L ribulose 5 phosphate 4 epimerase


Gene Symbol: L ribulose 5 phosphate 4 epimerase
Description: L-ribulose-5-phosphate 4-epimerase
Alias: ECK0062, JW0060
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. Lee D, Huo L, Schleif R. Repression of the araBAD promoter from araO1. J Mol Biol. 1992;224:335-41 pubmed
  2. Yao J, Zhong J, Lambowitz A. Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library. Nucleic Acids Res. 2005;33:3351-62 pubmed
    ..All such introns tested individually gave the desired specific disruption, some by switching to an alternate retrohoming mechanism targeting single-stranded DNA and using a nascent lagging DNA strand to prime reverse transcription. ..
  3. Schleif R. L-arabinose operon messenger of Escherichia coli. Its inducibility and translation efficiency relative to lactose operon messenger. J Mol Biol. 1971;61:275-9 pubmed
  4. Lee N, Gielow W, Martin R, Hamilton E, Fowler A. The organization of the araBAD operon of Escherichia coli. Gene. 1986;47:231-44 pubmed
    ..The most pronounced difference, found in the araD gene, is the deletion of a single nt in the S. typhimurium sequence. ..
  5. Bonner C, Hays S, McEntee K, Goodman M. DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1990;87:7663-7 pubmed
    ..The demonstration that DNA polymerase II is a component of the SOS response in E. coli suggests that it plays an important role in DNA repair and/or mutagenesis. ..
  6. Chen H, Lawrence C, Bryan S, Moses R. Aphidicolin inhibits DNA polymerase II of Escherichia coli, an alpha-like DNA polymerase. Nucleic Acids Res. 1990;18:7185-6 pubmed
  7. Andersson A, Schneider G, Lindqvist Y. Purification and preliminary X-ray crystallographic studies of recombinant L-ribulose-5-phosphate 4-epimerase from Escherichia coli. Protein Sci. 1995;4:1648-50 pubmed
    ..8 A and c = 281.4 A and diffract to at least 2.2 A resolution. Density measurements of these crystals are consistent with eight subunits in the asymmetric unit. ..
  8. Rodgers M, Schleif R. DNA tape measurements of AraC. Nucleic Acids Res. 2008;36:404-10 pubmed
    ..In the other class, the possible arm-DNA-binding domain interaction is trans, where it adds to the dimerization interface. ..
  9. Englesberg E, Anderson R, Weinberg R, Lee N, Hoffee P, HUTTENHAUER G, et al. L-Arabinose-sensitive, L-ribulose 5-phosphate 4-epimerase-deficient mutants of Escherichia coli. J Bacteriol. 1962;84:137-46 pubmed
    ..Glucose prevents and cures the l-arabinose inhibition. ..

More Information


  1. Luo Y, Samuel J, Mosimann S, Lee J, Tanner M, Strynadka N. The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. Biochemistry. 2001;40:14763-71 pubmed
    ..Detailed inspection of the epimerase structure, however, indicates that despite the close overall structural similarity to class II aldolases, the enzyme has evolved distinct active site features that promote its particular chemistry. ..
  2. Johnson A, Tanner M. Epimerization via carbon-carbon bond cleavage. L-ribulose-5-phosphate 4-epimerase as a masked class II aldolase. Biochemistry. 1998;37:5746-54 pubmed
    ..37 mM) but not of the wild-type enzyme. The mutation apparently causes the epimerase to become "leaky" and enables it to bind/generate the normal reaction intermediates from the unbound aldol cleavage products. ..
  3. Johnson C, Schleif R. In vivo induction kinetics of the arabinose promoters in Escherichia coli. J Bacteriol. 1995;177:3438-42 pubmed
    ..5, 5, and 1, respectively. These results provide a basis for subsequent studies to determine the mechanism(s) by which AraC protein activates transcription from the different arabinose promoters. ..
  4. Reeder T, Schleif R. Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon. J Bacteriol. 1991;173:7765-71 pubmed
    ..S. Naom, S. J. Morton, D. R. F. Leach, and R. G. Lloyd, Nucleic Acids Res. 17:8033-8044, 1989). The carboxyl region of SbcC has an amino acid sequence consistent with this region of SbcC forming an extended alpha-helical coiled-coil. ..
  5. Schleif R, Greenblatt J, Davis R. Dual control of arabinose genes on transducing phage lambda-dara. J Mol Biol. 1971;59:127-50 pubmed
  6. Lee D, Schleif R. In vivo DNA loops in araCBAD: size limits and helical repeat. Proc Natl Acad Sci U S A. 1989;86:476-80 pubmed
    ..As the spacing between araI and araO2 varied, the activity of PBAD oscillated with an 11.1-base-pair periodicity, implying that the in vivo helical repeat of this DNA is 11.1 base pairs per turn. ..
  7. Mineno J, Fukui H, Ishino Y, Kato I, Shinagawa H. Nucleotide sequence of the araD gene of Escherichia coli K12 encoding the L-ribulose 5-phosphate 4-epimerase. Nucleic Acids Res. 1990;18:6722 pubmed
  8. Lee N, Patrick J, Masson M. Crystalline L-ribulose 5-phosphate 4-epimerase from Escherichia coli. J Biol Chem. 1968;243:4700-5 pubmed
  9. Ariza R, Roldan Arjona T, Hera C, Pueyo C. A method for selection of forward mutations in supF gene carried by shuttle-vector plasmids. Carcinogenesis. 1993;14:303-5 pubmed
    ..Since shuttle-vectors replicate both in bacteria and mammalian cells, this method makes it possible to compare prokaryotic and eukaryotic mutational spectra. ..
  10. Iwasaki H, Ishino Y, Toh H, Nakata A, Shinagawa H. Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases. Mol Gen Genet. 1991;226:24-33 pubmed
    ..The recognition sequence of the LexA repressor (SOS box) was identified by a footprinting experiment. It overlaps the -35 sequence of the polB promoter. ..
  11. Lee L, Vu M, Cleland W. 13C and deuterium isotope effects suggest an aldol cleavage mechanism for L-ribulose-5-phosphate 4-epimerase. Biochemistry. 2000;39:4808-20 pubmed
    ..94 and 8.24. The CD spectra of L-ribulose 5-phosphate and D-xylulose 5-phosphate differ sufficiently that the epimerization reaction can be followed at 300 nm. ..
  12. Lee L, Poyner R, Vu M, Cleland W. Role of metal ions in the reaction catalyzed by L-ribulose-5-phosphate 4-epimerase. Biochemistry. 2000;39:4821-30 pubmed
  13. Samuel J, Luo Y, Morgan P, Strynadka N, Tanner M. Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase. Biochemistry. 2001;40:14772-80 pubmed
    ..Modeling of L-Ru5P into the active site of the epimerase structure suggests that Tyr229' is responsible for deprotonating L-Ru5P and Asp120' is responsible for deprotonating its epimer, D-Xu5P. ..
  14. Gross J, Englesberg E. Determination of the order of mutational sites governing L-arabinose utilization in Escherichia coli B/r bv transduction with phage Plbt. Virology. 1959;9:314-31 pubmed
  15. Chen H, Sun Y, Stark T, Beattie W, Moses R. Nucleotide sequence and deletion analysis of the polB gene of Escherichia coli. DNA Cell Biol. 1990;9:631-5 pubmed
    ..We have also demonstrated that the polB sequence is lacking in some strains. We conclude that DNA polymerase II is not a required protein in the cell. Sequence comparisons show that DNA polymerase II is an alpha-like DNA polymerase. ..
  16. Ebright R, Beckwith J. The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of the araBAD operon of Escherichia coli K-12. Mol Gen Genet. 1985;201:51-5 pubmed
    ..However, contrary to the results of Kline et al., we find that the action of IAA does not require CAP. Thus, IAA fully stimulates the transcription of araBAD in a strain which bears a complete deletion of the crp gene. ..
  17. Ibanez E, Gimenez R, Pedraza T, Baldoma L, Aguilar J, Badia J. Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose. J Bacteriol. 2000;182:4625-7 pubmed
    ..Similarity of YiaR to several 3-epimerases suggested that this protein could catalyze the conversion of L-xylulose-5-phosphate into L-ribulose-5-phosphate, thus completing the pathway between L-xylulose and the general metabolism. ..
  18. Casadaban M. Fusion of the Escherichia coli lac genes to the ara promoter: a general technique using bacteriophage Mu-1 insertions. Proc Natl Acad Sci U S A. 1975;72:809-13 pubmed
    ..These fusions extend the techniques available for studies on the lac operon to studies on the ara operon. It should be possible to fuse other operons by this method. ..