MetaCyc Enzyme: pectate lyase E

Gene: pelE Accession Number: G-12029 (MetaCyc)

Species: Dickeya dadantii 3937

The subunit structure of this enzyme has not been reported. The apparent molecular mass of the recombinant polypeptide was determined by SDS-PAGE [Tardy97].

Phytopathogenic and saprophytic bacteria and fungi produce variety of extracellular and intracellular enzymes that de-esterify and depolymerize pectin (see a pectin) and its derivatives. Pectin is a constituent of the plant cell wall. In pectinolytic bacteria the initial steps of pectin degradation to pectate (see a pectate) and oligogalacturonides involve the action of extracellularly secreted pectin methylesterases, pectin acetylesterases, pectin lyases, pectate hydrolases and pectate lyases. Pectate degrading hydrolases and lyases are also found in the cytoplasm and periplasm.

Pectinolytic enzymes may be present in several different isoforms and may vary among species and strains. Pectin-degrading enzymes are used in the food, fiber and animal feed industries. The development of inhibitors of enzymes that degrade pectin and its derivatives is of interest as a possible way to prevent crop spoilage, although none have been reported. In [MartensUzunova09] and reviewed in [HugouvieuxCotte96, Abbott08].

Pectate lyases have a major role in pectinolysis in this organism and contribute to plant soft rot disease. The isoelectric points of the endo-cleaving pectate lyase isozymes vary from acidic (pectate lyase A) to slightly alkaline (PelB and pectate lyase C) and very alkaline (PelD and this enzyme). An exo-cleaving pectate lyase, PelX, has also been characterized ([Tardy97] and reviewed in [HugouvieuxCotte96]).

Pectate lyase E is one of several pectate lyases secreted into the extracellular medium (reviewed in [HugouvieuxCotte96]). The recombinant enzyme from Dickeya dadantii 3937 (previously known as Erwinia chrysanthemi strain 3937) was overexpressed in Escherichia coli, purified and characterized [Tardy97].

The crystal structure of this enzyme from Erwinia chrysanthemi EC16 has been determined [Keen86, Yoder93, Lietzke94, Lietzke96].

See the summary for MetaCyc pathway 4-deoxy-L-threo-hex-4-enopyranuronate degradation.

Gene Citations: [Reverchon89]

Molecular Weight of Polypeptide: 43.094 kD (from nucleotide sequence), 42.5 kD (experimental) [Tardy97 ]

pI: 10.3 [Tardy97]

Unification Links: Entrez-Nucleotide:M33584 , UniProt:P0C1A5

Relationship Links: InterPro:IN-FAMILY:IPR002022 , InterPro:IN-FAMILY:IPR011050 , InterPro:IN-FAMILY:IPR012334 , Pfam:IN-FAMILY:PF00544 , Smart:IN-FAMILY:SM00656

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Created 14-May-2010 by Fulcher CA , SRI International

Enzymatic reaction of: pectate lyase

EC Number:

a pectate <=> n an unsaturated pectate oligosaccharide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

This endo-cleaving enzyme cleaves the internal glycosidic bonds of pectate (polygalacturonate) via a β-elimination mechanism. It produces oligogalacturonides containg a 4,5-unsaturated residue at the nonreducing end of the oligomer (reviewed in [HugouvieuxCotte96]).

The Km for pectate was 0.42 g/l. The enzyme retained 68% of its activity in the absence of Ca2+, but was inhibited by 1 mM Ca2+. Divalent ions Ba2+, Co2+, Cu2+, Mg2+, Mn2+, Sr2+ and Zn2+ could not activate the enzyme and Zn2+ was inhibitory. The enzyme was active on pectate substrates that had only a low degree of methylation. No product inhibition was observed [Tardy97].

Cofactors or Prosthetic Groups: Ca2+ [Tardy97]

Inhibitors (Unknown Mechanism): EDTA [Tardy97] , Zn2+ [Tardy97] , (-)-epicatechin [Tardy97] , salicylate [Tardy97]

T(opt): 50 °C [Tardy97]

pH(opt): 8 [Tardy97]


Abbott08: Abbott DW, Boraston AB (2008). "Structural biology of pectin degradation by Enterobacteriaceae." Microbiol Mol Biol Rev 72(2);301-16, table of contents. PMID: 18535148

Caffall09: Caffall KH, Mohnen D (2009). "The structure, function, and biosynthesis of plant cell wall pectic polysaccharides." Carbohydr Res 344(14);1879-900. PMID: 19616198

HugouvieuxCotte96: Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S (1996). "Regulation of pectinolysis in Erwinia chrysanthemi." Annu Rev Microbiol 50;213-57. PMID: 8905080

Keen86: Keen NT, Tamaki S (1986). "Structure of two pectate lyase genes from Erwinia chrysanthemi EC16 and their high-level expression in Escherichia coli." J Bacteriol 168(2);595-606. PMID: 3536853

Lietzke94: Lietzke SE, Yoder MD, Keen NT, Jurnak F (1994). "The Three-Dimensional Structure of Pectate Lyase E, a Plant Virulence Factor from Erwinia chrysanthemi." Plant Physiol 106(3);849-862. PMID: 12232373

Lietzke96: Lietzke SE, Scavetta RD, Yoder MD, Jurnak F (1996). "The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution." Plant Physiol 111(1);73-92. PMID: 12226275

MartensUzunova09: Martens-Uzunova ES, Schaap PJ (2009). "Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics." Fungal Genet Biol 46 Suppl 1;S170-S179. PMID: 19618506

Reginault08: Reginault, Ph., Valette-Collet , O., Boccara, M. (2008). "The importance of fungal pectinolytic enzymes in plant invasion, host adaptability and symptom type." Eur. J. Plant Pathol.

Reverchon89: Reverchon S, Huang Y, Bourson C, Robert-Baudouy J (1989). "Nucleotide sequences of the Erwinia chrysanthemi ogl and pelE genes negatively regulated by the kdgR gene product." Gene 85(1);125-34. PMID: 2695393

Richard09: Richard P, Hilditch S (2009). "D-galacturonic acid catabolism in microorganisms and its biotechnological relevance." Appl Microbiol Biotechnol 82(4);597-604. PMID: 19159926

Tardy97: Tardy F, Nasser W, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N (1997). "Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: enzyme characteristics and potential inhibitors." J Bacteriol 179(8);2503-11. PMID: 9098045

Yoder93: Yoder MD, Lietzke SE, Jurnak F (1993). "Unusual structural features in the parallel beta-helix in pectate lyases." Structure 1(4);241-51. PMID: 8081738

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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