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)

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

β-elimination endo-activity exo activity [2]

Kinetics and catalytic residues

Arg, Gln, His, Tyr form active site [4]

His removes negative charge of the substrate

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] PL 7 is a very well biochemical characterized family with almost 40 entries in the CAZy data base [6]. Structural insights on the other hand are still restricted with nine 3D structures from only eight bacterial strains (status at CAZy,org in August 2019). The first structure of a PL7 was determined fromPseudomonas aeruginosa by multiple isomorphpus replacement(MIR) at 2.0 Å resolution [5]. Just like PL14, Pl7 belongs to the jellyroll family, composing of

endo vs. exo [2]

Evolution of Aly PULs

[7]

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 [8]

References

1. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010 Dec 15;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. 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 Aug 9;288(32):23021-37. DOI:10.1074/jbc.M113.467217 |
3. Deng S, Ye J, Xu Q, and Zhang H. 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. A structural basis for depolymerization of alginate by polysaccharide lyase family-7. J Mol Biol. 2005 Sep 9;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. 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 Jul 23;279(30):31863-72. DOI:10.1074/jbc.M402466200 |
6. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, and Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5. DOI:10.1093/nar/gkt1178 |
7. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, and Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010 Apr 8;464(7290):908-12. DOI:10.1038/nature08937 |
8. Crystal Structure of Family 7 Alginate Lyase A1-II' H191N/Y284F in Complex with Substrate (GGMG)