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Difference between revisions of "Polysaccharide Lyase Family 9"
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== Substrate specificities == | == Substrate specificities == | ||
| − | + | Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrades homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Jenkins2004</cite>. | |
| − | |||
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | PL9 acts by an ''anti''-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 <cite>Jenkins2004</cite>. Similar to PL1 family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. <cite>Jenkins2004 Seyedarabi2010</cite>. | |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | The lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) <cite>Jenkins2004</cite>. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | PL9 structure of ''Erwinia chrysanthemi'' (Pel9A) was solved at a resolution of 1.6 Å ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1RU4 1RU4]) and displays a right-handed parallel β-helix fold. The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft <cite>Jenkins2004</cite>. | |
== Family Firsts == | == Family Firsts == | ||
| − | ;First | + | ;First description of catalytic activity: PelX from ''Erwinia chrysanthemi'' <cite>Brooks1990</cite>. |
| − | ;First catalytic | + | ;First catalytic base identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. |
| − | ;First | + | ;First catalytic divalent cation identification: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. |
| − | ;First 3-D structure: | + | ;First 3-D structure: Pel9A from ''Erwinia chrysanthemi'' <cite>Jenkins2004</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Jenkins2004 pmid=14670977 |
| − | # | + | #Seyedarabi2010 pmid=20000851 |
| + | #Brooks1990 pmid=2254266 | ||
</biblio> | </biblio> | ||
[[Category:Polysaccharide Lyase Families|PL009]] | [[Category:Polysaccharide Lyase Families|PL009]] | ||
Revision as of 14:43, 21 November 2015
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Ana Luis^^^
- Responsible Curator: ^^^Wade Abbott^^^
| Polysaccharide Lyase Family PL9 | |
| 3D Structure | β-helix |
| Mechanism | β-elimination |
| Charge neutraliser | calcium |
| Active site residues | known |
| CAZy DB link | |
| https://www.cazy.org/PL9.html | |
Substrate specificities
Polysaccharide lyases of family 9 (CAZy) degrades homogalacturonan, a pectin component present in the plant cell walls. PL9 are pectate lyases that cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism (EC 4.2.2.2) [1].
Kinetics and Mechanism
PL9 acts by an anti-β-elimination mechanism generating a 4,5-unsaturated galacturonic acid product and a new reducing end. The elimination of C5 proton is base-catalyzed by lysine 237 [1]. Similar to PL1 family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. [1, 2].
Catalytic Residues
The lysine 237 (K237) is the Brønstead base (responsible for the abstraction of the C5 proton from galacturonic acid at +1 subsite). The calcium coordination pocket is comprised of four aspartates (D209, D233, D234 and D237) [1].
Three-dimensional structures
PL9 structure of Erwinia chrysanthemi (Pel9A) was solved at a resolution of 1.6 Å (1RU4) and displays a right-handed parallel β-helix fold. The superhelical structure presents 10 complete coils and 3 β -sheets (PB1, PB2, PB3). A short α-helix at N-terminus caps the hydrophobic core of the parallel β -helix. The catalytic base K237 and calcium binding site are orientated in the structure cleft [1].
Family Firsts
- First description of catalytic activity
- PelX from Erwinia chrysanthemi [3].
- First catalytic base identification
- Pel9A from Erwinia chrysanthemi [1].
- First catalytic divalent cation identification
- Pel9A from Erwinia chrysanthemi [1].
- First 3-D structure
- Pel9A from Erwinia chrysanthemi [1].
References
- Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, and Pickersgill RW. (2004). The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem. 2004;279(10):9139-45. DOI:10.1074/jbc.M311390200 |
- Seyedarabi A, To TT, Ali S, Hussain S, Fries M, Madsen R, Clausen MH, Teixteira S, Brocklehurst K, and Pickersgill RW. (2010). Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase. Biochemistry. 2010;49(3):539-46. DOI:10.1021/bi901503g |
- Brooks AD, He SY, Gold S, Keen NT, Collmer A, and Hutcheson SW. (1990). Molecular cloning of the structural gene for exopolygalacturonate lyase from Erwinia chrysanthemi EC16 and characterization of the enzyme product. J Bacteriol. 1990;172(12):6950-8. DOI:10.1128/jb.172.12.6950-6958.1990 |