Polysaccharide Lyase Family 4 - Revision history

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

2021-12-18T21:15:56Z

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

Harry Brumer: Fixed broken link to Sorting the Diverse - new DOI link added

2020-04-19T01:13:21Z

Fixed broken link to Sorting the Diverse - new DOI link added

Harry Brumer: Fixed Davies & Sinnott ref.

2016-08-03T18:38:34Z

Fixed Davies & Sinnott ref.

Harry Brumer: /* Three-dimensional structures */

2014-09-08T15:49:22Z

Three-dimensional structures

Harry Brumer: Linked to Sine's user page

2014-09-08T15:18:24Z

Linked to Sine's user page

Harry Brumer at 15:14, 8 September 2014

2014-09-08T15:14:23Z

Harry Brumer: Added PL subfamily reference

2014-09-08T15:14:02Z

Added PL subfamily reference

Wade Abbott at 14:17, 8 September 2014

2014-09-08T14:17:13Z

Wade Abbott at 14:16, 8 September 2014

2014-09-08T14:16:13Z

Wade Abbott at 14:15, 8 September 2014

2014-09-08T14:15:08Z

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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]]: ^^^Leila LoLeggio^^^ and ^^^Sine Larsen^^^
+* [[Author]]: [[User:Leila LoLeggio|Leila LoLeggio]] and [[User:Sine Larsen|Sine Larsen]]
-* [[Responsible Curator]]:  ^^^Leila LoLeggio^^^
+* [[Responsible Curator]]:  [[User:Leila LoLeggio|Leila LoLeggio]]
 ----

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 #Mutter1998 pmid=9576783
 #Cantarel2009 pmid=18838391
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 Download PDF version].
 #Lombard2010 pmid=20925655
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL004]]

@@ Line 55: / Line 55: @@
 #Mutter1998 pmid=9576783
 #Cantarel2009 pmid=18838391
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
+#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
 #Lombard2010 pmid=20925655
 </biblio>
 [[Category:Polysaccharide Lyase Families|PL004]]

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 == Three-dimensional structures ==
 [[File:Figure_complex_PL4.png|thumb|300px|right|'''Structure of AaRGL4 K150A in complex with a hexasaccharide.''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [http://pymol.org pymol]]]
-The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite> [[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].
+The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite> [[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>.
 == 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]]: ^^^Leila LoLeggio^^^ and Sine Larsen
+* [[Author]]: ^^^Leila LoLeggio^^^ and ^^^Sine Larsen^^^
 * [[Responsible Curator]]:  ^^^Leila LoLeggio^^^
 ----

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 == Substrate specificities ==
-The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans) at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]). The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>. In [http://www.cazy.org/ CAZy] <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants) <cite>Lombard2010/cite>. Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences.
+The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans) at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]). The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>. In [http://www.cazy.org/ CAZy] <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants) <cite>Lombard2010</cite>. Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences.
 == Kinetics and Mechanism ==

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 == Kinetics and Mechanism ==
-Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing {{smallcaps|d}}-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the pectate lyases within PL family 1. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.
+Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing {{smallcaps|d}}-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.
 == Catalytic Residues ==
 Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.