Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Pathway: L-rhamnose degradation III

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: diketo-hydrolase pathway

Superclasses: Degradation/Utilization/Assimilation Carbohydrates Degradation Sugars Degradation L-rhamnose Degradation

Some taxa known to possess this pathway include ? : Sphingomonas sp. SKA58

Expected Taxonomic Range: Bacteria

Summary:
General Background

L-rhamnose is a 6-deoxy-aldohexose that occurs in nature. Some fungi and bacteria posess an L-rhamnose degradation pathway that involves non-phosphorylated intermediates (see pathway L-rhamnose degradation II), analogous to the Entner-Doudoroff pathway II (non-phosphorylative). Pathway L-rhamnose degradation II is in contrast to the known bacterial L-rhamnose degradation pathway which involves phosphorylated intermediates (see L-rhamnose degradation I). Genes encoding enzymes of pathway L-rhamnose degradation II in Scheffersomyces stipitis CBS 6054 (previously known as Pichia stipitis), Debaryomyces hansenii hansenii CBS767 and Azotobacter vinelandii NBRC 102612 have been cloned, expressed and their products functionally characterized. Phylogenetic studies of the fungal and bacterial 2-keto-3-deoxy-L-rhamnoate aldolases (L-KDR aldolases) suggested that they are unerelated evolutionarily. Their respective non-phosphorylative L-rhamnose degradation pathways appear to have evolved independently and are the result of convergent evolution (in [Watanabe08a] and in [Watanabe09]). In Sphingomonas sp. SKA58, a variation of this non-phosphorylative pathway was demonstrated in which 2-dehydro-3-deoxy-L-rhamnonate is oxidized to L-2,4-diketo-3-deoxyrhamnonate, followed by hydrolysis of this compound to pyruvate and (S)-lactate (L-lactate) [Watanabe09] (this pathway).

About This Pathway

The first reaction in this pathway shows the spontaneous conversion of the pyranose ring form of L-rhamnose to its furanose ring form L-rhamnofuranose (the α and β anomers of each form are not specified here). This reaction is shown because the reaction that follows is catalyzed by L-rhamnose 1-dehydrogenase (EC 1.1.1.173) which specifies L-rhamnofuranose as a substrate and L-rhamnono-1,4-lactone (L-rhamnono-γ-lactone) as a product. As noted in [Dahms72], a δ-lactone (1,5-lactone) would be produced by a pyranose ring form).

In Sphingomonas sp. SKA58 the first three enzymatic reactions are shared with pathway L-rhamnose degradation II, but the last two reactions of the pathway were shown to be catalyzed by L-2-keto-3-deoxyrhamnoate 4-dehydrogenase and L-2,4-diketo-3-deoxyrhamnoate hydrolase encoded by genes lra5 and lra6, respectively. pyruvate and (S)-lactate (L-lactate) are the end products of this variant and (S)-lactaldehyde is not produced [Watanabe09].

Variants: L-rhamnose degradation I , L-rhamnose degradation II

Credits:
Created 08-Feb-2011 by Fulcher CA , SRI International


References

Dahms72: Dahms AS, Anderson RL (1972). "D-Fucose metabolism in a pseudomonad. I. Oxidation of D-fucose to D-fucono- -lactone by a D-aldohexose dehydrogenase." J Biol Chem 247(7);2222-7. PMID: 4335867

Watanabe08a: Watanabe S, Saimura M, Makino K (2008). "Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism." J Biol Chem 283(29);20372-82. PMID: 18505728

Watanabe09: Watanabe S, Makino K (2009). "Novel modified version of nonphosphorylated sugar metabolism--an alternative L-rhamnose pathway of Sphingomonas sp." FEBS J 276(6);1554-67. PMID: 19187228

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

Ewaschuk05: Ewaschuk JB, Naylor JM, Zello GA (2005). "D-lactate in human and ruminant metabolism." J Nutr 135(7);1619-25. PMID: 15987839

Franks87: Franks F. (1987). "Physical chemistry of small carbohydrates-equilibrium solution properties." Pure & Appl. Chem. Vol. 59, No. 9, pp. 1189-1202.

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

Ma98a: Ma B, Schaefer HF 3rd, Allinger NL (1998). "Theoretical studies of the potential energy surfaces and compositions of the D-also- and D-ketohexoses." J. Am. Chem. Soc. 120, 3411-3422.

Rakus08: Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA (2008). "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase." Biochemistry 47(38);9944-54. PMID: 18754693

Rigo76: Rigo LU, Nakano M, Veiga LA, Feingold DS (1976). "L-rhamnose dehydrogenase of Pullularia pullulans." Biochimica et Biophysica Acta 445, 286-293.

Ryu04: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C (2004). "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." J Biol Chem 279(24);25544-8. PMID: 15060078


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 Fri Nov 28, 2014, BIOCYC13B.