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

1. 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 |
2. Moran F, Nasuno S, and Starr MP. (1968). Oligogalacturonide trans-eliminase of Erwinia carotovora. Arch Biochem Biophys. 1968;125(3):734-41. DOI:10.1016/0003-9861(68)90508-0 |
3. Abbott DW, Gilbert HJ, and Boraston AB. (2010). The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination. J Biol Chem. 2010;285(50):39029-38. DOI:10.1074/jbc.M110.153981 |
4. Kester HC, Magaud D, Roy C, Anker D, Doutheau A, Shevchik V, Hugouvieux-Cotte-Pattat N, Benen JA, and Visser J. (1999). Performance of selected microbial pectinases on synthetic monomethyl-esterified di- and trigalacturonates. J Biol Chem. 1999;274(52):37053-9. DOI:10.1074/jbc.274.52.37053 |
5. Shevchik VE, Condemine G, Robert-Baudouy J, and Hugouvieux-Cotte-Pattat N. (1999). The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937. J Bacteriol. 1999;181(13):3912-9. DOI:10.1128/JB.181.13.3912-3919.1999 |
6. Collmer A and Bateman DF. (1981). Impaired induction and self-catabolite repression of extracellular pectate lyase in Erwinia chrysanthemi mutants deficient in oligogalacturonide lyase. Proc Natl Acad Sci U S A. 1981;78(6):3920-4. DOI:10.1073/pnas.78.6.3920 |
7. Reverchon S and Robert-Baudouy J. (1987). Molecular cloning of an Erwinia chrysanthemi oligogalacturonate lyase gene involved in pectin degradation. Gene. 1987;55(1):125-33. DOI:10.1016/0378-1119(87)90255-1 |
8. Reverchon S, Huang Y, Bourson C, and Robert-Baudouy J. (1989). Nucleotide sequences of the Erwinia chrysanthemi ogl and pelE genes negatively regulated by the kdgR gene product. Gene. 1989;85(1):125-34. DOI:10.1016/0378-1119(89)90472-1 |
9. Yang S, Zhang Q, Guo J, Charkowski AO, Glick BR, Ibekwe AM, Cooksey DA, and Yang CH. (2007). Global effect of indole-3-acetic acid biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl Environ Microbiol. 2007;73(4):1079-88. DOI:10.1128/AEM.01770-06 |