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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Pathway: CMP-KDO biosynthesis I

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

Locations of Mapped Genes:

Genetic Regulation Schematic: ?

Synonyms: 3-deoxy-D-manno-octulosonate biosynthesis

Superclasses: Biosynthesis Carbohydrates Biosynthesis Polysaccharides Biosynthesis CMP-KDO Biosynthesis
Biosynthesis Carbohydrates Biosynthesis Sugars Biosynthesis Sugar Nucleotides Biosynthesis CMP-sugar Biosynthesis

Summary:
3-deoxy-D-manno-octulosonate (KDO) is a component of bacterial lipopolysaccharide (LPS). The majority of Gram-negative bacteria LPS contain at least one 2-keto 3-deoxy-D-manno-octulosonate molecule.

This pathway starts with the isomerization of D-ribulose 5-phosphate to D-arabinose 5-phosphate, followed by its conversion to 3-deoxy-D-manno-octulosonate 8-phosphate (KDOP), which is catalyzed by a family of enzymes called 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDOPS). The bacterial KDOPSs have been grouped in two classes, and plant KDOPSs belong to a third class [Wu04a].

In the next step the phosphate group is removed from 3-deoxy-D-manno-octulosonate 8-phosphate, generating KDO. The last step of the pathway is the activation of KDO to CMP-3-deoxy-D-manno-octulosonate.

Superpathways: superpathway of lipopolysaccharide biosynthesis , superpathway of (KDO)2-lipid A biosynthesis

Credits:
Created 15-Feb-2006 by Caspi R , SRI International


References

Wu04a: 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

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

Airoldi10: Airoldi C, Sommaruga S, Merlo S, Sperandeo P, Cipolla L, Polissi A, Nicotra F (2010). "Targeting bacterial membranes: NMR spectroscopy characterization of substrate recognition and binding requirements of D-arabinose-5-phosphate isomerase." Chemistry 16(6);1897-902. PMID: 20039350

Asojo01: Asojo O, Friedman J, Adir N, Belakhov V, Shoham Y, Baasov T (2001). "Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor." Biochemistry 40(21);6326-34. PMID: 11371194

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

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Badger05: Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ (2005). "Structural analysis of a set of proteins resulting from a bacterial genomics project." Proteins 60(4);787-96. PMID: 16021622

Bateman99: Bateman A (1999). "The SIS domain: a phosphosugar-binding domain." Trends Biochem Sci 24(3);94-5. PMID: 10203754

Bigham84: Bigham EC, Gragg CE, Hall WR, Kelsey JE, Mallory WR, Richardson DC, Benedict C, Ray PH (1984). "Inhibition of arabinose 5-phosphate isomerase. An approach to the inhibition of bacterial lipopolysaccharide biosynthesis." J Med Chem 27(6);717-26. PMID: 6429331

Biswas09: Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV (2009). "The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase." J Biol Chem 284(44);30594-603. PMID: 19726684

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Cieslewicz97: Cieslewicz M, Vimr E (1997). "Reduced polysialic acid capsule expression in Escherichia coli K1 mutants with chromosomal defects in kpsF." Mol Microbiol 26(2);237-49. PMID: 9383150

DAniello05: D'Aniello S, Spinelli P, Ferrandino G, Peterson K, Tsesarskia M, Fisher G, D'Aniello A (2005). "Cephalopod vision involves dicarboxylic amino acids: D-aspartate, L-aspartate and L-glutamate." Biochem J 386(Pt 2);331-40. PMID: 15491279

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

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

Fujishima02: Fujishima H, Nishimura A, Wachi M, Takagi H, Hirasawa T, Teraoka H, Nishimori K, Kawabata T, Nishikawa K, Nagai K (2002). "kdsA mutations affect FtsZ-ring formation in Escherichia coli K-12." Microbiology 148(Pt 1);103-12. PMID: 11782503

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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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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