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

Kinetics and Mechanism

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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

1. Mathieu S, Henrissat B, Labre F, Skjåk-Bræk G, and Helbert W. (2016). Functional Exploration of the Polysaccharide Lyase Family PL6. PLoS One. 2016;11(7):e0159415. DOI:10.1371/journal.pone.0159415 |

2. 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

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

4. Lyu Q, Zhang K, Shi Y, Li W, Diao X, and Liu W. (2019). Structural insights into a novel Ca(2+)-independent PL-6 alginate lyase from Vibrio OU02 identify the possible subsites responsible for product distribution. Biochim Biophys Acta Gen Subj. 2019;1863(7):1167-1176. DOI:10.1016/j.bbagen.2019.04.013 |
5. Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, and Chen XL. (2017). Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6. J Biol Chem. 2017;292(11):4457-4468. DOI:10.1074/jbc.M116.766030 |
6. Maki H, Mori A, Fujiyama K, Kinoshita S, and Yoshida T. (1993). Cloning, sequence analysis and expression in Escherichia coli of a gene encoding an alginate lyase from Pseudomonas sp. OS-ALG-9. J Gen Microbiol. 1993;139(5):987-93. DOI:10.1099/00221287-139-5-987 |
7. 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 |
8. Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, and Cygler M. (2004). The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. J Biol Chem. 2004;279(31):32882-96. DOI:10.1074/jbc.M403421200 |
9. 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 |