Structural highlights
Function
PLYL_DICD3 Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. Is effective in the maceration of plant tissue, and has an important role in soft-rot disease. Is 280-fold less active against polygalacturonate than the major pectate lyase PelB. When assayed on polygalacturonate, PelL releases oligogalacturonates of different sizes; upon prolonged incubation, PelL degrades the primary products to unsaturated tetramer and pentamer in addition to unsaturated dimer and trimer. When assayed on oligogalacturonates (degrees of polymerization of 2 to 8), it preferentially forms unsaturated tetramer, and displays the highest activity on the octamer.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The "family 9 polysaccharide lyase" pectate lyase L (Pel9A) from Erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. Pel9A has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family Pel1A pectate lyases, and there is strong evidence for a common second calcium ion that binds between enzyme and substrate in the "Michaelis" complex. Although the primary calcium ion binds substrate in subsite -1, it is the second calcium ion, whose binding site is formed by the coming together of enzyme and substrate, that facilitates abstraction of the C5 proton from the sacharride in subsite +1. The role of the second calcium is to withdraw electrons from the C6 carboxylate of the substrate, thereby acidifying the C5 proton facilitating its abstraction and resulting in an E1cb-like anti-beta-elimination mechanism. The active site geometries and mechanism of Pel1A and Pel9A are closely similar, but the catalytic base is a lysine in the Pel9A enzymes as opposed to an arginine in the Pel1A enzymes.
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.,Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW J Biol Chem. 2004 Mar 5;279(10):9139-45. Epub 2003 Dec 11. PMID:14670977[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Roy C, Kester H, Visser J, Shevchik V, Hugouvieux-Cotte-Pattat N, Robert-Baudouy J, Benen J. Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937. J Bacteriol. 1999 Jun;181(12):3705-9. PMID:10368144 doi:10.1128/JB.181.12.3705-3709.1999
- ↑ Lojkowska E, Masclaux C, Boccara M, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N. Characterization of the pelL gene encoding a novel pectate lyase of Erwinia chrysanthemi 3937. Mol Microbiol. 1995 Jun;16(6):1183-95. PMID:8577252 doi:10.1111/j.1365-2958.1995.tb02341.x
- ↑ Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW. The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem. 2004 Mar 5;279(10):9139-45. Epub 2003 Dec 11. PMID:14670977 doi:10.1074/jbc.M311390200
