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Difference between revisions of "Polysaccharide Lyase Family 7"
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− | + | == Mechanism == | |
− | + | Alginate lyases (Alys) of all families, PL5-7, PL14, PL15, PL17-18, cleave the glycosidic bond via β-elimination. Most PL7s are endo-active, i.e. acting within a poly- or oligosaccharide and releasing smaller alginate fragments. | |
− | + | exo activity <cite>Thomas2013</cite> | |
+ | == Kinetics and catalytic residues == | ||
+ | Arg, Gln, His, Tyr form active site <cite>Yamasaki2005</cite> | ||
− | + | His removes negative charge of the substrate | |
− | |||
− | + | == Substrate specificities == | |
− | |||
− | |||
− | + | The polysaccharide lyase family 7 (PL7) contains 5 subfamilies <cite>Lombard2010</cite>. All characterized PL7 enzymes were alginate lyases specific for the anionic, gel forming polysaccharide alginate. The substrate specificity depends on the source of alginate, i.e. derived from brown seaweed or mucoid bacteria ''Pseudomonas ''spp. and ''Azotobacter vinelandii'', as well as geographical and saisonal parameters. Alginate is an heteropolysaccharide, consisting of β-D-mannuronate(M) and α-L-guluronate (G). These monosaccharides can occur in homogenous and heterogenous blocks. Hence, PL7 lyases can be mannuronate (EC 4.2.2.3), guluronate (EC 4.2.2.11) or mixed link (EC 4.2.2.-) specific. Despite the pefernce for M- or G-enriched blocks, most PL7s also have a moderate to low processivity for the other building block. | |
− | |||
− | |||
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+ | 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 <cite>Deng2014</cite> | ||
== Three-dimensional structures == | == Three-dimensional structures == | ||
[[Image:...|thumb|400px|'''Figure 2.''' 3D Structure of endo- and exo-active PL7s (A,C) AlyA1 and (B, D) AlyA5 from ''Zobellia galaactinovorans'' DsijT. ]] | [[Image:...|thumb|400px|'''Figure 2.''' 3D Structure of endo- and exo-active PL7s (A,C) AlyA1 and (B, D) AlyA5 from ''Zobellia galaactinovorans'' DsijT. ]] | ||
− | PL 7 is a very well biochemical characterized family with almost 40 entries in the CAZy data base <cite>Lombard2014</cite>. 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 from''Pseudomonas aeruginosa'' by multiple isomorphpus replacement(MIR) at 2.0 Å resolution | + | PL 7 is a very well biochemical characterized family with almost 40 entries in the CAZy data base <cite>Lombard2014</cite>. 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 from''Pseudomonas aeruginosa'' by multiple isomorphpus replacement(MIR) at 2.0 Å resolution <cite>Yamasaki2004</cite>. Just like PL14, PL7 belongs to the jelly roll family with a wide open cleft harboring the active site. |
endo vs. exo <cite>Thomas2013</cite> | endo vs. exo <cite>Thomas2013</cite> | ||
+ | |||
== Evolution of Aly PULs == | == Evolution of Aly PULs == | ||
<cite>Hehemann2010</cite> | <cite>Hehemann2010</cite> | ||
+ | |||
== Family Firsts == | == Family Firsts == | ||
;First catalytic endo-activity: | ;First catalytic endo-activity: |
Revision as of 09:39, 31 July 2019
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Authors: ^^^Nadine Gerlach^^^ and ^^^Jan-Hendrik Hehemann^^^
- Responsible Curator: ^^^Jan-Hendrik Hehemann^^^
Polysaccharide Lyase Family PL7 | |
3D Structure | β jelly roll |
Mechanism | β-elimination |
Active site residues | known |
CAZy DB link | |
http://www.cazy.org/PL7.html |
Mechanism
Alginate lyases (Alys) of all families, PL5-7, PL14, PL15, PL17-18, cleave the glycosidic bond via β-elimination. Most PL7s are endo-active, i.e. acting within a poly- or oligosaccharide and releasing smaller alginate fragments.
exo activity [1]
Kinetics and catalytic residues
Arg, Gln, His, Tyr form active site [2]
His removes negative charge of the substrate
Substrate specificities
The polysaccharide lyase family 7 (PL7) contains 5 subfamilies [3]. All characterized PL7 enzymes were alginate lyases specific for the anionic, gel forming polysaccharide alginate. The substrate specificity depends on the source of alginate, i.e. derived from brown seaweed or mucoid bacteria Pseudomonas spp. and Azotobacter vinelandii, as well as geographical and saisonal parameters. Alginate is an heteropolysaccharide, consisting of β-D-mannuronate(M) and α-L-guluronate (G). These monosaccharides can occur in homogenous and heterogenous blocks. Hence, PL7 lyases can be mannuronate (EC 4.2.2.3), guluronate (EC 4.2.2.11) or mixed link (EC 4.2.2.-) specific. Despite the pefernce for M- or G-enriched blocks, most PL7s also have a moderate to low processivity for the other building block.
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 [4]
Three-dimensional structures
PL 7 is a very well biochemical characterized family with almost 40 entries in the CAZy data base [5]. 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 [6]. Just like PL14, PL7 belongs to the jelly roll family with a wide open cleft harboring the active site.
endo vs. exo [1]
Evolution of Aly PULs
[7]
Family Firsts
- First catalytic endo-activity
- First catalytic exo-activity
- AlyA5 from Zobellia galactanivorans DsijT [1]
- First 3-D apo-structure
- PA1167 from Pseudomonas aeruginosa [6]
- First 3-D holo-structure
- A1-II from Sphingomons sp. A1 [8]
References
- 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 |
- 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 |
- 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 |
- 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 |
- Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, and Henrissat B. (2014). The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(Database issue):D490-5. DOI:10.1093/nar/gkt1178 |
- 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 |
- 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 |