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 lyases of CAZy contain two subfamilies [1] and several outlier sequences. Originally referred to as oligogalacturonide trans-eliminases (OGTE)[2], Family 22 lyases are now commonly referred to as oligogalacturonide lyases (OGLs).

As the name suggests, OGLs are typically preferentially active on short chain oligomers of galacturonides. Several studies have been undertaken to evaluate the specificity of PL22s, and have found that optimal activity is seen with digalacturonate and Δ4,5-unsaturated digalacturonate [3][4]. Activity on trigalacturonate has been shown to be significantly lower than that on digalacturonate and although activity on the unsaturated dimer was lower than that of the saturated dimer, activity on Δ4,5-unsaturated trigalacturonate is comparable or higher than that of saturated trigalacturonate [4]. No assays on larger oligomers have been reported at this time however, OGLs lack activity on long chain polymers of α-(1,4)-linked polygalacturonate.

Activity has been demonstrated on methylated short chain galacturonides with differing levels of activity depending on the location of methylation [4]. Activity on 1-methyl digalacturonate was only half of what was seen on digalacturonate and no activity was found on 2-methyl digalacturonate. A similar trend was shown on trigalacturonate as well with roughly half the activity on 1-methyl trigalacturonate as on trigalacturonate and no activity on 2-methyl galacturonate. Interestingly though, nearly triple activity was seen on 3-methyl galacturonate as on unmethylated trigalacturonate.

Catalytic Residues

The Brønstead base for Family 22 lyases is a histidine. [3] H242 in YE1876 from Yersinia enterocolitica subsp. enterocolitica 8081 was the first and is to date, the only catalytic residue determined in a Family 22 lyase. This histidine is nearly perfectly conserved within Family 22 lyases reported in the CAZy database with a single exception, that of Candidatus Solibacter usitatus Ellin6076 (gi|116225114|) in which the histidine has been mutated to threonine T236.

The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088 H287, H353, H355; YeOGL 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 and several outlier sequences, this is not the case for subfamily 2 or archaeal sequences. The three archaeal sequences have similar histidines but the Q350 has been replaced in two cases with an aspartate and in one case, no residue has identity. In subfamily 2, there is a histidine in place of H287 however there is no residue identity with Q350 and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may result in a substantially different metal coordination pocket.

Three-dimensional structures

YePL22 in complex with Mn²⁺ and acetate

The first structure of a Family 22 Lyase was the Vibrio parahaemolyticus RIMD 2210633 PDBID: 3C5M fused to a c-terminal polyhistidine tag and was solved in 2008 by x-ray diffraction to 2.60 Å. This was followed in 2010 by Yersinia enterocolitica subsp. enterocolitica 8081 PDBID: 3PE7 which was solved in complex with Mn²⁺ and acetate by x-ray diffraction to 1.65 Å. The two proteins share ~69% sequence identity and highly similar 3D structures.

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. ([1])

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 |