ung

Summary

Gene Symbol: ung
Description: uracil-DNA-glycosylase
Alias: ECK2578, JW2564
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. ncbi Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung)
    U Varshney
    Department of Medical Biochemistry, Faculty of Medicine, University of Calgary, Canada
    J Biol Chem 263:7776-84. 1988
  2. ncbi Escherichia coli uracil- and ethenocytosine-initiated base excision DNA repair: rate-limiting step and patch size distribution
    Jung Suk Sung
    Departments of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331 7301, USA
    Biochemistry 42:4613-25. 2003
  3. pmc Negative regulation of DNA repair gene (ung) expression by the CpxR/CpxA two-component system in Escherichia coli K-12 and induction of mutations by increased expression of CpxR
    Hiroshi Ogasawara
    Department of Bioscience and Biotechnology, Graduate School of Agriculture of Kinki University, 3327 204 Nakamachi, Nara 631 8505, Japan
    J Bacteriol 186:8317-25. 2004
  4. pmc Enzymatic capture of an extrahelical thymine in the search for uracil in DNA
    Jared B Parker
    Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nature 449:433-7. 2007
  5. pmc Repair of chromosomal abasic sites in vivo involves at least three different repair pathways
    M Otterlei
    Institute of Cancer Research and Molecular Biology, The Faculty of Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    EMBO J 19:5542-51. 2000
  6. pmc X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG
    R Ravishankar
    Molecular Biophysics Unit and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 26:4880-7. 1998
  7. ncbi Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    J T Stivers
    Center for Advanced Research in Biotechnology, University of Maryland, National Institute for Standards and Technology, Rockville 20850, USA
    Biochemistry 38:952-63. 1999
  8. ncbi Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
    C D Putnam
    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
    J Mol Biol 287:331-46. 1999
  9. ncbi Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187
    A C Drohat
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, National Institute for Standards and Technology, Rockville, Maryland 20850, USA
    Biochemistry 38:11876-86. 1999
  10. ncbi Structure and function in the uracil-DNA glycosylase superfamily
    L H Pearl
    Section of Structural Biology and CRC DNA Repair Enzyme Group, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, SW3 6JB, London, UK
    Mutat Res 460:165-81. 2000

Scientific Experts

  • Isaac Wong
  • L H Pearl
  • James T Stivers
  • Narottam Acharya
  • J T Stivers
  • A C Drohat
  • P Handa
  • Umesh Varshney
  • Jared B Parker
  • Luciana Amado
  • U Varshney
  • Andrei Kuzminov
  • Yu Lin Jiang
  • Scott T Kimber
  • Priya Handa
  • D W Mosbaugh
  • S Roy
  • Grigory V Mechetin
  • Sanjay Kumar Bharti
  • Ramappa K Talawar
  • Haidong Huang
  • Shin Ichiro Yonekura
  • S E Bennett
  • K Saikrishnan
  • G Xiao
  • Helen Ting
  • M Saparbaev
  • M Vijayan
  • J S Sung
  • Samridhi C Goswami
  • S Kh Timchenko
  • Sibghat Ullah Lari
  • Hiroshi Ogasawara
  • G L Gilliland
  • K W Pankiewicz
  • R Ravishankar
  • Claude Saint-Ruf
  • M Tordova
  • Ryan W Shaw
  • K Purnapatre
  • M J Shroyer
  • J Jagadeesh
  • C D Putnam
  • Jung Suk Sung
  • D A Gonchar
  • E A Kubareva
  • Dwain I D'souza
  • E M Volkov
  • S Kh Degtiarev
  • Pingfang Liu
  • Erik J Spek
  • Keith R Fox
  • Tom Brown
  • A J Lundquist
  • E J Spek
  • C E Doneanu
  • R J Sanderson
  • Dmitry O Zharkov
  • M Sandigursky
  • M Otterlei
  • A E Sud'ina
  • M Ghosh
  • M Bidya Sagar
  • R M Werner
  • J Dong
  • Shuji Yonei
  • Nobuya Nakamura
  • J Laval
  • Qiu Mei Zhang-Akiyama
  • Marc M Greenberg
  • Elena A Kouzminova
  • J A Tainer
  • E Lutsenko
  • K A Watanabe
  • Daniel J Krosky
  • Mario A Bianchet
  • Joshua I Friedman
  • L Mario Amzel
  • Jung Hoon Yoon
  • O L Voronina
  • Beata G Vertessy
  • Samuel E Bennett
  • Gerd P Pfeifer
  • K Kimura
  • Jeff Morré
  • Cheng Yao Chen
  • Edith H Postel
  • Bozena M Abramczyk
  • M A Timchenko
  • V G Lunin

Detail Information

Publications77

  1. ncbi Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung)
    U Varshney
    Department of Medical Biochemistry, Faculty of Medicine, University of Calgary, Canada
    J Biol Chem 263:7776-84. 1988
    The complete nucleotide sequence of the Escherichia coli ung gene is described. Transcription initiation and termination sites were determined by S1 nuclease and RNase mapping...
  2. ncbi Escherichia coli uracil- and ethenocytosine-initiated base excision DNA repair: rate-limiting step and patch size distribution
    Jung Suk Sung
    Departments of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331 7301, USA
    Biochemistry 42:4613-25. 2003
    ..coli DNA ligase to the cell-free extract, whereas addition of E. coli Ung, Nfo, Fpg, or Pol I did not stimulate BER. Hence, DNA ligation was identified as the rate-limiting step in the E...
  3. pmc Negative regulation of DNA repair gene (ung) expression by the CpxR/CpxA two-component system in Escherichia coli K-12 and induction of mutations by increased expression of CpxR
    Hiroshi Ogasawara
    Department of Bioscience and Biotechnology, Graduate School of Agriculture of Kinki University, 3327 204 Nakamachi, Nara 631 8505, Japan
    J Bacteriol 186:8317-25. 2004
    In Escherichia coli K-12 overexpressing CpxR, transcription of the ung gene for uracil-DNA glycosylase was repressed, ultimately leading to the induction of mutation...
  4. pmc Enzymatic capture of an extrahelical thymine in the search for uracil in DNA
    Jared B Parker
    Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nature 449:433-7. 2007
    The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism...
  5. pmc Repair of chromosomal abasic sites in vivo involves at least three different repair pathways
    M Otterlei
    Institute of Cancer Research and Molecular Biology, The Faculty of Medicine, Norwegian University of Science and Technology, N 7489 Trondheim, Norway
    EMBO J 19:5542-51. 2000
    ..Spontaneous mutation spectra were generally strongly dependent upon the repair background. In conclusion, BER, recombination and TLS all contribute to the handling of chromosomal AP sites in E.coli in vivo...
  6. pmc X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG
    R Ravishankar
    Molecular Biophysics Unit and Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 26:4880-7. 1998
    ..Ec UDG could serve as a prototype for UDGs from pathogenic prokaryotes, and provide a framework for possible drug development against such pathogens with emphasis on features of the molecule that differ from those in the human enzyme...
  7. ncbi Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    J T Stivers
    Center for Advanced Research in Biotechnology, University of Maryland, National Institute for Standards and Technology, Rockville 20850, USA
    Biochemistry 38:952-63. 1999
    ..Thus, base flipping contributes little to the free energy of DNA binding but contributes greatly to specificity through an induced-fit mechanism...
  8. ncbi Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
    C D Putnam
    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
    J Mol Biol 287:331-46. 1999
    ....
  9. ncbi Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187
    A C Drohat
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, National Institute for Standards and Technology, Rockville, Maryland 20850, USA
    Biochemistry 38:11876-86. 1999
    ..Rather, we propose a concerted mechanism involving general base catalysis by Asp64 and electrophilic stabilization of the developing enolate on uracil O2 by a neutral His187...
  10. ncbi Structure and function in the uracil-DNA glycosylase superfamily
    L H Pearl
    Section of Structural Biology and CRC DNA Repair Enzyme Group, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, SW3 6JB, London, UK
    Mutat Res 460:165-81. 2000
    ....
  11. ncbi Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2
    A C Drohat
    Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology and the University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
    Biochemistry 39:11865-75. 2000
    ..The role of this H bond in catalysis by UDG and several approaches to quantify the H bond energy are discussed...
  12. ncbi Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase
    R M Werner
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and National Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
    Biochemistry 39:12585-94. 2000
    ..S., et al. (2000) Proc Natl. Acad. Sci. 94, 5083], there is no evidence that conformational strain of the glycosidic bond induced by serine pinching plays a major role in the 10(12)-fold rate enhancement brought about by UDG...
  13. ncbi The role of leucine 191 of Escherichia coli uracil DNA glycosylase in the formation of a highly stable complex with the substrate mimic, ugi, and in uracil excision from the synthetic substrates
    P Handa
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
    J Biol Chem 276:17324-31. 2001
    ..We also envisage a role for Leu191 in stabilizing the productive enzyme-substrate complex...
  14. pmc Nitric oxide-induced homologous recombination in Escherichia coli is promoted by DNA glycosylases
    Erik J Spek
    Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    J Bacteriol 184:3501-7. 2002
    ..we show that AP endonuclease-deficient cells can be protected from NO* toxicity by inactivation of the uracil (Ung) or formamidopyrimidine (Fpg) DNA glycosylases but not by inactivation of a 3-methyladenine (AlkA) DNA glycosylase...
  15. pmc Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and subs
    Priya Handa
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Nucleic Acids Res 30:3086-95. 2002
    ..We discuss their additional roles in conferring stability to the transition state enzyme-substrate complex and/or enhancing the leaving group quality of the uracilate anion during catalysis...
  16. pmc Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition
    Narottam Acharya
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
    Nucleic Acids Res 31:7216-26. 2003
    ....
  17. ncbi Excision of 5'-terminal deoxyribose phosphate from damaged DNA is catalyzed by the Fpg protein of Escherichia coli
    R J Graves
    Groupe Reparation des lesions Radio et Chimio Induites, Centre National de la Recherche Scientifique URA147, Institut Gustave Roussy, Villejuif, France
    J Biol Chem 267:14429-35. 1992
    ..The release of 5'-terminal dRp by crude extracts of E. coli from wild type and fpg-mutant strains shows that the Fpg protein is one of the major EDTA-resistant activities catalyzing this reaction...
  18. pmc A mutant of uracil DNA glycosylase that distinguishes between cytosine and 5-methylcytosine
    Scott T Kimber
    Centre for Biological Sciences, University of Southampton, Highfield, Southampton, United Kingdom
    PLoS ONE 9:e95394. 2014
    ..In contrast no cleavage is observed with any substrates that contain 5-methylcytosine. This enzyme may offer a new approach for discriminating between cytosine and 5-methylcytosine. ..
  19. ncbi Contrasting effects of mutating active site residues, aspartic acid 64 and histidine 187 of Escherichia coli uracil-DNA glycosylase on uracil excision and interaction with an inhibitor protein
    Priya Handa
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Indian J Biochem Biophys 39:312-7. 2002
    ..Thus, our findings provide further evidence to the primary function of D64 and H187 in catalysis...
  20. ncbi New substrates for old enzymes. 5-Hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2'-deoxyuridine is a substrate for uracil DNA N-glycos
    Z Hatahet
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington 05405
    J Biol Chem 269:18814-20. 1994
    ..Analysis of crude extracts obtained from wild type and endonuclease III deletion mutants of E. coli correlated well with data obtained with the purified enzymes...
  21. ncbi [Structure of Escherichia coli uracil DNA glycosylase and its complexes with nonhydrolyzable substrate analogues in solution observed by synchrotron small-angle X-ray scattering]
    S Kh Timchenko
    Biofizika 51:5-12. 2006
    ..A decrease in the ionic strength of solution results in a partial disruption of compact structure of the modified protein, without changes in its functional activity...
  22. ncbi An exponential dilution gradient system for nanoscale liquid chromatography in combination with MALDI or nano-ESI mass spectrometry for proteolytic digests
    C E Doneanu
    Department of Chemistry, Oregon State University, Corvallis 97331 4003, USA
    J Am Soc Mass Spectrom 12:1205-13. 2001
    ..The system was used to analyze a tryptic digest of Escherichia coli uracil DNA glycosylase (Ung; Mr = 25,563), a DNA-binding protein that initiates the uracil-excision DNA repair process by catalyzing the ..
  23. ncbi Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis
    Yu Lin Jiang
    Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 2185, USA
    J Biol Chem 277:15385-92. 2002
    ..These results suggest that electrostatic effects can effectively stabilize such an intermediate by at least -7 kcal/mol, without leading to anticatalytic stabilization of the substrate and products...
  24. ncbi Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism
    Isaac Wong
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
    J Biol Chem 277:19424-32. 2002
    ..The results define for the first time the proper sequence of events during a catalytic cycle and establish a "pull-push", as opposed to a "push-pull", mechanism for nucleotide flipping...
  25. pmc Multiple mutant of Escherichia coli synthesizing virtually thymineless DNA during limited growth
    H H El-Hajj
    Department of Pathology, University of Michigan Medical School, Ann Arbor 48109 0602
    J Bacteriol 174:4450-6. 1992
    ..bearing, in addition to these mutations, ones affecting the following genes and their corresponding products: ung, which produces uracil-DNA N-glycosylase, a repair enzyme that removes uracil from DNA; deoA, which produces ..
  26. ncbi Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG
    K Saikrishnan
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Acta Crystallogr D Biol Crystallogr 58:1269-76. 2002
    ..The comparative study also shows that the mobility of the molecule involves the rigid-body movement of the domains superposed on flexibility within domains...
  27. ncbi Substrate recognition by a family of uracil-DNA glycosylases: UNG, MUG, and TDG
    Pingfang Liu
    Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
    Chem Res Toxicol 15:1001-9. 2002
    ..The glycosylases studied here include Escherichia coli uracil-DNA glycosylase (UNG), E...
  28. pmc Repair of clustered uracil DNA damages in Escherichia coli
    Dwain I D'souza
    Department of Molecular and Cellular Physiology, Louisiana Health Sciences Center, Shreveport, LA, USA
    Nucleic Acids Res 31:4573-81. 2003
    ..the firefly luciferase coding region, transformed into bacteria (wild-type, uracil DNA glycosylase-deficient, ung-, or exonuclease III and endonuclease IV-deficient, xth-nfo-) and luciferase activity measured following repair...
  29. ncbi Use of sequence microdivergence in mycobacterial ortholog to analyze contributions of the water-activating loop histidine of Escherichia coli uracil-DNA glycosylase in reactant binding and catalysis
    Narottam Acharya
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
    Biochem Biophys Res Commun 320:893-9. 2004
    Uracil-DNA glycosylase (Ung), a DNA repair enzyme, pioneers uracil excision repair pathway...
  30. ncbi Contribution of a conserved phenylalanine residue to the activity of Escherichia coli uracil DNA glycosylase
    Ryan W Shaw
    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610 0245, USA
    DNA Repair (Amst) 3:1273-83. 2004
    ..Overall, the effects of the mutations on catalysis are best correlated with the polarity of the substituted residue such that an increase in polarity decreases the efficiency of uracil excision...
  31. pmc Stress and survival of aging Escherichia coli rpoS colonies
    Claude Saint-Ruf
    Laboratoire de Génétique Moléculaire Evolutive et Médicale, INSERM U571, Faculte de Medecine Necker Enfants Malades, Universite Paris V, 75730 Cedex 15, France
    Genetics 168:541-6. 2004
    ..By measuring cell viability and by transcriptome analysis, here we show that rpoS cells as well as wild-type cells survive when they form colonies on solid media...
  32. ncbi Recognition of an unnatural difluorophenyl nucleotide by uracil DNA glycosylase
    Yu Lin Jiang
    Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205 2185, USA
    Biochemistry 43:15429-38. 2004
    ....
  33. ncbi Uracil-initiated base excision DNA repair synthesis fidelity in human colon adenocarcinoma LoVo and Escherichia coli cell extracts
    R J Sanderson
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
    Prog Nucleic Acid Res Mol Biol 68:165-88. 2001
    ..coli uracil-DNA glycosylase (Ung) and endonuclease IV, indicating that complete uracil-initiated BER repair had occurred...
  34. ncbi The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision
    Luciana Amado
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801 3709, USA
    J Biol Chem 281:22635-46. 2006
    ..is unchanged by blocking linear DNA processing with a recBCD mutation or by blocking uracil excision with an ung mutation...
  35. ncbi Molecular and functional interactions between Escherichia coli nucleoside-diphosphate kinase and the uracil-DNA glycosylase Ung
    Samridhi C Goswami
    Laboratory of Biochemistry and Molecular Biology, Department of Pediatrics, Robert Wood Johnson Medical School University of Medicine and Dentistry of New Jersey, One Robert Wood Johnson Place, New Brunswick, NJ 08903 0019, USA
    J Biol Chem 281:32131-9. 2006
    ..and DNA repair activities, including the excision of uracil from DNA, an activity normally associated with the Ung and Mug uracil-DNA glycosylases (UDGs) in E. coli...
  36. pmc Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance
    Sibghat Ullah Lari
    Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331 7301, USA
    DNA Repair (Amst) 5:1407-20. 2006
    ..strains of Escherichia coli were measured and the influence of defects in the genes for uracil-DNA glycosylase (ung), double-strand uracil-DNA glycosylase (dug), and dUTP pyrophosphatase (dut) on uracil accumulation was determined...
  37. pmc Synthetic lethality with the dut defect in Escherichia coli reveals layers of DNA damage of increasing complexity due to uracil incorporation
    Helen Ting
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    J Bacteriol 190:5841-54. 2008
    ..Thus, we isolated mutants in functions involved in (i) uracil-DNA excision (ung, polA, and xthA); (ii) double-strand DNA break repair (recA, recBC, and ruvABC); and (iii) chromosomal-dimer ..
  38. pmc Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions
    Jared B Parker
    Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205 2185, USA
    Biochemistry 47:8614-22. 2008
    Uracil DNA glycosylase (UNG) is a powerful DNA repair enzyme that has been shown to stabilize a glycosyl cation reaction intermediate and a related tight binding inhibitor using electrostatic interactions with the +1 and -1, but not the +..
  39. ncbi Generation, biological consequences and repair mechanisms of cytosine deamination in DNA
    Shin Ichiro Yonekura
    Department of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Sakyo ku, Kyoto 606 8502, Japan
    J Radiat Res 50:19-26. 2009
    ..Uracil in DNA is also produced by the incorporation of dUMP during DNA replication. Uracil-DNA glycosylase (UNG) acts as a major repair enzyme that protects DNA from the deleterious consequences of uracil...
  40. pmc Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase
    Haidong Huang
    Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    J Am Chem Soc 131:1344-5. 2009
    ..A potential benefit of such a mechanism is that multiple incorporations can occur for longer DNA molecules leading to amplification of the inhibitory effect beyond that seen here with short DNA duplexes...
  41. pmc Polyphosphate accumulation in Escherichia coli in response to defects in DNA metabolism
    Luciana Amado
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    J Bacteriol 191:7410-6. 2009
    ..coli mutants with diverse defects in the DNA metabolism. We detected increased polyphosphate accumulation in the ligA, ligA recBCD, dut ung, and thyA mutants. Polyphosphate accumulation may thus be an indicator of general DNA stress.
  42. pmc Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli
    Sanjay Kumar Bharti
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    Nucleic Acids Res 38:2291-301. 2010
    Uracil DNA glycosylase (Ung) initiates the uracil excision repair pathway...
  43. pmc Mechanism of translocation of uracil-DNA glycosylase from Escherichia coli between distributed lesions
    Grigory V Mechetin
    SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave, Novosibirsk 630090, Russia
    Biochem Biophys Res Commun 414:425-30. 2011
    Uracil-DNA glycosylase (Ung) is a DNA repair enzyme that excises uracil bases from DNA, where they appear through deamination of cytosine or incorporation from a cellular dUTP pool...
  44. pmc DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I
    M Sandigursky
    Department of Radiology, Albert Einstein College of Medicine, Bronx, NY 10461
    Nucleic Acids Res 20:4699-703. 1992
    ..These results suggest that the dRpase activity may be important in pathways for both DNA repair and recombination...
  45. pmc The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair
    M Sandigursky
    Department of Radiology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 26:1282-7. 1998
    ..Repair synthesis carried out by repair-proficient ung, recJ and xon E...
  46. ncbi Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited
    G Xiao
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute for Standards and Technology, Rockville, 20850, USA
    Proteins 35:13-24. 1999
    ..The catalytic mechanism of UDG is critically discussed with respect to these results...
  47. ncbi Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis
    M J Shroyer
    Departments of Microbiology, Environmental and Molecular Toxicology, Biochemistry and Biophysics, and the Environmental Health Science Center, Oregon State University, Corvallis, Oregon 97331, USA
    Biochemistry 38:4834-45. 1999
    ..the conserved histidine-187 located in the leucine intercalation loop of Escherichia coli uracil-DNA glycosylase (Ung) was investigated...
  48. ncbi Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications
    E Lutsenko
    463 Chemistry Building, Department of Chemistry, Wayne State University, Detroit, MI 48202 3489, USA
    Mutat Res 437:11-20. 1999
    ..G mismatches by the uracil-DNA glycosylase (Ung)...
  49. ncbi Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase
    A C Drohat
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, National Institute for Standards and Technology, Rockville, Maryland 20850, USA
    Biochemistry 38:11866-75. 1999
    ..In the following paper of this issue we establish by crystallography and heteronuclear NMR spectroscopy that the imidazole of His187 is neutral during the catalytic cycle of UDG...
  50. pmc 3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase
    M Saparbaev
    Groupe Reparation des lesions Radio et Chimio Induites, UMR 1772, Centre National de la Recherche Scientifique, Institut Gustave Roussy, 94805 Villejuif Cedex, France
    Proc Natl Acad Sci U S A 95:8508-13. 1998
    ..coli dsUDG and hTDG proteins in vitro suggests that these enzymes may be responsible for the repair of this mutagenic lesion in vivo and be important contributors to genetic stability...
  51. ncbi Enzymology of the repair of etheno adducts in mammalian cells and in Escherichia coli
    M Saparbaev
    Groupe Reparation des lesions Radio et Chimio Induites, UMR 1772 CNRS Institut Gustave Roussy, Villejuif, France
    IARC Sci Publ . 1999
    ....
  52. pmc Structural basis for uracil DNA glycosylase interaction with uracil: NMR study
    M Ghosh
    Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
    Nucleic Acids Res 28:1906-12. 2000
    ..This study shows that UDG actively promotes the flipping of uracil from a stacked conformation and rules out the possibility of UDG recognizing the flipped out uracil bases...
  53. ncbi [A rapid method for testing the activity of the repair enzyme uracil-DNA-glycosylase]
    A E Sud'ina
    Chemical Faculty, Moscow State University, Vorob evy Gory, Russia
    Bioorg Khim 26:442-7. 2000
    ..The ammonia cleavage of the apyrimidine site formed in the enzymic reaction followed by the transition of the labeled oligonucleotide fragment from the solid phase into solution allowed the detection of the enzymic activity...
  54. ncbi Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein. Role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase
    A J Lundquist
    Department of Agricultural Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
    J Biol Chem 272:21408-19. 1997
    Bacteriophage PBS2 uracil-DNA glycosylase inhibitor (Ugi) protein inactivates uracil-DNA glycosylase (Ung) by acting as a DNA mimic to bind Ung in an irreversible complex...
  55. pmc Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli
    H H El-Hajj
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    J Bacteriol 170:1069-75. 1988
    ..compensatory mutations: dcd (dCTP deaminase) and cdd (deoxycytidine deaminase), which should reduce dUTP formation; ung (uracil-DNA glycosylase), which should reduce fatally excessive excision repair; deoA (thymidine phosphorylase), ..
  56. ncbi Fidelity of uracil-initiated base excision DNA repair in Escherichia coli cell extracts
    J S Sung
    Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon 97331 7301, USA
    J Biol Chem 276:2276-85. 2001
    ..The rate and extent of complete uracil-DNA repair were measured using uracil-DNA glycosylase (Ung)- or double-strand uracil-DNA glycosylase (Dug)-proficient and -deficient isogenic E. coli cells...
  57. ncbi Raman spectroscopy of uracil DNA glycosylase-DNA complexes: insights into DNA damage recognition and catalysis
    J Dong
    Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106 4935, USA
    Biochemistry 39:13241-50. 2000
    ..These observations are generally not apparent from the high-resolution crystal structures of UDG and its complexes with DNA; thus, Raman spectroscopy can provide unique and valuable insights into the nature of enzyme-DNA interactions...
  58. pmc Recombinational repair is critical for survival of Escherichia coli exposed to nitric oxide
    E J Spek
    Division of Bioengineering and Environmental Health, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    J Bacteriol 183:131-8. 2001
    ..that repair alkylation damage [alkA tag strain], oxidative damage [fpg nei nth strain], and deaminated cytosine [ung strain]) showed essentially wild-type levels of NO(.) resistance...
  59. pmc Release of 5'-terminal deoxyribose-phosphate residues from incised abasic sites in DNA by the Escherichia coli RecJ protein
    G Dianov
    Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire, UK
    Nucleic Acids Res 22:993-8. 1994
    ..Nevertheless, E. coli fpg recJ double mutants retain capacity to repair abasic sites in DNA, indicating the presence of a back-up excision function...
  60. ncbi Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases
    P Handa
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
    J Biol Chem 276:16992-7. 2001
    ..The mechanism of how the interactions between SSB and UDG could be important in uracil excision repair pathway has been discussed...
  61. pmc The rpoE gene of Escherichia coli, which encodes sigma E, is essential for bacterial growth at high temperature
    K Hiratsu
    Department of Molecular Microbiology, Osaka University, Japan
    J Bacteriol 177:2918-22. 1995
    ..We demonstrate that expression of htrA is completely dependent on the rpoE gene in vivo and that the rpoE gene is essential for bacterial growth at high temperature...
  62. pmc Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions
    M A Lonetto
    Department of Stomatology, University of California at San Francisco 94143 0512
    Proc Natl Acad Sci U S A 91:7573-7. 1994
    ..Available information suggests that all of them regulate extracytoplasmic functions and that they function as effector molecules responding to extracytoplasmic stimuli. A. eutrophus CnrH appears to be a plasmid-encoded factor...
  63. ncbi Use of a coupled transcriptional system for consistent overexpression and purification of UDG-Ugi complex and Ugi from Escherichia coli
    S Roy
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
    Protein Expr Purif 13:155-62. 1998
    ..Finally, the usefulness of the operon construct in convenient mutational analysis to study the mechanism of UDG-Ugi interaction is also discussed...
  64. ncbi DNA sequencing of the Escherichia coli ribonuclease III gene and its mutations
    H Nashimoto
    Mol Gen Genet 201:25-9. 1985
    ..coli...
  65. ncbi Suppressors of temperature-sensitive mutations in a ribosomal protein gene, rpsL (S12), of Escherichia coli K12
    H Nashimoto
    Mol Gen Genet 199:381-7. 1985
    ..coli chromosome and one group, named rbaA, mapped at the same locus as the suppressor mutation, showing close linkage to the RNAase III gene...
  66. pmc A GTP-binding protein of Escherichia coli has homology to yeast RAS proteins
    J Ahnn
    Proc Natl Acad Sci U S A 83:8849-53. 1986
    ..These data indicate that ras-related sequences occur not only in eukaryotes but also in prokaryotes...
  67. ncbi An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosomal subunit assembly
    K Nishi
    Max Planck Institut fur Molekulare Genetik, Abteilung Wittmann, Berlin, FRG
    Nature 336:496-8. 1988
    ..The RNA dependent ATPase activity of SrmB suggests that like, eIF-4A, it could be involved in specific alterations of RNA secondary structure...
  68. ncbi Characterization of the lep operon of Escherichia coli. Identification of the promoter and the gene upstream of the signal peptidase I gene
    P E March
    J Biol Chem 260:7206-13. 1985
    ..The DNA sequence immediately downstream of the lep gene contains features consistent with a rho factor-independent transcriptional termination site, indicating that the lep operon encodes only two proteins (lepA and lep)...
  69. ncbi Analysis of an Escherichia coli mutant strain resistant to the cell-killing function encoded by the gef gene family
    L K Poulsen
    Biotechnological Institute, Technical University of Denmark, Lyngby
    Mol Microbiol 6:895-905. 1992
    ..1 kDa. ORF178 and an upstream frame, ORF190, probably constitute an operon...
  70. ncbi Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB
    R Flachmann
    Institut fur Biochemie, Technische Hochschule Darmstadt, Federal Republic of Germany
    Eur J Biochem 175:221-8. 1988
    ..High-copy-number vectors, carrying either gene nadA, nadB or nadA + nadB, increased quinolinate production 1.5-fold, 2.0-fold and 15-fold respectively. Both gene products seem to be equally rate-limiting in quinolinate synthesis...
  71. pmc Functional equivalence of Escherichia coli sigma E and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa
    H Yu
    Department of Microbiology, University of Texas Health Science Center at San Antonio 78284 7758, USA
    J Bacteriol 177:3259-68. 1995
    ..aeruginosa and suggest that elements showing sequence similarity to those known to regulate AlgU activity in P. aeruginosa are also present in other bacteria...