Escherichia coli K-12 substr. MG1655 Pathway: GDP-L-fucose biosynthesis I (from GDP-D-mannose)

Pathway diagram: GDP-L-fucose biosynthesis I (from GDP-D-mannose)

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Synonyms: GDP-L-fucose biosynthesis I (de novo synthesis)

Superclasses: Biosynthesis Carbohydrates Biosynthesis Sugars Biosynthesis Sugar Nucleotides Biosynthesis GDP-sugar Biosynthesis

General Background

L-fucose is an important monosaccharide found in a diverse array of organisms. It is a carbohydrate component of bacterial lipopolysaccharides, mammalian and plant glycoproteins and various plant cell wall polysaccharides. Fucosylation is performed by fucosyltransferases which require the activated form GDP-L-fucose as the donor substrate. The formation of GDP-L-fucose occurs via two routes, a de novo synthesis route from GDP-α-D-mannose (this pathway), and a eukaryotic salvage pathway leading to the formation of UDP-fucose from free L-fucose (see GDP-L-fucose biosynthesis II (from L-fucose)).

The de novo synthesis of GDP-L-fucose from GDP-D-mannose comprises three catalytic steps: a 4,6-dehydration, a 3,5-epimerization, and a 4-reduction. The first reaction step is catalyzed by GDP-mannose 4,6-dehydratase, which involves the formation of the intermediate GDP-4-dehydro-6-deoxy-D-mannose. This compound is also a common intermediate in the synthesis of other bacterial deoxyhexoses derived from GDP-D-mannose (see MetaCyc pathways GDP-6-deoxy-D-talose biosynthesis GDP-D-perosamine biosynthesis GDP-D-rhamnose biosynthesis and GDP-L-colitose biosynthesis). In bacteria (including E. coli), fungi, plants and humans, the second and third reactions have been shown to be catalyzed by a single bifunctional polypeptide, GDP-fucose synthase [Nakayama03, Sullivan98, Tonetti96, Ren10].

In the Enterobacteriaceae colanic acid (M antigen) is a polyanionic extracellular heteropolysaccharide containing a repeat unit with D-glucose, L-fucose, D-galactose, and D-glucuronate sugars that are nonstoichiometrically decorated with O-acetyl and pyruvate side chains [Grant69, Garegg71]. The sugars must be activated in the form of nucleotide sugars (such as GDP-L-fucose) before their assembly [Stevenson96, Stout96] (see pathway COLANSYN-PWY). Colanic acid biosynthesis has been linked to a cluster of 19 wca genes that includes wcaG (fcl) encoding GDP-fucose synthase [Stevenson96, Andrianopoulos98].

About This Pathway

L-fucose is biosynthesized as the sugar nucleotide GDP-L-fucose. Its biosynthesis from GDP-D-mannose begins with dehydration of this compound to GDP-4-dehydro-6-deoxy-D-mannose by the product of gene gmd. Then the bifunctional GDP-fucose synthase catalyzes the two-step (epimerase/reductase) synthesis of GDP-fucose from GDP-4-dehydro-6-deoxy-D-mannose via a GDP-4-dehydro-6-L-deoxygalactose intermediate [Andrianopoulos98]. The overall reaction is defined by EC and is carried out at a single active site on the enzyme [Lau08].

This pathway requires NADPH as a reducing cofactor. Overexpression of endogenous NADPH-regenerating enzymes in recombinant E. coli increased GDP-L-fucose production under optimized conditions [Lee11a]. In another study, overexpression of inosine-guanosine kinase encoded by gene gsk led to a significant improvement of GDP-L-fucose production. This was attributed to the increased level of intracellular GMP as a source of GTP which is required for this pathway (as shown in the pathway link to GDP-mannose biosynthesis) [Lee12].

Superpathways: colanic acid building blocks biosynthesis

Last-Curated ? 25-Jan-2013 by Fulcher C , SRI International


Andrianopoulos98: Andrianopoulos K, Wang L, Reeves PR (1998). "Identification of the fucose synthetase gene in the colanic acid gene cluster of Escherichia coli K-12." J Bacteriol 1998;180(4);998-1001. PMID: 9473059

Garegg71: Garegg PJ, Lindberg B, Onn T, Sutherland IW (1971). "Comparative structural studies on the M-antigen from Salmonella typhimurium. Escherichia coli and Aerobacter cloacae." Acta Chem Scand 25(6);2103-8. PMID: 4941627

Grant69: Grant WD, Sutherland IW, Wilkinson JF (1969). "Exopolysaccharide colanic acid and its occurrence in the Enterobacteriaceae." J Bacteriol 100(3);1187-93. PMID: 4902806

Lau08: Lau ST, Tanner ME (2008). "Mechanism and active site residues of GDP-fucose synthase." J Am Chem Soc 130(51);17593-602. PMID: 19053199

Lee11a: Lee WH, Chin YW, Han NS, Kim MD, Seo JH (2011). "Enhanced production of GDP-L-fucose by overexpression of NADPH regenerator in recombinant Escherichia coli." Appl Microbiol Biotechnol 91(4);967-76. PMID: 21538115

Lee12: Lee WH, Shin SY, Kim MD, Han NS, Seo JH (2012). "Modulation of guanosine nucleotides biosynthetic pathways enhanced GDP-L-fucose production in recombinant Escherichia coli." Appl Microbiol Biotechnol 93(6);2327-34. PMID: 22159740

Nakayama03: Nakayama K, Maeda Y, Jigami Y (2003). "Interaction of GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase with GDP-mannose-4,6-dehydratase stabilizes the enzyme activity for formation of GDP-fucose from GDP-mannose." Glycobiology 13(10);673-80. PMID: 12881408

Ren10: Ren Y, Perepelov AV, Wang H, Zhang H, Knirel YA, Wang L, Chen W (2010). "Biochemical characterization of GDP-L-fucose de novo synthesis pathway in fungus Mortierella alpina." Biochem Biophys Res Commun 391(4);1663-9. PMID: 20035716

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

Stout96: Stout V (1996). "Identification of the promoter region for the colanic acid polysaccharide biosynthetic genes in Escherichia coli K-12." J Bacteriol 178(14);4273-80. PMID: 8763957

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

Tonetti96: Tonetti M, Sturla L, Bisso A, Benatti U, De Flora A (1996). "Synthesis of GDP-L-fucose by the human FX protein." J Biol Chem 271(44);27274-9. PMID: 8910301

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

Albermann01: Albermann C, Piepersberg W, Wehmeier UF (2001). "Synthesis of the milk oligosaccharide 2'-fucosyllactose using recombinant bacterial enzymes." Carbohydr Res 334(2);97-103. PMID: 11502265

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

Byun07: Byun SG, Kim MD, Lee WH, Lee KJ, Han NS, Seo JH (2007). "Production of GDP-L-fucose, L-fucose donor for fucosyloligosaccharide synthesis, in recombinant Escherichia coli." Appl Microbiol Biotechnol 74(4);768-75. PMID: 17111133

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

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 240:1926-1931. PMID: 14299611

Ginsburg61: Ginsburg V (1961). "Studies on the biosynthesis of guanosine diphosphate L-fucose." J Biol Chem 236;2389-93. PMID: 13705522

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Menon99: Menon S, Stahl M, Kumar R, Xu GY, Sullivan F (1999). "Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli." J Biol Chem 274(38);26743-50. PMID: 10480878

Rizzi98: Rizzi M, Tonetti M, Vigevani P, Sturla L, Bisso A, Flora AD, Bordo D, Bolognesi M (1998). "GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily." Structure 6(11);1453-65. PMID: 9817848

Rosano00: Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M (2000). "Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants." J Mol Biol 303(1);77-91. PMID: 11021971

Somers98: Somers WS, Stahl ML, Sullivan FX (1998). "GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site." Structure 6(12);1601-12. PMID: 9862812

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

Tonetti98: Tonetti M, Rizzi M, Vigevani P, Sturla L, Bisso A, De Flora A, Bolognesi M (1998). "Preliminary crystallographic investigations of recombinant GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from E. coli." Acta Crystallogr D Biol Crystallogr 54 ( Pt 4);684-6. PMID: 9761875

Tonetti98a: Tonetti M, Sturla L, Bisso A, Zanardi D, Benatti U, De Flora A (1998). "The metabolism of 6-deoxyhexoses in bacterial and animal cells." Biochimie 80(11);923-31. PMID: 9893952

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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