Polysaccharide Lyase Family 31

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• Author: Marie-Line Garron
• Responsible Curator: Marie-Line Garron

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Polysaccharide Lyase Family PL31
3D Structure	Right handed β-helix
Mechanism	β-elimination
Charge neutraliser	Divalent cation (based on docking)
Active site residues	Lysine (base) and Tyrosine (acid) (mutagenesis and docking)
CAZy DB link
https://www.cazy.org/PL31.html

Substrate specificities

The PL31 family is mainly a bacterial family distantly related to the PL41 family (PL31) [1]. The first activities were demonstrated against poly-glucuronan for Saccharophagus degradans 2-40 (ABD82242.1) and Streptomyces hygroscopicus subsp. jinggangensis (AGF62897.1) (EC 4.2.2.14) [2]. Shortly afterwards, another PL31 member with a different function was characterized. PsAly, from Paenibacillus sp. FPU-7, is an endo-alginate lyase specific for polymannuronate (EC 4.2.2.3) [3]. The poly-M specific alginate lyase function was confirmed by the characterization of paeh-aly, belonging to Paenibacillus ehimensis [4]. The two publications on poly-M alginate lyases also reported a significant increase in activity in the presence of divalent cations, mainly Mg²⁺ [3, 4].

Kinetics and Mechanism

Like the other family of PLs, the PL31 family follows the same β-elimination process, involving a neutralizer, a Brønstead base and an acid [5]. Based on the C5 and C4 orientation, there are two variations of the β-elimination, the syn-elimination, where the C4-oxygen of the glycosidic bond and the C5-abstracted proton are on the same side, and the inverse, the anti-elimination [5]. Poly-glucuronan (EC 4.2.2.14) or poly-M specific alginate lyase (EC 4.2.2.3) require a syn-elimination mechanism, in which case the Brønstead base and acid roles can be played, sometimes by the same amino acid. Several mutants of PsAly have been realized by Itoh and co-workers. Activity is completely lost for the Y184F and K221A mutants and greatly reduced when several charged amino acids in the catalytic pocket are mutated. To discriminate the exact role of Y184 and K221, and in the absence of structures with products or substrate, docking simulations were performed. Based on the docking, the authors hypothesis that K221 could be the Brønstead base and Y184 the Brønstead acid, while the carboxylate would be neutralized by a divalent cation [3].

Three-dimensional structures

PL31 presents a right handed β-helix fold, which is already found in several PL families such as PL1, 3 or the alginate family PL6 [6]. The only structure available has been solved at high resolution (0,89Å) (PDB 6KFN) and is composed of 10 β-stand coils and one α-helix capping the N-terminus extremity [3]. Despite the difference in function, the closest structural homologue is Pel9A, a pectate lyase of the PL9 family (PDB 1RU4)[3, 7]. The structure of PSAly was solved with 2 sodium ions in the catalityc cleft, identified by the authors on the basis of the structural homology.

Family Firsts

First desciption of catalytic activity

Glucuronan lyase was the first activity reported for the family PL31 [2].

First charge neutralizer identification

Based on the influence of cations on activity and the docking experiments, Itoh and co-workers hypothesised that divalent cations could be the neutralizer [3].

First Brønstead acid and base residue identification

The total loss of activity when PsAly is mutated on Y184 and K221, confirms their crucial role in catalysis. The base and acid functions were assigned on the basis of docking: Lys the base and Tyr the acid [3].

First 3-D structure

The structure of the poly-M specific alginate lyase, PSAly, was the first solved by X-ray diffraction at 0.89Å resolution (PDB 6KFN) [3].

References

1. 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 |
2. Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, and Henrissat B. (2019). Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space. Proc Natl Acad Sci U S A. 2019;116(13):6063-6068. DOI:10.1073/pnas.1815791116 |
3. Itoh T, Nakagawa E, Yoda M, Nakaichi A, Hibi T, and Kimoto H. (2019). Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7. Sci Rep. 2019;9(1):14870. DOI:10.1038/s41598-019-51006-1 |
4. Wang X, Xu W, Dai Q, Liu X, Guang C, Zhang W, and Mu W. (2023). Characterization of a thermostable PL-31 family alginate lyase from Paenibacillus ehimensis and its application for alginate oligosaccharides bioproduction. Enzyme Microb Technol. 2023;166:110221. DOI:10.1016/j.enzmictec.2023.110221 |
5. Garron ML and Cygler M. (2010). Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology. 2010;20(12):1547-73. DOI:10.1093/glycob/cwq122 |
6. Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, and Cygler M. (1999). Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution. J Mol Biol. 1999;294(5):1257-69. DOI:10.1006/jmbi.1999.3292 |
7. Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, and Pickersgill RW. (2004). The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem. 2004;279(10):9139-45. DOI:10.1074/jbc.M311390200 |