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Polysaccharide Lyase Family 22

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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
http://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. 432, 437-44. DOI:10.1042/BJ20101185 | PubMed ID:20925655 | HubMed [Lombard2010]
  2. Moran F, Nasuno S, and Starr MP. (1968) Oligogalacturonide trans-eliminase of Erwinia carotovora. Arch Biochem Biophys. 125, 734-41. PubMed ID:5671040 | HubMed [Moran1968]
  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. 285, 39029-38. DOI:10.1074/jbc.M110.153981 | PubMed ID:20851883 | HubMed [Abbott2010]
  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. 274, 37053-9. PubMed ID:10601263 | HubMed [Kester1999]
  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. 181, 3912-9. PubMed ID:10383957 | HubMed [Shevchik1989]
  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. 78, 3920-4. PubMed ID:16593039 | HubMed [Collmer1981]
  7. Reverchon S and Robert-Baudouy J. (1987) Molecular cloning of an Erwinia chrysanthemi oligogalacturonate lyase gene involved in pectin degradation. Gene. 55, 125-33. PubMed ID:3623103 | HubMed [Reverchon1987]
  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. 85, 125-34. PubMed ID:2695393 | HubMed [Reverchon1989]
  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. 73, 1079-88. DOI:10.1128/AEM.01770-06 | PubMed ID:17189441 | HubMed [Yang2007]
All Medline abstracts: PubMed | HubMed