MetaCyc Pathway: CMP-3-deoxy-D-manno-octulosonate biosynthesis II (from D-arabinose 5-phosphate)

Enzyme View:

Pathway diagram: CMP-3-deoxy-D-manno-octulosonate biosynthesis II (from D-arabinose 5-phosphate)

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: CMP-Kdo biosynthesis II (from D-arabinose 5-phosphate)

Superclasses: Biosynthesis Carbohydrates Biosynthesis Polysaccharides Biosynthesis CMP-3-deoxy-D-manno-octulosonate Biosynthesis
Biosynthesis Carbohydrates Biosynthesis Sugars Biosynthesis Sugar Nucleotides Biosynthesis CMP-sugar Biosynthesis

Some taxa known to possess this pathway include ? : Arabidopsis thaliana col , Pisum sativum , Solanum lycopersicum , Zea mays

Expected Taxonomic Range: Chlamydiae/Verrucomicrobia group , Cyanobacteria , Proteobacteria , Viridiplantae

General Background

The acid sugar 3-deoxy-D-manno-octulosonate (KDO), in addition to being an important component of the lipopolysaccharides of Gram-negative bacteria, is also a component of the rhamnogalacturonan II (RGII) pectin fraction of the primary cell walls of most higher plants, including dicots, monocots and gymnosperms [Albersheim94, Edashige98, York85, Shin97a]. To date, the specific contribution of KDO to RGII function, as well as the pathway leading to the synthesis, activation and incorporation of KDO into this polysaccharide remain largely unknown. In order to be incorporated into cell wall polymers, KDO requires to be activated; free KDO cannot be directly incorporated. This activation occurs through the unusual coupling of KDO to the monophosphonucleotide CMP, rather than to the more common diphosphonucleotides [Royo00].

Enzymatic steps:

The first two steps of this pathway deal with the formation of KDO from D-arabinose 5-phosphate. The first reaction is catalyzed by a family of genes called KDOPS (3-deoxy-D-manno-octulosonate-8-phosphate synthase). The bacterial KDOPSs are grouped in two classes: Class I and Class II. It has been proposed that the plant KDOPSs belong to a third class (stable against thermal denaturation, dimeric and non-metallo-enzymes) [Wu04]. No plant enzymes have yet been shown to catalyze reaction EC [Wu04]. The last step of the pathway corresponds to the activation step of KDO. This step is catalyzed by a 3-deoxy-manno-octulosonate cytidylyltransferase called CMP-3-deoxy-D-manno-2-octulosonate synthetase (CKS). To date the only characterized representative of plant CKSs is the maize ZmCKS [Royo00a].

Note on this pathway variant:

This pathway is almost identical to its variant CMP-3-deoxy-D-manno-octulosonate biosynthesis I. The difference lies in the first step. Indeed, in plants (represented in this pathway), the origin of D-arabinose 5-phosphate is unknown and it was therefore judged inappropriate to include the isomerisation step of D-ribulose 5-phosphate into D-arabinose 5-phosphate in this pathway. This conversion, however, has not been disproved; but remains to be ascertained in plants.

Citations: [Matsuura03, Delmas03]

Variants: CMP-3-deoxy-D-manno-octulosonate biosynthesis I , CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis

Unification Links: AraCyc:PWY-5111

Created 14-Feb-2006 by Tissier C , TAIR


Albersheim94: Albersheim P, An J, Freshour G, Fuller MS, Guillen R, Ham KS, Hahn MG, Huang J, O'Neill M, Whitcombe A (1994). "Structure and function studies of plant cell wall polysaccharides." Biochem Soc Trans 22(2);374-8. PMID: 7958328

Delmas03: Delmas F, Petit J, Joubes J, Seveno M, Paccalet T, Hernould M, Lerouge P, Mouras A, Chevalier C (2003). "The gene expression and enzyme activity of plant 3-deoxy-D-manno-2-octulosonic acid-8-phosphate synthase are preferentially associated with cell division in a cell cycle-dependent manner." Plant Physiol 133(1);348-60. PMID: 12970500

Edashige98: Edashige Y, Ishii T (1998). "Rhamnogalacturonan II from cell walls of Cryptomeria japonica." Phytochemistry 49(3);681-90. PMID: 9779594

Matsuura03: Matsuura K, Miyagawa I, Kobayashi M, Ohta D, Matoh T (2003). "Arabidopsis 3-deoxy-D-manno-oct-2-ulosonate-8-phosphate synthase: cDNA cloning and expression analyses." J Exp Bot 54(388);1785-7. PMID: 12754267

Royo00: Royo J, Gimez E, Hueros G (2000). "CMP-KDO synthetase: a plant gene borrowed from gram-negative eubacteria." Trends Genet 16(10);432-3. PMID: 11050325

Royo00a: Royo J, Gomez E, Hueros G (2000). "A maize homologue of the bacterial CMP-3-deoxy-D-manno-2-octulosonate (KDO) synthetases. Similar pathways operate in plants and bacteria for the activation of KDO prior to its incorporation into outer cellular envelopes." J Biol Chem 275(32);24993-9. PMID: 10829033

Shin97a: Shin, K.-S., Kiyohara, H., Matsumoto, T., Yamada, H. (1997). "Rhamnogalacturonan II from the leaves of Panax ginseng C.A. Meyer as a macrophage Fc receptor expression-enhancing polysaccharide." Carbohydr. Res. 300:239-249.

Wu04: Wu J, Patel MA, Sundaram AK, Woodard RW (2004). "Functional and biochemical characterization of a recombinant Arabidopsis thaliana 3-deoxy-D-manno-octulosonate 8-phosphate synthase." Biochem J 381(Pt 1);185-93. PMID: 15070398

York85: York, W.S., Davill, A.G., McNeil, M., Albersheim, P. (1985). "3-deoxy-D-manno-2-octulosonic acid (KDO) is a component of rhamnogalacturonan II, a pectic polysaccharide in the primary cell walls of plants." Carbohydr. Res. 139:109-126.

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

Baasov93: Baasov T, Sheffer-Dee-Noor S, Kohen A, Jakob A, Belakhov V (1993). "Catalytic mechanism of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase. The use of synthetic analogues to probe the structure of the putative reaction intermediate." Eur J Biochem 217(3);991-9. PMID: 8223657

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

Dotson93: Dotson GD, Nanjappan P, Reily MD, Woodard RW (1993). "Stereochemistry of 3-deoxyoctulosonate 8-phosphate synthase." Biochemistry 32(46);12392-7. PMID: 8241128

Dotson95: Dotson GD, Dua RK, Clemens JC, Wooten EW, Woodard RW (1995). "Overproduction and one-step purification of Escherichia coli 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase and oxygen transfer studies during catalysis using isotopic-shifted heteronuclear NMR." J Biol Chem 270(23);13698-705. PMID: 7775423

Furdui05: Furdui CM, Sau AK, Yaniv O, Belakhov V, Woodard RW, Baasov T, Anderson KS (2005). "The use of (E)- and (Z)-phosphoenol-3-fluoropyruvate as mechanistic probes reveals significant differences between the active sites of KDO8P and DAHP synthases." Biochemistry 44(19);7326-35. PMID: 15882071

Ghalambor66: Ghalambor MA, Heath EC (1966). "The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. IV. Purification and properties of cytidine monophosphate 3-deoxy-d-manno-octulosonate synthetase." J Biol Chem 1966;241(13);3216-21. PMID: 5330266

Goldman85: Goldman RC, Kohlbrenner WE (1985). "Molecular cloning of the structural gene coding for CTP:CMP-3-deoxy-manno-octulosonate cytidylyltransferase from Escherichia coli K-12." J Bacteriol 163(1);256-61. PMID: 2989246

Hedstrom88: Hedstrom L, Abeles R (1988). "3-Deoxy-D-manno-octulosonate-8-phosphate synthase catalyzes the C-O bond cleavage of phosphoenolpyruvate." Biochem Biophys Res Commun 157(2);816-20. PMID: 2904815

Heyes09: Heyes DJ, Levy C, Lafite P, Roberts IS, Goldrick M, Stachulski AV, Rossington SB, Stanford D, Rigby SE, Scrutton NS, Leys D (2009). "Structure-based mechanism of CMP-2-keto-3-deoxymanno-octulonic acid synthetase: convergent evolution of a sugar-activating enzyme with DNA/RNA polymerases." J Biol Chem 284(51);35514-23. PMID: 19815542

Howe03: Howe DL, Sundaram AK, Wu J, Gatti DL, Woodard RW (2003). "Mechanistic insight into 3-deoxy-D-manno-octulosonate-8-phosphate synthase and 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase utilizing phosphorylated monosaccharide analogues." Biochemistry 42(17);4843-54. PMID: 12718525

Kohen92: Kohen A, Jakob A, Baasov T (1992). "Mechanistic studies of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase from Escherichia coli." Eur J Biochem 208(2);443-9. PMID: 1521535

Kohlbrenner85: Kohlbrenner WE, Fesik SW (1985). "Determination of the anomeric specificity of the Escherichia coli CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase by 13C NMR spectroscopy." J Biol Chem 260(27);14695-700. PMID: 2997221

Kohlbrenner87: Kohlbrenner WE, Nuss MM, Fesik SW (1987). "31P and 13C NMR studies of oxygen transfer during catalysis by 3-deoxy-D-manno-octulosonate cytidylyltransferase from Escherichia coli." J Biol Chem 262(10);4534-7. PMID: 3031027

Krosky02: Krosky DJ, Alm R, Berg M, Carmel G, Tummino PJ, Xu B, Yang W (2002). "Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase is a zinc-metalloenzyme." Biochim Biophys Acta 1594(2);297-306. PMID: 11904225

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

Li05: Li Z, Sau AK, Furdui CM, Anderson KS (2005). "Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy-d-manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisecond time range." Anal Biochem 343(1);35-47. PMID: 15979047

Liang98: Liang PH, Lewis J, Anderson KS, Kohen A, D'Souza FW, Benenson Y, Baasov T (1998). "Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate." Biochemistry 37(46);16390-9. PMID: 9819231

Ray80: Ray PH (1980). "Purification and characterization of 3-deoxy-D-manno-octulosonate 8-phosphate synthetase from Escherichia coli." J Bacteriol 1980;141(2);635-44. PMID: 6988389

Ray80a: Ray PH, Benedict CD (1980). "Purification and characterization of specific 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Escherichia coli B." J Bacteriol 1980;142(1);60-8. PMID: 6246070

Ray81: Ray PH, Benedict CD, Grasmuk H (1981). "Purification and characterization of cytidine 5'-triphosphate:cytidine 5'-monophosphate-3-deoxy-D-manno-octulosonate cytidylyltransferase." J Bacteriol 1981;145(3);1273-80. PMID: 6259128

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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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