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: 5-dehydro-4-deoxy-D-glucuronate 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, Escherichia coli K-12 substr. MG1655, Pectobacterium carotovorum, Pseudomonas sp., Streptococcus agalactiae NEM316
Expected Taxonomic Range:
Many organisms produce large complex polymers that contain uronic acids. A few examples include pectin, an important component of plant cell walls that contains D-galacturonate, and glycosaminoglycans produced by animals, which include heparin, heparan sulfate, hyaluronan, chondroitin sulfate etc.
The bacterial degradation pathways for these polymers usually invovle an intial attack on the polymer that breaks it into short oligosaccharides. Two main types of enzymes that perform this task are the hydrolases and the endolyases. While hydrolases produce oligosaccharides that contain sugar residues similar to those in the polymer, lyases produce oligosaccharides that have a 4-5 unsaturated uronic acid at their non-reducing end. This is typically followed by the action of exolyases or hydrolases that cleave the oligosaccharides, resulting in the production of unstable unsaturated mono uronic acid monomers. Two forms of unsaturated uronic acids are formed, depending on the stereochemistry of the original acid - 4-deoxy-L-erythro-hex-4-enopyranuronate and 4-deoxy-L-threo-hex-4-enopyranuronate. The degradation of many polymers, including gellan, rhamnogalacturan, pectin, heparin, heparan sulfate, dermatan sulfate, hyaluronan and chondroitin results in formation the latter. 4-deoxy-L-threo-hex-4-enopyranuronate is unstable and the ring opens spontaneously, forming the keto acid 5-dehydro-4-deoxy-D-glucuronate. This pathway describes the degradation of that intermediate to metabolites of central metabolism.
About This Pathway
The pathway, which was first studied in detail in the pectin degrader Dickeya chrysanthemi, begins with the isomerization of 5-dehydro-4-deoxy-D-glucuronate (DKI) to 3-deoxy-D-glycero-2,5-hexodiulosonate (DKII). The kduI gene encoding the isomerase has been identified in this organism [Condemine91], but the enzyme has not been characterized. Earlier 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, a compound that 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 the kdgA gene, producing the central metabolites D-glyceraldehyde 3-phosphate and pyruvate.
The same pathway has also been characterized from the heparin/hyaluronan-degradating bacterium Streptococcus agalactiae NEM316 [Maruyama15]. Two of the enzymes ( EC 184.108.40.206, 5-dehydro-4-deoxy-D-glucuronate isomerase and EC 220.127.116.11, 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase) have been characterized in detail from this organism. While their actions are identical to those of the Dickeya chrysanthemi enzymes, they share very little sequence similarity and possess different structures, suggesting parallel evolution. The kduI and kduD genes are found in enterococci and clostridia, while the dhuI and dhuD genes are much less common and found primarily in streptococci [Maruyama15].
In Escherichia coli the aldolase encoded by gene eda is involved in the Entner-Doudoroff pathway I. However, in Dickeya 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, 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].
Relationship Links: KEGG:PART-OF:map00040
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Maruyama15: Maruyama Y, Oiki S, Takase R, Mikami B, Murata K, Hashimoto W (2015). "Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: Molecular identification and structure determination of streptococcal isomerase and dehydrogenase." J Biol Chem 290(10);6281-92. PMID: 25605731
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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
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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
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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.
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DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
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
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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
Kim06b: 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
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