Polysaccharide Lyase Family 4

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• Author: Leila Lo Leggio and Sine Larsen
• Responsible Curator: ^^^Leila LoLeggio^^^

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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. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC 4.2.2.23) The best characterized enzyme in the family, the Aspergillus aculeatus Rhamnogalacturonan Lyase (AaRGL4) cleaves the α-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with α-Δ-(4,5)- D-galacturonic acid at the non-reducing end [1]. the same study [1] 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. 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 [1]. In CAZY [2, 3], 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 [1]) 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

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Family Firsts

First demonstration of unsaturated product

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First catalytic base identification

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First general acid/base residue identification

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First 3-D structure

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References

1. Mutter M, Colquhoun IJ, Beldman G, Schols HA, Bakx EJ, and Voragen AG. (1998). Characterization of recombinant rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase from Aspergillus aculeatus. An enzyme that fragments rhamnogalacturonan I regions of pectin. Plant Physiol. 1998;117(1):141-52. DOI:10.1104/pp.117.1.141 |

2. 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

3. 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 |