deamination

Summary

Summary: The removal of an amino group (NH2) from a chemical compound.

Top Publications

  1. Prochnow C, Bransteitter R, Klein M, Goodman M, Chen X. The APOBEC-2 crystal structure and functional implications for the deaminase AID. Nature. 2007;445:447-51 pubmed
    ..Different APOBEC members use the same deamination activity to achieve diverse human biological functions...
  2. Yu A, Granvil C, Haining R, Krausz K, Corchero J, Küpfer A, et al. The relative contribution of monoamine oxidase and cytochrome p450 isozymes to the metabolic deamination of the trace amine tryptamine. J Pharmacol Exp Ther. 2003;304:539-46 pubmed
    ..It had been reported that deamination of tryptamine to tryptophol was mediated by CYP2D6, a cytochrome P450 that is expressed in human brain, ..
  3. Ali M, Alam M, Kawasaki T, Nakayama S, Nagatsugi F, Sasaki S. Sequence- and base-specific delivery of nitric oxide to cytidine and 5-methylcytidine leading to efficient deamination. J Am Chem Soc. 2004;126:8864-5 pubmed
    ..innovative method for sequence- and base-specific delivery of NO to a specific site of DNA followed by specific deamination. We designed a NO transfer reaction from S-nitroso thioguanine to an imino tautomer of cytosine...
  4. Teperek Tkacz M, Pasque V, Gentsch G, Ferguson Smith A. Epigenetic reprogramming: is deamination key to active DNA demethylation?. Reproduction. 2011;142:621-32 pubmed publisher
    ..These findings are also considered along with alternative demethylation pathways involving hydroxymethylation. ..
  5. Larijani M, Martin A. Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID. Mol Cell Biol. 2007;27:8038-48 pubmed
    ..Since transcription of target genes is required for deamination in vivo and AID exclusively mutates single-stranded DNA (ssDNA) in vitro, AID has been postulated to mutate ..
  6. Siebel A, Piato A, Capiotti K, Seibt K, Bogo M, Bonan C. PTZ-induced seizures inhibit adenosine deamination in adult zebrafish brain membranes. Brain Res Bull. 2011;86:385-9 pubmed publisher
    ..and adenosine deaminase (ADA) contributes to the regulation of this nucleoside concentration through its deamination. In this study, we tested the effect of pentylenetetrazole (PTZ)-induced seizures on ectonucleotidase and ADA ..
  7. Shivarov V, Shinkura R, Honjo T. Dissociation of in vitro DNA deamination activity and physiological functions of AID mutants. Proc Natl Acad Sci U S A. 2008;105:15866-71 pubmed publisher
    ..Two alternative mechanisms of DNA cleavage by AID have been proposed: RNA editing and DNA deamination. In support of the latter, AID has DNA deamination activity in cell-free systems that is assumed to represent ..
  8. Malim M. APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos Trans R Soc Lond B Biol Sci. 2009;364:675-87 pubmed publisher
  9. Holtz C, Sadler H, Mansky L. APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure. Nucleic Acids Res. 2013;41:6139-48 pubmed publisher
    ..specificity for cytosine dinucleotides, though only certain cytosine dinucleotides are 'hotspots' for cytosine deamination, and others experience little or no editing by A3G...

More Information

Publications62

  1. Mehler A, Tabor H. Deamination of histidine to form urocanic acid in liver. J Biol Chem. 1953;201:775-84 pubmed
  2. Choi J, Pfeifer G. The role of DNA polymerase eta in UV mutational spectra. DNA Repair (Amst). 2005;4:211-20 pubmed
    ..of Pol eta or low levels of remaining Pol eta, lesion replication is delayed allowing more time for cytosine deamination within CPDs to occur...
  3. Osuji G, Konan J, M Mbijjewe G. RNA synthetic activity of glutamate dehydrogenase: determination of enzyme purity, RNA characteristics, and deamination/amination ratio. Appl Biochem Biotechnol. 2004;119:209-28 pubmed
    ..The RNA synthetic activity of the enzyme was at least 50-fold more active in the deamination than in the amination direction, thus providing a robust technology for assay of the enzyme's activity...
  4. Bélanger K, Savoie M, Rosales Gerpe M, Couture J, Langlois M. Binding of RNA by APOBEC3G controls deamination-independent restriction of retroviruses. Nucleic Acids Res. 2013;41:7438-52 pubmed publisher
    ..This can occur by mechanisms dependent on catalytic activity, resulting in the mutagenic deamination of nascent viral cDNA, and/or by other means that are independent of its catalytic activity...
  5. Song Q, Cannistraro V, Taylor J. Rotational position of a 5-methylcytosine-containing cyclobutane pyrimidine dimer in a nucleosome greatly affects its deamination rate. J Biol Chem. 2011;286:6329-35 pubmed publisher
    ..mutations are proposed to arise from the insertion of A by DNA polymerase ? opposite the T that results from deamination of the methylC ((m)C) within the CPD...
  6. Singal R, Grimes S. Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction. Biotechniques. 2001;30:116-20 pubmed
  7. Glaser R, Wu H, Lewis M. Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation. J Am Chem Soc. 2005;127:7346-58 pubmed
    Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2...
  8. Neta P, Pu Q, Kilpatrick L, Yang X, Stein S. Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides. J Am Soc Mass Spectrom. 2007;18:27-36 pubmed
    ..that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is ..
  9. Chelico L, Prochnow C, Erie D, Chen X, Goodman M. Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G. J Biol Chem. 2010;285:16195-205 pubmed publisher
    ..monomer that binds single-stranded DNA, Alu RNA, and catalyzes processive C-->U deaminations with 3'-->5' deamination polarity, similar to native Apo3G. The CD1 domain is essential for both processivity and polarity...
  10. Senavirathne G, Jaszczur M, Auerbach P, Upton T, Chelico L, Goodman M, et al. Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution. J Biol Chem. 2012;287:15826-35 pubmed publisher
    ..We address the specific issue of deamination asymmetry within the general context of ssDNA scanning mechanisms and show that Apo3G scanning trajectories, ..
  11. Branco M, Ficz G, Reik W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet. 2011;13:7-13 pubmed publisher
    ..Although we have only started to scratch the surface, interesting clues on the role of 5-hydroxymethylcytosine are quickly emerging. ..
  12. Rayat S, Qian M, Glaser R. Nitrosative cytosine deamination. An exploration of the chemistry emanating from deamination with pyrimidine ring-opening. Chem Res Toxicol. 2005;18:1211-8 pubmed
    A discussion of nitrosative deamination of cytosine 1 is presented that argues for the formation of 6 by diazotization of 1 to cytosinediazonium ion 2 and its electrostatic complex 3, dediazoniation to 4 <--> 5, and amide-bond ..
  13. Connolly B. Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem Soc Trans. 2009;37:65-8 pubmed publisher
    ..The possible role of read-ahead recognition of uracil/hypoxanthine in DNA repair is discussed, as is the observation that the feature appears to be limited to replicative polymerases of the archaeal domain. ..
  14. Zhang H, Bren U, Kozekov I, Rizzo C, Stec D, Guengerich F. Steric and electrostatic effects at the C2 atom substituent influence replication and miscoding of the DNA deamination product deoxyxanthosine and analogs by DNA polymerases. J Mol Biol. 2009;392:251-69 pubmed publisher
    Deoxyinosine (dI) and deoxyxanthosine (dX) are both formed in DNA at appreciable levels in vivo by deamination of deoxyadenosine (dA) and deoxyguanosine (dG), respectively, and can miscode...
  15. Wanner R, Castor D, Güthlein C, Bottger E, Springer B, Jiricny J. The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination. J Bacteriol. 2009;191:6312-9 pubmed publisher
    Spontaneous hydrolytic deamination of DNA bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats...
  16. Hendriks G, Calléja F, Besaratinia A, Vrieling H, Pfeifer G, Mullenders L, et al. Transcription-dependent cytosine deamination is a novel mechanism in ultraviolet light-induced mutagenesis. Curr Biol. 2010;20:170-5 pubmed publisher
    ..Here we show that transcription-associated UV-induced nucleotide substitutions are caused by increased deamination of cytosines to uracil within photolesions at the transcribed strand, presumably at sites of stalled ..
  17. Ruszczycky M, Choi S, Liu H. Stoichiometry of the redox neutral deamination and oxidative dehydrogenation reactions catalyzed by the radical SAM enzyme DesII. J Am Chem Soc. 2010;132:2359-69 pubmed publisher
    DesII from Streptomyces venezuelae is a radical SAM (S-adenosyl-l-methionine) enzyme that catalyzes the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to form TDP-3-keto-4,6-dideoxy-d-glucose in the biosynthesis of TDP-d-desosamine...
  18. Heinl S, Hartinger D, Thamhesl M, Schatzmayr G, Moll W, Grabherr R. An aminotransferase from bacterium ATCC 55552 deaminates hydrolyzed fumonisin B?. Biodegradation. 2011;22:25-30 pubmed publisher
    ..FB? by microorganisms seems to comprise two essential steps: hydrolysis to hydrolyzed fumonisin B? (HFB?) and deamination of the hydrolysis product...
  19. Chahwan R, Wontakal S, Roa S. Crosstalk between genetic and epigenetic information through cytosine deamination. Trends Genet. 2010;26:443-8 pubmed publisher
    ..We therefore propose that the AID/APOBEC family of deaminases are likely to have acted as drivers throughout vertebrate evolution. ..
  20. Yu P, Wang M, Fan H, Deng Y, Gubisne Haberle D. Involvement of SSAO-mediated deamination in adipose glucose transport and weight gain in obese diabetic KKAy mice. Am J Physiol Endocrinol Metab. 2004;286:E634-41 pubmed
    ..This enzyme catalyzes deamination of methylamine and aminoacetone, leading to production of toxic formaldehyde and methylglyoxal, respectively, ..
  21. Lindahl T, Nyberg B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry. 1974;13:3405-10 pubmed
  22. Malina H, Martin X. Deamination of 3-hydroxykynurenine in bovine lenses: a possible mechanism of cataract formation in general. Graefes Arch Clin Exp Ophthalmol. 1995;233:38-44 pubmed
    ..7, 3.5, and 9.6 mumol/g of tissue per h in retina, iris/ciliary body, and lens respectively. The deamination of 3-hydroxykynurenine resulted in the formation of a fluorescent substance which was identified as oxidized ..
  23. Caulfield J, Wishnok J, Tannenbaum S. Nitric oxide-induced deamination of cytosine and guanine in deoxynucleosides and oligonucleotides. J Biol Chem. 1998;273:12689-95 pubmed
    The autoxidation of nitric oxide (NO.) forms the nitrosating agent N2O3, which can directly damage DNA by deamination of DNA bases following nitrosation of their primary amine functionalities...
  24. Frederico L, Kunkel T, Shaw B. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry. 1990;29:2532-7 pubmed
    Previously it has not been possible to determine the rate of deamination of cytosine in DNA at 37 degrees C because this reaction occurs so slowly...
  25. Fryxell K, Zuckerkandl E. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol Biol Evol. 2000;17:1371-83 pubmed
    DNA melting is rate-limiting for cytosine deamination, from which we infer that the rate of cytosine deamination should decline twofold for each 10% increase in GC content...
  26. Weiss B. Endonuclease V of Escherichia coli prevents mutations from nitrosative deamination during nitrate/nitrite respiration. Mutat Res. 2001;461:301-9 pubmed
    ..It thereby reduces the mutagenic effects of nitrous acid by attacking lesions caused by nitrosative deamination. Nitrosating agents may be produced endogenously when E...
  27. Sueoka N. Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses. Gene. 2002;300:141-54 pubmed
    ..2) The above result makes the deamination of cytosine due to double-strand breathing of DNA [Mol. Biol. Evol...
  28. Dickerson S, Market E, Besmer E, Papavasiliou F. AID mediates hypermutation by deaminating single stranded DNA. J Exp Med. 2003;197:1291-6 pubmed
    ..Finally, AID does not target mutational hotspots, thus mutational targeting to specific residues must be attributed to different factors. ..
  29. Byeon I, Ahn J, Mitra M, Byeon C, Hercík K, Hritz J, et al. NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat Commun. 2013;4:1890 pubmed publisher
    ..Our results afford novel mechanistic insights into APOBEC3A-mediated deamination and provide the structural basis for further molecular studies.
  30. MacDuff D, Harris R. Directed DNA deamination by AID/APOBEC3 in immunity. Curr Biol. 2006;16:R186-9 pubmed
  31. Rayat S, Glaser R. 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole and nitrosative guanine deamination. A theoretical study of geometries, electronic structures, and N-protonation. J Org Chem. 2003;68:9882-92 pubmed
    ..It is an immediate consequence of this result that the direct observation of the cations 8 and 9 should be possible in the gas phase only. ..
  32. Bhagwat A. DNA-cytosine deaminases: from antibody maturation to antiviral defense. DNA Repair (Amst). 2004;3:85-9 pubmed
    The deamination of cytosines in DNA to uracil, thought to be initiated by free water within the cells, is a well studied pathway by which C to T mutations occur...
  33. Beale R, Petersen Mahrt S, Watt I, Harris R, Rada C, Neuberger M. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. J Mol Biol. 2004;337:585-96 pubmed
  34. Gubisne Haberle D, Hill W, Kazachkov M, Richardson J, Yu P. Protein cross-linkage induced by formaldehyde derived from semicarbazide-sensitive amine oxidase-mediated deamination of methylamine. J Pharmacol Exp Ther. 2004;310:1125-32 pubmed
    ..Increased SSAO-mediated deamination may contribute to protein deposition, the formation of plaques, and inflammation, and thus may be involved in ..
  35. Rangam G, Schmitz K, Cobb A, Petersen Mahrt S. AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloud. PLoS ONE. 2012;7:e43279 pubmed publisher
    ..Here we demonstrate that AID's enzymatic activity is inversely proportional to the electron cloud size of C5-cytosine - H > F > methyl > hydroxymethyl. This makes AID an unlikely candidate to be part of 5 hmC removal. ..
  36. Yu P, Lu L, Fan H, Kazachkov M, Jiang Z, Jalkanen S, et al. Involvement of semicarbazide-sensitive amine oxidase-mediated deamination in lipopolysaccharide-induced pulmonary inflammation. Am J Pathol. 2006;168:718-26 pubmed
    ..Lysine residues of proteins were the primary targets for cross-linkage with formaldehyde derived from deamination of methylamine...
  37. Suspène R, Aynaud M, Vartanian J, Wain Hobson S. Efficient deamination of 5-methylcytidine and 5-substituted cytidine residues in DNA by human APOBEC3A cytidine deaminase. PLoS ONE. 2013;8:e63461 pubmed publisher
    b>Deamination of 5-methylcytidine (5MeC) in DNA results in a G:T mismatch unlike cytidine (C) deamination which gives rise to a G:U pair. Deamination of C was generally considered to arise spontaneously...
  38. Cooper D, Mort M, Stenson P, Ball E, Chuzhanova N. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum Genomics. 2010;4:406-10 pubmed
    ..is related to its role as the major site of cytosine methylation with the attendant risk of spontaneous deamination of 5-methylcytosine (5mC) to yield thymine...
  39. Nabel C, Jia H, Ye Y, Shen L, Goldschmidt H, Stivers J, et al. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol. 2012;8:751-8 pubmed publisher
    ..Although oxidation-dependent pathways for demethylation have been described, pathways involving deamination of either 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) have emerged as alternatives...
  40. Vuong B, Chaudhuri J. Combinatorial mechanisms regulating AID-dependent DNA deamination: interacting proteins and post-translational modifications. Semin Immunol. 2012;24:264-72 pubmed publisher
  41. Wang M, Rada C, Neuberger M. Altering the spectrum of immunoglobulin V gene somatic hypermutation by modifying the active site of AID. J Exp Med. 2010;207:141-53 pubmed publisher
    ..As a critical test of whether such DNA deamination activity underpins antibody diversification and to gain insight into the extent to which the antibody mutation ..
  42. Cannistraro V, Taylor J. Acceleration of 5-methylcytosine deamination in cyclobutane dimers by G and its implications for UV-induced C-to-T mutation hotspots. J Mol Biol. 2009;392:1145-57 pubmed publisher
    ..enhances CPD formation in sunlight, little is known about the effect of methylation and sequence context on the deamination of 5-methylcytosine ((m)C) and its contribution to mutagenesis at these hotspots...
  43. Bertoldi M, Cellini B, Montioli R, Borri Voltattorni C. Insights into the mechanism of oxidative deamination catalyzed by DOPA decarboxylase. Biochemistry. 2008;47:7187-95 pubmed publisher
    The unusual oxygen-consuming oxidative deamination reaction catalyzed by the pyridoxal 5'-phosphate (PLP) enzyme DOPA decarboxylase (DDC) was here investigated...
  44. Desrosiers M, Cembrola K, Fakir M, Stephens L, Jama F, Shameli A, et al. Adenosine deamination sustains dendritic cell activation in inflammation. J Immunol. 2007;179:1884-92 pubmed
    ..Our findings suggest a mechanism that DCs maintain their hyperreactive state in inflammation despite the general state of suppression, and reveal a regulatory role of adenosine deaminase in DC innate immune responses. ..
  45. Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat A. Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucleic Acids Res. 2006;34:3762-70 pubmed
    Hydrolytic deamination of cytosines in DNA creates uracil and, if unrepaired, these lesions result in C to T mutations...
  46. Coker H, Morgan H, Petersen Mahrt S. Genetic and in vitro assays of DNA deamination. Methods Enzymol. 2006;408:156-70 pubmed
    ..The application of these assays to future studies of the deaminase family will provide an indispensible tool in determining the potentially diverse functions of the remainder of this family of enzymes. ..
  47. Besmer E, Market E, Papavasiliou F. The transcription elongation complex directs activation-induced cytidine deaminase-mediated DNA deamination. Mol Cell Biol. 2006;26:4378-85 pubmed
    ..In this assay, which detects AID-mediated deamination in the context of transcription by Escherichia coli RNA polymerase, deamination targets either strand and ..
  48. Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U. The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. J Exp Med. 2005;202:1443-54 pubmed
    ..Thus, AID does not gain access to the 5' and constant regions of Ig genes. The implications for the role of transcription and Ung in SHM are discussed. ..
  49. Ohlson J, Ensterö M, Sjoberg B, Ohman M. A method to find tissue-specific novel sites of selective adenosine deamination. Nucleic Acids Res. 2005;33:e167 pubmed
    ..The RNA substrates were verified by RT-PCR, RNase protection and microarray. Using this method it is possible to uniquely identify novel single sites of selective A to I editing. ..
  50. Hodgen B, Rayat S, Glaser R. Nitrosative adenine deamination: facile pyrimidine ring-opening in the dediazoniation of adeninediazonium ion. Org Lett. 2003;5:4077-80 pubmed
    ..The results suggest that 4-cyano-5-isocyano-imidazole, 4, and 4,5-dicyanoimidazole, 5, might be formed to some extent in nitrosative deaminations of adenine. ..
  51. Neuberger M, Harris R, Di Noia J, Petersen Mahrt S. Immunity through DNA deamination. Trends Biochem Sci. 2003;28:305-12 pubmed
    ..Recent evidence indicates that all three processes are caused by the deamination of cytosine to uracil at sites within the immunoglobulin (Ig) loci, with the pattern of diversification ..
  52. Lee D, Pfeifer G. Deamination of 5-methylcytosines within cyclobutane pyrimidine dimers is an important component of UVB mutagenesis. J Biol Chem. 2003;278:10314-21 pubmed
    ..It is not known how these mutations might arise. One hypothesis is that UV-induced mutations occur only after deamination of the cytosine or 5-methylcytosine within the pyrimidine dimer...
  53. Hellsten Y, Richter E, Kiens B, Bangsbo J. AMP deamination and purine exchange in human skeletal muscle during and after intense exercise. J Physiol. 1999;520 Pt 3:909-20 pubmed
    1. The present study examined the regulation of human skeletal muscle AMP deamination during intense exercise and quantified muscle accumulation and release of purines during and after intense exercise. 2...