Polysaccharide Lyase Family 1 - Revision history

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

2021-12-18T21:16:53Z

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

Wade Abbott at 18:49, 7 August 2015

2015-08-07T18:49:12Z

Wade Abbott: /* Three-dimensional structures */

2015-08-07T18:48:05Z

Three-dimensional structures

Wade Abbott at 18:47, 7 August 2015

2015-08-07T18:47:28Z

Wade Abbott: /* Three-dimensional structures */

2015-08-07T18:42:24Z

Three-dimensional structures

Wade Abbott: /* Family Firsts */

2015-08-07T18:35:03Z

Family Firsts

Wade Abbott: /* Three-dimensional structures */

2015-08-07T02:13:05Z

Three-dimensional structures

Wade Abbott: /* Substrate specificities */

2015-08-07T01:59:24Z

Substrate specificities

Wade Abbott: /* Family Firsts */

2015-08-07T01:54:41Z

Family Firsts

Wade Abbott: /* Family Firsts */

2015-08-07T01:53:56Z

Family Firsts

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Richard Pickersgill^^^
+* [[Author]]: [[User:Richard Pickersgill|Richard Pickersgill]]
-* [[Responsible Curator]]:  ^^^Richard Pickersgill^^^
+* [[Responsible Curator]]:  [[User:Richard Pickersgill|Richard Pickersgill]]
 ----

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 == Three-dimensional structures ==
-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]] .
+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]].
 == Family Firsts ==

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 == Three-dimensional structures ==
-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]] .
+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]] .
 == Family Firsts ==

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 == Three-dimensional structures ==
-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.
+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]] .
 == Family Firsts ==

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 == Three-dimensional structures ==
-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.
+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.
 == Family Firsts ==

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 ;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.
 ;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>.
-;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>.
+;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>.
 == References ==

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 == Substrate specificities ==
 [[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]
 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.
 == Kinetics and Mechanism ==