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Difference between revisions of "Polysaccharide Lyase Family 7"

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== 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 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 <cite>Thomas2013</cite> 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.-)
+
== Mechanism ==
  
poly β-D-mannuronate lyase / M-specific alginate lyase (EC 4.2.2.3)
+
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.
  
poly α-L-guluronate lyase / G-specific alginate lyase (EC 4.2.2.11)
+
exo activity <cite>Thomas2013</cite>
 +
== Kinetics and catalytic residues ==
  
 +
Arg, Gln, His, Tyr form active site <cite>Yamasaki2005</cite>
  
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>
+
His removes negative charge of the substrate
  
== Mechanism ==
 
  
β-elimination
+
== Substrate specificities ==
endo-activity
 
exo activity <cite>Thomas2013</cite>
 
  
== Kinetics and catalytic residues ==
+
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.
  
Arg, Gln, His, Tyr form active site <cite>Yamasaki2005</cite>
 
 
His removes negative charge of the substrate
 
  
 +
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 <cite>Yamasaki2004</cite>. Just like PL14, PL7 belongs to the jelly roll family, composing of
+
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

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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

File:...
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 [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

  1. 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 | PubMed ID:23782694 [Thomas2013]
  2. 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 | PubMed ID:16081095 [Yamasaki2005]
  3. 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 | PubMed ID:20925655 [Lombard2010]
  4. 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 | PubMed ID:24050202 [Deng2014]
  5. 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 | PubMed ID:24270786 [Lombard2014]
  6. 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 | PubMed ID:15136569 [Yamasaki2004]
  7. 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 | PubMed ID:20376150 [Hehemann2010]
  8. [Ogura2007]

All Medline abstracts: PubMed