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Gene Review

ycjM  -  glycosidase

Escherichia coli O157:H7 str. EDL933

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Disease relevance of ycjM


High impact information on ycjM

  • Addition of uracil, a known inhibitor of the enzyme uracil-DNA glycosidase (Lindahl et al., 1977), increased total synthesis and shifted the incorporation to longer progeny strands [6].
  • These results indicate that this replacement of thymine by uracil in DNA does not seriously impair the biological functionality of T4 DNA, provided the DNA is not subjected to the breakdown (repair) pathway initiated by uracil--DNA glycosidase [1].
  • We suggest that the hotspots may result from the spontaneous deamination of 5-methylcytosine to thymine, which is not excised by the enzyme DNA-uracil glycosidase [7].
  • Using a sensitive approach that combines in-gel glycosidase and protease digestions, permethylation of released glycans, and mass spectrometry, we have elucidated for the first time the native glycoform structures of the mouse UPIa receptor and those of its non-binding homolog, UPIb, and have determined the glycosylation site occupancy [8].
  • The relative activities of the induced enzymes suggest that the rate-limiting steps in oligosaccharide catabolism are the glycosidase activities in the periplasm [9].

Chemical compound and disease context of ycjM

  • This uracil-containing DNA is competent for RNA transcription, and can be packaged into phage which are viable, if the host cells are deficient in uracil--DNA glycosidase activity [1].

Biological context of ycjM

  • Structural studies including monosaccharide and phosphate analysis, glycosidase and phosphatase treatments, methylation analysis, and periodate treatment indicated the structure of this compound to be NeuAc alpha 2-6Gal beta 1-4GlcNAc-6-P [10].
  • The gene cluster aec-35 to aec-37 of module 1 encodes proteins associated with carbohydrates assimilation such as a major facilitator superfamily transporter (Aec-36), a glycosidase (Aec-37), and a putative transcriptional regulator of the LacI family (Aec-35) [11].
  • Random mutagenesis of a plasmid-borne glycosidase gene and phenotypic selection of mutants in Escherichia coli [12].
  • In simulations of the substrate complexed with the native protein conformation, the sugar ring in the -1 binding site was observed to make a spontaneous transition from the (4)C(1) conformation to a twist-boat conformer, consistent with generally accepted glycosidase mechanisms [13].
  • RESULTS: Forty GH1 genes could be identified in rice databases, including 2 possible endophyte genes, 2 likely pseudogenes, 2 gene fragments, and 34 apparently competent rice glycosidase genes [14].

Anatomical context of ycjM


Associations of ycjM with chemical compounds

  • Mechanism-based glycosidase inhibitors are of considerable use in studies of enzyme mechanism, in studies of glycoprotein processing, and possibly therapeutically in control of sugar uptake [17].
  • Furthermore, the Ki values of acarbose, which is thought to be a transition-state analog of glycosidase catalysis, were 2-3 orders of magnitude larger in asparagine-replaced CGTases than that in wild-type CGTase [18].
  • Since the ung mutation is phenotypically expressed as a defect in uracil DNA glycosidase, this observation supports the contention that treatment of cells with nitrous acid causes deamination of cytosine to uracil [19].
  • Synthesis and biological evaluation of potent glycosidase inhibitors: N-phenyl cyclic isourea derivatives of 5-amino- and 5-amino-C-(hydroxymethyl)-1,2,3,4-cyclopentanetetraols [20].
  • Saccharolytic organisms growing in the SRB fermenter utilized more starch, but less galactose-containing polymers, which correlated with the observed glycosidase activities [21].

Analytical, diagnostic and therapeutic context of ycjM


  1. In vivo synthesis and properties of uracil-containing DNA. Warner, H.R., Duncan, B.K. Nature (1978) [Pubmed]
  2. DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli. Lindahl, T., Ljungquist, S., Siegert, W., Nyberg, B., Sperens, B. J. Biol. Chem. (1977) [Pubmed]
  3. Mechanism of the family 1 beta-glucosidase from Streptomyces sp: catalytic residues and kinetic studies. Vallmitjana, M., Ferrer-Navarro, M., Planell, R., Abel, M., Ausín, C., Querol, E., Planas, A., Pérez-Pons, J.A. Biochemistry (2001) [Pubmed]
  4. Serratia marcescens chitobiase is a retaining glycosidase utilizing substrate acetamido group participation. Drouillard, S., Armand, S., Davies, G.J., Vorgias, C.E., Henrissat, B. Biochem. J. (1997) [Pubmed]
  5. Molecular cloning and characterization of Bifidobacterium bifidum 1,2-alpha-L-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95). Katayama, T., Sakuma, A., Kimura, T., Makimura, Y., Hiratake, J., Sakata, K., Yamanoi, T., Kumagai, H., Yamamoto, K. J. Bacteriol. (2004) [Pubmed]
  6. Formation of Okazaki fragments in polyoma DNA synthesis caused by misincorporation of uracil. Brynolf, K., Eliasson, R., Reichard, P. Cell (1978) [Pubmed]
  7. Molecular basis of base substitution hotspots in Escherichia coli. Coulondre, C., Miller, J.H., Farabaugh, P.J., Gilbert, W. Nature (1978) [Pubmed]
  8. Distinct glycan structures of uroplakins Ia and Ib: structural basis for the selective binding of FimH adhesin to uroplakin Ia. Xie, B., Zhou, G., Chan, S.Y., Shapiro, E., Kong, X.P., Wu, X.R., Sun, T.T., Costello, C.E. J. Biol. Chem. (2006) [Pubmed]
  9. Chitin utilization by marine bacteria. Degradation and catabolism of chitin oligosaccharides by Vibrio furnissii. Bassler, B.L., Yu, C., Lee, Y.C., Roseman, S. J. Biol. Chem. (1991) [Pubmed]
  10. Occurrence of N-acetylglucosamine 6-phosphate in complex carbohydrates. Characterization of a phosphorylated sialyl oligosaccharide from bovine colostrum. Parkkinen, J., Finne, J. J. Biol. Chem. (1985) [Pubmed]
  11. A selC-associated genomic island of the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is involved in carbohydrate uptake and virulence. Chouikha, I., Germon, P., Brée, A., Gilot, P., Moulin-Schouleur, M., Schouler, C. J. Bacteriol. (2006) [Pubmed]
  12. Random mutagenesis of a plasmid-borne glycosidase gene and phenotypic selection of mutants in Escherichia coli. Lopez-Camacho, C., Polaina, J. Mutat. Res. (1993) [Pubmed]
  13. Computational and experimental studies of the catalytic mechanism of Thermobifida fusca cellulase Cel6A (E2). André, G., Kanchanawong, P., Palma, R., Cho, H., Deng, X., Irwin, D., Himmel, M.E., Wilson, D.B., Brady, J.W. Protein Eng. (2003) [Pubmed]
  14. Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 beta-glucosidase. Opassiri, R., Pomthong, B., Onkoksoong, T., Akiyama, T., Esen, A., Ketudat Cairns, J.R. BMC Plant Biol. (2006) [Pubmed]
  15. The low expression level of pokeweed antiviral protein (PAP) gene in Escherichia coli by the inducible lac promoter is due to inefficient transcription and translation and not to the toxicity of the PAP. Xu, J., Kaloyanova, D., Ivanov, I.G., AbouHaidar, M.G. Arch. Biochem. Biophys. (1998) [Pubmed]
  16. Gene XV of bacteriophage PRD1 encodes a lytic enzyme with muramidase activity. Caldentey, J., Hänninen, A.L., Bamford, D.H. Eur. J. Biochem. (1994) [Pubmed]
  17. 2-Deoxy-2-fluoro-D-glycosyl fluorides. A new class of specific mechanism-based glycosidase inhibitors. Withers, S.G., Rupitz, K., Street, I.P. J. Biol. Chem. (1988) [Pubmed]
  18. Three histidine residues in the active center of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011: effects of the replacement on pH dependence and transition-state stabilization. Nakamura, A., Haga, K., Yamane, K. Biochemistry (1993) [Pubmed]
  19. Repair of nitrous acid damage to DNA in Escherichia coli. Da Roza, R., Friedberg, E.C., Duncan, B.K., Warner, H.R. Biochemistry (1977) [Pubmed]
  20. Synthesis and biological evaluation of potent glycosidase inhibitors: N-phenyl cyclic isourea derivatives of 5-amino- and 5-amino-C-(hydroxymethyl)-1,2,3,4-cyclopentanetetraols. Uchida, C., Kimura, H., Ogawa, S. Bioorg. Med. Chem. (1997) [Pubmed]
  21. Growth of a human intestinal Desulfovibrio desulfuricans in continuous cultures containing defined populations of saccharolytic and amino acid fermenting bacteria. Newton, D.F., Cummings, J.H., Macfarlane, S., Macfarlane, G.T. J. Appl. Microbiol. (1998) [Pubmed]
  22. Shiga toxin binds human platelets via globotriaosylceramide (Pk antigen) and a novel platelet glycosphingolipid. Cooling, L.L., Walker, K.E., Gille, T., Koerner, T.A. Infect. Immun. (1998) [Pubmed]
  23. Characterization of a salt-tolerant family 42 beta-galactosidase from a psychrophilic antarctic Planococcus isolate. Sheridan, P.P., Brenchley, J.E. Appl. Environ. Microbiol. (2000) [Pubmed]
  24. Identification of a collagen-like protein gene from white spot syndrome virus. Li, Q., Chen, Y., Yang, F. Arch. Virol. (2004) [Pubmed]
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