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MetaCyc Pathway: D-glucarate degradation II

Enzyme View:

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.

Superclasses: Degradation/Utilization/Assimilation Carboxylates Degradation Sugar Acids Degradation D-Glucarate Degradation
Degradation/Utilization/Assimilation Secondary Metabolites Degradation Sugar Derivatives Degradation Sugar Acids Degradation D-Glucarate Degradation

Some taxa known to possess this pathway include ? : Acinetobacter sp. ADP1 , Agrobacterium fabrum C58 , Agrobacterium tumefaciens , Delftia acidovorans , Pseudomonas putida , Pseudomonas sp. , Pseudomonas syringae

Expected Taxonomic Range: Bacteria

Summary:
General Background

D-glucarate is a naturally occurring dicarboxylate that can be used by some species of bacteria. Enterobacteria such as Escherichia coli and Klebsiella aerogenes utilize it by a different pathway than the one shown here (see pathway D-glucarate degradation I). Both pathways start with a dehydratase that produces 5-dehydro-4-deoxy-D-glucarate [Jeffcoat69]. Some bacteria possess an inducible uronate dehydrogenase that catalyzes the conversion of D-glucuronate to D-glucarate as shown in the pathway link. Although the genes in the pathway shown here remain uncharacterized in most of the organisms listed, more recent work in Acinetobacter sp. ADP1 (previously known as Acinetobacter baylyi ADP1) identified the genes involved in this pathway and pathway D-galactarate degradation II, including a D-glucararte/D-galactarate permease [Aghaie08].

About This Pathway

In Acinetobacter sp. ADP1 genes encoding enzymes for the degradation of D-glucarate and D-galactarate were identified by mutant analysis and complementation studies and the recombinant gene products were characterized. Intermediates in the pathway were identified by LC/MS [Aghaie08]. Genes included a D-glucarate/D-galactarate permease; separate, specific dehydratases for D-glucarate and D-galactarate; a 5-dehydro-4-deoxy-D-gluccarate dehydratase; and a 2-oxoglutarate semialdehyde dehydrogenase (also see pathway D-galactarate degradation II). The 2-oxoglutarate (α-ketoglutarate) produced in the pathway can be metabolized in the TCA cycle I (prokaryotic) as shown in the pathway link, or used in many other pathways.

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

Variants: D-glucarate degradation I

Credits:
Created 23-Apr-2010 by Fulcher CA , SRI International


References

Aghaie08: Aghaie A, Lechaplais C, Sirven P, Tricot S, Besnard-Gonnet M, Muselet D, de Berardinis V, Kreimeyer A, Gyapay G, Salanoubat M, Perret A (2008). "New insights into the alternative D-glucarate degradation pathway." J Biol Chem 283(23);15638-46. PMID: 18364348

Jeffcoat69: Jeffcoat R, Hassall H, Dagley S (1969). "The metabolism of D-glucarate by Pseudomonas acidovorans." Biochem J 115(5);969-76. PMID: 4311826

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

BLUMENTHAL63: BLUMENTHAL HJ, FISH DC (1963). "Bacterial conversion of D-glucarate to glycerate and pyruvate." Biochem Biophys Res Commun 11;239-43. PMID: 13971911

Blumenthal66: Blumenthal H "D-Glucarate Dehydrase." Meth Enz 1966;9:660-665.

Brouns06: Brouns SJ, Walther J, Snijders AP, van de Werken HJ, Willemen HL, Worm P, de Vos MG, Andersson A, Lundgren M, Mazon HF, van den Heuvel RH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, van der Oost J (2006). "Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment." J Biol Chem 281(37);27378-88. PMID: 16849334

Dagley75: Dagley S, Jeffcoat R (1975). "D-4-deoxy-5-ketoglucarate hydro-lyase (decarboxylating)." Methods Enzymol 42;272-6. PMID: 237186

Gulick00: Gulick AM, Hubbard BK, Gerlt JA, Rayment I (2000). "Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli." Biochemistry 2000;39(16);4590-602. PMID: 10769114

Gulick01: Gulick AM, Hubbard BK, Gerlt JA, Rayment I (2001). "Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli." Biochemistry 40(34);10054-62. PMID: 11513584

Gulick98: Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I (1998). "Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida." Biochemistry 37(41);14358-68. PMID: 9772161

Hubbard98: Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA (1998). "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli." Biochemistry 1998;37(41);14369-75. PMID: 9772162

Jeffcoat69a: Jeffcoat R, Hassall H, Dagley S (1969). "Purification and properties of D-4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating)." Biochem J 115(5);977-83. PMID: 4982840

Jeffcoat75: Jeffcoat R (1975). "Studies on the subunit structure of 4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating) from Pseudomonas acidovorans." Biochem J 145(2);305-9. PMID: 1156361

Johnsen09: Johnsen U, Dambeck M, Zaiss H, Fuhrer T, Soppa J, Sauer U, Schonheit P (2009). "D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii." J Biol Chem 284(40);27290-303. PMID: 19584053

Koo74: Koo PH, Adams E (1974). "Alpha-ketoglutaric semialdehyde dehydrogenase of Pseudomonas. Properties of the separately induced isoenzymes." J Biol Chem 249(6);1704-16. PMID: 4206401

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

Palmer96: Palmer D.R.J., Gerlt J.A. (1996). "Evolution of enzymatic activities: Multiple pathways for generating and partitioning a common enolic intermediate by glucarate dehydratase from Pseudomonas putida." J. Am. Chem. Soc. 118, 10323-10324.

Palmer98: Palmer DR, Hubbard BK, Gerlt JA (1998). "Evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (D)-glucarate dehydratase from Pseudomonas putida." Biochemistry 37(41);14350-7. PMID: 9772160

Watanabe12: Watanabe S, Morimoto D, Fukumori F, Shinomiya H, Nishiwaki H, Kawano-Kawada M, Sasai Y, Tozawa Y, Watanabe Y (2012). "Identification and characterization of D-hydroxyproline dehydrogenase and Delta1-pyrroline-4-hydroxy-2-carboxylate deaminase involved in novel L-hydroxyproline metabolism of bacteria: metabolic convergent evolution." J Biol Chem 287(39);32674-88. PMID: 22833679


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC14B.