CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.
Difference between revisions of "Polysaccharide Lyase Family 9"
| Line 30: | Line 30: | ||
<!-- This is the end of the table --> | <!-- This is the end of the table --> | ||
== Substrate specificities == | == Substrate specificities == | ||
| − | Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan | + | Polysaccharide lyases of family 9 ([http://www.cazy.org/PL9.html CAZy]) degrade homogalacturonan,a pectin component present in the plant cell walls. An enzyme in PL9 was described as active on sheath, a thioloic glycoconjugate secreted by ''Sphaerotilus natans'' <cite>Takeda2000</cite>. The main activity in characterized PL9 is pectate lyases. These enzymes 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>. Other additional activities include: exopolygalacturonic lyase ([http://www.enzyme-database.org/query.php?ec=4.2.2.9 EC 4.2.2.9]) |
| − | |||
| − | |||
| − | |||
Revision as of 12:00, 14 September 2017
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) degrade homogalacturonan,a pectin component present in the plant cell walls. An enzyme in PL9 was described as active on sheath, a thioloic glycoconjugate secreted by Sphaerotilus natans [1]. The main activity in characterized PL9 is pectate lyases. These enzymes cleave non-methylated α-(1-4)-linked D-galacturonic acid by a β-elimination mechanism (EC 4.2.2.2)[2]. Other additional activities include: exopolygalacturonic lyase (EC 4.2.2.9)
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 [2]. Similar to PL1 family, a calcium ion interacts with the substrate carboxylate at +1 subsite promoting the C5 proton acidification. [2, 3].
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) [2].
Three-dimensional structures
[[
File:PL9.png|thumb|300px|right|Figure 1. Pel9A in complex with Ca2+ (1RU4) A. Schematic representation of Pel9A parallel β-helix fold colour ramped from blue (N-terminal) to red (C-terminal). The active site is represented as sticks and highlighted inside the black box. The calcium is represented as sphere (gray) B. Blow up of the active site. The residues interacting with calcium and the proposed catalytic base (K237) are represented as stick in green and yellow, respectively.]]
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 (Figure 1A). 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 (Figure 1B) [2].
Family Firsts
- First description of catalytic activity
- PelX from Erwinia chrysanthemi [4].
- First catalytic base identification
- Pel9A from Erwinia chrysanthemi [2].
- First catalytic divalent cation identification
- Pel9A from Erwinia chrysanthemi [2].
- First 3-D structure
- Pel9A from Erwinia chrysanthemi [2].
References
- Takeda M, Iohara K, Shinmaru S, Suzuki I, and Koizumi JI. (2000). Purification and properties of an enzyme capable of degrading the sheath of Sphaerotilus natans. Appl Environ Microbiol. 2000;66(11):4998-5004. DOI:10.1128/AEM.66.11.4998-5004.2000 |
- 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 |
- Kondo K, Takeda M, Ejima W, Kawasaki Y, Umezu T, Yamada M, Koizumi J, Mashima T, and Katahira M. (2011). Study of a novel glycoconjugate, thiopeptidoglycan, and a novel polysaccharide lyase, thiopeptidoglycan lyase. Int J Biol Macromol. 2011;48(2):256-62. DOI:10.1016/j.ijbiomac.2010.11.009 |