Difference between revisions of "Polysaccharide Lyase Family 2"

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Author: ^^^Wade Abbott^^^
Responsible Curator: ^^^Wade Abbott^^^

Polysaccharide Lyase Family PL2
3D Structure	(α/α)₇ barrel
Mechanism	β-elimination
Charge neutraliser	manganese
Active site residues	known
CAZy DB link
https://www.cazy.org/PL2.html

Substrate specificities

PL2 activity has been demonstrated on α-(1,4)-linked polygalacturonic acid (i.e. homogalacturonan or pectate) and α-(1,4)-linked oligogalacturonides [1, 2]. There are two subfamilies in PL2 [3]. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of sequence entries are from the genomes of phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species [4]. Several outliers exist, including the single copy PaePL2 from Paenibacillus sp.Y412MC10, which may reflect the ancestral endolytic activity [4].

Kinetics and Mechanism

Use of a β-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn²⁺ or Mg²⁺) for acidification of the β-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 [1, 4], which is substantially lower than the pK_a of arginine. These effects have been attributed to localized pK_a effects within the active site. β-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other nascent sugar chain end (residue in the +1 subsite).

Catalytic Residues

The Brønstead base for the PL2 family is an arginine, which is consistent with most pectate lyase families. R171 in YePL2A was the first catalytic base described for the family and it is completely conserved within the family [1, 4]. The metal coordination pocket in YePL2A consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130).

Three-dimensional structures

YePL22 in complex with Mn²⁺ and acetate

The structure of the endolytic PL2A from Yersinia enterocolitica (YePL2A) was the first PL2 structure to be reported [1]. In this study, structural differences were noted between a native-form (PDB 2v8i, 1.50 Å), and complexes with trigalacturonate (PDB 2v8k, 2.1 Å) and a transition metal (PDB 2v8j, 2.01 Å). Family 2 PLs adopt a rare α/α₇ barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.

Family Firsts

First catalytic activity: PelY/YpsPL2 from Yersinia pseudotuberculosis macerated cucumber [5].
First catalytic base identification: YePL2A (YE4069) R171 from Yersinia enterocolitica [1].
First catalytic divalent cation identification: PelW/DdPL2 (Dda3937_03361) from Dickeya Dadantii 3937 (previously Erwinia chrysanthemi3937) [2].

First 3-D structure: YePL2A (YE4069) from Yersinia enterocolitica [1] (PDB 2v8i, PDB 2v8j, PDB 2v8k).

References

All Medline abstracts: PubMed

@@ Line 42: / Line 42: @@
 == Three-dimensional structures ==
-[[Image:PL2A.png|thumb|230px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k],  2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.
+[[Image:PL2A.png|thumb|350px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) was the first PL2 structure to be reported <cite>Abbott2007</cite>. In this study, structural differences were noted between a native-form ([{{PDBlink}}2v8i PDB 2v8i], 1.50 Å), and complexes with trigalacturonate ([{{PDBlink}}2v8k PDB 2v8k],  2.1 Å) and a transition metal ([{{PDBlink}}2v8j PDB 2v8j], 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;<sub>7</sub> barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate.
 == Family Firsts ==