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)
 
Chemical Compound Review

Hydroxyl     hydroxide

Synonyms: HYDROXY, oxidanide, hydroxide ion, Hydroxide(1-), hydroxyl ion, ...
 
 
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 Hydroxyl radical

  • M1 RNA (the catalytic subunit) alone and the RNAase P holoenzyme from E. coli cleave the tRNA-like structure of TYMV RNA in vitro at the 5' side of the quasi-helical structure to generate 5' phosphate and 3' hydroxyl groups in the cleavage products [1].
  • We show that virions and purified viral cores contain a unique endonuclease that cleaves RNAs containing a 5' methylated cap structure (m7GpppXm) preferentially at purine residues 10 to 14 nucleotides from the cap, generating fragments with 3'-terminal hydroxyl groups [2].
  • In the crystal structure of the tyrosyl tRNA synthetase (of Bacillus stearothermophilus), the side-chain hydroxyl of Thr 51 appears to make a weak hydrogen bond with the AMP moiety of the substrate intermediate, tyrosyl adenylate [3].
  • A major portion of the toxicity of hydrogen peroxide in Escherichia coli is attributed to DNA damage mediated by a Fenton reaction that generates active forms of hydroxyl radicals from hydrogen peroxide, DNA-bound iron, and a constant source of reducing equivalents [4].
  • The DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein [5].
 

Psychiatry related information on Hydroxyl radical

 

High impact information on Hydroxyl radical

  • This suggests a model of the RAG protein active site in which two divalent metal ions serve alternating and opposite roles as activators of attacking hydroxyl groups and stabilizers of oxyanion leaving groups [11].
  • The metal-activated hydroxide ion is a critical nucleophile in metalloenzymes that catalyze hydrolysis or hydration reactions [12].
  • Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing [13].
  • During TPRT, the LINE-1 endonuclease cleaves genomic DNA, freeing a 3' hydroxyl that serves as a primer for reverse transcription of LINE-1 RNA by LINE-1 reverse transcriptase [14].
  • The observed nonhomologous recombinations are entirely dependent on the 3' hydroxyl group of the 5' fragment, and are due to a splicing-like reaction in which RNA secondary structure guides the attack of this 3' hydroxyl on phosphoester bonds within the 3' fragment [15].
 

Chemical compound and disease context of Hydroxyl radical

 

Biological context of Hydroxyl radical

  • TFIID binding in the minor groove of DNA at the TATA element was demonstrated by methylation interference and hydroxyl radical footprinting assays, and by binding studies with thymine analog substituted oligonucleotides [20].
  • Moreover, elimination of a single transmembrane hydroxyl group severely inhibits antigen presentation without affecting signal transduction, suggesting that these two functions are mediated by different protein interactions [21].
  • We have used oligodeoxynucleotide-directed mutagenesis to construct two point mutants at this site: one to remove the hydroxyl group (Thr 51 leads to Ala 51) and the other, in addition, to distort the local polypeptide backbone (Thr 51 leads to Pro 51) [3].
  • Current estimates of CH3Br and CH3Cl emissions from oceanic sources, terrestrial plants and fungi, biomass burning and anthropogenic inputs do not balance their losses owing to oxidation by hydroxyl radicals, oceanic degradation, and consumption in soils, suggesting that additional natural terrestrial sources may be important [22].
  • For both spliceosomal and group II introns, the first-step reaction occurs by nucleophilic attack on the 5' splice junction by the 2' hydroxyl of an internal adenosine, forming a 2'-5' phosphodiester branch in the intron [23].
 

Anatomical context of Hydroxyl radical

 

Associations of Hydroxyl radical with other chemical compounds

 

Gene context of Hydroxyl radical

  • The reduction of copper(II) to copper(I) by APP involves an electron-transfer reaction and could enhance the production of hydroxyl radicals, which could then attack nearby sites [35].
  • The hydroxyl radical (OH.) scavenger dimethyl sulfoxide (DMSO) was found to dose-dependently inhibit interleukin 8 (IL-8) production in LPS-stimulated human whole blood [36].
  • C4B reacts much more effectively with hydroxyl groups than C4A and this is reversed for reaction with amino groups in spite of the very small difference in amino acid sequence between the two forms of C4 [37].
  • A quantification of the hydroxyl radical footprints allowed us to compare further the affinity of the LexA repressor for the recA operator with that of its isolated DNA binding domain [38].
  • When probed with hydroxyl radicals, ssDNA-RAD52 complexes exhibit a four-nucleotide repeat hypersensitivity pattern [39].
 

Analytical, diagnostic and therapeutic context of Hydroxyl radical

References

  1. Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA. Guerrier-Takada, C., van Belkum, A., Pleij, C.W., Altman, S. Cell (1988) [Pubmed]
  2. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Plotch, S.J., Bouloy, M., Ulmanen, I., Krug, R.M. Cell (1981) [Pubmed]
  3. A large increase in enzyme-substrate affinity by protein engineering. Wilkinson, A.J., Fersht, A.R., Blow, D.M., Carter, P., Winter, G. Nature (1984) [Pubmed]
  4. DNA damage and oxygen radical toxicity. Imlay, J.A., Linn, S. Science (1988) [Pubmed]
  5. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Kamtekar, S., Berman, A.J., Wang, J., Lázaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A. Mol. Cell (2004) [Pubmed]
  6. Sodium hydroxide decontamination of Creutzfeldt-Jakob disease virus. Brown, P., Rohwer, R.G., Gajdusek, D.C. N. Engl. J. Med. (1984) [Pubmed]
  7. Prooxidant-antioxidant shift induced by androgen treatment of human prostate carcinoma cells. Ripple, M.O., Henry, W.F., Rago, R.P., Wilding, G. J. Natl. Cancer Inst. (1997) [Pubmed]
  8. Inhibition of amyloid beta protein aggregation and neurotoxicity by rifampicin. Its possible function as a hydroxyl radical scavenger. Tomiyama, T., Shoji, A., Kataoka, K., Suwa, Y., Asano, S., Kaneko, H., Endo, N. J. Biol. Chem. (1996) [Pubmed]
  9. Molecular structure of a cross-reactive idiotype on autoantibodies recognizing parenchymal self. Karp, S.L., Kieber-Emmons, T., Sun, M.J., Wolf, G., Neilson, E.G. J. Immunol. (1993) [Pubmed]
  10. Reactive oxygen species-induced gastric ulceration: protection by melatonin. Bandyopadhyay, D., Chattopadhyay, A. Current medicinal chemistry. (2006) [Pubmed]
  11. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Fugmann, S.D., Lee, A.I., Shockett, P.E., Villey, I.J., Schatz, D.G. Annu. Rev. Immunol. (2000) [Pubmed]
  12. Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes. Christianson, D.W., Cox, J.D. Annu. Rev. Biochem. (1999) [Pubmed]
  13. Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Lancaster, L., Kiel, M.C., Kaji, A., Noller, H.F. Cell (2002) [Pubmed]
  14. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Morrish, T.A., Gilbert, N., Myers, J.S., Vincent, B.J., Stamato, T.D., Taccioli, G.E., Batzer, M.A., Moran, J.V. Nat. Genet. (2002) [Pubmed]
  15. Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure. Chetverin, A.B., Chetverina, H.V., Demidenko, A.A., Ugarov, V.I. Cell (1997) [Pubmed]
  16. Hydrogen peroxide-mediated toxicity for Leishmania donovani chagasi promastigotes. Role of hydroxyl radical and protection by heat shock. Zarley, J.H., Britigan, B.E., Wilson, M.E. J. Clin. Invest. (1991) [Pubmed]
  17. 5-Aminosalicylic acid protects against ischemia/reperfusion-induced gastric bleeding in the rat. Kvietys, P.R., Smith, S.M., Grisham, M.B., Manci, E.A. Gastroenterology (1988) [Pubmed]
  18. Elevated free nitrotyrosine levels, but not protein-bound nitrotyrosine or hydroxyl radicals, throughout amyotrophic lateral sclerosis (ALS)-like disease implicate tyrosine nitration as an aberrant in vivo property of one familial ALS-linked superoxide dismutase 1 mutant. Bruijn, L.I., Beal, M.F., Becher, M.W., Schulz, J.B., Wong, P.C., Price, D.L., Cleveland, D.W. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  19. Cytochrome P-450 mediates tissue-damaging hydroxyl radical formation during reoxygenation of the kidney. Paller, M.S., Jacob, H.S. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  20. Interaction of TFIID in the minor groove of the TATA element. Lee, D.K., Horikoshi, M., Roeder, R.G. Cell (1991) [Pubmed]
  21. Mutations of immunoglobulin transmembrane and cytoplasmic domains: effects on intracellular signaling and antigen presentation. Shaw, A.C., Mitchell, R.N., Weaver, Y.K., Campos-Torres, J., Abbas, A.K., Leder, P. Cell (1990) [Pubmed]
  22. Natural methyl bromide and methyl chloride emissions from coastal salt marshes. Rhew, R.C., Miller, B.R., Weiss, R.F. Nature (2000) [Pubmed]
  23. Group II intron splicing in vivo by first-step hydrolysis. Podar, M., Chu, V.T., Pyle, A.M., Perlman, P.S. Nature (1998) [Pubmed]
  24. Hydroxyl radical formation in neutrophils. Britigan, B.E., Cohen, M.S., Rosen, G.M. N. Engl. J. Med. (1988) [Pubmed]
  25. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Wilson, K.S., Noller, H.F. Cell (1998) [Pubmed]
  26. Hydroxyl radical scavengers inhibit human natural killer cell activity. Suthanthiran, M., Solomon, S.D., Williams, P.S., Rubin, A.L., Novogrodsky, A., Stenzel, K.H. Nature (1984) [Pubmed]
  27. Chemical evidence for production of hydroxyl radicals during microsomal electron transfer. Cohen, G., Cederbaum, A.I. Science (1979) [Pubmed]
  28. Sulfation preceding deiodination of iodothyronines in rat hepatocytes. Otten, M.H., Mol, J.A., Visser, T.J. Science (1983) [Pubmed]
  29. Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Ohndorf, U.M., Rould, M.A., He, Q., Pabo, C.O., Lippard, S.J. Nature (1999) [Pubmed]
  30. Lariat RNA's as intermediates and products in the splicing of messenger RNA precursors. Padgett, R.A., Konarska, M.M., Grabowski, P.J., Hardy, S.F., Sharp, P.A. Science (1984) [Pubmed]
  31. Prooxidant activity of transferrin and lactoferrin. Klebanoff, S.J., Waltersdorph, A.M. J. Exp. Med. (1990) [Pubmed]
  32. The specificity of cellular immune responses in guinea pigs. I. T cells specific for 2,4-dinitrophenyl-o-tyrosyl residues. Janeway, C.A., Cohen, B.E., Ben-Sasson, S.Z., Paul, W.E. J. Exp. Med. (1975) [Pubmed]
  33. Evidence for hydroxyl radical generation by human Monocytes. Weiss, S.J., King, G.W., LoBuglio, A.F. J. Clin. Invest. (1977) [Pubmed]
  34. DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants. Margolin, Y., Shafirovich, V., Geacintov, N.E., DeMott, M.S., Dedon, P.C. J. Biol. Chem. (2008) [Pubmed]
  35. The amyloid precursor protein of Alzheimer's disease in the reduction of copper(II) to copper(I). Multhaup, G., Schlicksupp, A., Hesse, L., Beher, D., Ruppert, T., Masters, C.L., Beyreuther, K. Science (1996) [Pubmed]
  36. Oxygen radical scavengers selectively inhibit interleukin 8 production in human whole blood. DeForge, L.E., Fantone, J.C., Kenney, J.S., Remick, D.G. J. Clin. Invest. (1992) [Pubmed]
  37. A comparison of the properties of two classes, C4A and C4B, of the human complement component C4. Law, S.K., Dodds, A.W., Porter, R.R. EMBO J. (1984) [Pubmed]
  38. Contacts between the LexA repressor--or its DNA-binding domain--and the backbone of the recA operator DNA. Hurstel, S., Granger-Schnarr, M., Schnarr, M. EMBO J. (1988) [Pubmed]
  39. Precise binding of single-stranded DNA termini by human RAD52 protein. Parsons, C.A., Baumann, P., Van Dyck, E., West, S.C. EMBO J. (2000) [Pubmed]
  40. Model for binding of transcription factor TFIIB to the TBP-DNA complex. Lee, S., Hahn, S. Nature (1995) [Pubmed]
  41. DNA footprinting with hydroxyl radical. Tullius, T.D. Nature (1988) [Pubmed]
  42. Mononuclear phagocytes have the potential for sustained hydroxyl radical production. Use of spin-trapping techniques to investigate mononuclear phagocyte free radical production. Britigan, B.E., Coffman, T.J., Adelberg, D.R., Cohen, M.S. J. Exp. Med. (1988) [Pubmed]
  43. Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Takamoto, K., Chance, M.R. Annual review of biophysics and biomolecular structure. (2006) [Pubmed]
  44. Familial giant cell hepatitis associated with synthesis of 3 beta, 7 alpha-dihydroxy-and 3 beta,7 alpha, 12 alpha-trihydroxy-5-cholenoic acids. Clayton, P.T., Leonard, J.V., Lawson, A.M., Setchell, K.D., Andersson, S., Egestad, B., Sjövall, J. J. Clin. Invest. (1987) [Pubmed]
 
WikiGenes - Universities