Polysaccharide Lyase Family 9

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• Author: ^^^Ana Luis^^^
• Responsible Curator: ^^^Wade Abbott^^^

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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) degrade 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

1. 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 |
2. 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 |
3. 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 |