https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Wade+AbbottCAZypedia - User contributions [en-ca]2026-05-04T15:14:53ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=User:Wade_Abbott&diff=15661User:Wade Abbott2020-07-24T14:31:02Z<p>Wade Abbott: </p>
<hr />
<div>[[File:Wade.jpg|300 px|right]]<br />
Dr. Abbott received his PhD from the [http://www.uvic.ca/ University of Victoria] in 2005. He then studied the molecular basis of protein-carbohydrate interactions under Dr. ^^^Alisdair Boraston^^^ at the [http://www.uvic.ca/ University of Victoria]. In 2008, Dr. Abbott joined Dr. ^^^Harry Gilbert^^^'s group at the [http://www.ccrc.uga.edu/ Complex Carbohydrate Research Centre], at the [http://uga.edu/ University of Georgia] where he investigated the functional genomics of carbohydrate utilization pathways from intestinal bacteria. Currently, Dr. Abbott is a Research Scientist for [https://www.agr.gc.ca/eng/agriculture-and-agri-food-canada/?id=1395690825741/ AAFC] based at the [http://www.agr.gc.ca/eng/science-and-innovation/research-centres/alberta/lethbridge-research-centre/?id=1180547946064/ Lethbridge Research Centre] and Adjunct Professor at the [http://www.uleth.ca/ University of Lethbridge]. His research program investigates the mechanisms of complex carbohydrate modification by intestinal bacteria, and is developing applications for carbohydrates in animal agriculture and human intestinal health. See [https://profils-profiles.science.gc.ca/en/profile/d-wade-abbott-phd/ Abbott Group] and [https://scholar.google.ca/citations?user=ZuZ0rZoAAAAJ&hl=en/ Abbott Google Scholar] for more information on research activities.<br />
<br />
Dr. Abbott has contributed to structure-function studies of the following CAZyme Families:<br />
<br />
'''Glycoside Hydrolases'''<br />
*[[GH20]] ''Streptococcus pneumoniae'' exo-β-D-N-acetylglucosaminidase (SpnGH20AB/StrH) <cite>Pluvinage2013, Pluvinage2011</cite>.<br />
<br />
*[[GH28]] ''Yersinia enterocolitica'' exopolygalacturonase (YeGH28) <cite>Abbott2007a</cite>. *Family First<br />
<br />
*[[GH85]] ''Streptococcus pneumoniae'' endo-β-D-glucosaminidase D (SpGH85/EndoD) <cite>Abbott2009a</cite>. *Family First<br />
<br />
'''Polysaccharide Lyases'''<br />
*[[PL2]] ''Yersinia enterocolitica'' perplasmic pectate lyase (YePL2A) <cite>Abbott2007c</cite>. ''Paenibacillus sp. Y412MC10'' Cytoplasmic endolytic pectate lyase (PaePL2) <cite>Abbott2013</cite>. *Family First. ''Vibrio vulnificus sp. YJ016'' endolytic pectate lyase (VvPL2) <cite>McLean2015</cite>.<br />
*[[PL22]] ''Yersinia enterocolitica'' Cytoplasmic oligogalacturonate lyase (YePL22/Ogl) <cite>Abbott2010a</cite>. *Family First<br />
<br />
'''Carbohydrate Binding Modules'''<br />
*[[CBM6]] <cite>Abbott2009b Abbott2014</cite><br />
*[[CBM32]] ''Yersinia enterocolitica'' polygalacturonic acid binding protein (YeCBM32) <cite>Abbott2007b</cite>. ''Streptococcus pneumoniae'' EndoD CBM (SpnCBM32) <cite>Abbott2011</cite>.<br />
*[[CBM35]] <cite>Correia2010 Abbott2014</cite><br />
*[[CBM51]] ''Clostridium perfringens'' blood group binding CBMs (GH95CBM51 and GH98CBM51) <cite>Finn2008</cite><br />
<br />
'''Carbohydrate Esterases'''<br />
*[[CE8]] ''Yersinia enterocolitica'' pectin methylesterase <cite>Abbott2012</cite><br />
<br />
'''Glycosyl Transferase'''<br />
*[[GT32]] ''Bacteroides thetaiotaomicron VPI-5482'' α-1,3-mannosyltransferase (BT3775), α-1,6-mannosyltransferase (BT3776) <cite>cuskin2015</cite><br />
<br />
----<br />
'''References'''<br />
<biblio><br />
#Abbott2007a pmid=17397864<br />
#Abbott2007b pmid=17292916<br />
#Abbott2007c pmid=17881361<br />
#Finn2008 pmid=18292090<br />
#Abbott2009a pmid=19181667<br />
#Abbott2009b pmid=19181667<br />
#Abbott2010a pmid=20851883<br />
#Correia2010 pmid=20496884<br />
#Abbott2011 pmid=21505233<br />
#Pluvinage2011 pmid=22078560<br />
#Abbott2012 pmid=22297983<br />
#Pluvinage2013 pmid=23154168<br />
#Abbott2013 pmid=24013861<br />
#Abbott2014 pmid=25108190<br />
#McLean2015 pmid=26160170<br />
#Cuskin2015 pmid=25567280<br />
<br />
</biblio><br />
<br />
[[Category:Contributors|Abbott, Wade]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15374Polysaccharide Lyase Family 92020-06-16T22:55:34Z<p>Wade Abbott: </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]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyase. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan) by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two PL9 endo-acting lyases have been shown to be active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([{{EClink}}4.2.2.- EC 4.2.2.-]) <cite>Brooks1990 Kondo2011</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. The characterization of the ''Bacteroides thetaiotaomicron'' rhamnogalacturonan lyase (BT4170) revealed an additional calcium ion also interacting with the substrate and playing a role in catalysis (Figure 1) <cite>Luis2018</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[File:Active site PL9 1.png|thumb|300px|right|'''Figure 1.''' '''BT4170 ([{{PDBlink}}5OLR PDB ID 5OLR]) and Pel9A ([{{PDBlink}}1RU4 PDB ID 1RU4]) active site'''. Superimposed active residues of BT4170 (cyan) and Pel9A (green). The calcium ions are represented as spheres (gray). The first calcium is found in both structures. However, Ca<sup>2+</sup>_2 is only present in BT4170 struture.]]<br />
In Pel9A the lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family (Figure 1) <cite>Luis2018</cite>. In BT4170 rhamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases (Figure 1) <cite>Luis2018</cite>.<br />
== Three-dimensional structures ==<br />
[[File:PL9.png|thumb|300px|right|'''Figure 2.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([{{PDBlink}}1RU4 PDB ID 1RU4]) '''A.''' Schematic representation of Pel9A parallel β-helix fold colour ramped from blue (N-terminal) to red (C-terminal). The active site is represented as sticks and highlighted inside the black box. The calcium is represented as sphere (gray) '''B.''' Blow up of the active site. The residues interacting with calcium and the proposed catalytic base (K237) are represented as stick in green and yellow, respectively.]]<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([{{PDBlink}}1RU4 PDB ID 1RU4]) and displays a right-handed parallel β-helix fold (Figure 2A). The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft (Figure 2B) <cite>Jenkins2004</cite>. The structure of the rhamnogalacturonan lyase (BT4170) in complex with the enzyme product showed that apart from the catalytic apparatus, there is little conservation of substrate binding residues between this enzyme and the pectate lyase Pel9A <cite>Luis2018</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_9&diff=15373Polysaccharide Lyase Family 92020-06-16T22:54:09Z<p>Wade Abbott: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ana Luis^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL9'''<br />
|-<br />
|'''3D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL9.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) are active on pectins, a major plant cell wall polysaccharide. The main activity in characterized PL9 is pectate lyase. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid (homogalacturonan) by a β-elimination mechanism ([{{EClink}}4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. Two PL9 endo-acting lyases have been shown to be active on rhamnogalacturonan-I ([{{EClink}}4.2.2.23 EC 4.2.2.23]) <cite>Luis2018</cite>. Additional activities include: exopolygalacturonic lyase ([{{EClink}}4.2.2.9 EC 4.2.2.9]) and thiopeptidoglycan lyase ([{{EClink}}4.2.2.- EC 4.2.2.-]) <cite>Brooks1990 Kondo2011</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to the [[PL1]] family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. The characterization of the ''Bacteroides thetaiotaomicron'' rhamnogalacturonan lyase (BT4170) revealed an additional calcium ion also interacting with the substrate and playing a role in catalysis (Figure 1) <cite>Luis2018</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[File:Active site PL9 1.png|thumb|300px|right|'''Figure 1.''' '''BT4170 ([{{PDBlink}}5OLR PDB ID 5OLR]) and Pel9A ([{{PDBlink}}1RU4 PDB ID 1RU4]) active site'''. Superimposed active residues of BT4170 (cyan) and Pel9A (green). The calcium ions are represented as spheres (gray). The first calcium is found in both structures. However, Ca<sup>2+</sup>_2 is only present in BT4170 struture.]]<br />
In Pel9A the lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. These residues are essential in catalysis and invariant in PL9 family (Figure 1) <cite>Luis2018</cite>. In BT4170 rhamnogalacturonan lyase, the residues G212, D246 and D280 comprise a second calcium binding site that is not conserved in pectate lyases (Figure 1) <cite>Luis2018</cite>.<br />
== Three-dimensional structures ==<br />
[[File:PL9.png|thumb|300px|right|'''Figure 2.''' '''Pel9A in complex with Ca<sup>2+</sup>''' ([{{PDBlink}}1RU4 PDB ID 1RU4]) '''A.''' Schematic representation of Pel9A parallel β-helix fold colour ramped from blue (N-terminal) to red (C-terminal). The active site is represented as sticks and highlighted inside the black box. The calcium is represented as sphere (gray) '''B.''' Blow up of the active site. The residues interacting with calcium and the proposed catalytic base (K237) are represented as stick in green and yellow, respectively.]]<br />
PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([{{PDBlink}}1RU4 PDB ID 1RU4]) and displays a right-handed parallel β-helix fold (Figure 2A). The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft (Figure 2B) <cite>Jenkins2004</cite>. The structure of the rhamnogalacturonan lyase (BT4170) in complex with the enzyme product showed that apart from the catalytic apparatus, there is little conservation of substrate binding residues between this enzyme and the pectate lyase Pel9A <cite>Luis2018</cite>. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. <br />
;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Jenkins2004 pmid=14670977<br />
#Luis2018 pmid=29255254<br />
#Kondo2011 pmid=21095202<br />
#Seyedarabi2010 pmid=20000851<br />
#Brooks1990 pmid=2254266<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL009]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10931Polysaccharide Lyase Family 12015-08-07T18:49:12Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These PL1 structures are remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. The β-helix fold is conserved in other PL families including [[PL3]] and [[PL9]].<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 structure from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10930Polysaccharide Lyase Family 12015-08-07T18:48:05Z<p>Wade Abbott: /* Three-dimensional structures */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These PL1 structures are remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. The β-helix fold is conserved in other PL families including [[PL3]] and [[PL9]] .<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 structure from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10929Polysaccharide Lyase Family 12015-08-07T18:47:28Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These PL1 structures are remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. The β-helix fold is conserved in other PL families including *[[PL3]] and *[[PL9]] .<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 structure from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10928Polysaccharide Lyase Family 12015-08-07T18:42:24Z<p>Wade Abbott: /* Three-dimensional structures */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These PL1 structures are remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. The β-helix fold is conserved in other PL families including PL3 and PL9.<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 structure from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10927Polysaccharide Lyase Family 12015-08-07T18:35:03Z<p>Wade Abbott: /* Family Firsts */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin.<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 structure from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10925Polysaccharide Lyase Family 12015-08-07T02:13:05Z<p>Wade Abbott: /* Three-dimensional structures */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin.<br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10919Polysaccharide Lyase Family 12015-08-07T01:59:24Z<p>Wade Abbott: /* Substrate specificities */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10918Polysaccharide Lyase Family 12015-08-07T01:54:41Z<p>Wade Abbott: /* Family Firsts */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1s reported were PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10917Polysaccharide Lyase Family 12015-08-07T01:53:56Z<p>Wade Abbott: /* Family Firsts */</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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: The first structures of PL1 are PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi''. The first PL1 from ''Bacillus subtilis'' was reported in 1994 <cite>Pickersgill1994</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=User:Wade_Abbott&diff=10916User:Wade Abbott2015-08-07T00:35:34Z<p>Wade Abbott: </p>
<hr />
<div>[[File:Wade.jpg|300 px|right]]<br />
Dr. Abbott received his PhD from the [http://www.uvic.ca/ University of Victoria] in 2005. He then studied the molecular basis of protein-carbohydrate interactions under Dr. ^^^Alisdair Boraston^^^ at the [http://www.uvic.ca/ University of Victoria]. In 2008, Dr. Abbott joined Dr. ^^^Harry Gilbert^^^'s group at the [http://www.ccrc.uga.edu/ Complex Carbohydrate Research Centre], at the [http://uga.edu/ University of Georgia] where he investigated the functional genomics of carbohydrate utilization pathways from intestinal bacteria. Currently, Dr. Abbott is a Research Scientist for [http://www.agr.gc.ca/index_e.php/ Agriculture and Agri-Food Canada] based at the [http://www.agr.gc.ca/eng/science-and-innovation/research-centres/alberta/lethbridge-research-centre/?id=1180547946064/ Lethbridge Research Centre] and Adjunct Professor at the [http://www.uleth.ca/ University of Lethbridge]. His research program investigates the mechanisms of complex carbohydrate modification by intestinal bacteria, and is developing applications for carbohydrates in animal agriculture and human intestinal health. <br />
<br />
Dr. Abbott has contributed to structure-function studies of the following CAZyme Families:<br />
<br />
'''Glycoside Hydrolases'''<br />
*[[GH20]] ''Streptococcus pneumoniae'' exo-β-D-N-acetylglucosaminidase (SpnGH20AB/StrH) <cite>Pluvinage2013, Pluvinage2011</cite>.<br />
<br />
*[[GH28]] ''Yersinia enterocolitica'' exopolygalacturonase (YeGH28) <cite>Abbott2007a</cite>. *Family First<br />
<br />
*[[GH85]] ''Streptococcus pneumoniae'' endo-β-D-glucosaminidase D (SpGH85/EndoD) <cite>Abbott2009a</cite>. *Family First<br />
<br />
'''Polysaccharide Lyases'''<br />
*[[PL2]] ''Yersinia enterocolitica'' perplasmic pectate lyase (YePL2A) <cite>Abbott2007c</cite>. ''Paenibacillus sp. Y412MC10'' Cytoplasmic endolytic pectate lyase (PaePL2) <cite>Abbott2013</cite>. *Family First. ''Vibrio vulnificus sp. YJ016'' endolytic pectate lyase (VvPL2) <cite>McLean2015</cite>.<br />
*[[PL22]] ''Yersinia enterocolitica'' Cytoplasmic oligogalacturonate lyase (YePL22/Ogl) <cite>Abbott2010a</cite>. *Family First<br />
<br />
'''Carbohydrate Binding Modules'''<br />
*[[CBM6]] <cite>Abbott2009b Abbott2014</cite><br />
*[[CBM32]] ''Yersinia enterocolitica'' polygalacturonic acid binding protein (YeCBM32) <cite>Abbott2007b</cite>. ''Streptococcus pneumoniae'' EndoD CBM (SpnCBM32) <cite>Abbott2011</cite>.<br />
*[[CBM35]] <cite>Correia2010 Abbott2014</cite><br />
*[[CBM51]] ''Clostridium perfringens'' blood group binding CBMs (GH95CBM51 and GH98CBM51) <cite>Finn2008</cite><br />
<br />
'''Carbohydrate Esterases'''<br />
*[[CE8]] ''Yersinia enterocolitica'' pectin methylesterase <cite>Abbott2012</cite><br />
<br />
'''Glycosyl Transferase'''<br />
*[[GT32]] ''Bacteroides thetaiotaomicron VPI-5482'' α-1,3-mannosyltransferase (BT3775), α-1,6-mannosyltransferase (BT3776) <cite>cuskin2015</cite><br />
<br />
----<br />
'''References'''<br />
<biblio><br />
#Abbott2007a pmid=17397864<br />
#Abbott2007b pmid=17292916<br />
#Abbott2007c pmid=17881361<br />
#Finn2008 pmid=18292090<br />
#Abbott2009a pmid=19181667<br />
#Abbott2009b pmid=19181667<br />
#Abbott2010a pmid=20851883<br />
#Correia2010 pmid=20496884<br />
#Abbott2011 pmid=21505233<br />
#Pluvinage2011 pmid=22078560<br />
#Abbott2012 pmid=22297983<br />
#Pluvinage2013 pmid=23154168<br />
#Abbott2013 pmid=24013861<br />
#Abbott2014 pmid=25108190<br />
#McLean2015 pmid=26160170<br />
#Cuskin2015 pmid=25567280<br />
<br />
</biblio><br />
<br />
[[Category:Contributors|Abbott, Wade]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=User:Wade_Abbott&diff=10915User:Wade Abbott2015-08-07T00:30:30Z<p>Wade Abbott: </p>
<hr />
<div>[[File:Wade.jpg|300 px|right]]<br />
Dr. Abbott received his PhD from the [http://www.uvic.ca/ University of Victoria] in 2005. He then studied the molecular basis of protein-carbohydrate interactions under Dr. ^^^Alisdair Boraston^^^ at the [http://www.uvic.ca/ University of Victoria]. In 2008, Dr. Abbott joined Dr. ^^^Harry Gilbert^^^'s group at the [http://www.ccrc.uga.edu/ Complex Carbohydrate Research Centre], at the [http://uga.edu/ University of Georgia] where he investigated the functional genomics of carbohydrate utilization pathways from intestinal bacteria. Currently, Dr. Abbott is a Research Scientist for [http://www.agr.gc.ca/index_e.php/ Agriculture and Agri-Food Canada] based at the [http://www.agr.gc.ca/eng/science-and-innovation/research-centres/alberta/lethbridge-research-centre/?id=1180547946064/ Lethbridge Research Centre] and Adjunct Professor at the [http://www.uleth.ca/ University of Lethbridge]. His research program investigates the mechanisms of complex carbohydrate modification by intestinal bacteria, and is developing applications for carbohydrates in animal agriculture and human intestinal health. <br />
<br />
Dr. Abbott has contributed to structure-function studies of the following CAZyme Families:<br />
<br />
'''Glycoside Hydrolases'''<br />
*[[GH20]] ''Streptococcus pneumoniae'' exo-β-D-N-acetylglucosaminidase (SpnGH20AB/StrH) <cite>Pluvinage2013, Pluvinage2011</cite>.<br />
<br />
*[[GH28]] ''Yersinia enterocolitica'' exopolygalacturonase (YeGH28) <cite>Abbott2007a</cite>. *Family First<br />
<br />
*[[GH85]] ''Streptococcus pneumoniae'' endo-β-D-glucosaminidase D (SpGH85/EndoD) <cite>Abbott2009a</cite>. *Family First<br />
<br />
'''Polysaccharide Lyases'''<br />
*[[PL2]] ''Yersinia enterocolitica'' perplasmic pectate lyase (YePL2A) <cite>Abbott2007c</cite>. ''Paenibacillus sp. Y412MC10'' Cytoplasmic endolytic pectate lyase (PaePL2) <cite>Abbott2013</cite>. *Family First. ''Vibrio vulnificus sp. YJ016'' endolytic pectate lyase (VvPL2) <cite>McLean2015</cite>.<br />
*[[PL22]] ''Yersinia enterocolitica'' Cytoplasmic oligogalacturonate lyase (YePL22/Ogl) <cite>Abbott2010a</cite>. *Family First<br />
<br />
'''Carbohydrate Binding Modules'''<br />
*[[CBM6]] <cite>Abbott2009b Abbott2014</cite><br />
*[[CBM32]] ''Yersinia enterocolitica'' polygalacturonic acid binding protein (YeCBM32) <cite>Abbott2007b</cite>. ''Streptococcus pneumoniae'' EndoD CBM (SpnCBM32) <cite>Abbott2011</cite>.<br />
*[[CBM35]] <cite>Correia2010 Abbott2014</cite><br />
*[[CBM51]] ''Clostridium perfringens'' blood group binding CBMs (GH95CBM51 and GH98CBM51) <cite>Finn2008</cite><br />
<br />
'''Carbohydrate Esterases'''<br />
*[[CE8]] ''Yersinia enterocolitica'' pectin methylesterase <cite>Abbott2012</cite><br />
<br />
<br />
----<br />
'''References'''<br />
<biblio><br />
#Abbott2007a pmid=17397864<br />
#Abbott2007b pmid=17292916<br />
#Abbott2007c pmid=17881361<br />
#Finn2008 pmid=18292090<br />
#Abbott2009a pmid=19181667<br />
#Abbott2009b pmid=19181667<br />
#Abbott2010a pmid=20851883<br />
#Correia2010 pmid=20496884<br />
#Abbott2011 pmid=21505233<br />
#Pluvinage2011 pmid=22078560<br />
#Abbott2012 pmid=22297983<br />
#Pluvinage2013 pmid=23154168<br />
#Abbott2013 pmid=24013861<br />
#Abbott2014 pmid=25108190<br />
#McLean2015 pmid=26160170<br />
<br />
</biblio><br />
<br />
[[Category:Contributors|Abbott, Wade]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10910Polysaccharide Lyase Family 12015-08-06T16:14:36Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10909Polysaccharide Lyase Family 12015-08-06T16:12:15Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-(1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10908Polysaccharide Lyase Family 12015-08-06T16:10:05Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave &alpha;-1,4)-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10907Polysaccharide Lyase Family 12015-08-06T16:08:12Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave α1,4-linked {{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([{{PDBlink}}2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10905Polysaccharide Lyase Family 12015-08-06T14:50:18Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>. The structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10904Polysaccharide Lyase Family 12015-08-06T14:48:36Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine was identified as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10903Polysaccharide Lyase Family 12015-08-06T14:36:21Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC]) and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10902Polysaccharide Lyase Family 12015-08-06T14:35:25Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC] and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10901Polysaccharide Lyase Family 12015-08-06T14:33:10Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC], [http://www.proteopedia.org/wiki/index.php/2pcu 2PCU], [http://www.proteopedia.org/wiki/index.php/1bn8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10900Polysaccharide Lyase Family 12015-08-06T14:30:12Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC], [http://www.proteopedia.org/wiki/index.php/2pcu 2PCU], [http://www.proteopedia.org/wiki/index.php/1BN8 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10899Polysaccharide Lyase Family 12015-08-06T14:28:39Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([http://www.proteopedia.org/wiki/index.php/2pec 2PEC], [{{PDBlink}} 1bn8], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10897Polysaccharide Lyase Family 12015-08-06T14:22:19Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10896Polysaccharide Lyase Family 12015-08-06T14:21:18Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10895Polysaccharide Lyase Family 12015-08-06T14:15:05Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html/ PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10894Polysaccharide Lyase Family 12015-08-06T14:14:05Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html/ PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10893Polysaccharide Lyase Family 12015-08-06T14:13:48Z<p>Wade Abbott: </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]]: ^^^Richard Pickersgill^^^<br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<br />
----<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html/ PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10892Polysaccharide Lyase Family 12015-08-06T14:13:13Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html/ PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10891Polysaccharide Lyase Family 12015-08-06T14:11:41Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases (http://www.cazy.org/PL1.html/ PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10890Polysaccharide Lyase Family 12015-08-06T14:10:30Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2/ EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10/ EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10889Polysaccharide Lyase Family 12015-08-06T14:03:28Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10888Polysaccharide Lyase Family 12015-08-06T14:00:25Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10887Polysaccharide Lyase Family 12015-08-06T13:56:35Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}2pec PDB 2pec], [{{PDBlink}}2pcl PDB 2pcl], [{{PDBlink}}1bn8 PDB 1bn8](2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10886Polysaccharide Lyase Family 12015-08-06T13:52:18Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10885Polysaccharide Lyase Family 12015-08-06T13:51:43Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10884Polysaccharide Lyase Family 12015-08-06T13:50:45Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10883Polysaccharide Lyase Family 12015-08-06T13:49:43Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10882Polysaccharide Lyase Family 12015-08-06T13:47:55Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase. R and R’ are additional galacturonan residues]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10881Polysaccharide Lyase Family 12015-08-06T13:42:09Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> (2PEC, 1PCL, 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10880Polysaccharide Lyase Family 12015-08-06T13:34:16Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}2PEC], [{{PDBlink}}1PCL PDB 1PCL],[{{PDBlink}}1BN8 PDB 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10879Polysaccharide Lyase Family 12015-08-06T13:31:58Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> [{{PDBlink}}2PEC PDB 2PEC], [{{PDBlink}}1PCL PDB 1PCL],[{{PDBlink}}1BN8 PDB 1BN8]. These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10878Polysaccharide Lyase Family 12015-08-06T13:27:41Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}2PEC, ([{{PDBlink}}1PCL, ([{{PDBlink}}1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10874Polysaccharide Lyase Family 12015-08-06T13:21:10Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using B''acillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modelled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}3c5m PDB 2PEC, 1PCL, 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_1&diff=10873Polysaccharide Lyase Family 12015-08-06T13:09:35Z<p>Wade Abbott: </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]]: <br />
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^<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 PL1'''<br />
|-<br />
|'''3-D Structure''' <br />
|&beta;-helix<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|calcium<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL1.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase]]<br />
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>.<br />
<br />
In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond. <br />
<br />
== Kinetics and Mechanism ==<br />
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>. <br />
<br />
== Catalytic Residues ==<br />
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using B''acillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modelled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]<br />
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.<br />
<br />
== Three-dimensional structures ==<br />
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}}3c5m PDB 2PEC, 1PCL, 1BN8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin. <br />
<br />
== Family Firsts ==<br />
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>. <br />
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues. <br />
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>. <br />
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Albersheim1962 pmid=13860094<br />
#Edstrom1964a pmid=14235515<br />
#Edstrom1964b pmid=14235514<br />
#Gerlt1993 pmid=8218268<br />
#Scavetta1999 pmid=10368179<br />
#Herron2000 pmid=10922032<br />
#Seyedarabi2010 pmid=20000851<br />
#Yoder1993 pmid=8502994<br />
#Lietzke1994 pmid=12232373<br />
#Pickersgill1994 pmid=7634076<br />
#Mayans1997 pmid=9195887<br />
#Vitali1998 pmid=9449837<br />
#Charnock2002 pmid=12221284<br />
</biblio><br />
<br />
6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.<br />
<br />
7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.<br />
<br />
8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.<br />
<br />
9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.<br />
<br />
10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.<br />
<br />
11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.<br />
<br />
12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.<br />
<br />
13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.<br />
<br />
14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.<br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL001]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_2&diff=10872Polysaccharide Lyase Family 22015-08-06T11:16:34Z<p>Wade Abbott: /* References */</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]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL2'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>7</sub> barrel<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|manganese<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL2.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
PL2 activity has been demonstrated on &alpha;-(1,4)-linked polygalacturonic acid (i.e. homogalacturonan or pectate) and &alpha;-(1,4)-linked oligogalacturonides <cite>Abbott2007, Shevchik1999</cite>. There are two subfamilies in PL2 <cite>#Lombard2010</cite>. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of sequence entries are from the genomes of phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species <cite>Abbott2013</cite>. Several outliers exist, including the single copy PaePL2 from ''Paenibacillus sp.''Y412MC10, which may reflect the ancestral endolytic activity <cite>Abbott2013</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticity in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.<br />
<br />
== Catalytic Residues ==<br />
The Brønstead base for the PL2 family is an arginine, which is consistent with most pectate lyase families. R171 in YePL2A was the first catalytic base described for the family and it is completely conserved within the family <cite>Abbott2007, Abbott2013</cite>. The metal coordination pocket in YePL2A consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130).<br />
<br />
== Three-dimensional structures ==<br />
[[Image:PL2A.png|thumb|350px|[{{PDBlink}}2v8j YePL2A] in complex with Mn<sup>2+</sup>]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k], 2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.<br />
<br />
== Family Firsts ==<br />
;First catalytic activity: PelY/YpsPL2 from ''Yersinia pseudotuberculosis'' macerated cucumber <cite>Manulis1988</cite>. <br />
;First catalytic base identification: YePL2A (YE4069) R171 from ''Yersinia enterocolitica'' <cite>Abbott2007</cite>.<br />
;First catalytic divalent cation identification: PelW/DdPL2 (Dda3937_03361) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi''3937) <cite>Shevchik1999</cite>. <br />
<br />
;First 3-D structure: YePL2A (YE4069) from ''Yersinia enterocolitica'' <cite>Abbott2007</cite> ([{{PDBlink}}2v8i PDB 2v8i], [{{PDBlink}}2v8j PDB 2v8j], [{{PDBlink}}2v8k PDB 2v8k]).<br />
<br />
== References ==<br />
<biblio><br />
#Abbott2007 pmid=17881361<br />
#Shevchik1999 pmid=10383957<br />
#Manulis1988 pmid=2832382<br />
#Abbott2013 pmid=24013861<br />
#Lombard2010 pmid=20925655<br />
#McLean2015 pmid=26160170<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL002]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_2&diff=10871Polysaccharide Lyase Family 22015-08-06T11:14:43Z<p>Wade Abbott: /* Kinetics and Mechanism */</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]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL2'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>7</sub> barrel<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|manganese<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL2.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
PL2 activity has been demonstrated on &alpha;-(1,4)-linked polygalacturonic acid (i.e. homogalacturonan or pectate) and &alpha;-(1,4)-linked oligogalacturonides <cite>Abbott2007, Shevchik1999</cite>. There are two subfamilies in PL2 <cite>#Lombard2010</cite>. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of sequence entries are from the genomes of phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species <cite>Abbott2013</cite>. Several outliers exist, including the single copy PaePL2 from ''Paenibacillus sp.''Y412MC10, which may reflect the ancestral endolytic activity <cite>Abbott2013</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticity in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.<br />
<br />
== Catalytic Residues ==<br />
The Brønstead base for the PL2 family is an arginine, which is consistent with most pectate lyase families. R171 in YePL2A was the first catalytic base described for the family and it is completely conserved within the family <cite>Abbott2007, Abbott2013</cite>. The metal coordination pocket in YePL2A consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130).<br />
<br />
== Three-dimensional structures ==<br />
[[Image:PL2A.png|thumb|350px|[{{PDBlink}}2v8j YePL2A] in complex with Mn<sup>2+</sup>]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k], 2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.<br />
<br />
== Family Firsts ==<br />
;First catalytic activity: PelY/YpsPL2 from ''Yersinia pseudotuberculosis'' macerated cucumber <cite>Manulis1988</cite>. <br />
;First catalytic base identification: YePL2A (YE4069) R171 from ''Yersinia enterocolitica'' <cite>Abbott2007</cite>.<br />
;First catalytic divalent cation identification: PelW/DdPL2 (Dda3937_03361) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi''3937) <cite>Shevchik1999</cite>. <br />
<br />
;First 3-D structure: YePL2A (YE4069) from ''Yersinia enterocolitica'' <cite>Abbott2007</cite> ([{{PDBlink}}2v8i PDB 2v8i], [{{PDBlink}}2v8j PDB 2v8j], [{{PDBlink}}2v8k PDB 2v8k]).<br />
<br />
== References ==<br />
<biblio><br />
#Abbott2007 pmid=17881361<br />
#Shevchik1999 pmid=10383957<br />
#Manulis1988 pmid=2832382<br />
#Abbott2013 pmid=24013861<br />
#Lombard2010 pmid=20925655<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL002]]</div>Wade Abbotthttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_2&diff=10870Polysaccharide Lyase Family 22015-08-06T11:14:22Z<p>Wade Abbott: /* Kinetics and Mechanism */</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]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL2'''<br />
|-<br />
|'''3D Structure''' <br />
|(&alpha;/&alpha;)<sub>7</sub> barrel<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|manganese<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL2.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
PL2 activity has been demonstrated on &alpha;-(1,4)-linked polygalacturonic acid (i.e. homogalacturonan or pectate) and &alpha;-(1,4)-linked oligogalacturonides <cite>Abbott2007, Shevchik1999</cite>. There are two subfamilies in PL2 <cite>#Lombard2010</cite>. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of sequence entries are from the genomes of phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species <cite>Abbott2013</cite>. Several outliers exist, including the single copy PaePL2 from ''Paenibacillus sp.''Y412MC10, which may reflect the ancestral endolytic activity <cite>Abbott2013</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Use of a &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the p''K''<sub>a</sub> of arginine. These effects have been attributed to localized p''K''<sub>a</sub> effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite). Full kinetics with a library of metals have been performed for the YePL2A and YePL2B <cite>McLean2015</cite>. Both paralogs have the best catalytic efficiency with Mn<sup>2+</sup>; however, the secreted YePL2A demonstrates more plasticty in metal utilization; whereas, the cytoplasmic YePL2B is selective for Mn<sup>2+</sup>.<br />
<br />
== Catalytic Residues ==<br />
The Brønstead base for the PL2 family is an arginine, which is consistent with most pectate lyase families. R171 in YePL2A was the first catalytic base described for the family and it is completely conserved within the family <cite>Abbott2007, Abbott2013</cite>. The metal coordination pocket in YePL2A consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130).<br />
<br />
== Three-dimensional structures ==<br />
[[Image:PL2A.png|thumb|350px|[{{PDBlink}}2v8j YePL2A] in complex with Mn<sup>2+</sup>]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k], 2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.<br />
<br />
== Family Firsts ==<br />
;First catalytic activity: PelY/YpsPL2 from ''Yersinia pseudotuberculosis'' macerated cucumber <cite>Manulis1988</cite>. <br />
;First catalytic base identification: YePL2A (YE4069) R171 from ''Yersinia enterocolitica'' <cite>Abbott2007</cite>.<br />
;First catalytic divalent cation identification: PelW/DdPL2 (Dda3937_03361) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi''3937) <cite>Shevchik1999</cite>. <br />
<br />
;First 3-D structure: YePL2A (YE4069) from ''Yersinia enterocolitica'' <cite>Abbott2007</cite> ([{{PDBlink}}2v8i PDB 2v8i], [{{PDBlink}}2v8j PDB 2v8j], [{{PDBlink}}2v8k PDB 2v8k]).<br />
<br />
== References ==<br />
<biblio><br />
#Abbott2007 pmid=17881361<br />
#Shevchik1999 pmid=10383957<br />
#Manulis1988 pmid=2832382<br />
#Abbott2013 pmid=24013861<br />
#Lombard2010 pmid=20925655<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL002]]</div>Wade Abbott