Polysaccharide Lyase Family 42

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• Author: Alan Cartmell
• Responsible Curator: Alan Cartmell

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Polysaccharide Lyase Family PL42
Clan	None
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/PL42.html

Substrate specificities

Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic [1, 2].

Kinetics and Mechanism

NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism [1]. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes [3, 4]. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage [1]. Further work is needed to confirm the mechanism by which GH145 operates.

Catalytic Residues

A single catalytic histidine, His48 in BT3686, has been shown to be critical for activity. This was the only residue mutated (to Gln, Ala and Gly) that caused loss of activity and is thought to act as an acid/base. Several homologues of BT3686 exist, which although >80 % identical are inactive due to having Gln at the equivalent position to His48 in BT3686. The introduction of a histidine at into related enzymes BACINT_00347 and BACCELL_00856, from Bacteroides intestinalis and Bacteroides cellulosilyticus, generating the mutants Q48H in both proteins, is sufficient to introduce rhamnosidase activity into these, otherwise inactive, enzymes [1]. No second catalytic residue to could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, portonating its own O4 and activating a water molecule.

Three-dimensional structures

GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity [1, 5].

Family Firsts

First stereochemistry determination

Determined for the bacteroides thetaiotaomicron enzyme BT3686 [1].

First catalytic acid/base residue identification

Predicted to be a histidine [1].

Second general acid/base residue identification

Predicted to be provided by the substrate [1].

First 3-D structure

BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms bacteroides thetaiotaomicron, bacteroides intestinalis and bacteroides cellulosilyticus, respectively. [1].

References

1. Munoz-Munoz J, Cartmell A, Terrapon N, Henrissat B, and Gilbert HJ. (2017). Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Proc Natl Acad Sci U S A. 2017;114(19):4936-4941. DOI:10.1073/pnas.1701130114 |
2. Cartmell A, Muñoz-Muñoz J, Briggs JA, Ndeh DA, Lowe EC, Baslé A, Terrapon N, Stott K, Heunis T, Gray J, Yu L, Dupree P, Fernandes PZ, Shah S, Williams SJ, Labourel A, Trost M, Henrissat B, and Gilbert HJ. (2019). Author Correction: A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation. Nat Microbiol. 2019;4(11):2021-2023. DOI:10.1038/s41564-019-0584-5 |
3. Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stütz AE, Butters TD, Williams SJ, and Davies GJ. (2012). Structural and mechanistic insight into N-glycan processing by endo-α-mannosidase. Proc Natl Acad Sci U S A. 2012;109(3):781-6. DOI:10.1073/pnas.1111482109 |
4. Fernandes PZ, Petricevic M, Sobala L, Davies GJ, and Williams SJ. (2018). Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. Chemistry. 2018;24(29):7464-7473. DOI:10.1002/chem.201800435 |
5. Ulaganathan T, Boniecki MT, Foran E, Buravenkov V, Mizrachi N, Banin E, Helbert W, and Cygler M. (2017). New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. ACS Chem Biol. 2017;12(5):1269-1280. DOI:10.1021/acschembio.7b00126 |