Polysaccharide Lyase Family 7

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• Authors: ^^^Nadine Gerlach^^^ and ^^^Jan-Hendrik Hehemann^^^
• Responsible Curator: ^^^Jan-Hendrik Hehemann^^^

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Polysaccharide Lyase Family PL7
3D Structure	β jelly roll
Mechanism	β-elimination
Active site residues	known
CAZy DB link
https://www.cazy.org/PL7.html

Substrate specificities

The polysaccharide lyase family 7 (PL7) contains 5 subfamilies [1]. All characterized PL7 enzymes were alginate lyases specific for the anionic, gel forming polysaccharide alginate which is from brown seaweed such as kelps or from certain types of bacteria. Alginate consists of beta-D-mannuronate and alpha-L-guluronate, which occur in homogenous or heterogenous blocks. Hence, PL7 can be mannuronate, guluronate or mixed link lyases. PL7 enzymes are often found in marine bacteria such as the seaweed associated Flavobacterium Zobellia galactanivorans [2] or in coastal, planktonic gammaproteobacteria such as Vibrio spp. PL7 alginate lyases also occur in terrestrial bacteria.

poly-(MG)-lyase / MG-specific alginate lyase (EC 4.2.2.-)

poly β-D-mannuronate lyase / M-specific alginate lyase (EC 4.2.2.3)

poly α-L-guluronate lyase / G-specific alginate lyase (EC 4.2.2.11)

endo-β-1,4-glucuronan lyase (EC 4.2.2.14)

Substitution of hydrophobic amino acids in the isoleucine site of domain QIH could have an enormous influence on the high-affinity to pM or pG. This isoleucine was reconfirmed to be indispensable for recognition of the pG or G-G bond [3]

Mechanism and catalytic residues

β-elimination

endo-activity

exo activity [2] Arg, Gln, His, Tyr form active site [4]

Three-dimensional structures

File:...

Figure 2. 3D Structure of endo- and exo-active PL7s (A,C) AlyA1 and (B, D) AlyA5 from Zobellia galaactinovorans DsijT.

β-jelly roll fold [5] only 9 PL7s structure from 8 bacterial strains so far (CAZY, August 2019) endo vs. exo [2]

Evolution of Aly PULs

[6]

Family Firsts

First catalytic endo-activity

First catalytic exo-activity

AlyA5 from Zobellia galactanivorans DsijT [2]

First 3-D apo-structure

PA1167 from Pseudomonas aeruginosa [5]

First 3-D holo-structure

A1-II from Sphingomons sp. A1 [7]

References

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 |
2. Thomas F, Lundqvist LC, Jam M, Jeudy A, Barbeyron T, Sandström C, Michel G, and Czjzek M. (2013). Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate. J Biol Chem. 2013;288(32):23021-37. DOI:10.1074/jbc.M113.467217 |
3. Deng S, Ye J, Xu Q, and Zhang H. (2014). Structural and functional studies on three alginate lyases from Vibrio alginolyticus. Protein Pept Lett. 2014;21(2):179-87. DOI:10.2174/09298665113206660094 |
4. Yamasaki M, Ogura K, Hashimoto W, Mikami B, and Murata K. (2005). A structural basis for depolymerization of alginate by polysaccharide lyase family-7. J Mol Biol. 2005;352(1):11-21. DOI:10.1016/j.jmb.2005.06.075 |
5. Yamasaki M, Moriwaki S, Miyake O, Hashimoto W, Murata K, and Mikami B. (2004). Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold. J Biol Chem. 2004;279(30):31863-72. DOI:10.1074/jbc.M402466200 |
6. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, and Michel G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010;464(7290):908-12. DOI:10.1038/nature08937 |

7. Crystal Structure of Family 7 Alginate Lyase A1-II' H191N/Y284F in Complex with Substrate (GGMG)