Polysaccharide Lyase Family 15

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• Author: ^^^Emil Stender^^^
• Responsible Curator: ^^^Birte Svensson^^^

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Polysaccharide Lyase Family 15
3D structure	(α/α)6 barrel + anti-parallel β-sheet
Mechanism	β-elimination
Charge neutralizer	Arginine and histidine
Active site residues	known
CAZy DB link
http://www.cazy.org/PL15.html

Substrate specificities

PL15 currently contains 2 subfamilies [1] as well as several proteins currently not assigned to any subfamily. Subfamily one has been shown to only degrade alginate [2, 3, 4, 5] while subfamily 2 has been found to be heparin and heparan sulfate lyases [6, 7]. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks [8, 9]. Heparin consisting of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-L-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-D-glucuronic acid with a considerably more variable sulfation and acetylation pattern [10].

Kinetics and Mechanism

Figure 1 +1 subsite of the alginate lyase Atu3025

The β-elimination catalyzed by the PL15 enzymes results in the formation of a C4-C5 unsaturated sugar at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by the conserved H531 and R314 (Atu3025 numbering)[3]. This lowers the pKa value of the C5-proton allowing for abstraction by the catalytic base (Figure 1). A catalytic acid then donates a proton to the glycosidic linkage resulting in the β-elimination.

Catalytic Residues

After charge neutralization a histidine functions as the catalytic base and a tyrosine the acid. They were originally identified as H311 and Y365 in Atu3025 from Agrobacterium fabrum [3].

Three-dimensional structures

Figure 2 Crystal structures of the substrate complex of the monomeric Atu3025 (PDB: 3AFL) with the substrate in blue.

There is only a single crystal structure available in PL15. That of the alginate lyase Atu3025 from Agrobacterium fabrum (Figure 2) [3]. The catalytic domains consists of an N-terminal (α/α)6 barrel domain and a C-terminal anti-parallel β-sheet domain. The catalytic site is located between the two domains with the catalytic residues and the arginine charge neutralizer located in the (α/α)₆ barrel and the histidine neutralizer in a loop extending into the active site from the anti-parallel β-sheet domain [3].

Family Firsts

First catalytic activity

Alginate lyase IV from Sphingomonas sp [2].

First catalytic base/acid

Atu3025 from Agrobacterium fabrum [3].

First charge neutralizer

Atu3025 from Agrobacterium fabrum [3].

First 3-D structure

Atu3025 from Agrobacterium fabrum [3].

References

<biblio>

1. Lombard2010 pmid=20925655
2. Miyake2003 pmid=12729723
3. Ochiai2010 pmid=20507980
4. Jagtap2014 pmid=24795372
5. Hashimoto20005 pmid=16233753
6. Cartmell2017 pmid=28630303
7. Helbert2019 pmid=30850540
8. Haug1967 Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704
9. Haug1966 Haug, A., Larsen, B., and Smidsrod, O. (1966) A study of constitution of alginic acid by partial acid hydrolysis. Acta Chem. Scand. 20, 183–190
10. Garron2010 pmid=20805221