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MetaCyc Pathway: GDP-D-rhamnose biosynthesis
Traceable author statement to experimental supportInferred from experiment

Enzyme View:

Pathway diagram: GDP-D-rhamnose 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: GDP-α-D-rhamnose biosynthesis

Superclasses: BiosynthesisCarbohydrates BiosynthesisSugars BiosynthesisSugar Nucleotides BiosynthesisGDP-sugar Biosynthesis
BiosynthesisCell Structures BiosynthesisLipopolysaccharide BiosynthesisO-Antigen Biosynthesis

Some taxa known to possess this pathway include : Aneurinibacillus thermoaerophilus L420-91, Burkholderia cepacia, Campylobacter fetus, Helicobacter pylori, Pseudomonas aeruginosa, Pseudomonas syringae, Xanthomonas campestris

Expected Taxonomic Range: Firmicutes, Proteobacteria

Although the deoxyhexose rhamnose is found in glycoconjugates of bacteria and plants (but not animals), the rare D-isoform is found only in the outer cell surface of bacteria. α-D-rhamnose is a constituent of the lipopolysaccharide of the plant pathogens Xanthomonas campestris and Pseudomonas syringae, and animal pathogens Pseudomonas aeruginosa, Burkholderia cepacia, Campylobacter fetus and Helicobacter pylori [Webb04, Maki02, Kneidinger01a] and reviewed in [Rocchetta99]).

α-D-rhamnose is the nucleotide-activated donor of D-rhamnose units to the A-band lipopolysaccharide in Pseudomonas aeruginosa. This gram-negative organism synthesizes two variants of lipopolysaccharide, designated A-band and B-band. The O-antigen of the A-band lipopolysaccharide is a homopolymer of D-rhamnose residues arranged in repeating trisaccharide units, whereas the O-antigen of the B-band is a heteropolymer containing many different monosaccharides. Pseudomonas aeruginosa TAU-5 is a pathogen that causes opportunistic infections in animals and plants, and the lipopolysaccharide of the outer membrane contributes to its virulence. In [Webb04], in [Maki02], and reviewed in [Rocchetta99]). The biosynthesis of O-antigen in Escherichia coli is shown in MetaCyc pathway O-antigen building blocks biosynthesis (E. coli), although its composition is different from that of Pseudomonas aeruginosa TAU-5.

Aneurinibacillus thermoaerophilus L420-91 also has D-rhamnose residues on its surface. However, they are in the S-layer, a crystalline protein layer found on the outermost cell surface of many bacteria and archaea. The S-layer of this gram-positive, thermophilic bacterium is glycosylated with identical repeats of D-rhamnose and 3-acetamido-3,6-dideoxy-α-D-galactopyranose units (in [Kneidinger01a]).

In this pathway, the final product is the D-rhamnose donor, GDP-D-rhamnose. It is synthesized from GDP-D-mannose in two steps, involving a dehydratase and a reductase. The precursor GDP-4-keto-6-deoxy-D-mannose is also a common intermediate for the synthesis of other GDP-monodeoxyhexoses such as: GDP-L-fucose, GDP-4-deoxy-D-talose, and GDP-deoxy-D-altrose; the GDP-dideoxyhexose GDP-colitose; and the GDP-dideoxy amino sugar GDP-D-perosamine (in [Webb04], in [Maki02], and in [Kneidinger01a]). The biosynthesis of the starting substrate, GDP-D-mannose, is shown in the pathway link.

Citations: [Overbeek98]

Superpathways: superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis

Revised 10-Jan-2007 by Fulcher CA, SRI International


Kneidinger01a: Kneidinger B, Graninger M, Adam G, Puchberger M, Kosma P, Zayni S, Messner P (2001). "Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T." J Biol Chem 276(8);5577-83. PMID: 11096116

Maki02: Maki M, Jarvinen N, Rabina J, Roos C, Maaheimo H, Renkonen R, , (2002). "Functional expression of Pseudomonas aeruginosa GDP-4-keto-6-deoxy-D-mannose reductase which synthesizes GDP-rhamnose." Eur J Biochem 269(2);593-601. PMID: 11856318

Overbeek98: Overbeek, R, Larsen, N, Selkov, EE, Maltsev, M "The WIT Database." 1998 WWW URL http://www.cme.msu.edu/WIT/.

Rocchetta99: Rocchetta HL, Burrows LL, Lam JS (1999). "Genetics of O-antigen biosynthesis in Pseudomonas aeruginosa." Microbiol Mol Biol Rev 63(3);523-53. PMID: 10477307

Webb04: Webb NA, Mulichak AM, Lam JS, Rocchetta HL, Garavito RM (2004). "Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway." Protein Sci 13(2);529-39. PMID: 14739333

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

Albermann01: Albermann C, Piepersberg W (2001). "Expression and identification of the RfbE protein from Vibrio cholerae O1 and its use for the enzymatic synthesis of GDP-D-perosamine." Glycobiology 11(8);655-61. PMID: 11479276

Bonin97: Bonin CP, Potter I, Vanzin GF, Reiter WD (1997). "The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP-D-mannose-4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP-L-fucose." Proc Natl Acad Sci U S A 94(5);2085-90. PMID: 9050909

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

Chen03b: Chen S, Huang X, Zhou X, Bai L, He J, Jeong KJ, Lee SY, Deng Z (2003). "Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex." Chem Biol 10(11);1065-76. PMID: 14652074

Elbein65: Elbein AD, Heath EC (1965). "The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-d-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose." J Biol Chem 240;1926-31. PMID: 14299611

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

Mulichak02: Mulichak AM, Bonin CP, Reiter WD, Garavito RM (2002). "Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity." Biochemistry 41(52);15578-89. PMID: 12501186

Somoza00: Somoza JR, Menon S, Schmidt H, Joseph-McCarthy D, Dessen A, Stahl ML, Somers WS, Sullivan FX (2000). "Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose." Structure Fold Des 2000;8(2);123-35. PMID: 10673432

Sturla97: Sturla L, Bisso A, Zanardi D, Benatti U, De Flora A, Tonetti M (1997). "Expression, purification and characterization of GDP-D-mannose 4,6-dehydratase from Escherichia coli." FEBS Lett 1997;412(1);126-30. PMID: 9257704

Sullivan98: Sullivan FX, Kumar R, Kriz R, Stahl M, Xu GY, Rouse J, Chang XJ, Boodhoo A, Potvin B, Cumming DA (1998). "Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro." J Biol Chem 273(14);8193-202. PMID: 9525924

Suzuki02e: Suzuki N, Nakano Y, Yoshida Y, Nezu T, Terada Y, Yamashita Y, Koga T (2002). "Guanosine diphosphate-4-keto-6-deoxy-d-mannose reductase in the pathway for the synthesis of GDP-6-deoxy-d-talose in Actinobacillus actinomycetemcomitans." Eur J Biochem 269(23);5963-71. PMID: 12444986

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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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