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MetaCyc Pathway: UDP-D-xylose biosynthesis
Inferred from experiment

Enzyme View:

Pathway diagram: UDP-D-xylose biosynthesis

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: UDP-xylose biosynthesis, UDPXyl biosynthesis

Superclasses: BiosynthesisCarbohydrates BiosynthesisSugars BiosynthesisSugar Nucleotides BiosynthesisUDP-sugar Biosynthesis

Some taxa known to possess this pathway include : Arabidopsis thaliana col, Glycine max, Mus musculus, Nicotiana tabacum, Sinorhizobium meliloti 1021

Expected Taxonomic Range: Eukaryota, Rhizobiaceae

General Background

UDP-α-D-xylose is a nucleotide sugar involved in the synthesis of diverse plant cell wall hemicelluloses (xyloglucan, xylan) and minor plant metabolites. It is also required for the synthesis of glycoproteins, animal proteoglycans and fungal polysaccharides (for review see [Harper02]).

This Pathway in Plants:

In plants, the biosynthesis of UDP-α-D-xylose occurs both in the cytosol and in membrane-bound compartments. The major biosynthesis route occurs through the conversion of UDP-α-D-glucose (UDP-Glc). This conversion involves two enzymatic steps: the oxidation of UDP-α-D-glucose to UDP-α-D-glucuronate (UDP-GlcA) by a UDP-glucose dehydrogenase and the subsequent decarboxylation to UDP-α-D-xylose by a UDP-glucuronate decarboxylase. Regulation of these enzymes is important in understanding the partitioning of carbon into hemicellulose away from starch, sucrose and cellulose, which are irreversible processes. Biochemical evidence suggests that the timing of expression of UDP-glucose dehydrogenase and to some extent that of UDP-glucuronate decarboxylase may control the flux of carbon into hemicellulose in vascular differentiating tissues.

Key Notes on the Enzymes:

In plants, two different types of UDP-Glc dehydrogenases have been identified so far: the first type, exemplified by the UDP-Glc dehydrogenase isolated from soybean nodules [Tenhaken96], has a unique catalytic activity towards UDP-Glc (EC; the second type exemplified by the mammalian-like tobacco dehydrogenase [Bindschedler05] has dual dehydrogenase activities towards UDP-Glc (EC and ethanol (EC Similarly, biochemical analysis of UDP-glucuronate decarboxylases suggests that this enzyme may come in different forms [Bindschedler05].

This Pathway in Bacteria:

There is also evidence for this pathway in plant-associated bacteria belonging to the family Rhizobiaceae. Rhizobia are soil bacteria that fix nitrogen in the root nodules of some leguminous plants. In Sinorhizobium meliloti 1021 an operon was identified that contains genes uxe and uxs1 encoding UDP-xylose 4-epimerase and UDP-xylose synthase 1, respectively. Data from real-time 1H-NMR spectroscopy demonstrated the conversion of UDP-α-D-glucuronate to UDP-α-D-xylose, and UDP-α-D-xylose to UDP-β-L-arabinopyranose. These UDP-sugars are then used for the biosynthesis of xylose-containing and arabinose-containing cell surface glycans. Their pathways and the roles that they play in nodulation are only beginning to be elucidated [Gu11].

Two orthologs of each gene encoding active enzymes were also identified in other rhizobial species including Rhizobium leguminosarum bv. viciae 3841 (loci R10559 and R10078 for uxe, R10560 and R10077 for uxs). These observations were cited in [Gu11] as unpublished data.

Superpathways: UDP-sugars interconversion

Subpathways: UDP-α-D-glucuronate biosynthesis (from UDP-glucose)

Unification Links: AraCyc:PWY-4821


Bindschedler05: Bindschedler LV, Wheatley E, Gay E, Cole J, Cottage A, Bolwell GP (2005). "Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue." Plant Mol Biol 57(2);285-301. PMID: 15821883

Gu11: Gu X, Lee SG, Bar-Peled M (2011). "Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase." Microbiology 157(Pt 1);260-9. PMID: 20847005

Harper02: Harper AD, Bar-Peled M (2002). "Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms." Plant Physiol 130(4);2188-98. PMID: 12481102

Pattathil05: Pattathil S, Harper AD, Bar-Peled M (2005). "Biosynthesis of UDP-xylose: characterization of membrane-bound AtUxs2." Planta 221(4);538-48. PMID: 15655675

Tenhaken96: Tenhaken R, Thulke O (1996). "Cloning of an enzyme that synthesizes a key nucleotide-sugar precursor of hemicellulose biosynthesis from soybean: UDP-glucose dehydrogenase." Plant Physiol 112(3);1127-34. PMID: 8938413

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

Arrecubieta94: Arrecubieta C, Lopez R, Garcia E (1994). "Molecular characterization of cap3A, a gene from the operon required for the synthesis of the capsule of Streptococcus pneumoniae type 3: sequencing of mutations responsible for the unencapsulated phenotype and localization of the capsular cluster on the pneumococcal chromosome." J Bacteriol 176(20);6375-83. PMID: 7929009

Baron72: Baron D, Wellmann E, Grisebach H (1972). "Purification and properties of an enzyme from cell suspension cultures of parsley catalyzing the synthesis of UDP-apiose and UDP-D-xylose from UDP-D-glucuronic acid." Biochim Biophys Acta 258(1);310-8. PMID: 4333589

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

Brett90: Brett C., Wladron K. "Physiology and biochemistry of plant cell walls." Topics in plant physiology, vol2. M. Black, J. Chapman (Eds.) 1990, pp. 4-57.

Garcia93: Garcia E, Garcia P, Lopez R (1993). "Cloning and sequencing of a gene involved in the synthesis of the capsular polysaccharide of Streptococcus pneumoniae type 3." Mol Gen Genet 239(1-2);188-95. PMID: 8510646

Grangeasse03: Grangeasse C, Obadia B, Mijakovic I, Deutscher J, Cozzone AJ, Doublet P (2003). "Autophosphorylation of the Escherichia coli protein kinase Wzc regulates tyrosine phosphorylation of Ugd, a UDP-glucose dehydrogenase." J Biol Chem 278(41);39323-9. PMID: 12851388

Hempel94: Hempel J, Perozich J, Romovacek H, Hinich A, Kuo I, Feingold DS (1994). "UDP-glucose dehydrogenase from bovine liver: primary structure and relationship to other dehydrogenases." Protein Sci 3(7);1074-80. PMID: 7920253

Jaenicke86: Jaenicke R, Rudolph R, Feingold DS (1986). "Dissociation and in vitro reconstitution of bovine liver uridine diphosphoglucose dehydrogenase. The paired subunit nature of the enzyme." Biochemistry 25(23);7283-7. PMID: 3099833

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

Lazarowski03: Lazarowski ER, Shea DA, Boucher RC, Harden TK (2003). "Release of cellular UDP-glucose as a potential extracellular signaling molecule." Mol Pharmacol 63(5);1190-7. PMID: 12695547

Lind99: Lind T, Falk E, Hjertson E, Kusche-Gullberg M, Lidholt K (1999). "cDNA cloning and expression of UDP-glucose dehydrogenase from bovine kidney." Glycobiology 9(6);595-600. PMID: 10336992

Matern77: Matern U, Grisebach H (1977). "UDP-apiose/UDP-xylose synthase. Subunit composition and binding studies." Eur J Biochem 74(2);303-12. PMID: 192551

Molhoj03: Molhoj M, Verma R, Reiter WD (2003). "The biosynthesis of the branched-chain sugar d-apiose in plants: functional cloning and characterization of a UDP-d-apiose/UDP-d-xylose synthase from Arabidopsis." Plant J 35(6);693-703. PMID: 12969423

Reiter01: Reiter WD, Vanzin GF (2001). "Molecular genetics of nucleotide sugar interconversion pathways in plants." Plant Mol Biol 47(1-2);95-113. PMID: 11554483

Schiller73: Schiller JG, Bowser AM, Feingold DS (1973). "Partial purification and properties of UDPG dehydrogenase from Escherichia coli." Biochim Biophys Acta 293(1);1-10. PMID: 4568129

Seifert04: Seifert GJ (2004). "Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside." Curr Opin Plant Biol 7(3);277-84. PMID: 15134748

Sennett12: Sennett NC, Kadirvelraj R, Wood ZA (2012). "Cofactor binding triggers a molecular switch to allosterically activate human UDP-α-D-glucose 6-dehydrogenase." Biochemistry 51(46);9364-74. PMID: 23106432

Shigeoka79: Shigeoka S, Nakano Y, Kitaoka S (1979). "The biosynthetic pathway of L-ascorbic acid in Euglena gracilis Z." J Nutr Sci Vitaminol (Tokyo) 25(4);299-307. PMID: 118242

Spicer98: Spicer AP, Kaback LA, Smith TJ, Seldin MF (1998). "Molecular cloning and characterization of the human and mouse UDP-glucose dehydrogenase genes." J Biol Chem 273(39);25117-24. PMID: 9737970

Stevenson96: Stevenson G, Andrianopoulos K, Hobbs M, Reeves PR (1996). "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid." J Bacteriol 1996;178(16);4885-93. PMID: 8759852

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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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