Polysaccharide Lyase Family 22

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• Author: Richard McLean and Wade Abbott
• Responsible Curator: Wade Abbott

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Polysaccharide Lyase Family PL22
3D Structure	β7 propeller
Mechanism	β-elimination
Charge neutraliser	manganese
Active site residues	known
CAZy DB link
https://www.cazy.org/PL22.html

Substrate specificities

Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences [1]. Originally known as oligogalacturonide transeliminases (OGTE) [2], PL22s are now commonly referred to as oligogalacturonide lyases (OGLs). This enzyme family is found primarily in phytopathogenic or intestinal bacteria where it plays a role in the metabolism of pectin.

PL22s remove 5-keto-4-deoxyuronate (4-deoxy-l-threo-5-hexosulose uronic acid, DKI) from short chain oligalacturonides and display preferential activity on digalacturonate and Δ4,5-unsaturated digalacturonate [3, 4]. Activity on trigalacturonate is significantly lower and PL22s appear to completely lack activity on long chain polymers of α-(1,4)-linked polygalacturonate [3, 4]. Differing levels of activity has been reported on methylated short chain oligogalacturonides depending on the location of methylation [4].

Kinetics and Mechanism

PL22s harness a β-elimination mechanism to cleave the glycosidic bonds in oligogalacturonides. This process requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn²⁺ or Mg²⁺) for acidification of the α-proton and charge neutralization of the oxyanion intermediate. YePL22 (YE1876 from Yersinia enterocolitica subsp. enterocolitica 8081; gi|123442156|) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) [3], which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate.

Catalytic Residues

Within the structure of YePL22, H242 is the only basic residue that is in proximity to the α-proton of a modelled galacturonate [3]. This histidine is highly conserved within PL22s with only Candidatus Solibacter usitatus Ellin6076 (gi|116225114|) displaying an alternative residue (T236); however, whether this protein is a lyase has yet to be determined. The 'stabilizing arginine' [3] (YE1876: R217) is completely conserved across the PL22 family.

The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088: H287, H353, H355; YE1876: H287, H353, H355) and one glutamine (VPA0088: Q350; YeOGL: Q350). It is of note however that although these residues are perfectly conserved in all reported subfamily 1 sequences and several outlier sequences, there are minor differences in subfamily 2 [1]: H287 is invariant, Q350 is not conserved, and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may alter the chemistry of metal coordination selectivity. Further experimentation will be required to define this relationship.

Three-dimensional structures

YePL22 in complex with Mn²⁺ and acetate

The first structure of a PL22 determined was from Vibrio parahaemolyticus RIMD 2210633 (PDB 3C5M) in 2008 by x-ray diffraction to 2.60 Å (Northeast Structural Genomics Consortium). This was followed in 2010 by YePL2A from Yersinia enterocolitica subsp. enterocolitica 8081 (PDB 3PE7), which was solved in complex with Mn²⁺ and acetate by x-ray diffraction to 1.65 Å [3]. The two proteins share ~69% sequence identity and highly similar 3D structures. The PL22 fold is a β₇ propeller with the catalytic machinery and metal coordination pocket housed at the center of the enzyme.

Family Firsts

First catalytic activity

OGTE from Pectobacterium carotovorum ICPB EC153 (previously Erwinia carotovora) [2].

First catalytic base identification

YeOGL (YE1876) H242 from Yersinia enterocolitica subsp. enterocolitica 8081 [3].

First catalytic divalent cation identification

OGL (Dda3937_03686) from Dickeya Dadantii 3937 (previously Erwinia chrysanthemi 3937) [5].

First 3-D structure

VPA0088 from Vibrio parahaemolyticus RIMD 2210633 (Unpublished: PDB 3C5M).

References

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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 |