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Difference between revisions of "Polysaccharide Lyase Family 22"
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== Substrate specificities == | == Substrate specificities == | ||
− | Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally | + | Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally known as oligogalacturonide transeliminases (OGTE) <cite>Moran1968</cite>, 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-{{smallcaps|l}}-threo-5-hexosulose uronic acid, DKI) from short chain oligalacturonides and display preferential activity on digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010 Kester1999</cite>. Activity on trigalacturonate is significantly lower and PL22s appear to completely lack activity on long chain polymers of α-(1,4)-linked polygalacturonate <cite>Abbott2010 Kester1999</cite>. Differing levels of activity has been reported on methylated short chain oligogalacturonides depending on the location of methylation <cite>Kester1999</cite>. | |
− | |||
== Kinetics and Mechanism == | == 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. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the α-proton and charge neutralization of the oxyanion intermediate. YePL22 (YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081; [http://www.ncbi.nlm.nih.gov/protein/123442156 gi|123442156|]) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) <cite>Abbott2010</cite>, which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate. | |
== Catalytic Residues == | == 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 <cite>Abbott2010</cite>. This histidine is highly conserved within PL22s with only ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) displaying an alternative residue (T236); however, whether this protein is a lyase has yet to be determined. The 'stabilizing arginine' <cite>Abbott2010</cite> (YE1876: R217) is completely conserved across the PL22 family. | |
− | |||
− | The | ||
+ | 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 <cite>Lombard2010</cite>: 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 == | == Three-dimensional structures == | ||
− | [[Image:3pe7.png|thumb| | + | [[Image:3pe7.png|thumb|400px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The first structure of a PL22 determined was from ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]) in 2008 by x-ray diffraction to 2.60 Å ([http://www.nesg.org/ Northeast Structural Genomics Consortium]). This was followed in 2010 by YePL2A from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 ([{{PDBlink}}3pe7 PDB 3PE7]), which was solved in complex with Mn<sup>2+</sup> and acetate by x-ray diffraction to 1.65 Å <cite>Abbott2010</cite>. The two proteins share ~69% sequence identity and highly similar 3D structures. The PL22 fold is a β<sub>7</sub> propeller with the catalytic machinery and metal coordination pocket housed at the center of the enzyme. |
− | |||
== Family Firsts == | == Family Firsts == | ||
− | ;First catalytic activity: OGTE from ''Pectobacterium carotovorum'' ICPB EC153 (previously ''Erwinia carotovora'') | + | ;First catalytic activity: OGTE from ''Pectobacterium carotovorum'' ICPB EC153 (previously ''Erwinia carotovora'') <cite>Moran1968</cite>. |
− | ;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 | + | ;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 <cite>Abbott2010</cite>. |
− | ;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937) | + | ;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937) <cite>Shevchik1989</cite>. |
− | ;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633 | + | ;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633 (''Unpublished:'' [{{PDBlink}}3c5m PDB 3C5M]). |
== References == | == References == |
Latest revision as of 14:20, 18 December 2021
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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
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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |