The world's first wiki where authorship really matters (Nature Genetics, 2008). Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts. Search thousands of articles and collaborate with scientists around the globe.

wikigene or wiki gene protein drug chemical gene disease author authorship tracking collaborative publishing evolutionary knowledge reputation system wiki2.0 global collaboration genes proteins drugs chemicals diseases compound
Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
Gene Review

LH0168  -  nuclease

Escherichia coli

Welcome! If you are familiar with the subject of this article, you can contribute to this open access knowledge base by deleting incorrect information, restructuring or completely rewriting any text. Read more.

Disease relevance of LH0168

  • A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region [1].
  • Overexpression of dominant-negative mutants of various viral proteins can result in 'intracellular immunization'. Here we describe a new approach to interfering with viral replication in which a nuclease is fused to a capsid component so that the nuclease is encapsidated inside the virion where it can inactivate viral nucleic acid [2].
  • These enzymes are phospholipase C from Bacillus cereus (structure at 1.5-A resolution) (43) and P1 nuclease from Penicillium citrinum (structure at 2.8-A resolution) (74) [3].
  • A phage T4 inhibitor of DNA restriction activates anticodon nuclease, but other T4 proteins restore tRNALys [4].
  • Detection of a homologous system in Neisseria and a different anticodon nuclease in colicin E5 suggest ubiquity and diversity of such tRNA toxins [4].

High impact information on LH0168

  • S1 nuclease mapping of in vivo transcripts from an E. coli gyrase temperature-sensitive mutant harboring the plasmids indicates that the bulk of the transcripts at either permissive or nonpermissive temperatures can proceed through the CG sequence, suggesting that the sequence is normally in the B helical form in vivo [5].
  • Plasmid deletions generated with Bal 31 nuclease show that the DNA sequence CTGCCACCC in the -44 to -36 region of this promoter is necessary for its heat shock activity [6].
  • We interpret the nuclease protection pattern and sequence data as evidence for three Mu A protein binding sites at each end of Mu [7].
  • The ligated junction is resistant to nuclease P1 and RNAase T2 but sensitive to venom phosphodiesterase and alkaline hydrolysis, consistent with a 2',5' linkage [8].
  • On the 3' side of pyrimidine dimers, the UVRABC nuclease cut the fourth or the fifth phosphodiester bond 3' to pyrimidine dimers [1].

Chemical compound and disease context of LH0168

  • The reassociation kinetics of Escherichia coli DNA were measured by S1 nuclease resistance and hydroxyapatite binding [9].
  • In vitro introduction of phosphorothioate linkages into one end of a linearized replicative plasmid, followed by exonuclease III and S1 nuclease treatments, gives rise to truncated forms that, upon circularization by blunt-end ligation, transform E. coli and replicate in vivo [10].
  • Using the Escherichia coli lac UV5 and trp EDCBA promoters as in vitro models of open complex formation, we have identified the sites inside these transcription bubbles that are accessible for hybridization by short, nuclease-resistant, non-extendable oligoribonucleotides (ORNs) [11].
  • RNase D, a putative tRNa processing nuclease, has been purified about 1,000-fold from extracts of Escherichia coli to apparent homogeneity, as judged by acrylamide gel electrophoresis under nondenaturing and denaturing conditions and by gel electrofocusing [12].
  • It has been suggested previously that Ndk, similar to its human counterparts, possesses nuclease 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 [13].

Biological context of LH0168

  • We constructed fusion genes consisting of the region encoding the N-terminal portion of the TYA/TYB open reading frames of retrotransposon Ty1 and either of two different nuclease genes [2].
  • The ABC excision nuclease of Escherichia coli is an ATP-dependent DNA repair enzyme composed of three protein subunits, UvrA, UvrB and UvrC [14].
  • AlkB has no detectable nuclease, DNA glycosylase or methyltransferase activity; however, Escherichia coli alkB mutants are defective in processing methylation damage generated in single-stranded DNA [15].
  • The first view of the 5' nuclease domain, responsible for excising the Okazaki RNA in lagging-strand DNA replication, shows a cluster of conserved divalent metal-ion-binding carboxylates at the bottom of a cleft [16].
  • The four major structural domains created by the base-pairing scheme correspond closely to RNA fragments isolated after nuclease digestion in the presence of bound ribosomal proteins [17].

Anatomical context of LH0168

  • Several KB cell RNAs with long half-lives in vivo, including 5S and bulk 4S RNA, are not cleaved by this nuclease [18].
  • A nuclease that cuts specifically in the ribosome binding site of some T4 mRNAs [19].
  • The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering translocation of the toxin across the OM [20].
  • Mung bean nuclease analysis mapped the bacterial transcriptional start site of the promoter to the U3 region of the LTR, in contrast to transcription in eukaryotic cells, which initiates in the U3-R boundary of the LTR [21].
  • Comparison of the hairpins derived from the DNA of morula, blastula, and gastrula stage embryos shows that during embryogenesis there are changes in the average number and position of S1 nuclease-sensitive base pair mismatch sites on the majority of the hairpin stems [22].

Associations of LH0168 with chemical compounds

  • Substrates for phospholipase C are phosphatidylinositol and phosphatidylcholine, while P1 nuclease is an endonuclease hydrolyzing single stranded ribo- and deoxyribonucleotides [3].
  • Thus, the T4-induced anticodon nuclease cleaves lysine tRNA 5' to the wobble position, yielding 2':3'-P greater than and 5'-OH termini [23].
  • We report high-resolution 13C and 15N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca2+ [24].
  • Here, we show that purified, cloned endk is a DNA repair nuclease whose substrate is uracil misincorporated into DNA [25].
  • Equations are derived that describe the observed form of reassociation kinetics as measured with hydroxyapatite and with single strand specific nuclease [26].

Other interactions of LH0168

  • The purification procedure resulted in > 90% pure TrwC protein, which was free of contaminating nuclease activities [27].

Analytical, diagnostic and therapeutic context of LH0168

  • Consistent with filter-binding and nuclease-protection studies, complexes of 20 to 30 dnaA monomers are visualized at oriC and other sites by electron microscopy [28].
  • To map the protein-protein and protein-DNA interactions involved in lambda site-specific recombination, Int cleavage assays with suicide substrates, nuclease protection patterns, gel retardation experiments, and quantitative Western blotting were applied to wild-type attL and attL mutants [29].
  • The nuclease-resistant junction dinucleotide comigrates with authentic (2',5') APA marker in thin-layer chromatography [8].
  • The experimental approach made use of S1 nuclease protection assays on in vivo synthesized transcripts, site-directed mutagenesis and construction of chimeric plasmids, dissection of the processing reaction by RNA mobility retardation experiments, and in vitro RNA degradation assays with cellular extracts [30].
  • The DNA helix at the tandemly repeated, 13mer sequence is thermodynamically unstable, as evidenced by hypersensitivity to single-strand-specific nuclease in a negatively supercoiled plasmid, and demonstrated by stable DNA unwinding seen after two-dimensional gel electrophoresis of topoisomers [31].


  1. A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region. Sancar, A., Rupp, W.D. Cell (1983) [Pubmed]
  2. New antiviral strategy using capsid-nuclease fusion proteins. Natsoulis, G., Boeke, J.D. Nature (1991) [Pubmed]
  3. Structure and mechanism of alkaline phosphatase. Coleman, J.E. Annual review of biophysics and biomolecular structure. (1992) [Pubmed]
  4. Anticodon nucleases. Kaufmann, G. Trends Biochem. Sci. (2000) [Pubmed]
  5. Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence. Peck, L.J., Wang, J.C. Cell (1985) [Pubmed]
  6. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Taylor, W.E., Straus, D.B., Grossman, A.D., Burton, Z.F., Gross, C.A., Burgess, R.R. Cell (1984) [Pubmed]
  7. Site-specific recognition of the bacteriophage Mu ends by the Mu A protein. Craigie, R., Mizuuchi, M., Mizuuchi, K. Cell (1984) [Pubmed]
  8. RNA ligase in bacteria: formation of a 2',5' linkage by an E. coli extract. Greer, C.L., Javor, B., Abelson, J. Cell (1983) [Pubmed]
  9. Studies on nucleic acid reassociation kinetics: reactivity of single-stranded tails in DNA-DNA renaturation. Smith, M.J., Britten, R.J., Davidson, E.H. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  10. A DNA fragment with an alpha-phosphorothioate nucleotide at one end is asymmetrically blocked from digestion by exonuclease III and can be replicated in vivo. Putney, S.D., Benkovic, S.J., Schimmel, P.R. Proc. Natl. Acad. Sci. U.S.A. (1981) [Pubmed]
  11. An approach to gene-specific transcription inhibition using oligonucleotides complementary to the template strand of the open complex. Milne, L., Xu, Y., Perrin, D.M., Sigman, D.S. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  12. Escherichia coli RNase D. Purification and structural characterization of a putative processing nuclease. Cudny, H., Zaniewski, R., Deutscher, M.P. J. Biol. Chem. (1981) [Pubmed]
  13. Molecular and Functional Interactions between Escherichia coli Nucleoside-diphosphate Kinase and the Uracil-DNA Glycosylase Ung. Goswami, S.C., Yoon, J.H., Abramczyk, B.M., Pfeifer, G.P., Postel, E.H. J. Biol. Chem. (2006) [Pubmed]
  14. Domainal evolution of a prokaryotic DNA repair protein and its relationship to active-transport proteins. Doolittle, R.F., Johnson, M.S., Husain, I., Van Houten, B., Thomas, D.C., Sancar, A. Nature (1986) [Pubmed]
  15. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Trewick, S.C., Henshaw, T.F., Hausinger, R.P., Lindahl, T., Sedgwick, B. Nature (2002) [Pubmed]
  16. Crystal structure of Thermus aquaticus DNA polymerase. Kim, Y., Eom, S.H., Wang, J., Lee, D.S., Suh, S.W., Steitz, T.A. Nature (1995) [Pubmed]
  17. Secondary structure of 16S ribosomal RNA. Noller, H.F., Woese, C.R. Science (1981) [Pubmed]
  18. Identification of a ribonuclease P-like activity from human KB cells. Koski, R.A., Bothwell, A.L., Altman, S. Cell (1976) [Pubmed]
  19. A nuclease that cuts specifically in the ribosome binding site of some T4 mRNAs. Uzan, M., Favre, R., Brody, E. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  20. Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. Loftus, S.R., Walker, D., Maté, M.J., Bonsor, D.A., James, R., Moore, G.R., Kleanthous, C. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  21. Human immunodeficiency viral long terminal repeat is functional and can be trans-activated in Escherichia coli. Kashanchi, F., Wood, C. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  22. Evidence for translocation of DNA sequences during sea urchin embryogenesis. Dickinson, D.G., Baker, R.F. Proc. Natl. Acad. Sci. U.S.A. (1978) [Pubmed]
  23. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. Amitsur, M., Levitz, R., Kaufmann, G. EMBO J. (1987) [Pubmed]
  24. Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints. Cole, H.B., Sparks, S.W., Torchia, D.A. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  25. Escherichia coli nucleoside diphosphate kinase is a uracil-processing DNA repair nuclease. Postel, E.H., Abramczyk, B.M. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  26. Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation. Britten, R.J., Davidson, E.H. Proc. Natl. Acad. Sci. U.S.A. (1976) [Pubmed]
  27. Purification and biochemical characterization of TrwC, the helicase involved in plasmid R388 conjugal DNA transfer. Grandoso, G., Llosa, M., Zabala, J.C., de la Cruz, F. Eur. J. Biochem. (1994) [Pubmed]
  28. The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Fuller, R.S., Funnell, B.E., Kornberg, A. Cell (1984) [Pubmed]
  29. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in lambda attL. Kim, S., Moitoso de Vargas, L., Nunes-Düby, S.E., Landy, A. Cell (1990) [Pubmed]
  30. Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Alifano, P., Rivellini, F., Piscitelli, C., Arraiano, C.M., Bruni, C.B., Carlomagno, M.S. Genes Dev. (1994) [Pubmed]
  31. The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. Kowalski, D., Eddy, M.J. EMBO J. (1989) [Pubmed]
WikiGenes - Universities