5-Hydroxymethyluracil (BioDeep_00000001265)

 

Secondary id: BioDeep_00000400049

human metabolite PANOMIX_OTCML-2023 Endogenous blood metabolite BioNovoGene_Lab2019


代谢物信息卡片


5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

化学式: C5H6N2O3 (142.03784059999998)
中文名称: 5-(羟甲基)脲嘧啶
谱图信息: 最多检出来源 Homo sapiens(blood) 2.74%

分子结构信息

SMILES: C1=C(C(=O)NC(=O)N1)CO
InChI: InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)

描述信息

5-Hydroxymethyluracil (5hmU), also known as alpha-hydroxythymine, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5hmU has been identified as a thymine base modification found in the genomes of a diverse range of organisms (PMID: 28137275). 5-hydroxymethyluracil has been detected in bacteriophages, dinoflagellates, leishmania, and in eukaryotic genomes where its level appears to be cell type-specific. 5-Hydroxymethyluracil arises from the oxidation of thymine. 5-Hydroxymethyluracil is produced by the enzyme thymine dioxygenase (EC 1.14.11.6) which catalyzes the chemical reaction thymine + 2-oxoglutarate + O2 <-> 5-hydroxymethyluracil + succinate + CO2. The 3 substrates of this enzyme are thymine, 2-oxoglutarate, and O2, whereas its 3 products are 5-hydroxymethyluracil, succinate, and CO2. The 5hmU base can also be generated by oxidation/hydroxylation of thymine by the Ten-Eleven-Translocation (TET) proteins or result from deamination of 5hmC (PMID: 29184924). DNA containing 5hmU has been reported to be more flexible and hydrophilic (PMID: 29184924).
5-Hydroxymethyluracil is an oxidation damage product derived from thymine or 5-methylcytosine. It is a product of thymine dioxygenase [EC 1.14.11.6]. (KEGG)
D005765 - Gastrointestinal Agents > D000897 - Anti-Ulcer Agents
D007155 - Immunologic Factors
5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase.
5-Hydroxymethyluracil is a product of oxidative DNA damage. 5-Hydroxymethyluracil can be used as a potential epigenetic mark enhancing or inhibiting transcription with bacterial RNA polymerase.

同义名列表

12 个代谢物同义名

5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione; 5-(Hydroxymethyl)-1,3-dihydropyrimidine-2,4-dione; 5-(hydroxymethyl)-1H-pyrimidine-2,4-dione hydrate; 5-(Hydroxymethyl)-2,4(1H,3H)-pyrimidinedione; 5-(Hydroxymethyl)uracil; 5-HYDROXYMETHYL uracil; α-Hydroxythymine; 5-Hydroxymethyluracil; alpha-Hydroxythymine; Hydroxymethyluracil; a-Hydroxythymine; Bmse000443



数据库引用编号

19 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(0)

BioCyc(0)

PlantCyc(0)

代谢反应

1 个相关的代谢反应过程信息。

Reactome(0)

BioCyc(0)

WikiPathways(1)

Plant Reactome(0)

INOH(0)

PlantCyc(0)

COVID-19 Disease Map(0)

PathBank(0)

PharmGKB(0)

3 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有：

  • PubMed: 来源于PubMed文献库中的文献信息，我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表，这个列表按照代谢物同时出现的文献数量降序排序，取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘，得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序，取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中，存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称，可以跳转到相关代谢物的信息页面。



文献列表

  • Georgi K Marinov, Xinyi Chen, Matthew P Swaffer, Tingting Xiang, Arthur R Grossman, William J Greenleaf. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. Genome biology. 2024 May; 25(1):115. doi: 10.1186/s13059-024-03261-3. [PMID: 38711126]
  • Martyna Modrzejewska, Maciej Gawronski, Magdalena Skonieczna, Ewelina Zarakowska, Marta Starczak, Marek Foksinski, Joanna Rzeszowska-Wolny, Daniel Gackowski, Ryszard Olinski. Vitamin C enhances substantially formation of 5-hydroxymethyluracil in cellular DNA. Free radical biology & medicine. 2016 12; 101(?):378-383. doi: 10.1016/j.freeradbiomed.2016.10.535. [PMID: 27833031]
  • Ryszard Olinski, Marta Starczak, Daniel Gackowski. Enigmatic 5-hydroxymethyluracil: Oxidatively modified base, epigenetic mark or both?. Mutation research. Reviews in mutation research. 2016 Jan; 767(?):59-66. doi: 10.1016/j.mrrev.2016.02.001. [PMID: 27036066]
  • Rafal Rozalski, Daniel Gackowski, Agnieszka Siomek-Gorecka, Marta Starczak, Martyna Modrzejewska, Zbigniew Banaszkiewicz, Ryszard Olinski. Urinary 5-hydroxymethyluracil and 8-oxo-7,8-dihydroguanine as potential biomarkers in patients with colorectal cancer. Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals. 2015; 20(5):287-91. doi: 10.3109/1354750x.2015.1068860. [PMID: 26329524]
  • Daniel Gackowski, Ewelina Zarakowska, Marta Starczak, Martyna Modrzejewska, Ryszard Olinski. Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships. PloS one. 2015; 10(12):e0144859. doi: 10.1371/journal.pone.0144859. [PMID: 26660343]
  • Berta Mendes, Pedro Silva, Isabel Mendonça, Jorge Pereira, José S Câmara. A new and fast methodology to assess oxidative damage in cardiovascular diseases risk development through eVol-MEPS-UHPLC analysis of four urinary biomarkers. Talanta. 2013 Nov; 116(?):164-72. doi: 10.1016/j.talanta.2013.04.064. [PMID: 24148388]
  • Berta Mendes, Pedro Silva, Fernando Aveiro, Jorge Pereira, José S Câmara. A micro-extraction technique using a new digitally controlled syringe combined with UHPLC for assessment of urinary biomarkers of oxidatively damaged DNA. PloS one. 2013; 8(3):e58366. doi: 10.1371/journal.pone.0058366. [PMID: 23484022]
  • Jolyon Terragni, Jurate Bitinaite, Yu Zheng, Sriharsa Pradhan. Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes. Biochemistry. 2012 Feb; 51(5):1009-19. doi: 10.1021/bi2014739. [PMID: 22229759]
  • Daniela Pelclova, Tomas Navratil, Zdenka Fenclova, Stepanka Vlckova, Karel Kupka, Pavel Urban, Petr Ridzon, Vit Zikan, Ludmila Landova, Kamila Syslova, Marek Kuzma, Petr Kacer. Increased oxidative/nitrosative stress markers measured non- invasively in patients with high 2,3,7,8-tetrachloro-dibenzo-p-dioxin plasma level. Neuro endocrinology letters. 2011; 32 Suppl 1(?):71-6. doi: . [PMID: 22167218]
  • Marcus S Cooke, Paul T Henderson, Mark D Evans. Sources of extracellular, oxidatively-modified DNA lesions: implications for their measurement in urine. Journal of clinical biochemistry and nutrition. 2009 Nov; 45(3):255-70. doi: 10.3164/jcbn.sr09-41. [PMID: 19902015]
  • Hauh-Jyun Candy Chen, Chan-Fu Wu, Ju-Li Huang. Measurement of urinary excretion of 5-hydroxymethyluracil in human by GC/NICI/MS: correlation with cigarette smoking, urinary TBARS and etheno DNA adduct. Toxicology letters. 2005 Mar; 155(3):403-10. doi: 10.1016/j.toxlet.2004.11.009. [PMID: 15649624]
  • Marek Foksinski, Rafal Rozalski, Jolanta Guz, Barbara Ruszkowska, Paulina Sztukowska, Maciej Piwowarski, Arne Klungland, Ryszard Olinski. Urinary excretion of DNA repair products correlates with metabolic rates as well as with maximum life spans of different mammalian species. Free radical biology & medicine. 2004 Nov; 37(9):1449-54. doi: 10.1016/j.freeradbiomed.2004.07.014. [PMID: 15454284]
  • Rafal Rozalski, Agnieszka Siomek, Daniel Gackowski, Marek Foksinski, Christine Gran, Arne Klungland, Ryszard Olinski. Diet is not responsible for the presence of several oxidatively damaged DNA lesions in mouse urine. Free radical research. 2004 Nov; 38(11):1201-5. doi: 10.1080/10715760400017350. [PMID: 15621697]
  • Tomiko Kuhara, Chie Ohdoi, Morimasa Ohse, André B P van Kuilenburg, Albert H van Gennip, Satoshi Sumi, Tetsuya Ito, Yoshiro Wada, Isamu Matsumoto. Rapid gas chromatographic-mass spectrometric diagnosis of dihydropyrimidine dehydrogenase deficiency and dihydropyrimidinase deficiency. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences. 2003 Jul; 792(1):107-15. doi: 10.1016/s1570-0232(03)00044-8. [PMID: 12829003]
  • J L Ravanat, P Guicherd, Z Tuce, J Cadet. Simultaneous determination of five oxidative DNA lesions in human urine. Chemical research in toxicology. 1999 Sep; 12(9):802-8. doi: 10.1021/tx980194k. [PMID: 10490501]
  • S Pourcelot, H Faure, F Firoozi, V Ducros, M Tripier, J Hee, J Cadet, A Favier. Urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine and 5-(hydroxymethyl) uracil in smokers. Free radical research. 1999 Mar; 30(3):173-80. doi: 10.1080/10715769900300191. [PMID: 10711787]
  • I Kato, J H Vogelman, V Dilman, J Karkoszka, K Frenkel, N P Durr, N Orentreich, P Toniolo. Effect of supplementation with chromium picolinate on antibody titers to 5-hydroxymethyl uracil. European journal of epidemiology. 1998 Sep; 14(6):621-6. doi: 10.1023/a:1007442203258. [PMID: 9794131]
  • E Christensen, I Cezanne, S Kjaergaard, H Hørlyk, V Faurholt Pedersen, P Vreken, A B van Kuilenburg, A H Van Gennip. Clinical variability in three Danish patients with dihydropyrimidine dehydrogenase deficiency all homozygous for the same mutation. Journal of inherited metabolic disease. 1998 Jun; 21(3):272-5. doi: 10.1023/a:1005328424310. [PMID: 9686373]
  • H Faure, M Mousseau, J Cadet, C Guimier, M Tripier, H Hida, A Favier. Urine 8-oxo-7,8-dihydro-2-deoxyguanosine vs. 5-(hydroxymethyl) uracil as DNA oxidation marker in adriamycin-treated patients. Free radical research. 1998 Apr; 28(4):377-82. doi: 10.3109/10715769809070806. [PMID: 9684982]
  • G D Castro, M I Díaz Gómez, J A Castro. DNA bases attack by reactive metabolites produced during carbon tetrachloride biotransformation and promotion of liver microsomal lipid peroxidation. Research communications in molecular pathology and pharmacology. 1997 Mar; 95(3):253-8. doi: . [PMID: 9144833]
  • H Faure, C Coudray, M Mousseau, V Ducros, T Douki, F Bianchini, J Cadet, A Favier. 5-Hydroxymethyluracil excretion, plasma TBARS and plasma antioxidant vitamins in adriamycin-treated patients. Free radical biology & medicine. 1996; 20(7):979-83. doi: 10.1016/0891-5849(95)02187-6. [PMID: 8743984]
  • H Faure, M F Incardona, C Boujet, J Cadet, V Ducros, A Favier. Gas chromatographic-mass spectrometric determination of 5-hydroxymethyluracil in human urine by stable isotope dilution. Journal of chromatography. 1993 Jun; 616(1):1-7. doi: 10.1016/0378-4347(93)80465-g. [PMID: 8376480]
  • V A Myshkin, S A Bashkatov, A F Vakaritsa, G A Sofronov, G A Tolstikov, D A Enikeev. [Effect of hydroxymethyluracil and atropine on free radical oxidation of lipids and membrane status in rats in carbofos poisoning]. Patologicheskaia fiziologiia i eksperimental'naia terapiia. 1993 Mar; ?(2):47-9. doi: ". [PMID: 8058386]
  • E B Berkhin, V V Lampatov, G P Ul'ianov. [Effect of 5-hydroxymethyluracil and dimephosphon on the tubular secretion of xenobiotics in the kidney]. Farmakologiia i toksikologiia. 1987 Sep; 50(5):37-8. doi: NULL. [PMID: 3691775]
  • R Berger, S A Stoker-de Vries, S K Wadman, M Duran, F A Beemer, P K de Bree, J J Weits-Binnerts, T J Penders, J K van der Woude. Dihydropyrimidine dehydrogenase deficiency leading to thymine-uraciluria. An inborn error of pyrimidine metabolism. Clinica chimica acta; international journal of clinical chemistry. 1984 Aug; 141(2-3):227-34. doi: 10.1016/0009-8981(84)90014-7. [PMID: 6488556]
  • A Leyva, J H Schornagel, I Kraal, S K Wadman, H M Pinedo. Clinical and biochemical studies of high-dose thymidine treatment in patients with solid tumors. Journal of cancer research and clinical oncology. 1984; 107(3):211-6. doi: 10.1007/bf01032609. [PMID: 6736109]