Polysaccharide Lyase Family 6

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

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Polysaccharide Lyase Family 6
3D structure	parralel β-helix
Mechanism	β-elimination
Charge neutralizer	calcium or water
Active site residues	known
CAZy DB link
https://www.cazy.org/PL6.html

Substrate specificities

PL6 currently contains 3 subfamilies [1] all of which contain members catalyzing the depolymerisation of alginate [2]. 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 [3, 4]. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks [2], while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid [5, 6], poly-mannuronic acid [7], poly-mannuronic/guluronic acid [2] as well as dermatan sulfate (formerly chrondroitin B) [2, 8, 9].

Kinetics and Mechanism

Figure 1. Syn – or anti – β-elimination catalyzed by PL6 enzymes acting on alginate. M represents mannuronic acid and G guluronic acid. n represents the continued sugar chain.

The β-elimination catalyzed by the PL6 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 a calcium [6, 9] or by water [5]. 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. This can be done in syn with the acid and base on the same side of the sugar ring in the transition state (the case for D-mannuronic acid) or anti where they are on opposite sides of the sugar ring (the case for L-guluronic acid) [10, 11].

Catalytic Residues

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Three-dimensional structures

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Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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References

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1. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. (2010). A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010;432(3):437-44. DOI:10.1042/BJ20101185 |

3. 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

4. Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704

10. 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 |