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Uracil-DNA GlycosidaseUracilDNA GlycosylasesN-Glycosyl HydrolasesDNA-Formamidopyrimidine GlycosylaseThymine DNA GlycosylaseDeoxyribonuclease (Pyrimidine Dimer)DNA RepairPentoxylTaxesGuanineDNA-(Apurinic or Apyrimidinic Site) LyaseEndodeoxyribonucleasesDeoxyribonuclease IV (Phage T4-Induced)ThymineDeoxyuracil NucleotidesCytosineDNA DamageDNASubstrate SpecificityBase Pair MismatchEscherichia coliAdenineCarbon-Oxygen LyasesApurinic AcidDeaminationMolecular Sequence DataBase SequenceUracil Nucleotides5-MethylcytosineEscherichia coli ProteinsGuanosineOligonucleotidesKineticsDeoxyguanosineHypoxanthineNucleotide Transport ProteinsMutationAmino Acid SequenceAlkylationHydantoinsDNA AdductsBromouracilState GovernmentTobacco IndustryCatalytic DomainOligodeoxyribonucleotidesDNA, BacterialBinding SitesCatalysisPyrimidine DimersCommercePentosyltransferasesBase PairingLabor UnionsModels, MolecularMutagenesisProtein BindingCloning, MolecularUracil MustardSequence Homology, Amino AcidCytidine DeaminaseAlkylating AgentsMethyl MethanesulfonateNucleic Acid HeteroduplexesComet AssayUridine MonophosphatePlasmidsUltraviolet RaysPyrophosphatasesLobbyingHeLa CellsDeoxyuridineExonucleasesSomatic Hypermutation, ImmunoglobulinDNA Breaks, Single-StrandedThermoproteaceaeUridine PhosphorylaseNucleic Acid ConformationDNA ReplicationSequence AlignmentDihydrouracil Dehydrogenase (NADP)PyrimidinesEndonucleasesDNA Transposable ElementsRecombinant ProteinsTegafurBorohydridesArabinofuranosyluracilUridineProtein Structure, TertiaryIntegrasesDNA PrimersCrystallography, X-RayDNA-Directed DNA PolymeraseCell LineThiouracilSulfites

EnzymeThymineCytosineDouble-strandedBasesAdenineEnzymesSubstratesAbasicRecognitionReactionFamilyCellsSitesFoundStructureMethylpurine DNA GlycosylaseOGG1Family of enzymesEndonucleaseLyaseLesionsUridineOxidativePyrimidinePathwaysVitroDuplexLacksReplicationRecognizeProteinActsInteractionsHumanLasting damageComplexTerms

Enzyme6

• This enzyme would therefore recognize and cut out both types of uracil - the one incorporated naturally, and the one formed due to cytosine deamination, which would trigger unnecessary and inappropriate repair processes. (wikipedia.org)
• The N123D mutation generates an enzyme that excises cytosine. (ox.ac.uk)
• In the first stage of the base excision repair pathway the enzyme uracil DNA glycosylase (UNG) recognizes and excises uracil (U) from DNA filaments. (sissa.it)
• Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1), previously thought to be a backup enzyme for uracil-DNA glycosylase, has recently been shown to excise 5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU) bearing an oxidized group at ring C5 as well as an uracil. (elsevierpure.com)
• The enzyme hydrolyzes uracil glycosidic bonds at U-DNA in single- and double-stranded DNA excising uracil and creating alkali sensitive abasic sites in the DNA. (apslabs.in)
• The enzyme is inactive on RNA and native, uracil-free DNA. (apslabs.in)

Thymine11

• In DNA, the uracil nucleobase is replaced by thymine (T). Uracil is a demethylated form of thymine. (wikipedia.org)
• In RNA, uracil base-pairs with adenine and replaces thymine during DNA transcription. (wikipedia.org)
• Methylation of uracil produces thymine. (wikipedia.org)
• In DNA, the evolutionary substitution of thymine for uracil may have increased DNA stability and improved the efficiency of DNA replication (discussed below). (wikipedia.org)
• Methylated uracil is identical to thymine. (wikipedia.org)
• Hence the hypothesis that, over time, thymine became standard in DNA instead of uracil. (wikipedia.org)
• Apparently, either there was no evolutionary pressure to replace uracil in RNA with the more complex thymine, or uracil has some chemical property that is useful in RNA, which thymine lacks. (wikipedia.org)
• Uracil is selected over cytosine by a pattern of specific hydrogen bonds, and thymine is excluded by steric clash of its 5-methyl group with Y66. (ox.ac.uk)
• Integration of the present results and the structural data elucidates how hSMUG1 accepts uracil, hoU, hmU and fU as substrates, but not other oxidized pyrimidines such as 5-hydroxycytosine, 5-formylcytosine and thymine glycol, and intact pyrimidines such as thymine and cytosine. (elsevierpure.com)
• This occurs through deamination, where the hydrolysis of cytosine, turning it into uracil, causes the base to mispair with adenine during replication, and ultimately be replaced by thymine. (ukessays.com)
• Thymine dimers are excised in bacteria by UvrABC proteins in a process known as nucleotide excision repair (NER) as illustrated in Figure 29.29. (pharmacy180.com)

Cytosine6

• The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. (wikipedia.org)
• This is because cytosine can deaminate spontaneously to produce uracil through hydrolytic deamination. (wikipedia.org)
• Therefore, if there were an organism that used uracil in its DNA, the deamination of cytosine (which undergoes base pairing with guanine) would lead to formation of uracil (which would base pair with adenine) during DNA synthesis. (wikipedia.org)
• The first reaction is the simplest of the syntheses, by adding water to cytosine to produce uracil and ammonia: C4H5N3O + H2O → C4H4N2O2 + NH3 The most common way to synthesize uracil is by the condensation of malic acid with urea in fuming sulfuric acid: C4H4O4 + NH2CONH2 → C4H4N2O2 + 2 H2O + CO Uracil can also be synthesized by a double decomposition of thiouracil in aqueous chloroacetic acid. (wikipedia.org)
• A mutant of uracil DNA glycosylase that distinguishes between cytosine and 5-methylcytosine. (ox.ac.uk)
• Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (abcam.cn)

Double-stranded1

• Uracil-DNA glycosylase excises uracil bases from double-stranded DNA. (wikipedia.org)

Bases2

• In the present study, we used site-directed mutagenesis to construct a series of mutants of human SMUG1 (hSMUG1), and tested their activity for uracil, hoU, hmU, fU and other bases to elucidate the catalytic and damage-recognition mechanism of hSMUG1. (elsevierpure.com)
• This tends to occur with bases uracil and guanine, as the pairing is less specific. (ukessays.com)

Adenine2

• Uracil pairs with adenine through hydrogen bonding. (wikipedia.org)
• When base pairing with adenine, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor. (wikipedia.org)

Enzymes3

• Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. (kaist.ac.kr)
• The mechanism requires a family of enzymes called glycosylases. (news-medical.net)
• In mismatch repair, the missed errors are later corrected by enzymes which recognize and excise the mismatched base to restore the original sequence. (news-medical.net)

Substrates2

• Degradation of uracil produces the substrates β-alanine, carbon dioxide, and ammonia. (wikipedia.org)
• This N123D:L191A mutant excises C when it is mispaired with A or opposite an abasic site, but not when it is paired with G. In contrast no cleavage is observed with any substrates that contain 5-methylcytosine. (ox.ac.uk)

Abasic1

• Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. (kaist.ac.kr)

Recognition1

• Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. (sissa.it)

Reaction2

• Uracil DNA glycosylase (UDG) efficiently removes uracil from DNA in a reaction in which the base is flipped into the enzyme's active site. (ox.ac.uk)
• Subsequent PCR/LAMP reaction mixes must be pre-treated with Uracil-DNA Glycosylase (UNG), thermo labile prior to PCR/LAMP to degrade uracil containing DNA. (apslabs.in)

Family2

• The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. (kaist.ac.kr)
• Belongs to the uracil-DNA glycosylase family. (abcam.cn)

Cells1

• So cells continue to use uracil in RNA, and not in DNA, because RNA is shorter-lived than DNA, and any potential uracil-related errors do not lead to lasting damage. (wikipedia.org)

Sites1

• In the gas phase, uracil has four sites that are more acidic than water. (wikipedia.org)

Found1

• Uracil is rarely found in DNA, and this may have been an evolutionary change to increase genetic stability. (wikipedia.org)

Structure1

• The lactam structure is the most common form of uracil. (wikipedia.org)

Methylpurine DNA Glycosylase1

• The excision of base damage is initiated by a specific DNA glycosylase: Hypoxanthine is bound and excised efficiently by human N -methylpurine-DNA glycosylase (MPG, also known as AAG, ANPG, APNG, or MDG) [ 6 ]. (biomedcentral.com)

OGG16

• 5. Stimulation of DNA glycosylase activity of OGG1 by NEIL1: functional collaboration between two human DNA glycosylases. (nih.gov)
• 8. Catalytic and DNA-binding properties of the human Ogg1 DNA N-glycosylase/AP lyase: biochemical exploration of H270, Q315 and F319, three amino acids of the 8-oxoguanine-binding pocket. (nih.gov)
• 9. Cloning and characterization of an ascidian homolog of the human 8-oxoguanine DNA glycosylase (Ogg1) that is involved in the repair of 8-oxo-7,8-dihydroguanine in DNA in Ciona intestinalis. (nih.gov)
• 14. The C-terminal alphaO helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial beta-Ogg1 lacks this domain and does not have glycosylase activity. (nih.gov)
• 15. The Ogg1 protein of Saccharomyces cerevisiae: a 7,8-dihydro-8-oxoguanine DNA glycosylase/AP lyase whose lysine 241 is a critical residue for catalytic activity. (nih.gov)
• 16. Dimerization and opposite base-dependent catalytic impairment of polymorphic S326C OGG1 glycosylase. (nih.gov)

Family of enzymes1

• The mechanism requires a family of enzymes called glycosylases. (news-medical.net)

Endonuclease4

• The putative AP-endonuclease (mvAPE) specifically cleaves at the abasic site created by the glycosylase while also exhibiting the 3'-5' exonuclease activity. (bvsalud.org)
• 3. Specificity of stimulation of human 8-oxoguanine-DNA glycosylase by AP endonuclease. (nih.gov)
• 10. Mechanism of interaction between human 8-oxoguanine-DNA glycosylase and AP endonuclease. (nih.gov)
• 19. Coordination of MYH DNA glycosylase and APE1 endonuclease activities via physical interactions. (nih.gov)

Lyase2

• 13. Adenine Glycosylase MutY of Corynebacterium pseudotuberculosis presents the antimutator phenotype and evidences of glycosylase/AP lyase activity in vitro. (nih.gov)
• The process called BASE EXCISION REPAIR can be completed by a DNA -(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA . (nih.gov)

Lesions3

• We found that AAG bound to a wide variety of purine and pyrimidine lesions but excised only a few of them. (nih.gov)
• Therefore, additional enzymes are required to excise the dI lesions in the EndoV-mediated repair process. (biomedcentral.com)
• 12. Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2. (nih.gov)

Uridine2

• In RNA, uracil binds with a ribose sugar to form the ribonucleoside uridine. (wikipedia.org)
• citation needed] Organisms synthesize uracil, in the form of uridine monophosphate (UMP), by decarboxylating orotidine 5'-monophosphate (orotidylic acid). (wikipedia.org)

Oxidative2

• C4H4N2O2→ H3NCH2CH2COO− + NH+4 + CO2 Oxidative degradation of uracil produces urea and maleic acid in the presence of H2O2 and Fe2+ or in the presence of diatomic oxygen and Fe2+. (wikipedia.org)
• The human 3-methyladenine DNA glycosylase (AAG) recognizes and excises a broad range of purines damaged by alkylation and oxidative damage, including 3-methyladenine, 7-methylguanine, hypoxanthine (Hx), and 1,N(6)-ethenoadenine (epsilonA). (nih.gov)

Pyrimidine2

• Uracil is a common and naturally occurring pyrimidine derivative. (wikipedia.org)
• In contrast to the purine nucleotides, the pyrimidine ring (orotidylic acid) that leads uracil is synthesized first and then linked to ribose phosphate, forming UMP. (wikipedia.org)

Pathways1

• Complementary pathways, initiated by the uracil-DNA glycosylase (UNG) or the mismatch repair factor MSH2/MSH6, must process the deoxyuridine to initiate class-switch recombination (CSR) and somatic hypermutation. (aai.org)

Vitro1

• Furthermore, we show that when reconstituted in vitro, mvUDG, mvAPE, and mvPolX function cohesively to repair a uracil-containing DNA predominantly by long patch BER and together, may participate in the BER pathway during the early phase of Mimivirus life-cycle. (bvsalud.org)

Duplex1

• In addition, we found that both the full-length and truncated AAG excised 1,N(2)-ethenoguanine (1,N(2)-epsilonG), albeit weakly, from duplex DNA. (nih.gov)

Lacks1

• Apparently, either there was no evolutionary pressure to replace uracil in RNA with the more complex thymine, or uracil has some chemical property that is useful in RNA, which thymine lacks. (wikipedia.org)

Replication1

• In DNA, the evolutionary substitution of thymine for uracil may have increased DNA stability and improved the efficiency of DNA replication (discussed below). (wikipedia.org)

Recognize1

• In Escherichia coli , early studies indicated that the DNA glycosylase encoded by alkA gene could recognize and release hypoxanthine residues from DNA [ 1 ]. (biomedcentral.com)

Protein1

• 2. A functional analysis of the DNA glycosylase activity of mouse MUTYH protein excising 2-hydroxyadenine opposite guanine in DNA. (nih.gov)

Acts1

• When base pairing with adenine, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor. (wikipedia.org)

Interactions1

• We believe that """"""""recognition"""""""" of damage by DNA glycosylases is not limited to interactions in the enzyme's active site but, rather, is part of a dynamic process involving a series of conformational changes, each of which may ultimately contribute to lesion specificity. (grantome.com)

Human1

• 18. Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase. (nih.gov)

Lasting damage1

• So cells continue to use uracil in RNA, and not in DNA, because RNA is shorter-lived than DNA, and any potential uracil-related errors do not lead to lasting damage. (wikipedia.org)

Complex1

• The complex then excises the mis-match. (flashcardmachine.com)

Terms1

• This problem is believed to have been solved in terms of evolution, that is by "tagging" (methylating) uracil. (wikipedia.org)