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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 referred to as oligogalacturonide trans-eliminases (OGTE)<cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs).
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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.
  
As the name suggests, OGLs are preferentially active on short chain oligomers of galacturonides. PL22s are preferentially active on digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010</cite><cite>Kester1999</cite>. Activity on trigalacturonate has been shown to be significantly lower than 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 <cite>Kester1999</cite>. 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 <cite>Kester1999</cite>. 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.
+
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 &alpha;-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 ==
The Brønstead base for PL22s is predicted to be a histidine <cite>Abbott2010</cite>. H242 in YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 was the first and is to date, the only catalytic residue determined reported to be in proximity to the &alpha;-proton of galacturonate. This histidine is highly conserved within Family 22 lyases with only ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) displaying a threonine (T236); however, whether this gene product functions as a lyase has yet to be determined.
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Within the structure of YePL22, H242 is the only basic residue that is in proximity to the &alpha;-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 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 sequences and several outlier sequences, subfamily 2 or archaeal sequences display different signatures <cite>Lombard2010</cite>. The archaeal sequences have conserved histidines but there is variations Q350. In subfamily 2, H287 is invariant; however, Q350 is not conserved and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications likely alter the chemistry of metal coordination selectivity.  
 
  
 +
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|230px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The first structure of a PL22 determined was the ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]) solved in 2008 by x-ray diffraction to 2.60 Å (http://www.nesg.org/, Northeast Structural Genomics Consortium). This was followed in 2010 by ''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. The two proteins share ~69% sequence identity and highly similar 3D structures.
+
[[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 &beta;<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''). <cite>Moran1968</cite>
+
;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. <cite>Abbott2010</cite>
+
;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). <cite>Shevchik1989</cite>.  
+
;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. ([{{PDBlink}}3c5m PDB 3C5M])
+
;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633 (''Unpublished:'' [{{PDBlink}}3c5m PDB 3C5M]).
  
 
== References ==
 
== References ==

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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. 2010;432(3):437-44. DOI:10.1042/BJ20101185 | PubMed ID:20925655 [Lombard2010]
  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 | PubMed ID:5671040 [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. 2010;285(50):39029-38. DOI:10.1074/jbc.M110.153981 | PubMed ID:20851883 [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. 1999;274(52):37053-9. DOI:10.1074/jbc.274.52.37053 | PubMed ID:10601263 [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. 1999;181(13):3912-9. DOI:10.1128/JB.181.13.3912-3919.1999 | PubMed ID:10383957 [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. 1981;78(6):3920-4. DOI:10.1073/pnas.78.6.3920 | PubMed ID:16593039 [Collmer1981]
  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 | PubMed ID:3623103 [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. 1989;85(1):125-34. DOI:10.1016/0378-1119(89)90472-1 | PubMed ID:2695393 [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. 2007;73(4):1079-88. DOI:10.1128/AEM.01770-06 | PubMed ID:17189441 [Yang2007]

All Medline abstracts: PubMed