CHEBI:132931 - α-putrescinylthymine

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ChEBI Name α-putrescinylthymine ChEBI ID CHEBI:132931 ChEBI ASCII Name alpha-putrescinylthymine Definition An N-substituted putrescine that is thymine in which a hydrogen of the methyl group has been replaced by one of the amino groups of putrescine. It replaces about half of the thymine residues in the DNA of bacetriophage φW-14. Stars This entity has been manually annotated by the ChEBI Team. Supplier Information No supplier information found for this compound. Download Molfile XML SDF Find compounds which contain this structure Find compounds which resemble this structure Take structure to the Advanced Search Formula C9H16N4O2 Net Charge 0 Average Mass 212.249 Monoisotopic Mass 212.12733 InChI InChI=1S/C9H16N4O2/c10-3-1-2-4-11-5-7-6-12-9(15)13-8(7)14/h6,11H,1-5,10H2,(H2,12,13,14,15) InChIKey IBOLVNKLOOYDDG-UHFFFAOYSA-N SMILES N1C=C(C(NC1=O)=O)CNCCCCN Roles Classification Chemical Role(s): Bronsted base A molecular entity capable of accepting a hydron from a donor (Bronsted acid). (via organic amino compound ) View more via ChEBI Ontology ChEBI Ontology Outgoing α-putrescinylthymine (CHEBI:132931) has functional parent thymine (CHEBI:17821) α-putrescinylthymine (CHEBI:132931) is a N-substituted putrescine (CHEBI:26406) α-putrescinylthymine (CHEBI:132931) is a pyrimidine nucleobase (CHEBI:26432) α-putrescinylthymine (CHEBI:132931) is a pyrimidone (CHEBI:38337) α-putrescinylthymine (CHEBI:132931) is a secondary amino compound (CHEBI:50995) α-putrescinylthymine (CHEBI:132931) is a tertiary amino compound (CHEBI:50996) IUPAC Name 5-{[(4-aminobutyl)amino]methyl}pyrimidine-2,4(1H,3H)-dione Synonyms Sources 5-(4-aminobutylaminomethyl)uracil ChemIDplus N-thyminylputrescine ChEBI Putthy ChemIDplus Registry Number Type Source 40451-54-5 CAS Registry Number ChemIDplus Citations Miller PB, Wakarchuk WW, Warren RA (1985) alpha-Putrescinylthymine and the sensitivity of bacteriophage phi W-14 DNA to restriction endonucleases. Nucleic acids research 13, 2559-2568 [PubMed:2987859] [show Abstract] The modified base alpha-putrescinylthymine (putT) in phi W-14 DNA blocks cleavage of the DNA by 17 of 32 Type II restriction endonucleases. The enzymes cleaving the DNA do so to widely varying extents. The frequencies of cleavage of three altered forms of the DNA show that putT blocks recognition sites either when it occurs within the site or when it is in a sequence flanking the site. The blocking is dependent on both charge and steric factors. The charge effects can be greater than the steric effects for some of the enzymes tested. All the enzymes cleaving phi W-14 DNA release discrete fragments, showing that the distribution of putT is ordered. The cleavage frequencies for different enzymes suggest that the sequence CAputTG occurs frequently in the DNA. Only TaqI of the enzymes tested appeared not to be blocked by putT, but it was slowed down. TaqI generated fragments are joinable by T4 DNA ligase. Miller PB, Scraba DG, Leyritz-Wills M, Maltman KL, Warren RA (1983) Formation and possible functions of alpha-putrescinylthymine in bacteriophage phi W-14 DNA: analysis of bacteriophage mutants with decreased levels of alpha-putrescinylthymine in their DNAs. Journal of virology 47, 399-405 [PubMed:6620460] [show Abstract] The DNA synthesized in the nonpermissive host by the noncomplementing mutants am36 and am42 of bacteriophage phi W-14 contains about half the wild-type level of alpha-putrescinylthymine (putThy) and a correspondingly greater level of thymine. The mechanisms whereby thymine nucleotides are excluded from replicating DNA are functional in both mutants because neither of them incorporates exogenous thymidine into DNA. It is proposed that (i) in wild-type phi W-14, the conversion of hydroxymethyluracil to putThy at the polynucleotide level is sequence specific, but that to thymine is nonspecific; and (ii) in the mutants, the sequence-specific recognition is impaired so that more thymine and less putThy are formed. The thymine-rich DNA can be packaged into phage particles. In the case of am42, the phage particles are morphologically indistinguishable from and have essentially the same polypeptide composition as wild-type particles. However, the DNA molecules they contain are about 11% shorter than those in wild-type phage, am42rev4, a revertant of am42, contains DNA with about 70% of the normal level of putThy; these molecules are about 3% shorter than wild-type DNA. The properties of am42 and am42rev4 are consistent with the suggestion that putThy facilitates the very tight packing of phi W-14 DNA (Scraba et al., Virology 124:152-160, 1983). It also appears that the putThy content of phi W-14 DNA can be reduced by no more than 30% without adversely affecting the production of viable progeny; for example, the burst size of am42rev4 is about 25% of that of the wild type. Kropinski AM, Maltman KL, Warren RA (1983) alpha-Putrescinylthymine. Methods in enzymology 94, 422-428 [PubMed:6621398] Takeda T, Ikeda K (1983) Synthesis of oligonucleotides containing the hypermodified base, alpha-putrescinylthymine. Nucleic acids symposium series75-78 [PubMed:6664879] [show Abstract] Self-complementary decadeoxyribonucleotides containing alpha-putrescinyl-thymidine (Put Thd), AAGAATTPCTT, AAGAATTCTPT, AAGAATTPCTPT, (p is the abbreviation of alpha-putrescinyl residue) were prepared by the phosphotriester method. Nuclease activities and Tm for their oligomers were investigated by comparison of AAGAATTCTT. Gerhard B, Warren RA (1982) Reactivity of the alpha-putrescinylthymine amino groups in phi W-14 deoxyribonucleic acid. Biochemistry 21, 5458-5462 [PubMed:6816277] [show Abstract] Bacteriophage phi W-14 DNA contains the hypermodified pyrimidine alpha-putrescinylthymine (putThy) [Kropinski, A. M. B., Bose, R. J., & Warren, R. A. J. (1973) Biochemistry 12, 151]. The primary amino groups of the putrescinyl side chains react with trinitrobenzenesulfonate (TNBS) but at a much slower rate than the reactive lysine side chains of proteins. Both primary and secondary amino groups in the putrescinyl side chains react with acetic anhydride, but the reaction does not go to completion under the conditions employed. Some of the secondary amino groups react faster with acetic anhydride than do some of the primary amino groups. Acetylation lowers the thermal transition temperature (Tm) of phi W-14 DNA, confirming that the unusually high Tm of this DNA is due to the charged putrescinyl groups, but it does not affect the buoyant density. The extent of lowering of the Tm is proportional to the degree of acetylation. Since some of the secondary amino groups are acetylated before some of the primary amino groups, the effect of acetylation on the Tm suggests that both the primary and secondary amino groups can neutralize negative charge repulsion in phi W-14 DNA. Only the putThy residues in the DNA are modified by TNBS and acetic anhydride. Maltman KL, Neuhard J, Warren RA (1981) 5-[(Hydroxymethyl)-O-pyrophosphoryl]uracil, an intermediate in the biosynthesis of alpha-putrescinylthymine in deoxyribonucleic acid of bacteriophage phi W-14. Biochemistry 20, 3586-3591 [PubMed:7260058] [show Abstract] In a nonpermissive host, an amber mutant, am 37, of bacteriophage phi W-14 synthesizes deoxyribonucleic acid (DNA) of considerably greater buoyant density than the DNA synthesized by wild-type phage. The am 37 DNA lacks the hypermodified pyrimidine, alpha-putrescinylthymine (putThy). Instead, it contains a new modified base, 5-[(hydroxymethyl)-O-pyrophosphoryl]uracil (hmPPUra). Extracts of cells infected with wild-type phi W-14 convert the hmPPUra in am 37 DNA to putThy when incubated with putrescine. Maltman KL, Neuhard J, Lewis HA, Warren RA (1980) Synthesis of thymine and alpha-putrescinylthymine in bacteriophage phi W-14-infected Pseudomonas acidovorans. Journal of virology 34, 354-359 [PubMed:6445427] [show Abstract] Host DNA synthesis stopped about 10 min after the infection of Pseudomonas acidovorans with bacteriophage phi W-14, but host DNA was not degraded to acid-soluble fragments. The synthesis of host but not of phage DNA was inhibited by 5-fluorodeoxyuridine. The nucleotide pools of infected cells did not contain dTTP, and infection resulted in the appearance of dTTPase activity. Although ornithine labeled the alpha-putrescinylthymine residues of phi W-14 DNA, ornithine-labeled nucleotides were not detected in infected cells. A new deoxynucleoside triphosphate did appear in infected cells, but it was not labeled by ornithine. It is concluded that the thymine and alpha-putrescinylthymine in phi W-14 DNA are synthesized at the polynucleotide level. Kropinski AM, Bose RJ, Warren RA (1973) 5-(4-Aminobutylaminomethyl)uracil, an unusual pyrimidine from the deoxyribonucleic acid of bacteriophage phiW-14. Biochemistry 12, 151-157 [PubMed:4683479] Kelln RA, Warren RA (1973) Studies on the biosynthesis of alpha-putrescinylthymine in bacteriophage phi W-14-infected Pseudomonas acidovorans. Journal of virology 12, 1427-1433 [PubMed:4586777] [show Abstract] The alpha-putrescinylthymine (putThy) in bacteriophage phiW-14 DNA is synthesized at the mononucleotide level: it is labeled by uracil or deoxyuridine but not by thymidine, and it appears in the acid-soluble pool of infected cells before the onset of phage DNA synthesis. The methylene group at the C-5 position of the pyrimidine moiety of putThy is derived in vivo from a C(1) unit. Extracts of a phage infected thymidine auxotroph of the host, Pseudomonas acidovorans, apparently contain a phage-specific thymidylate synthetase and a phage-specific activity which forms 5-hydroxymethyl dUMP from N(5), N(10)-methylene-tetrahydrofolate and dUMP. Last Modified 06 August 2016