MetaCyc Pathway: 5-dehydro-4-deoxy-D-glucuronate degradation

Enzyme View:

Pathway diagram: 5-dehydro-4-deoxy-D-glucuronate degradation

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: pectin degradation, 4,5-dihydroxy-2,6-dioxohexanoate degradation

Superclasses: Degradation/Utilization/Assimilation Secondary Metabolites Degradation Sugar Derivatives Degradation

Some taxa known to possess this pathway include ? : Dickeya dadantii 3937 , Erwinia chrysanthemi EC16 , Pectobacterium carotovorum , Pseudomonas sp.

Expected Taxonomic Range: Bacteria

General Background

5-dehydro-4-deoxy-D-glucuronate is a metabolite resulting from the bacterial degradation of pectin, a complex polymer found in plant cell walls. 5-dehydro-4-deoxy-D-glucuronate is produced by the action of cytoplasmic exopolygalacturonate lyase W and oligogalacturonate lyase and is catabolized in the pathway shown here, as described below in About This Pathway.

The initial steps of pectin degradation to oligogalacturonides in pectinolytic bacteria involve the action of extracellularly secreted pectin methylesterases, pectin acetylesterases, pectate hydrolases (polygalacturonases) and pectate lyases. Pectate degrading hydrolases and lyases are found in the cytoplasm, periplasm and extracellular space. Extracellularly secreted hydrolases can also produce free D-galacturonate which is an important carbon source for microorganisms that catabolize plant material. Pectinolytic enzymes may be present in several different isoforms and may vary among species and strains. In [Kester99] and reviewed in [HugouvieuxCotte96].

Pectin is a heteropolymer present in plant cell walls. It s involved in crosslinking cellulose and hemicellulose fibers, which provides rigidity to the cell wall. The uronic acid D-galacturonate is the main monomeric constituent of pectin. In pectin the D-galacturonate monomers are in the α-pyranose form connected through a 1,4 linkage to form long chains. Homogalacturonan (polygalacturonate) (see a homogalacturonan), a polymer of α-1,4-linked-d-galacturonic acid, is the simplest form of pectin. Other structural classes are rhamnogalacturonan-I, rhamnogalacturonan-II, apiogalacturonan and xylogalacturonan. In natural pectin the carboxyl groups of D-galacturonate may be methyl esterified and some plants also contain acetylated D-galacturonate residues. The degree of esterification varies among plants. Non-esterified carboxyl groups may be linked through divalent cations such as Mg2+ or Ca2+, causing pectin to form a gel.

Pectin is used in the animal feed industry and in the food industry as a gelling agent. Phytopathogenic and saprophytic bacteria and fungi can produce variety of extracellular and intracellular enzymes that degrade pectin and its derivatives. Pectinolytic enzymes such as esterases, hydrolases and lyases, are used in the food, fiber and animal feed industries. There is commercial interest in pectinolytic enzymes to convert the pectin-rich by-products from citrus peel and sugar beet processing to higher value material. In [MartensUzunova09] [Abbott08] and reviewed in [Richard09, Reginault08, HugouvieuxCotte96]. Pectin structure is reviewed in [Caffall09].

About This Pathway

The degradation of pectin by bacteria has been extensively studied in Dickeya dadantii 3937 (previously known as Erwinia chrysanthemi strain 3937), a plant pathogen that causes soft rot disease. Multiple isozymes excreted from the cell (virulence factors) de-esterify and cleave homogalacturonan (polygalacturonate) into pectate oligogalacturonides which then enter the cell (see a pectate). They are degraded by periplasmic enzymes to shorter oligogalacturonides which are then transported through the inner membrane and metabolized. The oligogalacturonide-degrading enzymes involved each have preferences for oligogalacturonides of various lengths. Oligogalacturonide transport proteins involved include the porin KdgM [Blot02] and the inner membrane transporters TogMNAB complex and TogT. The inner membrane permease KdgT, and the ExuT transporter allow uptake of pathway metabolites. Low levels of 5-dehydro-4-deoxy-D-glucuronate, 3-deoxy-D-glycero-2,5-hexodiulosonateI and 2-dehydro-3-deoxy-D-gluconate can act as inducers (in [Blot02] and reviewed in [HugouvieuxCotte96]).

The entire series of reactions (not shown) spans three compartments, the extracellular space, the periplasm and the cytoplasm (see [Blot02]). Initial pectin degradation reactions include its extracellular demethylation to pectate by secreted pectin methylesterase A (PemA) as well as deacetylation by pectin acetylesterase Y (PaeY), and production of oligogalacturonides by at least eight isoforms of pectate lyase (PelA, PelB, PelC, PelD, PelE, PelI, PelZ and PelL) (see pectate lyase A, pectate lyase C and pectate lyase E). After passage into the periplasm via the porin KdgM, any remaining methylated oligogalacturonides can be demethylated by pectin methylesterase B (PemB). Demethylated oligogalacturonides can be further processed by exo- hydrolytic cleavage (PehX) (see exopolygalacturonan hydrolase X), or exo- lyase cleavage (PelX) before transport into the cytoplasm. A periplasmic binding protein may aid in retention and accumulation of oligogalacturonides (in [Abbott08]). In Pectobacterium carotovorum (previously known as Erwinia carotovora) a secreted endo-polygalacturonase PehA [Saarilahti90, Pickersgill98] and a pectin lyase (Pnl) [Nishida90] have been identified.

In the cytoplasm the action of exopolygalacturonate lyase W (PelW) releases unsaturated digalacturonate (4-(4-deoxy-α-D-galact-4-enuronosyl)-D-galacturonate). The subsequent action of oligogalacturonate lyase (Ogl) on unsaturated digalacturonate produces two molecules of 5-dehydro-4-deoxy-D-glucuronate, whereas its action on saturated digalacturonate produces equimolar amounts of 5-dehydro-4-deoxy-D-glucuronate and D-galacturonate. D-galacturonate is catabolized as shown in pathway D-galacturonate degradation I. In [Kester99, Shevchik99] and reviewed in [HugouvieuxCotte96].

In Erwinia chrysanthemi this is the main pathway for pectin degradation. Due to the relatively low activity of polygalacturonases in this organism, little D-galacturonate is produced. The reactions shown here begin with the isomerization of 5-dehydro-4-deoxy-D-glucuronate (also referred to as DKI) to 3-deoxy-D-glycero-2,5-hexodiulosonate (DKII). The kduI gene encoding the putatuve isomerase in Erwinia chrysanthemi has been identified [Condemine91], but the enzyme has not been characterized. Early work characterized this enzyme in a pseudomonad [Preiss63]. 3-deoxy-D-glycero-2,5-hexodiulosonate is reduced to the common metabolite 2-dehydro-3-deoxy-D-gluconate. This compound is also an intermediate in D-galacturonate degradation I. 2-dehydro-3-deoxy-D-gluconate is phosphorylated and then cleaved by an aldolase encoded by gene kdgA which produces the central metabolites D-glyceraldehyde 3-phosphate and pyruvate.

In Escherichia coli the aldolase encoded by gene eda is involved in the Entner-Doudoroff pathway I. However, in Erwinia chrysanthemi this enzyme does not appear to be involved in D-gluconate catabolism and no product of the edd gene that encodes the phosphogluconate dehydratase could be detected in various species of Erwinia. These observations question the existence of the Entner-Doudoroff pathway in these organisms ([HugouvieuxCotte94] and reviewed in [HugouvieuxCotte96]).

Most of the enzymes in this pathway are controlled by kdgR a transcriptional regulator that is induced by 2-dehydro-3-deoxy-D-gluconate [Reverchon91, Nasser91]. A comparative genomics analysis of the kdgR regulon in eight enterobacteria including Dickeya dadantii 3937 and Pectobacterium carotovorum and two members of the genus Vibrio, yielded a metabolic map of pectin and pectin-derivative degradation in these organisms [Rodionov04].

Superpathways: superpathway of microbial D-galacturonate and D-glucuronate degradation

Relationship Links: KEGG:PART-OF:map00040

Created 30-Apr-2010 by Fulcher CA , SRI International


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

Blot02: Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G (2002). "The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family." J Biol Chem 277(10);7936-44. PMID: 11773048

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

Condemine91: Condemine G, Robert-Baudouy J (1991). "Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation." Mol Microbiol 1991;5(9);2191-202. PMID: 1766386

HugouvieuxCotte94: Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1994). "Molecular analysis of the Erwinia chrysanthemi region containing the kdgA and zwf genes." Mol Microbiol 11(1);67-75. PMID: 8145647

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

Kester99: Kester HC, Magaud D, Roy C, Anker D, Doutheau A, Shevchik V, Hugouvieux-Cotte-Pattat N, Benen JA, Visser J (1999). "Performance of selected microbial pectinases on synthetic monomethyl-esterified di- and trigalacturonates." J Biol Chem 274(52);37053-9. PMID: 10601263

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

Nasser91: Nasser W, Condemine G, Plantier R, Anker D, Robert-Baudouy J (1991). "Inducing properties of analogs of 2-keto-3-deoxygluconate on the expression of pectinase genes of Erwinia chrysanthemi." FEMS Microbiol Lett 65(1);73-8. PMID: 1874406

Nishida90: Nishida T, Suzuki T, Ito K, Kamio Y, Izaki K (1990). "Cloning and expression of pectin lyase gene from Erwinia carotovora in Escherichia coli." Biochem Biophys Res Commun 168(2);801-8. PMID: 2185758

Pickersgill98: Pickersgill R, Smith D, Worboys K, Jenkins J (1998). "Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora." J Biol Chem 273(38);24660-4. PMID: 9733763

Preiss63: Preiss J, Ashwell G (1963). "Polygalacturonic acid metabolism in bacteria. II. Formation and metabolism of 3-deoxy-D-glycero-2, 5-hexodiulosonic acid." J Biol Chem 238;1577-83. PMID: 13986017

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.

Reverchon91: Reverchon S, Nasser W, Robert-Baudouy J (1991). "Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation." Mol Microbiol 5(9);2203-16. PMID: 1840643

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

Rodionov04: Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N (2004). "Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria." Microbiology 150(Pt 11);3571-90. PMID: 15528647

Saarilahti90: Saarilahti HT, Heino P, Pakkanen R, Kalkkinen N, Palva I, Palva ET (1990). "Structural analysis of the pehA gene and characterization of its protein product, endopolygalacturonase, of Erwinia carotovora subspecies carotovora." Mol Microbiol 4(6);1037-44. PMID: 2215212

Shevchik99: Shevchik VE, Condemine G, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N (1999). "The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937." J Bacteriol 181(13);3912-9. PMID: 10383957

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Condemine84: Condemine G, Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1984). "An enzyme in the pectinolytic pathway of Erwinia chrysanthemi: 2-keto-3-deoxygluconate oxidoreductase." Journal of General Microbiology 130, 2839-2844.

Condemine86: Condemine G, Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1986). "Isolation of Erwinia chrysanthemi kduD mutants altered in pectin degradation." J Bacteriol 165(3);937-41. PMID: 3949717

Crowther05: Crowther RL, Georgiadis MM (2005). "The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli." Proteins 61(3);680-4. PMID: 16152643

Cynkin60: Cynkin MA, Ashwell G (1960). "Uronic acid metabolism in bacteria. IV. Purification and properties of 2-keto-3-deoxy-D-gluconokinase in Escherichia coli." J Biol Chem 235;1576-9. PMID: 13813474

Egan92: Egan SE, Fliege R, Tong S, Shibata A, Wolf RE, Conway T (1992). "Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon." J Bacteriol 1992;174(14);4638-46. PMID: 1624451

Griffiths02: Griffiths JS, Wymer NJ, Njolito E, Niranjanakumari S, Fierke CA, Toone EJ (2002). "Cloning, isolation and characterization of the Thermotoga maritima KDPG aldolase." Bioorg Med Chem 10(3);545-50. PMID: 11814840

HugouvieuxCotte94a: Hugouvieux-Cotte-Pattat N, Nasser W, Robert-Baudouy J (1994). "Molecular characterization of the Erwinia chrysanthemi kdgK gene involved in pectin degradation." J Bacteriol 176(8);2386-92. PMID: 8157608

Kim06: Kim S, Lee SB (2006). "Characterization of Sulfolobus solfataricus 2-keto-3-deoxy-D-gluconate kinase in the modified Entner-Doudoroff pathway." Biosci Biotechnol Biochem 70(6);1308-16. PMID: 16794308

Lamble05: Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ (2005). "Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus." FEBS Lett 579(30);6865-9. PMID: 16330030

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Miller13: Miller KA, Phillips RS, Mrazek J, Hoover TR (2013). "Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes." J Bacteriol. PMID: 23836865

Patil92: Patil RV, Dekker EE (1992). "Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene." J Bacteriol 1992;174(1);102-7. PMID: 1339418

Pouyssegur71: Pouyssegur JM, Stoeber FR (1971). "[The common degradative pathway for hexuronates in Escherichia coli K 12. Purification, properties and individuality of 2-keto-3-deoxy-6-phospho-D-gluconate aldolase]." Eur J Biochem 1971;21(3);363-73. PMID: 4936448

Pouyssegur71a: Pouyssegur J, Stoeber F (1971). "[Study of the common degradative pathway of hexuronates in Escherichia coli K 12. Purification, properties and individuality of 2-keto-3-deoxy-D-gluconnokinase]." Biochimie 53(6);771-81. PMID: 4944816

Rodionova12: Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA (2012). "Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima." Environ Microbiol 14(11);2920-34. PMID: 22925190

Siebers04: Siebers B, Tjaden B, Michalke K, Dorr C, Ahmed H, Zaparty M, Gordon P, Sensen CW, Zibat A, Klenk HP, Schuster SC, Hensel R (2004). "Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data." J Bacteriol 186(7);2179-94. PMID: 15028704

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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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