Polysaccharide Lyase Family 2

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

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Polysaccharide Lyase Family PL2
Mechanism	β-elimination
Metal Cofactor	Manganese
Active site residues	known
CAZy DB link
http://www.cazy.org/PL2.html

Substrate specificities

Activity have been demonstrated on homogalacturonan (α1,4-polygalacturonic acid or pectate) and (α1,4)-linked oligogalacturonides [1, 2].

Kinetics and Mechanism

The β-elimination of 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, 3], which is substantially lower than the pKa of arginine. These effects have been attributed to localized pKa 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-unsaturation (residue in the +1 subsite).

Catalytic Residues

The Brønstead base for the PL2 family is an ariginine, which is consistent with most pectate lyase families. R218 in YePL2A was the first catalytic base described for the family and it is completely conserved in the family [1, 3]. The metal coordination pocket consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130).

Subfamilies

There are two PL2 subfamilies in PL2. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of entries belong to phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species [3]. Several outliers exist within PL2, including the single copy PaePL2 from Paenibacillus sp. Y412MC10, which his suggested to represent an ancestral endolytic activity [3].

Three-dimensional structures

The structure of the endolytic PL2A from Yersinia enterocolitica (YePL2A) is the only only PL2 structure to be reported [1]. Three different models for YePL2A have been deposited, including a native-form (2V8I, 1.50 Å), and a complex with trigalacturonate (2V8K, 2.1 Å) and a transitional metal (2V8J, 2.01 Å). Family 2 PLs adopt a rare α/α-7 barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. The active site centre, consisting of the metal coordination pocket and catalytic arginine, is positioned at one end of the cleft. Substrate binding induces a conformational change and the arms close about the substrate.

Family Firsts

First catalytic activity

PelY from Yersinia pseudotuberculosis macerated cucumber [4].

First catalytic base identification

YePL2A (YE4069) Arg218 from Yersinia enterocolitica [1].

First catalytic divalent cation identification

DdPL2/PelW(Dda3937_03361) from Dickeya Dadantii 3937 (Previously Erwinia chrysanthemi3937) [2].

First 3-D structure

PL2A (YE4069) from Yersinia enterocolitica [1].

References

<biblio>

1. Abbott2007 pmid=17881361
2. Shevchik1999 pmid=10383957
3. Manulis1988 pmid=2832382
4. Abbott2013 pmid=24013861