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 188.8.131.52, 5-dehydro-4-deoxy-D-glucuronate isomerase and EC 184.108.40.206, 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
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
Hovingh70: Hovingh P, Linker A (1970). "The enzymatic degradation of heparin and heparitin sulfate. 3. Purification of a heparitinase and a heparinase from flavobacteria." J Biol Chem 245(22);6170-5. PMID: 5484472
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
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
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
Murphy04: Murphy KJ, Merry CL, Lyon M, Thompson JE, Roberts IS, Gallagher JT (2004). "A new model for the domain structure of heparan sulfate based on the novel specificity of K5 lyase." J Biol Chem 279(26);27239-45. PMID: 15047699
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
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
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
Rosenberg97: Rosenberg RD, Shworak NW, Liu J, Schwartz JJ, Zhang L (1997). "Heparan sulfate proteoglycans of the cardiovascular system. Specific structures emerge but how is synthesis regulated?." J Clin Invest 99(9);2062-70. PMID: 9151776
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.
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
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
Hannemann07: Hannemann F, Bernhardt R, Jose J (2007). "Biocatalytic synthesis of 4-pregnen-20,21-diol-3-one, a selective inhibitor of human 5alpha-reductase type II." J Enzyme Inhib Med Chem 22(5);570-6. PMID: 18035825
Hu10: Hu W, Tedesco S, McDonagh B, Barcena JA, Keane C, Sheehan D (2010). "Selection of thiol- and disulfide-containing proteins of Escherichia coli on activated thiol-Sepharose." Anal Biochem 398(2);245-53. PMID: 19903445
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
Showing only 20 references. To show more, press the button "Show all references".
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493