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Topic: Deamination

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	Deamination (Site not responding. Last check: 2007-10-22)
		Spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing ammonia in the process.
		In DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) and replacement with cytosine.
		Spontaneous deamination of 5-methylcytosine results in thymine and ammonia.
	www.serebella.com /encyclopedia/article-Deamination.html (196 words)

	Methylation inhibitors can increase the rate of cytosine deamination by (cytosine-5)-DNA methyltransferase -- Zingg et ...
		Since a mechanism-based inhibitor of the deamination reaction is not available and since deamination occurs with a much lower rate than the methyltransfer reaction, it is unlikely that the crystal structure of the methyltransferase with DNA shows the structure formed before or during the deamination reaction (40, 41).
		A caveat to this reaction is the formation of the 5,6-dihydrocytidine intermediate in the absence of AdoMet or AdoHcy and the presence of solvent water that deaminates with increased frequency (58).
		Deamination also requires protonation at N3 mediated by the enzyme and at the activated C5 of cytosine, followed by hydrolytic attack at the activated C4 of the 5,6-dihydrocytidine intermediate by water (52).
	nar.oxfordjournals.org /cgi/content/full/24/16/3267 (5905 words)

	Deamination -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-22)
		Deamination is the removal of an (A compound derived from ammonia by replacing hydrogen atoms by univalent hydrocarbon radicals) amine group from a ((physics and chemistry) the simplest structural unit of an element or compound) molecule.
		In ((biochemistry) a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix; associated with the transmission of genetic information) DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) and replacement with cytosine.
		Spontaneous deamination of 5-methylcytosine results in (A base found in DNA (but not in RNA) and derived from pyrimidine; pairs with adenine) thymine and ammonia.
	www.absoluteastronomy.com /encyclopedia/d/de/deamination.htm (192 words)

	Cytosine Deamination and Evolution: A View From Both Sides
		I have previously illustrated that the effects of cytosine deamination, expressed through the conventional genetic code, appear to bias mutational consequences by increasing a protein's hydrophobicity and predisposition to form secondary structures.
		Cytosines in the NTS are up to 10 times more likely to deaminate to uracil than those in the TS (1, 3), and in a strain of Escherichia coli defective in uracil excision (genotype ung), this causes a strand-dependent increase in C-to-T mutations.
		The extent of this susceptibility of cytosines in the NTS to deamination is roughly proportional to the frequency of transcription of the gene (1).
	www.idthink.net /biot/deam2 (1929 words)

	Full text - RNA editing in plant mitochondria, cytoplasmic male sterility and plant breeding.
		The latter approaches suggested that a deamination or a transamination mechanism may be involved in plant RNA editing.
		Although the double-labeling approach using partially purified mitochondrial extracts suggests strongly that a deamination process is operating in plant mitochondria, further experiments are necessary to ascertain that a transamination step is not involved in RNA editing.
		However, the observation that RNA editing occurs in intronic regions and in the stem of plant mitochondrial tRNA by correcting a mispairing of the stem indicates that formation of double stranded structures RNA may be associated to the mechanism of RNA editing in these organelles (Maréchal-Drouard et al., 1996; Marchfelder et al., 1996.
	www.ejbiotechnology.info /content/vol1/issue1/full/4/index.html (6493 words)

	Activation and Deactivation of a Broad-Spectrum Antiviral Drug by a Single Enzyme: Adenosine Deaminase Catalyzes Two ...
		The spontaneous hydrolytic deamination of viramidine to ribavirin
		Proposed deamination reaction mechanism of viramidine and ribavirin by adenosine deaminase.
		Deamination of adenosine analogs with calf intestine adenosine deaminase.
	aac.asm.org /cgi/content/full/47/1/426 (3116 words)

	Evolution's Design
		The bottom line is that spontaneous deamination of cytosine can lead to a base substitution known as a transition, where C is replaced by T (and G is replaced by A on the other strand of DNA).
		We might expect such mutations to be quite common, as the rate constant for cytosine deamination at 37 degree C in single stranded DNA translates into a half-life for any specific cytosine of about 200 years [3].
		Given that guanine deaminates at rates similar to adenine, and thymine lacks an exocyclic base, and thus experiences no deamination, we can see that the simple process of deamination would strongly favor cytosine as a target (figure 1).
	www.idthink.net /biot/deam/index.html (2743 words)

	Synthetic substrate analogs for the RNA-editing adenosine deaminase ADAR-2 -- Yi-Brunozzi et al. 27 (14): 2912 -- ...
		Deamination rates were shown to be sensitive to structural changes at the 2[prime]-carbon of the edited adenosine.
		Methylation of the 2[prime]-OH caused a large decrease in deamination rate, whereas 2[prime]-deoxyadenosine and 2[prime]-deoxy-2[prime]-fluoroadenosine were deaminated at a rate similar to adenosine.
		This identification and initial characterization of synthetic RNA editing substrate analogs further defines elements in the RNA that are important for the deamination reaction, and sets the stage for the analysis of other substrate and transition state analogs of increased structural complexity as well as detailed structural, thermodynamic and kinetic studies of this enzyme.
	nar.oupjournals.org /cgi/content/full/27/14/2912 (3435 words)

	Advantages and Disadvantages of Cytidine Deamination -- Cascalho 172 (11): 6513 -- The Journal of Immunology
		Cytidine deamination and diversification of the Ig genes
		cytidine to be deaminated at the apex of the loop (44, 45).
		DNA deamination mediates innate immunity to retroviral infection.
	www.jimmunol.org /cgi/content/full/172/11/6513 (4229 words)

	Catecholamine Metabolism: A Contemporary View with Implications for Physiology and Medicine -- Eisenhofer et al. 56 ...
		Deamination of norepinephrine to DOPEGAL by MAO and subsequent reduction to DHPG by aldehyde reductase (AR) occurs mainly in sympathetic nerves and represents the major pathway of norepinephrine metabolism.
		deamination pathway in the periphery and the latter a reductive
		Brown M (1984) Simultaneous assay of noradrenaline and its deaminated metabolite, dihydroxyphenylglycol, in plasma: a simplified approach to the exclusion of pheochromocytoma in patients with borderline elevation of plasma noradrenaline concentration.
	pharmrev.aspetjournals.org /cgi/pmidlookup?view=full&pmid=15317907 (7478 words)

	61 - Abstract (11th CROI) (Site not responding. Last check: 2007-10-22)
		Targeted deamination of dC?dU in the immunoglobulin locus is performed by the AID enzyme.
		Deamination within the immunoglobulin variable (IgV) gene are resolved by pathways that lead to changes in the DNA sequence and thereby generate IgV gene sequence diversity.
		Deamination that occurs within the immunoglobulin switch region is resolved by a process involving deletional recombination and this recombination (class-switch recombination) mediates the change in immunoglobulin isotype from IgM to IgG, IgE, or IgA.
	www.retroconference.org /2004/cd/Abstract/61.htm (306 words)

	Oxidative Deamination
		Deamination is also an oxidative reaction that occurs under aerobic conditions in all tissues but especially the liver.
		During oxidative deamination, an amino acid is converted into the corresponding keto acid by the removal of the amine functional group as ammonia and the amine functional group is replaced by the ketone group.
		The answer is that a combination of transamination and deamination of glutamic acid occurs which is a recycling type of reaction for glutamic acid.
	www.elmhurst.edu /~chm/vchembook/632oxdeam.html (281 words)

	Catecholamine Metabolism: A Contemporary View with Implications for Physiology and Medicine -- Eisenhofer et al. 56 ...
		deamination of norepinephrine and epinephrine by monoamine oxidase
		The deaminated aldehyde metabolites of catecholamines are short-lived
		DOPAL, the deaminated aldehyde metabolite of dopamine, and DOPEGAL,
	pharmrev.aspetjournals.org /cgi/content/full/56/3/331 (7478 words)

	Deamination (Site not responding. Last check: 2007-10-22)
		Spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing ammonia in theprocess.
		In DNA, this spontaneous deamination is corrected for by the removal of uracil (product ofcytosine deamination and not part of DNA) and replacement with cytosine.
		InDNA, this reaction cannot be corrected because the repair mechanisms do not recognize thymine as erroneous (as opposed touracil), and unless it affects the function of the gene, the mutation will persist.
	www.therfcc.org /deamination-87835.html (162 words)

	Physical Organic Chemistry of deamination and denitrosation of nitrosoamides(nitrosamides) (Site not responding. Last check: 2007-10-22)
		We are working on aspects of the fundamental physical organic chemistry of deamination, especially of N-alkyl-N-nitrosoamides, as well as applications of deaminative technology to carbocationic addition polymerization (for which a patent is pending), to cancer chemotherapy, to mechanistic elucidation, and to organic synthesis.
		We are also investigating the deaminative preparations and fates of high energy carbocations including cyclopropanyl as well as the ability of deaminatively generated carbocations to intercept low nucleophilicity species including sigma-bond donors (e.g., cyclopropane).
		New deaminative methods, including those that are designed to generate longer-lived carbocations and to maximize derivatization of solvents are being developed.
	faculty.mcneese.edu /rdarbeau/research.html (632 words)

	CDC - Multiple rpoB Mutants of Mycobacterium tuberculosis and Second-order Selection
		Both are cytosine-to-tymine transitions, which easily occur by spontaneous cytosine deamination to uracil.
		This deamination process is normally counteracted by uracil-N-glycosylase, the product of the ung gene, and organisms defective in the removal of uracil from DNA have an increased spontaneous mutation rate and more G:C→ A:T base-pair transitions (7).
		Deamination of single-stranded DNA cytosine residues in aerobic nitric oxide solution at micromolar total NO exposures.
	www.cdc.gov /ncidod/eid/vol10no7/03-0598.htm (1107 words)

	deamination - General Practice Notebook (Site not responding. Last check: 2007-10-22)
		Deamination is a means of amino acid degradation that predominantly occurs in the liver.
		It entails the loss of an amino (-NH2) group that is used to produce ammonia.
		Examples of enzymes involved in oxidative deamination include amino acid oxidase and glutamate dehydrogenase.
	www.gpnotebook.co.uk /cache/282067002.htm (185 words)

	Encyclopedia: Deamination (Site not responding. Last check: 2007-10-22)
		Ammonia Amines are organic compounds containing nitrogen as the key atom in the amine functional group.
		It is a minor end-product of nitrogen metabolism in the human body (the main product being urea), and is found in small amounts in urine.
		Space-filling model of a section of DNA molecule Deoxyribonucleic acid (DNA) or deoxyribose nucleic acid is a nucleic acid that contains the genetic instructions specifying the biological development of all cellular forms of life (and many viruses).
	www.nationmaster.com /encyclopedia/Deamination (773 words)

	APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase -- ...
		deamination of cytidines in the minus DNA strand.
		The base specific deamination frequencies among a collection of 431 sequences from all the reactions are given as a function of local sequence context.
		Harris,R.S., Bishop,K.N., Sheehy,A.M., Craig,H.M., Petersen-Mahrt,S.K., Watt,I.N., Neuberger,M.S. and Malim,M.H. (2003) DNA deamination mediates innate immunity to retroviral infection.
	nar.oxfordjournals.org /cgi/content/full/32/8/2421 (4232 words)

	Brainstorms: Cytosine Deamination from Both Sides
		First, it reviewed the evidence that deamination of cytosine gave uracil, which meant that mutations couldn't be fixed.
		This is obviously detrimental to fitness, and hence one would expect that organisms that replaced uracil or cytosine would have a selective advantage; apparently uracil was replaced, which at partially solved the problem (in the context of error-repair mechanisms).
		Recall that my original thesis for the utility of cytosine deamination is not a generic "stand alone" but is tied to the originally specified conditions.
	www.iscid.org /boards/ubb-get_topic-f-6-t-000290-p-3.html (8106 words)

	ASCO - Abstracts - PubMed Abstract View (Site not responding. Last check: 2007-10-22)
		Deamination of glutamine is a prerequisite for optimal asparagine deamination by asparaginases in vivo (CCG-1961).
		The percentages of Asn and Gln deamination were predicted by ASNase activity in patients' sera.
		Deamination of Gln correlates with enhanced serum Asn deamination in vivo.
	www.asco.org /ac/1,1003,_12-002867-00_18-0015154634,00.asp?SearchNames= (458 words)

	Involvement of SSAO-mediated deamination in adipose glucose transport and weight gain in obese diabetic KKAy mice -- Yu ...
		Assessment of the deamination of aminoacetone, an endogenous substrate for semicarbazide-sensitive amine oxidase.
		Oxidative deamination of methylamine by semicarbazide-sensitive amine oxidase leads to cytotoxic damage in endothelial cells: possible consequence for diabetes.
		Formaldehyde produced endogenously via deamination of methylamine: a potential risk factor for initiation of endothelial injury.
	ajpendo.physiology.org /cgi/content/full/286/4/E634 (3620 words)

	RNA-specific Adenosine Deaminases -- Neurotransmitter.net
		Deamination of adenosines changes the coding capacity of the RNA, as inosine is decoded as guanosine, and alters the structure because A-U base pairs are replaced by I*U wobble pairs.
		We find that ADAR1 and ADAR2 deaminate a given RNA with the same selectivity, and this appears to be dictated by features of the RNA substrate.
		One form involves the deamination of adenosine to form inosine, which is subsequently translated as guanosine.
	www.neurotransmitter.net /adar.html (17685 words)

	A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site -- Sartori et al. 21 (12): ... (Site not responding. Last check: 2007-10-22)
		Horst,J.P. and Fritz,H.J. (1996) Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF.
		Lindahl,T. and Nyberg,B. (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid.
		Nilsen,H., Haushalter,K.A., Robins,P., Barnes,D.E., Verdine,G.L. and Lindahl,T. (2001) Excision of deaminated cytosine from the vertebrate genome: role of the SMUG1 uracil-DNA glycosylase.
	embojournal.npgjournals.com /cgi/content/full/21/12/3182 (6351 words)

	Reactome: Carmichael, GG
		In humans the deamination of adenosines to inosines is the m...
		Deamination at C6 position of adenosine in Editosome (ADAR1) [Homo sapiens]
		Deamination at C6 position of adenosine in Editosome (ADAR2) [Homo sapiens]
	www.genomeknowledge.org /cgi-bin/eventbrowser?DB=gk_current&ID=75057& (154 words)

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