ''T. maritima'''s AXE had no demonstrated activity and the acetyl xylan esterase, Axe1, from ''Thermoanerobacterium saccharolyticum'' strain JW/SL-YS485 had no activity in one study and 5.2 U/mg (8-fold lower than the ''B. pumilus'' enzyme) in another study<cite>Levisson2012,Lorenz1997,Degrassi1998,Shao1995</cite>. In light of the apparent low/no activity against acetylated xylan, the enzymes from ''T maritima'' and ''T. saccharolyticum'' were assayed against smaller substrates, where the ''T maritima'' AXE (TM0077) had high activity against glucose pentaacetate with a ''k''<sub>cat</sub> of 2900 s<sup>-1</sup> and Axe1 from ''T. saccharolyticum'' had high activity against xylose tetraacetate with separately reported specific activities of 210 and 740 U/mg<cite>Levisson2012,Lorenz1997,Shao1995</cite>. Lastly, CAH from ''B. subtilis'' has been kinetically characterized with regards to activity towards cephalosporin C with a ''K''<sub>M</sub> of 24 mM and a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 7.0 s<sup>-1</sup>mM<sup>-1</sup>, which has supported its naming as a cephalosporin C deacetylase<cite>Takimoto1994</cite>.<br />
== Three-dimensional structures ==<br />
There are six resolved structures currently reported for the CE7 family. These include the AXE from ''B. pumilus'' ([{{PDBlink}}2XLB PDB ID 2XLB]), cephalosporin c deacetylase (CAH) from ''B. subtilis'' strain 168 ([{{PDBlink}}1ODS PDB ID 1ODS]), the AXE from ''Paenibacillus'' sp. R4 ([{{PDBlink}}6AGQ PDB ID 6AGQ]), acetyl xylan esterase 1 (Axe1) from ''T. saccharolyticum'' strain JW/SL-YS485 ([{{PDBlink}}3FCY PDB ID 3FCY]), the AXE (TM0077) from ''T. maritima'' ([{{PDBlink}}1VLQ PDB ID 1VLQ]) and, lastly, an unclassified protein named Axe1-NaM1 ([{{PDBlink}}6FKX PDB ID 6FKX]).<br />
<br />
Enzymes in the CE7 family contain high levels of multimerization, with quaternary structures containing 4, 5, 6 and 8 subunits described<cite>Vincent2003</cite>. For each of the six resolved structures from the CE7 family, individual subunits adopt a classic α/β-hydrolase fold that consists of a central eight-stranded β-sheet surrounded by α-helices on both sides (See Fig. 1A)<cite>Levisson2012</cite>. Together, the multimerized subunits adopt a donut-like shape that results in the formation of a tunnel leading to the centre of the protein (See Fig. 1B). Each of the active sites from the individual multimers are arranged so that they face into the centre of the tunnel<cite>Vincent2003</cite>.<br />
<br />
== Family Firsts ==<br />
;First Characterized:The first cephalosporin-C deacetylase (CAH) of this family to be characterized was from ''B. subtilis'' strain 168 in 1975<cite>Abbot1975</cite>. CAH is able to deacetylate cephalosporin-C, as well as cephalosporin-C derivatives (eg., cephalosporanic acid and cephalothin) at the 3’ position<cite>Abbot1975</cite>. The first acetyl xylan esterase to be characterized was Axe1, from the anaerobic thermophilic bacterium ''T. saccharolyticum'' strain JW/SL-YS485 in 1995<cite>Shao1995</cite>. When in the presence of acetylated xylan, Axe1 showed esterase activity that liberated acetate, leading to its name<cite>Shao1995</cite>. However, Axe1 has also demonstrated active against other acetylated sugars<cite>Shao1995</cite>. <br />
;First Mechanistic Insight: The first mechanistic insight into the CE7 family came from the CAH enzyme from ''B. subtilis'' in 1994 when Takimoto and coworkers tested the effects of various chemicals (''eg.'', EDTA, PMSF, diisopropyl flurophosphate) on CAH activity and concluded that serine is likely important for catalysis<cite>Takimoto1994</cite>. Almost 10 years later in 2003, Vincent and colleagues resolved the crystal structure of CAH, confirming that serine was present in the active site and that an aspartate and histidine completed the catalytic triad<cite>Vincent2003</cite>. More recently, co-crystallization of the AXE (TM0077) from ''T. martitima'' with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, led to trapping of the tetrahedral intermediate; thereby providing further support for the serine-histidine-aspartate mediated mechanism described for this family. <br />
;First 3-D Structure:The first resolved structure in this family was the cephalosporin-C deacetylase, CAH ([{{PDBlink}}1ODS PDB ID 1ODS]) from ''B. subtilis'' strain 168 in 2003<cite>Vincent2003</cite>. The quaternary structure consisted of a trimer of dimers to make up a donut-shaped homohexamer with 32kDa subunits that each adopt the α/β hydrolase fold (See Fig. 1A)<cite>Vincent2003</cite>. The hydrophobic core containing the six active site centers is thought to help exclude large substrates and is shielded from solvents through a lid-like domain<cite>Vincent2003</cite>. In order for the hexamer to form, there are α-helix interactions as well as a β-strand-like interface associating between monomers (See Fig. 1A)<cite>Vincent2003,Sista_Kameshwar2018</cite>.<br />
== References ==<br />
<biblio><br />
#Nakamura2017 Nakamura, AM, Nascimento, AS and Polikarpov, I. (2017) Structural diversity of carbohydrate esterases. ''Biotechnol. Res. Innov.'', vol. 1, pp. 35-51. [https://doi.org/10.1016/j.biori.2017.02.001].<br />
#Levisson2012 pmid=22411095<br />
#Krastanova2005 pmid=15769599<br />
#Lorenz1997 pmid=9286998<br />
#Vincent2003 pmid=12842474<br />
#Degrassi2000 pmid=10878123<br />
#Biely2012 pmid=22580218<br />
#Mitsushima1995 pmid=7793942<br />
#Sista_Kameshwar2018 pmid=30533253<br />
#Ollis1992 pmid=1409539<br />
#Takimoto1994 Takimoto, A, Mitsushima, K, Yagi, S. and Sonoyama, T. (1994) Purification, Characterization and Partial Amino Acid Sequences of a Novel Cephalosporin-C Deacetylase from ''Bacillus subtilis''. ''J. Fermentation Bioeng.'', vol. 77, no. 1, pp. 17-22.<br />
#Park2018 pmid=30379876<br />
#Degrassi1998 pmid=10215579<br />
#Shao1995 pmid=7574610<br />
#Abbot1975 pmid=241292<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE007]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_7&diff=15642Carbohydrate Esterase Family 72020-07-23T02:45:52Z<p>Michael Suits: </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]]: ^^^Emily Rodriguez^^^<br />
* [[Responsible Curator]]s: ^^^Michael Suits^^^ and ^^^Joel Weadge^^^<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" |'''Carbohydrate Esterase Family CE7'''<br />
|-<br />
|'''Clan''' <br />
|(α/β/α)-Sandwich<br />
|-<br />
|'''Mechanism'''<br />
|Serine Hydrolase<br />
|-<br />
|'''Active site residues'''<br />
|Known, Catalytic Triad<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE7.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Carbohydrate Esterase Family 7 currently contains enzymes classified as acetyl xylan esterases (AXEs) and cephalosporin-C deacetylases<cite>Nakamura2017</cite>. One exception is the AXE from ''Thermotoga martitima'' that lacks detectable activity towards acetylated xylan, but rather, shorter acetylated xylo-oligomers<cite>Levisson2012</cite>. A common feature of the oligomeric enzymes belonging to this family is that they usually serve as multifunctional deacetylases and are active on a broad range of small substrates with relatively low acetyl-positional specificity<cite>Levisson2012,Krastanova2005,Lorenz1997,Vincent2003</cite>. Some examples include xylose tetraacetate, glucose pentaacetate, α-napthyl acetate, 4-methylumbelliferyl acetate and ''p''-nitrophenyl acetate (''p''NP-acetate)<cite>Degrassi2000</cite>. Substrate binding is proposed to be largely mediated through non-specific hydrophobic interactions with surface amino acid residues<cite>Vincent2003</cite>. <br />
== Catalytic Residues ==<br />
Members of this family use the catalytic triad of serine, histidine and aspartate<cite>Biely2012</cite>. The aspartate promotes the amphoteric nature of the histidine residue so that it can abstract a proton from the serine residue to render the serine nucleophilic<cite>Levisson2012</cite>. The Gly-X-Ser-X-Gly motif, containing the nucleophilic serine, is common amongst the broad α/β-hydrolase family to which the CE7 enzymes belong<cite>Mitsushima1995</cite>. The glycine residues near the catalytic serine are important to prevent any steric hindrance that may occur from amino acids with larger side chains and form the basis for the nucleophilic “elbow” turn motif that is present in these enzymes<cite>Levisson2012</cite>. [[Image:CAH Bsubtilis CE7.jpg|thumb|300px|Figure 1: CAH from B. subtilis ([{{PDBlink}}1ODS PDB ID 1ODS]). A) An individual monomer from the overall CAH structure showing the α/β-hydrolase fold formed by each subunit and the β-strand-like interface domain needed for association of the monomers. The catalytic triad of Ser181, Asp 269 and His 298 are highlighted in cyan. B) Characteristic donut-shaped quaternary structure of the CAH hexamer. Each monomer is represented in a different colour.]]<br />
== Kinetics and Mechanism ==<br />
The CE7 family of esterases catalyze the removal of O-acetyl groups from cephalosporin C, xylan and xylo-oligosaccharides<cite>Vincent2003,Biely2012</cite>. Members of this family present their active site residues in typical positions observed for α/β-hydrolases<cite>Sista_Kameshwar2018</cite>. The catalytic triad residues responsible for de-O-acetylation are found on loops near the C-terminus of the β-strands 5, 7 and 8 for the catalytic serine, aspartate and histidine, respectively<cite>Ollis1992</cite>. Similar to other α/β-hydrolases, the CE7 enzymes follow a mechanism where the serine is deprotonated by the histidine imidazole side chain; thereby allowing for nucleophilic attack of the serine on the incoming carbonyl of the substrate’s acetyl group<cite>Sista_Kameshwar2018</cite>. The result is a transient tetrahedral oxyanion intermediate, which is stabilized by the backbone amide group of a highly conserved glutamate residue (found in a signature RGQ motif adjacent to the nucleophilic serine at the end of β-strand 4) and a less conserved tyrosine that together form the oxyanion hole of the enzyme<cite>Levisson2012,<cite>Vincent2003</cite>. The tetrahedral intermediate then collapses resulting in an acetyl-enzyme intermediate and release of the de-O-acetylated product. A water molecule entering the active site is deprotonated by histidine and then nucleophilic attack by water on the acetyl-enzyme takes place to liberate acetate and the free enzyme<cite>Sista_Kameshwar2018</cite>. A recent study on the CE7 AXE (TM0077) from ''T. martitima'' provided further support into the catalytic mechanism<cite>Levisson2012</cite>. TM0077 was co-crystallized with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, that led to a 110° rotation of the catalytic serine and the formation of a covalent tetrahedral intermediate that was unable to collapse back to the starting materials (TM0077 and PMSF/paraoxan)<cite>Levisson2012</cite>. Trapping the tetrahedral intermediate is strong evidence that CE7 enzymes proceed by the proposed mechanism. <br />
<br />
Kinetic parameters and specific activities have been determined for some members of CE7. CAH from ''Bacillus subtilis'', AXE from ''Paenibacillus'' sp. R4 and AXE (TM0077) from ''T. maritima'' were assayed for their activity against ''p''NP-acetate and were found to have ''K''<sub>M</sub> values of 0.29 +/- 0.01, 0.15 +/- 0.01 and 0.19 +/- 0.03 mM, respectively, and ''k''<sub>cat</sub>/''K''<sub>M</sub> values of 260, 360 and 310 s<sup>-1</sup>mM<sup>-1</sup>, respectively<cite>Levisson2012,Vincent2003,Takimoto1994,Park2018</cite>. There has been discrepancy regarding the ability of these CE7 enzymes to utilize acetylated xylan as a substrate. While a ''Bacillus pumilus'' AXE has demonstrated a specific activity against acetylated xylan of 41 +/- 8 U/mg, ''T. maritima'''s AXE had no demonstrated activity and the acetyl xylan esterase, Axe1, from ''Thermoanerobacterium saccharolyticum'' strain JW/SL-YS485 had no activity in one study and 5.2 U/mg (8-fold lower than the ''B. pumilus'' enzyme) in another study<cite>Levisson2012,Lorenz1997,Degrassi1998,Shao1995</cite>. In light of the apparent low/no activity against acetylated xylan, the enzymes from ''T maritima'' and ''T. saccharolyticum'' were assayed against smaller substrates, where the ''T maritima'' AXE (TM0077) had high activity against glucose pentaacetate with a ''k''<sub>cat</sub> of 2900 s<sup>-1</sup> and Axe1 from ''T. saccharolyticum'' had high activity against xylose tetraacetate with separately reported specific activities of 210 and 740 U/mg<cite>Levisson2012,Lorenz1997,Shao1995</cite>. Lastly, CAH from ''B. subtilis'' has been kinetically characterized with regards to activity towards cephalosporin C with a ''K''<sub>M</sub> of 24 mM and a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 7.0 s<sup>-1</sup>mM<sup>-1</sup>, which has supported its naming as a cephalosporin C deacetylase<cite>Takimoto1994</cite>.<br />
== Three-dimensional structures ==<br />
There are six resolved structures currently reported for the CE7 family. These include the AXE from ''B. pumilus'' ([{{PDBlink}}2XLB PDB ID 2XLB]), cephalosporin c deacetylase (CAH) from ''B. subtilis'' strain 168 ([{{PDBlink}}1ODS PDB ID 1ODS]), the AXE from ''Paenibacillus'' sp. R4 ([{{PDBlink}}6AGQ PDB ID 6AGQ]), acetyl xylan esterase 1 (Axe1) from ''T. saccharolyticum'' strain JW/SL-YS485 ([{{PDBlink}}3FCY PDB ID 3FCY]), the AXE (TM0077) from ''T. maritima'' ([{{PDBlink}}1VLQ PDB ID 1VLQ]) and, lastly, an unclassified protein named Axe1-NaM1 ([{{PDBlink}}6FKX PDB ID 6FKX]).<br />
<br />
Enzymes in the CE7 family contain high levels of multimerization, with quaternary structures containing 4, 5, 6 and 8 subunits described<cite>Vincent2003</cite>. For each of the six resolved structures from the CE7 family, individual subunits adopt a classic α/β-hydrolase fold that consists of a central eight-stranded β-sheet surrounded by α-helices on both sides (See Fig. 1A)<cite>Levisson2012</cite>. Together, the multimerized subunits adopt a donut-like shape that results in the formation of a tunnel leading to the centre of the protein (See Fig. 1B). Each of the active sites from the individual multimers are arranged so that they face into the centre of the tunnel<cite>Vincent2003</cite>.<br />
<br />
== Family Firsts ==<br />
;First Characterized:The first cephalosporin C deacetylase (CAH) of this family to be characterized was from ''B. subtilis'' strain 168 in 1975<cite>Abbot1975</cite>. CAH is able to deacetylate cephalosporin C, as well as cephalosporin C derivatives (eg., cephalosporanic acid and cephalothin) at the 3’ position<cite>Abbot1975</cite>. The first acetyl xylan esterase to be characterized was Axe1, from the anaerobic thermophilic bacterium ''T. saccharolyticum'' strain JW/SL-YS485 in 1995<cite>Shao1995</cite>. When in the presence of acetylated xylan, Axe1 showed esterase activity that liberated acetate, leading to its name<cite>Shao1995</cite>. However, Axe1 has also demonstrated active against other acetylated sugars<cite>Shao1995</cite>. <br />
;First Mechanistic Insight: The first mechanistic insight into the CE7 family came from the CAH enzyme from ''B. subtilis'' in 1994 when Takimoto and coworkers tested the effects of various chemicals (''eg.'', EDTA, PMSF, diisopropyl flurophosphate) on CAH activity and concluded that serine is likely important for catalysis<cite>Takimoto1994</cite>. Almost 10 years later in 2003, Vincent and colleagues resolved the crystal structure of CAH, confirming that serine was present in the active site and that an aspartate and histidine completed the catalytic triad<cite>Vincent2003</cite>. More recently, co-crystallization of the AXE (TM0077) from ''T. martitima'' with PMSF and paraoxan ([{{PDBlink}}3M82 PDB ID 3M82] and [{{PDBlink}}3M83 PDB ID 3M83], respectively), two known serine protease inhibitors, led to trapping of the tetrahedral intermediate; thereby providing further support for the serine-histidine-aspartate mediated mechanism described for this family. <br />
;First 3-D Structure:The first resolved structure in this family was the cephalosporin C deacetylase, CAH ([{{PDBlink}}1ODS PDB ID 1ODS]) from ''B. subtilis'' strain 168 in 2003<cite>Vincent2003</cite>. The quaternary structure consisted of a trimer of dimers to make up a donut-shaped homohexamer with 32kDa subunits that each adopt the α/β hydrolase fold (See Fig. 1A)<cite>Vincent2003</cite>. The hydrophobic core containing the six active site centers is thought to help exclude large substrates and is shielded from solvents through a lid-like domain<cite>Vincent2003</cite>. In order for the hexamer to form, there are α-helix interactions as well as a β-strand-like interface associating between monomers (See Fig. 1A)<cite>Vincent2003,Sista_Kameshwar2018</cite>.<br />
== References ==<br />
<biblio><br />
#Nakamura2017 Nakamura, AM, Nascimento, AS and Polikarpov, I. (2017) Structural diversity of carbohydrate esterases. ''Biotechnol. Res. Innov.'', vol. 1, pp. 35-51. [https://doi.org/10.1016/j.biori.2017.02.001].<br />
#Levisson2012 pmid=22411095<br />
#Krastanova2005 pmid=15769599<br />
#Lorenz1997 pmid=9286998<br />
#Vincent2003 pmid=12842474<br />
#Degrassi2000 pmid=10878123<br />
#Biely2012 pmid=22580218<br />
#Mitsushima1995 pmid=7793942<br />
#Sista_Kameshwar2018 pmid=30533253<br />
#Ollis1992 pmid=1409539<br />
#Takimoto1994 Takimoto, A, Mitsushima, K, Yagi, S. and Sonoyama, T. (1994) Purification, Characterization and Partial Amino Acid Sequences of a Novel Cephalosporin-C Deacetylase from ''Bacillus subtilis''. ''J. Fermentation Bioeng.'', vol. 77, no. 1, pp. 17-22.<br />
#Park2018 pmid=30379876<br />
#Degrassi1998 pmid=10215579<br />
#Shao1995 pmid=7574610<br />
#Abbot1975 pmid=241292<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE007]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_3&diff=15226Carbohydrate Esterase Family 32020-06-10T00:06:49Z<p>Michael Suits: </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]]: ^^^Stefen Stangherlin^^^<br />
* [[Responsible Curator]]s: ^^^Joel Weadge^^^ and ^^^Michael Suits^^^<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" |'''Carbohydrate Esterase Family CE3'''<br />
|-<br />
|'''Clan''' <br />
|(α/β/α)-Sandwich<br />
|-<br />
|'''Mechanism'''<br />
<br />
|Serine Hydrolase<br />
<br />
|-<br />
|'''Active site residues'''<br />
|Known, Catalytic Triad<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE3.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Carbohydrate Esterase Family 3 is currently comprised entirely of de-''O''-acetylxylan esterases. Xylan is a plant cell-wall polysaccharide composed of β-1,4-linked xylose decorated with α-arabinofuranose and α-glucuronic acid substituents <cite>Faik2010</cite>.<br />
== Catalytic Residues ==<br />
Functionally characterized CE3 members are all known to contain the classical catalytic triad of Ser-His-Asp, typical of the SGNH hydrolase family of enzymes (see Fig. 1) <cite>Polgar2005 Molgaard2000</cite>. The active site residues are presented via four conserved consensus sequences (Blocks I-III and V), and have an altered nucleophilic “elbow” turn motif (-GxSxT- as opposed to the canonical -GxSxG- motif) compared to other related members of the α/β-hydrolase family <cite>UptonBuckley1995 Akoh2004</cite>. The catalytic triad along with the Block II Gly and Block III Asn residues that comprise the oxyanion hole, are universally conserved across all characterized CE3 enzymes. The Block V Asp residue mediates the amphoteric nature of the Block V His residue, which abstracts a proton from the Block I Ser to render it nucleophilic.[[Image:CE3_Figure.png|thumb|300px|Figure 1:''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]). Colours correspond to α-helices (cyan), β-sheets (magenta), loops (wheat), disulfide bond (yellow), calcium ion (orange) and the active site residues (green).]]<br />
<br />
== Kinetics and Mechanism ==<br />
CE3 esterases catalyze the hydrolysis of O-linked acetyl groups from xylan oligo- and poly-saccharides. The Block V His residue abstracts a proton from the Block I Ser, rendering it nucleophilic, which attacks the electrophilic carbonyl carbon of the acetyl group of the xylan substrate; generating a tetrahedral oxyanion transition state that is stabilized by the backbone amides of the Block I Ser and Block II Gly, as well as the sidechain amide of the Block III Asn, together forming the oxyanion hole in the active site <cite>Uechi2016</cite>. Collapse of the oxyanion intermediate results in the formation of a transient acyl-enzyme intermediate and alcohol by-product <cite>Uechi2016</cite>. A hydrolytic water molecule is then deprotonated by the Block V His residue, and attacks the acyl-enzyme intermediate; hydrolyzing the bond and releasing acetate and the free enzyme <cite>Uechi2016</cite>. In the process, the Ser (Block I) is re-protonated and ready for another catalytic cycle.<br />
<br />
The kinetics for two enzymes from the CE3 family have been studied. ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) was found to have a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 2.5 and 1.2 mM<sup>-1</sup>s<sup>-1</sup> for ''p''-nitrophenyl acetate (''p''NP-Ac) and acetylated xylan, respectively <cite>Correia2008</cite>. In other studies, ''Tc''AE206 ([{{PDBlink}}5B5S PDB ID 5B5S]) was not assayed against acetylated xylan, but the ''k''<sub>cat</sub>/''K''<sub>M</sub> with ''p''NP-Ac and ''p''-nitropheyl butyrate (''p''NP-B) were reported as 44.7 and 4.1 mM<sup>-1</sup>s<sup>-1</sup>, respectively, while no activity was detected with ''p''‐nitrophenyl octanoate (''p''NO) as the substrate <cite>Watanabe2015</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Two members of the CE3 family have been structurally resolved, ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.<br />
<br />
== Family Firsts ==<br />
'''First characterized'''<br />
<br />
In 1994, the sequence of XynB from ''Ruminococcus flavefaciens'' 17 was found to be related to family G xylanases <cite>Zhang1994</cite>. In 1997, BnaC from ''Neocallimastix patriciarum'' was found to have close relation to XynB and other enzymes known to be members of a diverse family of esterases <cite>Dalrymple1997</cite>. It wasn’t until 2000 that CesA from ''R. flavefaciens'' 17, which was shown to have significant sequence identity to XynB, was characterized with the ability to deacetylate acetylated xylans; thereby representing the first characterized enzymes of family 3 CEs <cite>Aurilia2000</cite>.<br />
<br />
'''First mechanistic insight'''<br />
<br />
In 2000, CesA, XynB, and BnaC were aligned and shown to contain what was thought to be a Ser-His-Asp catalytic triad responsible for the observed esterase activity <cite>Aurilia2000</cite>. This was later confirmed by the structural resolution of ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) <cite>Correia2008</cite>.<br />
<br />
'''First 3-D structure'''<br />
<br />
The first resolved structure was ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum''), displaying the (α/β/α)-sandwich fold and Ser-His-Asp catalytic triad typical of SGNH hydrolases <cite>Correia2008</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Faik2010 pmid=20375115<br />
#Polgar2005 pmid=16003488 <br />
#Molgaard2000 pmid=10801485<br />
#UptonBuckley1995 pmid=7610479<br />
#Akoh2004 pmid=15522763<br />
#Uechi2016 pmid=27329813<br />
#Watanabe2015 pmid=25825334<br />
#Correia2008 pmid=18436237<br />
#Zhang1994 pmid=7816035<br />
#Dalrymple1997 pmid=9274014<br />
#Aurilia2000 pmid=10846217<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE003]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_3&diff=15225Carbohydrate Esterase Family 32020-06-10T00:06:22Z<p>Michael Suits: </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]]: ^^^Stefen Stangherlin^^^<br />
* [[Responsible Curator]]s: ^^^Joel Weadge^^^ and ^^^Michael Suits^^^<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" |'''Carbohydrate Esterase Family CE3'''<br />
|-<br />
|'''Clan''' <br />
|(α/β/α)-sandwich<br />
|-<br />
|'''Mechanism'''<br />
<br />
|Serine hydrolase<br />
<br />
|-<br />
|'''Active site residues'''<br />
|Known, Catalytic Triad<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE3.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Carbohydrate Esterase Family 3 is currently comprised entirely of de-''O''-acetylxylan esterases. Xylan is a plant cell-wall polysaccharide composed of β-1,4-linked xylose decorated with α-arabinofuranose and α-glucuronic acid substituents <cite>Faik2010</cite>.<br />
== Catalytic Residues ==<br />
Functionally characterized CE3 members are all known to contain the classical catalytic triad of Ser-His-Asp, typical of the SGNH hydrolase family of enzymes (see Fig. 1) <cite>Polgar2005 Molgaard2000</cite>. The active site residues are presented via four conserved consensus sequences (Blocks I-III and V), and have an altered nucleophilic “elbow” turn motif (-GxSxT- as opposed to the canonical -GxSxG- motif) compared to other related members of the α/β-hydrolase family <cite>UptonBuckley1995 Akoh2004</cite>. The catalytic triad along with the Block II Gly and Block III Asn residues that comprise the oxyanion hole, are universally conserved across all characterized CE3 enzymes. The Block V Asp residue mediates the amphoteric nature of the Block V His residue, which abstracts a proton from the Block I Ser to render it nucleophilic.[[Image:CE3_Figure.png|thumb|300px|Figure 1:''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]). Colours correspond to α-helices (cyan), β-sheets (magenta), loops (wheat), disulfide bond (yellow), calcium ion (orange) and the active site residues (green).]]<br />
<br />
== Kinetics and Mechanism ==<br />
CE3 esterases catalyze the hydrolysis of O-linked acetyl groups from xylan oligo- and poly-saccharides. The Block V His residue abstracts a proton from the Block I Ser, rendering it nucleophilic, which attacks the electrophilic carbonyl carbon of the acetyl group of the xylan substrate; generating a tetrahedral oxyanion transition state that is stabilized by the backbone amides of the Block I Ser and Block II Gly, as well as the sidechain amide of the Block III Asn, together forming the oxyanion hole in the active site <cite>Uechi2016</cite>. Collapse of the oxyanion intermediate results in the formation of a transient acyl-enzyme intermediate and alcohol by-product <cite>Uechi2016</cite>. A hydrolytic water molecule is then deprotonated by the Block V His residue, and attacks the acyl-enzyme intermediate; hydrolyzing the bond and releasing acetate and the free enzyme <cite>Uechi2016</cite>. In the process, the Ser (Block I) is re-protonated and ready for another catalytic cycle.<br />
<br />
The kinetics for two enzymes from the CE3 family have been studied. ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) was found to have a ''k''<sub>cat</sub>/''K''<sub>M</sub> of 2.5 and 1.2 mM<sup>-1</sup>s<sup>-1</sup> for ''p''-nitrophenyl acetate (''p''NP-Ac) and acetylated xylan, respectively <cite>Correia2008</cite>. In other studies, ''Tc''AE206 ([{{PDBlink}}5B5S PDB ID 5B5S]) was not assayed against acetylated xylan, but the ''k''<sub>cat</sub>/''K''<sub>M</sub> with ''p''NP-Ac and ''p''-nitropheyl butyrate (''p''NP-B) were reported as 44.7 and 4.1 mM<sup>-1</sup>s<sup>-1</sup>, respectively, while no activity was detected with ''p''‐nitrophenyl octanoate (''p''NO) as the substrate <cite>Watanabe2015</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Two members of the CE3 family have been structurally resolved, ''Tc''AE206 from ''Talaromyces cellulolyticus'' ([{{PDBlink}}5B5S PDB ID 5B5S]) (see Fig. 1) and ''Ct''Ces3-1 from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum'') ([{{PDBlink}}2VPT PDB ID 2VPT]). Both structures adopt an (α/β/α)-sandwich fold typical of the SGNH hydrolase family. The (α/β/α)-sandwich contains five central parallel β-strands forming a curved β-sheet, which is flanked by 5-6 α-helices <cite>Correia2008 Uechi2016</cite>. Additionally, both structures contain a calcium binding loop motif (DXVGX<sub>7</sub>DX<sub>n</sub>(D/N)) located above the N-terminal end of the central β-strand (β2) <cite>Watanabe2015</cite>. This binding motif is conserved across all currently characterized CE3s. A coordinated zinc ion was also observed next to a calcium ion in a ''Tc''AE206_S10A variant ([{{PDBlink}}5B5L PDB ID 5B5L]), however this was attributed to the use of ZnSO<sub>4</sub> in the crystallization conditions <cite>Uechi2016</cite>. Unique to ''Tc''AE206 is a disulfide bond formed near the N-terminus (see Fig. 1) that is thought to position the catalytic Ser by stabilizing neighbouring areas, including a β-turn (β1) that involves the catalytic Ser <cite>Uechi2016 Watanabe2015</cite>.<br />
<br />
== Family Firsts ==<br />
'''First characterized'''<br />
<br />
In 1994, the sequence of XynB from ''Ruminococcus flavefaciens'' 17 was found to be related to family G xylanases <cite>Zhang1994</cite>. In 1997, BnaC from ''Neocallimastix patriciarum'' was found to have close relation to XynB and other enzymes known to be members of a diverse family of esterases <cite>Dalrymple1997</cite>. It wasn’t until 2000 that CesA from ''R. flavefaciens'' 17, which was shown to have significant sequence identity to XynB, was characterized with the ability to deacetylate acetylated xylans; thereby representing the first characterized enzymes of family 3 CEs <cite>Aurilia2000</cite>.<br />
<br />
'''First mechanistic insight'''<br />
<br />
In 2000, CesA, XynB, and BnaC were aligned and shown to contain what was thought to be a Ser-His-Asp catalytic triad responsible for the observed esterase activity <cite>Aurilia2000</cite>. This was later confirmed by the structural resolution of ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) <cite>Correia2008</cite>.<br />
<br />
'''First 3-D structure'''<br />
<br />
The first resolved structure was ''Ct''Ces3-1 ([{{PDBlink}}2VPT PDB ID 2VPT]) from ''Hungateiclostridium thermocellum'' (formerly ''Clostridium thermocellum''), displaying the (α/β/α)-sandwich fold and Ser-His-Asp catalytic triad typical of SGNH hydrolases <cite>Correia2008</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Faik2010 pmid=20375115<br />
#Polgar2005 pmid=16003488 <br />
#Molgaard2000 pmid=10801485<br />
#UptonBuckley1995 pmid=7610479<br />
#Akoh2004 pmid=15522763<br />
#Uechi2016 pmid=27329813<br />
#Watanabe2015 pmid=25825334<br />
#Correia2008 pmid=18436237<br />
#Zhang1994 pmid=7816035<br />
#Dalrymple1997 pmid=9274014<br />
#Aurilia2000 pmid=10846217<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE003]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_9&diff=13580Carbohydrate Esterase Family 92019-02-28T20:16:25Z<p>Michael Suits: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Alex Anderson^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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" |'''Carbohydrate Esterase Family 9'''<br />
|-<br />
|'''Acid/alcohol sugar substrate''' <br />
|Alcohol<br />
|-<br />
|'''Metal-dependent'''<br />
|Yes<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
CE family 9 esterases catalyze the deacetylation of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate. This reaction has been demonstrated to be important for both amino sugar metabolism and peptidoglycan cell wall recycling in bacteria <cite>#Park2001</cite>. Experimental substrate specificity profiles for two CE9 enzymes demonstrated that they are active on other structurally similar amino sugar phosphates, such as N-acetyl- galactosamine-6-phosphate and N-acetyl-mannosamine-6-phosphate, although their reported affinities are 40-fold and 6-fold lower, respectively <cite>#Ahangar2018</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Removal of the acetate group by CE9 enzymes is proposed to be carried out by nucleophilic attack of the acetate carbon by a metal-bound hydroxide ion <cite>#Vincent2004</cite>. A proton is donated to the amine leaving group by a catalytic acid residue, and the tetrahedral transition state is stabilized either by the interaction of a second metal ion with the polarized carbonyl oxygen <cite>#Vincent2004</cite>, or by a catalytic base residue where a second metal ion is absent from the active site, although the latter has not been experimentally demonstrated. <br />
<br />
== Catalytic Residues ==<br />
The precise mechanism of catalysis has yet to be elucidated for CE9, although several conserved features in the active sites of resolved CE9 members suggest they play an important role in their function. In ''Bacillus subtilis'' NagA, ''Thermotoga maritima'' NagA, and ''Mycobacterium smegmatis'' NagA, four histidine residues are responsible for coordination of the metal cofactor(s), along with a glutamate in ''B. subtilis'' and ''T. maritima'', and an aspartic acid in ''M. smegmatis'' <cite>#Vincent2004,#Osipiuk2002,#Ferreira2006</cite>. The ''Escherichia coli'' NagA appears to have a glutamine, gluatamate, asparagine and an aspartate as the coordination enviroment, although this structure crystallized as the apoenzyme, and so this configuration is uncertain <cite>#Ferreira2006</cite>. In all structures, a strictly conserved aspartic acid residue is then thought to serve as a base to activate a water molecule, and then as an acid to protonate the leaving amine <cite>#Vincent2004</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The resolved structures of CE9 enzymes demonstrate variability in their organization and metal binding. For example, ''Vibrio cholerae'' NagA and ''B. subtilis'' NagA form dimers in their biologically relevant assemblies <cite>#Osipiuk2002, #Vincent2004</cite>, while ''E. coli'' NagA forms a tetramer <cite>#Ferreira2006</cite>. Additionally, these same enzymes appear to contain a Ni<sup>2+</sup> ion <cite>#Osipiuk2002</cite>, two Fe<sup>2+</sup> ions <cite>#Vincent2004</cite>, and a Zn<sup>2+</sup> ion <cite>#Ferreira2006</cite> in their active sites, respectively. All resolved CE9 enzymes contain a distorted (β/α)<sub>8</sub> fold containing the active site, and a small β-sheet domain comprising residues from both the N- and C-termini.<br />
<br />
== Family Firsts ==<br />
;First characterized: The ''E. coli'' N-acetylglucosamine-6-phosphate deacetylase NagA was the first CE9 enzyme to have its activity demonstrated <cite>#White1967</cite>.<br />
;First 3-D structure: The first structure of a CE9 enzyme published was the ''B. subtilis'' NagA, containing a two-Fe<sup>2+</sup> catalytic center <cite>#Vincent2004</cite>.<br />
;First mechanistic insight: The structure of the ''B. subtilis'' NagA enzyme was reported with a bound N-acetylglucosamine-6-phosphate molecule and provided evidence for the proposed metal-dependent catalytic mechanism <cite>#Vincent2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Park2001 pmid=11395446<br />
#Osipiuk2002 PDB entry [{{PDBlink}}3EGJ 3egj], unpublished.<br />
#Vincent2004 pmid=14557261<br />
#Ferreira2006 pmid=16630633<br />
#Ahangar2018 pmid=29728457<br />
#White1967 pmid=4861885<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE009]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Carbohydrate_Esterase_Family_4&diff=13508Carbohydrate Esterase Family 42019-02-04T16:33:27Z<p>Michael Suits: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Alex Anderson^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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" |'''Carbohydrate Esterase Family 4'''<br />
|-<br />
|'''Acid/alcohol sugar substrate''' <br />
|Alcohol<br />
|-<br />
|'''Metal-dependent'''<br />
|Yes (with exception)<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CE4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
CE family 4 esterases catalyze the de-acylation of polysaccharides. Known activities of CE family 4 members include acetylxylan esterases, chitin deacetylases, chitooligosaccharide deacetylases, and peptidoglycan deacetylases. Peptidoglycan, the essential bacterial cell wall polymer, consists of alternating β-(1,4) linked N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-muramic acid (MurNAc) <cite>Hayhurst2008</cite>. All but one of the characterized PG deacetylases belonging to CE family 4 deacetylate GlcNAc. The one characterized exception, PdaA from ''Bacillus subtilis'', deacetylates peptidoglycan MurNAc <cite>Fukushima2005</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
CE4 enzymes cleave acetyl groups by binding a catalytic water molecule on their metal cofactor <cite>Blair2005</cite> (usually Zn<sup>2+</sup>, but Co<sup>2+</sup> is observed in some structures <cite>Taylor2006</cite>). The catalytic base residue is responsible for proton abstraction from the catalytic water, and generates a nucleophilic attack on the carbonyl carbon of the acetyl substrate by that water molecule <cite>Blair2005</cite>. The resulting intermediate is a tetrahedral oxyanion, stabilized by the metal cofactor <cite>Blair2005</cite>. The catalytic acid residue then protonates the nitrogen atom of the intermediate, generating the free amine, along with the acetate product bound to the metal cofactor <cite>Blair2005</cite>.<br />
<br />
== Catalytic Residues ==<br />
Characterized CE4 members have been shown to possess a prototypical NodB conserved domain, containing an Asp-His-His triad responsible for coordinating a Zn<sup>2+</sup> ion, an Asp residue as the catalytic base, and a His residue as the catalytic acid <cite>Blair2005</cite>. These catalytic residues are invariant in all characterized CE4 family members, with the exception of two homologous acetylxylan esterases, the enzymes SlCE4 from ''Streptomyces lividans ''and CtCE4 from ''Clostridium thermocellum ''<cite>Taylor2006</cite>. Both SlCE4 and CtCE4 showed preference for Co<sup>2+</sup> in place of Zn<sup>2+</sup>'', ''and in CtCE4, four water molecules assisted two Asp-His residues in coordination of the Co<sup>2+</sup> in place of the His-His-Asp triad typical for the family <cite>Taylor2006</cite>.<br />
<br />
== Three-dimensional structures ==<br />
All CE4 members contain a NodB domain that houses the catalytic core. This NodB domain contains the triad responsible for coordinating the essential metal cofactor along with the catalytic acid/base pair, all of which are conserved and located in five separate motifs shared across CE4 enzymes. This NodB domain adopts a (β/α)<sub>7</sub> fold in all known structures. A notable exception for the family is PgdA from ''Streptococcus pneumoniae'' <cite>Blair2005</cite>. PgdA, a peptidoglycan GlcNAc deacetylase, contains the canonical NodB catalytic domain at its C-terminal, but the N and C termini are at opposite ends of the barrel as compared to other known CE4 structures <cite>Blair2005</cite>. PgdA is also atypical of the family in that it possesses two accessory domains that are not found in other CE4 members, nor shown any significant predicted to homology to non-CE4 members <cite>Blair2005</cite>. Other CE family 4 enzymes show considerable structural diversity outside their catalytic NodB domain, with some representative members also containing accessory CBM <cite>Andres2014</cite>, β sandwich <cite>Arnaouteli2015</cite>, α-helical <cite>Deng2009</cite>, and α/β <cite>Blair2005</cite> domains, although they are less common. In those CE4 members that do possess accessory domains, they are typically appended to the C-terminal <cite>Nishiyama2013</cite>, although presence at the N-terminal <cite>Deng2009</cite>, or flanking the NodB domain has been observed <cite>Blair2005</cite>. The length of CE4 enzymes are thus variable, but commonly near 300 residues in a prototypical, unappended CE4 member, but can range to as large as 700 residues in those appended with accessory domain(s).<br />
<br />
== Family Firsts ==<br />
;First characterized: TLC and HPLC experiments demonstrated that rhizobial NodB was a chitooligosaccharide deacetylase, and that it did not deacetylate GlcNAc monomers, only chitooligomers, and only at their nonreducing end <cite>John1993</cite>.<br />
;First mechanistic insight: The highly conserved His-His-Asp triad and His-Asp acid/base pair were first demonstrated to be catalytic in the structure of the SpPdgA peptidoglycan deacetylase from ''S. pneumoniae'' <cite>Blair2005</cite>. <br />
;First 3-D structure: The first CE4 structure, the peptidoglycan N-acetylmuramic acid deacetylase from ''B. subtilis'', demonstrates the canonical NodB domain adopting the (β/α)<sub>7</sub> fold, along with the His-His-Asp triad and the catalytic His/Asp acid/base pair <cite>Blair2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Hayhurst2008 pmid=18784364<br />
#Fukushima2005 pmid=15687192<br />
#Blair2005 pmid=16221761<br />
#Taylor2006 pmid=16431911<br />
#Andres2014 pmid=24810719<br />
#Arnaouteli2015 pmid=25825488<br />
#Deng2009 pmid=18978064<br />
#Nishiyama2013 pmid=23275162<br />
#John1993 pmid=8421697<br />
#Blair2004 pmid=15251431<br />
<br />
</biblio><br />
<br />
[[Category:Carbohydrate Esterase Families|CE004]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10361Polysaccharide Lyase Family 82014-10-21T21:30:24Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|His399 (''S. pneumoniae'')<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: hyaluronan (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, chondroitin AC (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, xanthan (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and chondroitin ABC (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations of the ''S. pneumoniae'' enzyme suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three dimensional structure ==<br />
The enzymatic PL8 domain is comprised by an N-terminal α-helical and C-terminal β-sheet domain, which constitute incomplete α<sub>5</sub>/α<sub>5</sub>-barrel and anti-parallel β-sheet structures, respectively. A deep cleft is located in the N-terminal α-helical domain facing the interface between the two domains that accommodates the substrate. <br />
<br />
'''Three dimensional structures by activity''':<br/><br />
Chondroitin AC lyase (EC 4.2.2.5) - ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br/><br />
Chondroitin ABC lyase (EC 4.2.2.20) – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]).<br/><br />
Hyaluronan lyase (EC 4.2.2.1) – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br/><br />
Xanthan lyase (EC 4.2.2.12) – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br/><br />
<br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R <cite>Rapport1951</cite>.<br />
;First catalytic base correctly identified: Xanthanase Y315 from 'Bacillus'' sp. GL1 <cite>Maruyama2005</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10360Polysaccharide Lyase Family 82014-10-21T20:29:23Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|His399 (''S. pneumoniae'')<br />
|-<br />
|'''Active site residues'''<br />
|Try408, His399 (''S. penumoniae'') <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations of the ''S. pneumoniae'' enzyme suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]).<br />
;N-terminal Hyaluronan Binding Module – ''S. pneumoniae'' Tigr4 <cite>Suits2014</cite>([{{PDBlink}}4d0q PDB 4D0Q]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R <cite>Rapport1951</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Suits2014 pmid=25100731<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10359Polysaccharide Lyase Family 82014-10-21T18:00:00Z<p>Michael Suits: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|His399 (''S. pneumoniae'')<br />
|-<br />
|'''Active site residues'''<br />
|Try408, His399 (''S. penumoniae'') <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations of the ''S. pneumoniae'' enzyme suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]).<br />
;N-terminal Hyaluronan Binding Module – ''S. pneumoniae'' Tigr4 <cite>Suits2014</cite>([{{PDBlink}}4d0q PDB 4D0Q]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R <cite>Rapport1951</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Suits2014 pmid=25100731<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyases&diff=10317Polysaccharide Lyases2014-10-09T17:23:41Z<p>Michael Suits: </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: ^^^Michael Suits^^^ and ^^^Wade Abbott^^^<br />
* Responsible Curator: ^^^Spencer Williams^^^<br />
----<br />
<br />
== Introduction ==<br />
Polysaccharide lyases (PLs) cleave uronic acid-containing polysaccharides via a β-elimination mechanism to generate an unsaturated hexenuronic acid residue and a new reducing end at the point of cleavage <cite>Lombard2010 Garron2010</cite>. PLs have been grouped into families and subfamilies within the Carbohydrate-Active Enzyme (CAZy) framework and that the PLs included are restricted to those operating via ''syn''- and ''anti''-elimination mechanisms <cite>Lombard2010</cite>. In this way, they are distinct from carbon-oxygen lyases that modify polysaccharide composition. Broadly, the mechanism of PL action can be described as consisting of three events: (i) abstraction of the C-5 proton on the sugar ring of a uronic acid or ester by a charge stabilizing cation such as Ca<sup>2+</sup> or a basic amino acid side chain, (ii) stabilization of the resulting anion by charge delocalization onto the C-6 carbonyl group, and (iii) lytic cleavage of the O-4:C-4 bonding that is facilitated by proton donation from a catalytic acid <cite>Lombard2010</cite>. Please see the following reviews on PL classification, specificities, and structures <cite>Lombard2010 Garron2010</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Lombard2010 pmid=20925655<br />
#Garron2010 pmid=20805221<br />
</biblio><br />
<br />
<br />
[[Category:Definitions and explanations]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10114Polysaccharide Lyase Family 82014-09-03T14:47:54Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|His399 (''S. pneumoniae'')<br />
|-<br />
|'''Active site residues'''<br />
|Try408, His399 (''S. penumoniae'') <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations of the ''S. pneumoniae'' enzyme suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]).<br />
;N-terminal Hyaluronan Binding Module – ''S. pneumoniae'' Tigr4 <cite>Suits2014</cite>([{{PDBlink}}4d0q PDB 4D0Q]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R <cite>Rapport1951</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Suits2014 pmid=25100731<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10113Polysaccharide Lyase Family 82014-09-03T14:36:38Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|His399 (S. pneumoniae)<br />
|-<br />
|'''Active site residues'''<br />
|Try408, His399 (S. penumoniae) <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R<cite>Rapport1951</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=10112Polysaccharide Lyase Family 82014-09-03T14:32:16Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|None<br />
|-<br />
|'''Active site residues'''<br />
|Known <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R<cite>Rapport1951</cite>.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9457Polysaccharide Lyase Family 82013-11-14T16:33:42Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R<cite>Rapport1951</cite>.<br />
;First catalytic base identification: Please refer to "Kinetics and Mechanism" and "Catalytic Residues" sections above.<br />
;First divalent acid identification: Please refer to "Kinetics and Mechanism" and "Catalytic Residues" sections above.<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9456Polysaccharide Lyase Family 82013-11-14T15:50:31Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: The hydrolysis of hyaluronan was attributed to a pneumococcal hyaluronidase from Pneumococcus type II strain D39R<cite>Rapport1951</cite>.<br />
;First catalytic base identification: (Please refer to "Kinetics and Mechanism" and "Catalytic Residue" sections above).<br />
;First divalent acid identification: (Please refer to "Kinetics and Mechanism" and "Catalytic Residue" sections above).<br />
;First 3-D structure: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9454Polysaccharide Lyase Family 82013-11-07T18:25:40Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with His399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that a combination of opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domain underlies processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''P. vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <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: Chondroitin AC lyase – ''F. heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9453Polysaccharide Lyase Family 82013-11-07T17:05:26Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. With respect to chondroitin AC and chondroitin ABC substrate specificity; structural comparisons of the ''Flavobacterium heparinum'' chondroitin AC lyase with the ''Proteus vulgaris'' chondroitin ABC lyase suggests that an Asp444 for an Asn differential in the ''Proteus vulgaris'' active centre provides the mechanism for enzymatic distinguishing between the two epimers <cite>Fethiere1999, Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''Flavobacterium heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''Proteus vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <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: Chondroitin AC lyase – ''Flavobacterium heparinum'' <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9452Polysaccharide Lyase Family 82013-11-07T16:43:58Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in ''Proteus vulgaris'' was suggested to provide the mechanism for enzymatic distinguishing between the two epimers <cite>Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
'''Structure by Activity''':<br />
;Hyaluronan lyase – ''S. pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – ''Bacteroides stercoris'' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – ''Proteus vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <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: Chondroitin AC lyase – ''B. stercoris'' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9451Polysaccharide Lyase Family 82013-11-07T16:33:59Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Activities and Substrate Specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including: '''hyaluronan''' (EC 4.2.2.1) [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' (EC 4.2.2.5) [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' (EC 4.2.2.12) [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' (EC 4.2.2.20) [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in ''Proteus vulgaris'' was suggested to provide the mechanism for enzymatic distinguishing between the two epimers <cite>Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Structure by Activity:<br />
;Hyaluronan lyase – 'S. pneumoniae' R6 <cite>Li2000</cite>([{{PDBlink}}1ojm PDB 1OJM]).<br />
;Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
;Xanthan lyase – 'Bacillus' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1j0m PDB 1J0M]).<br />
;Chondroitin ABC lyase – 'Proteus vulgaris' <cite>Huang2003</cite>([{{PDBlink}}1hn0 PDB 1HN0]). <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: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1cb8 PDB 1CB8]).<br />
<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9448Polysaccharide Lyase Family 82013-11-07T14:50:28Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20) actions.<br />
<br />
== Substrate specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including '''hyaluronan''' [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in ''Proteus vulgaris'' was suggested to provide the mechanism for enzymatic distinguishing between the two epimers <cite>Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Structure by Activity:<br />
Hyaluronidase – 'S. pneumoniae' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
Xanthanase – 'Bacillus' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
Chondroitin ABC lyase – 'Proteus vulgaris' <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]). <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: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
<br />
== First Structures by Activity ==<br />
;Hyaluronan lyase: ''Streptococcus pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
;Chondroitin AC lyase: ''Bacteroides stercoris'' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
;Xanthan lyase: ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
;Chondroitin ABC lyase: ''Proteus vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]).<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9447Polysaccharide Lyase Family 82013-11-06T22:51:46Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|Pneumonococcal hyaluronidase: Asn249, His399, Tyr408. <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20).<br />
<br />
== Substrate specificities ==<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including '''hyaluronan''' [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<br />
== Kinetics and Mechanism ==<br />
One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''S. pneumoniae'' hyaluronidase His399 acts as the general base, Asn349 act to neutralize the C5-carboxylate group, and Tyr408 is the protein donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that equivalent tyrosine residues served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggest the latter hypothesis is favored, with H399 participating in the neutralization of the C5 <cite>Zheng2013</cite>. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel and anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>. <br />
<br />
== Catalytic Residues ==<br />
In Streptococcus pneumoniae, mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng et al. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in Proteus vulgaris was suggested to provide the mechanism for distinguishing between the two epimers <cite>Huang2003</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Structure by Activity:<br />
Hyaluronidase – 'Streptococcus pneumoniae' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
Xanthanase – 'Bacillus' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
Chondroitin ABC lyase – 'Proteus vulgaris' <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]). <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: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
<br />
== First Structure by Activity ==<br />
;Hyaluroniate lyase: Streptococcus pneumoniae R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
;Chondroitin AC lyase: Bacteroides stercoris HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
;Xanthan lyase: Bacillus sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
;Chondroitin ABC lyase: Proteus vulgaris <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]).<br />
<br />
== References ==<br />
<biblio><br />
<br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
#Maruyama2005 pmid=15979090<br />
#Kelly2001 pmid=11358878<br />
#Elmabrouk2011 pmid=21287626<br />
#Zheng2013 pmid=23944739<br />
#Joshi2009 pmid=19089975<br />
<br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9446Polysaccharide Lyase Family 82013-11-06T18:34:59Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20).<br />
== Substrate specificities ==<br />
<br />
PL8s are active on a variety of uronic acid-containing polysaccharides including '''hyaluronan''' [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<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 />
Structure by Activity:<br />
Hyaluronidase – “Streptococcus pneumoniae” R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
Xanthanase – “Bacillus” sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
Chondroitin ABC lyase – “Proteus vulgaris” <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]). <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: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
First Structure by Activity:<br />
Hyaluronidase – “Streptococcus pneumoniae” R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
Xanthanase – “Bacillus” sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
Chondroitin ABC lyase – “Proteus vulgaris” <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]).<br />
<br />
== References ==<br />
<biblio><br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
<br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9445Polysaccharide Lyase Family 82013-11-06T18:28:48Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); chondroitin ABC lyase (EC 4.2.2.20).<br />
== Substrate specificities ==<br />
<br />
PL8 activity has been demonstrated on a variety of uronic acid-containing polysaccharides including '''hyaluronan''' [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<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 />
Structure by Activity:<br />
Hyaluronidase – “Streptococcus pneumoniae” R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).<br />
Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
Xanthanase – “Bacillus” sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).<br />
Chondroitin ABC lyase – “Proteus vulgaris” <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]). <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: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).<br />
<br />
== References ==<br />
<biblio><br />
#Rapport1951 pmid=14917676 <br />
#Li2000 pmid=10716923<br />
<br />
#Fethiere1999 pmid=10329169 <br />
#Sato1994 pmid=7512814 <br />
#Huang2003 pmid=12706721 <br />
<br />
#Hashimoto1998 pmid=9758797 <br />
#Hashimoto2003 pmid=16348550 <br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9444Polysaccharide Lyase Family 82013-11-06T17:18:37Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); chondroitin ABC lyase (EC 4.2.2.20).<br />
== Substrate specificities ==<br />
<br />
PL8 activity has been demonstrated on a variety of uronic acid-containing polysaccharides including '''hyaluronan''' [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, '''chondroitin AC''' [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, '''xanthan''' [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and '''chondroitin ABC''' [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<br />
<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9439Polysaccharide Lyase Family 82013-11-06T15:14:55Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''''3D Structure''''' <br />
|(&alpha;/&alpha;)<sub>6</sub> barrel + anti-parallel &beta;-sheet<br />
|-<br />
|'''Mechanism'''<br />
|&beta;-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); chondroitin ABC lyase (EC 4.2.2.20).<br />
== Substrate specificities ==<br />
<br />
PL8 activity has been demonstrated on a variety of uronic acid-containing polysaccharides including <u>'''hyaluronan'''</u> [4)-&beta;-D-Glucuronate-1,3-&beta; -D-N-Acetyl-Glucosamine(1]<sub>n</sub>, <u>'''chondroitin AC'''</u> [4)-&beta;-D-Glucuronate-1,3-&beta;-D-N-Acetyl-Galactosamine&Delta;4,6S(1]<sub>n</sub>, <u>'''xanthan'''</u> [4)-&beta;-D-Glucuronate-1,4-&beta;-D-Glucuronate (1]<sub>n</sub>, and <u>'''chondroitin ABC'''</u> [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-&beta;-L-Iduronate2S-1,3-&beta;-D-N-Acetyl-Galactosamine4S(1]<sub>n</sub>.<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=User:Michael_Suits&diff=9438User:Michael Suits2013-11-06T14:42:33Z<p>Michael Suits: </p>
<hr />
<div>Michael Suits obtained his BScH in Biochemistry from Queen's University (Canada) and completed his PhD under the supervision of Zongchao Jia at Queen's University. In 2007 he obtained an EMBO Long-term Fellowship to work with Gideon Davies at the York Structural Biology Lab (University of York, York, UK) where his work focused on glycoside hydrolases from families 26, 38, 85, and 92, and glycosyltransferase family 78. In 2007 he joined Alisdair Boraston at the University of Victoria (Canada) and was awarded a Michael Smith Foundation for Health Research Fellowship in 2008 to continue work on microbial CAZymes. He is now an Assistant Professor in the Department of Chemistry at [http://www.wlu.ca/homepage.php?grp_id=13670 Wilfrid Laurier University] (Canada) where his work uses X-ray crystallography and various biophysical tools to characterize carbohydrate metabolizing factors.<br />
<br />
Michael and colleagues have characterized the X-ray crystal structures of:<br />
<br />
* [[CBM32-4, CBM32-5, CBM32-6]] ''Clostridium perfringens'' appended to exo-α-D-N-acetylglucosaminidase (GH89) [1]<br />
* [[GH26]] ''Cellvibrio japonicus'' GH26 mannanase [2]<br />
* [[GH38]] ''Streptococcus pyogenes'' α-mannosidase [3]<br />
* [[GH85]] ''Arthrobacter protophormiae'' endo-beta-D-N-acetylglucosaminidases (EndoA) [4]<br />
* [[GH92]] Bacteroides thetaiotaomicron α-mannosidase [5]<br />
* [[GH-Non-Classified]] Streptococcus pyogenes plasmin and fibronectin binding protein A (PfbA) [6]<br />
* [[GT78]] Rhodothermus marinus mannosylglycerate synthase [7]<br />
----<br />
<br />
<biblio><br />
<br />
#Ficko-Blean2012 pmid=22479408<br />
#Cartmell2008 pmid=18799462<br />
#Suits2010 pmid=20140249<br />
#Ling&Suits2009 pmid=19327363<br />
#Zhu2010 pmid=20081828<br />
#Suits2013 pmid=23894284<br />
#Nielsen2011 pmid=21288903<br />
</biblio></div>Michael Suitshttps://www.cazypedia.org/index.php?title=User:Michael_Suits&diff=9437User:Michael Suits2013-11-05T22:32:32Z<p>Michael Suits: </p>
<hr />
<div>Michael Suits obtained his BScH in Biochemistry from Queen's University (Canada) and completed his PhD under the supervision of Zongchao Jia at Queen's University. In 2007 he obtained an EMBO Long-term Fellowship to work with Gideon Davies at the York Structural Biology Lab (University of York, York, UK) where his work focused on glycoside hydrolases from families 26, 38, 85, and 92, and glycosyltransferase family 78. In 2007 he joined Alisdair Boraston at the University of Victoria (Canada) and was awarded a Michael Smith Foundation for Health Research Fellowship in 2008 to work on microbial CAZymes. He is now an Assistant Professor in the Department of Chemistry at Wilfrid Laurier University (Canada) where his work uses X-ray crystallography and various biophysical tools to characterize carbohydrate metabolizing factors.<br />
<br />
Michael and colleagues have characterized the X-ray crystal structures of:<br />
<br />
* [[CBM32-4, CBM32-5, CBM32-6]] ''Clostridium perfringens'' appended to exo-α-D-N-acetylglucosaminidase (GH89) [1]<br />
* [[GH26]] ''Cellvibrio japonicus'' GH26 mannanase [2]<br />
* [[GH38]] ''Streptococcus pyogenes'' α-mannosidase [3]<br />
* [[GH85]] ''Arthrobacter protophormiae'' endo-beta-D-N-acetylglucosaminidases (EndoA) [4]<br />
* [[GH92]] Bacteroides thetaiotaomicron α-mannosidase [5]<br />
* [[GH-Non-Classified]] Streptococcus pyogenes plasmin and fibronectin binding protein A (PfbA) [6]<br />
* [[GT78]] Rhodothermus marinus mannosylglycerate synthase [7]<br />
----<br />
<br />
<biblio><br />
<br />
#Ficko-Blean2012 pmid=22479408<br />
#Cartmell2008 pmid=18799462<br />
#Suits2010 pmid=20140249<br />
#Ling&Suits2009 pmid=19327363<br />
#Zhu2010 pmid=20081828<br />
#Suits2013 pmid=23894284<br />
#Nielsen2011 pmid=21288903<br />
</biblio></div>Michael Suitshttps://www.cazypedia.org/index.php?title=User:Michael_Suits&diff=9436User:Michael Suits2013-11-05T22:18:02Z<p>Michael Suits: </p>
<hr />
<div>Michael Suits obtained his BScH in Biochemistry from Queen's University (Canada) and completed his PhD under the supervision of Zongchao Jia at Queen's University. In 2007 he obtained an EMBO Long-term Fellowship to work with Gideon Davies at the York Structural Biology Lab (University of York, York, UK) where his work focused on glycoside hydrolases from families 26, 38, 85, and 92, and glycosyltransferase family 78. In 2007 he joined Alisdair Boraston at the University of Victoria (Canada) and was awarded a Michael Smith Foundation for Health Research Fellowship in 2008 to work on microbial CAZymes. He is now an Assistant Professor in the Department of Chemistry at Wilfrid Laurier University (Canada) where his work uses X-ray crystallography and various biophysical tools to characterize carbohydrate metabolizing factors.<br />
<br />
Michael and colleagues have characterized the X-ray crystal structures of:<br />
<br />
CBM32-4, CBM32-5, CBM32-6 ''Clostridium perfringens'' appended to exo-α-D-N-acetylglucosaminidase (GH89) [1]<br />
GH26 ''Cellvibrio japonicus'' GH26 mannanase [2]<br />
GH38 ''Streptococcus pyogenes'' α-mannosidase [3]<br />
GH85 ''Arthrobacter protophormiae'' endo-beta-D-N-acetylglucosaminidases (EndoA) [4]<br />
GH92 Bacteroides thetaiotaomicron α-mannosidase [5]<br />
GH-Non-classified Streptococcus pyogenes plasmin and fibronectin binding protein A (PfbA) [6]<br />
GT78 Rhodothermus marinus mannosylglycerate synthase [7]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9435Polysaccharide Lyase Family 82013-11-05T15:22:36Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|'''''3D Structure''''' <br />
|(alpha/alpha)<sub>6</sub> barrel + anti-parallel beta-sheet<br />
|-<br />
|'''Mechanism'''<br />
|beta-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Known Activities ==<br />
hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); chondroitin ABC lyase (EC 4.2.2.20).<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suitshttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_8&diff=9434Polysaccharide Lyase Family 82013-11-05T15:16:38Z<p>Michael Suits: </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]]: ^^^Michael Suits^^^<br />
* [[Responsible Curator]]: ^^^Michael Suits^^^<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 PL8'''<br />
|-<br />
|''''''3D Structure'''''' <br />
|(alpha/alpha)6 barrel + anti-parallel beta-sheet<br />
|-<br />
|'''Mechanism'''<br />
|beta-elimination<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL8.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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL008]]</div>Michael Suits