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Difference between revisions of "Polysaccharide Lyase Family 4"
| Line 29: | Line 29: | ||
== Substrate specificities == | == 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 [α-L-Rha-(1,4)-α-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. These enzymes are therefore Rhamnogalacturonan lyases (EC 4.2.2.-) The best characterized enzymes in the family, exemplified by the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4)cleave the α-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids. Biochemical studies by Mutter et al. show 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. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactan side chains reduces activity. | + | 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 [α-L-Rha-(1,4)-α-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. These enzymes are therefore Rhamnogalacturonan lyases (EC 4.2.2.-) The best characterized enzymes in the family, exemplified by the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4)cleave the α-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids. Biochemical studies by Mutter et al. show 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. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactan side chains reduces activity. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. |
| − | |||
| − | In | ||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | Degradation of rhamnogalacturonan is via β-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. | |
| − | + | ||
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| Line 43: | Line 41: | ||
== Family Firsts == | == Family Firsts == | ||
| − | ;First | + | ;First demonstration of unsaturated product: Content is to be added here. |
| − | ;First catalytic | + | ;First catalytic base identification: Content is to be added here. |
;First general acid/base residue identification: Content is to be added here. | ;First general acid/base residue identification: Content is to be added here. | ||
;First 3-D structure: Content is to be added here. | ;First 3-D structure: Content is to be added here. | ||
Revision as of 00:18, 4 September 2014
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: Leila Lo Leggio and Sine Larsen
- Responsible Curator: ^^^Leila LoLeggio^^^
| Polysaccharide Lyase Family PL4 | |
| Mechanism | β-elimination |
| Charge neutraliser | none |
| Active site residues | known |
| CAZy DB link | |
| https://www.cazy.org/PL4.html | |
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 [α-L-Rha-(1,4)-α-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. These enzymes are therefore Rhamnogalacturonan lyases (EC 4.2.2.-) The best characterized enzymes in the family, exemplified by the Aspergillus aculeatus Rhamnogalacturonan Lyase (AaRGL4)cleave the α-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids. Biochemical studies by Mutter et al. show 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. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactan side chains reduces activity. In CAZY [1, 2], PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, 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
Degradation of rhamnogalacturonan is via β-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism.
Catalytic Residues
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.
Three-dimensional structures
Content is to be added here.
Family Firsts
- First demonstration of unsaturated product
- Content is to be added here.
- First catalytic base identification
- Content is to be added here.
- First general acid/base residue identification
- Content is to be added here.
- First 3-D structure
- Content is to be added here.
References
-
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). DOI: 10.1042/BJ20080382
- Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |