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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Pathway: ribose degradation

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

Locations of Mapped Genes:

Genetic Regulation Schematic: ?

Synonyms: ribose catabolism

Superclasses: Degradation/Utilization/Assimilation Carbohydrates Degradation Sugars Degradation

Summary:
D-ribose, which can serve as a total source of carbon and energy for E. coli, enters the cell via a high-affinity ABC transport system and hence in unphosphorylated form. The crystal structure of the periplasmic ribose binding protein of the ribose ABC transporter showed it to bind (and thus presumably to facilitate transport of) β-D-ribopyranose [Mowbray92]. ribose pyranase accelerates the conversion between the pyranose and furanose forms of β-D-ribose. Interconversion of the α- and β-anomers of D-ribofuranose is fast and spontaneous [Ryu04]. ribokinase then converts it to D-ribose 5-phosphate, an intermediate of the pentose phosphate pathway, and hence it flows through the pathways of central metabolism to satisfy the cell's need for precursor metabolites, reducing power, and metabolic energy.

Review: Mayer, C. and W. Boos, Hexose/Pentose and Hexitol/Pentitol Metabolism. EcoSal Module 3.4.1 [ECOSAL]

Credits:
Created 09-Sep-1994 by Riley M , Marine Biological Laboratory
Revised 09-Jun-2006 by Ingraham JL , UC Davis
Revised 06-Nov-2007 by Keseler I , SRI International


References

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Mowbray92: Mowbray SL, Cole LB (1992). "1.7 A X-ray structure of the periplasmic ribose receptor from Escherichia coli." J Mol Biol 225(1);155-75. PMID: 1583688

Ryu04: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C (2004). "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." J Biol Chem 279(24);25544-8. PMID: 15060078

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

Anderson69: Anderson A, Cooper RA (1969). "The significance of ribokinase for ribose utilization by Escherichia coli." Biochim Biophys Acta 177(1);163-5. PMID: 4889152

Andersson02: Andersson CE, Mowbray SL (2002). "Activation of ribokinase by monovalent cations." J Mol Biol 315(3);409-19. PMID: 11786021

Bell86: Bell AW, Buckel SD, Groarke JM, Hope JN, Kingsley DH, Hermodson MA (1986). "The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12." J Biol Chem 261(17);7652-8. PMID: 3011793

Bork93: Bork P, Sander C, Valencia A (1993). "Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases." Protein Sci 2(1);31-40. PMID: 8382990

Chuvikovsky06: Chuvikovsky DV, Esipov RS, Skoblov YS, Chupova LA, Muravyova TI, Miroshnikov AI, Lapinjoki S, Mikhailopulo IA (2006). "Ribokinase from E. coli: expression, purification, and substrate specificity." Bioorg Med Chem 14(18);6327-32. PMID: 16784868

Collier02: Collier J, Binet E, Bouloc P (2002). "Competition between SsrA tagging and translational termination at weak stop codons in Escherichia coli." Mol Microbiol 45(3);745-54. PMID: 12139620

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

Feng06a: Feng Y, Jiao W, Fu X, Chang Z (2006). "Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein." Protein Sci 15(6);1441-8. PMID: 16731978

Feng09c: Feng Y, Zhang M, Hu M, Zheng J, Jiao W, Chang Z (2009). "Disassembly intermediates of RbsD protein remain oligomeric despite the loss of an intact secondary structure." Sci China C Life Sci 52(11);997-1002. PMID: 19937196

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."

Hayes02: Hayes CS, Bose B, Sauer RT (2002). "Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli." Proc Natl Acad Sci U S A 99(6);3440-5. PMID: 11891313

Hope86: Hope JN, Bell AW, Hermodson MA, Groarke JM (1986). "Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase." J Biol Chem 261(17);7663-8. PMID: 3011794

Iida84: Iida A, Harayama S, Iino T, Hazelbauer GL (1984). "Molecular cloning and characterization of genes required for ribose transport and utilization in Escherichia coli K-12." J Bacteriol 158(2);674-82. PMID: 6327617

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kim01d: Kim MS, Oh H, Park C, Oh BH (2001). "Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli RbsD, a component of the ribose-transport system with unknown biochemical function." Acta Crystallogr D Biol Crystallogr 57(Pt 5);728-30. PMID: 11320319

Kim03: Kim MS, Shin J, Lee W, Lee HS, Oh BH (2003). "Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture." J Biol Chem 278(30);28173-80. PMID: 12738765

Kim04b: Kim I, Kim E, Yoo S, Shin D, Min B, Song J, Park C (2004). "Ribose utilization with an excess of mutarotase causes cell death due to accumulation of methylglyoxal." J Bacteriol 186(21);7229-35. PMID: 15489434

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

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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, BIOCYC14B.