Modification Summary
5-methyluridine
[show modification pathway]
Summary
| Full name | 5-methyluridine |
| Short name | m5U |
| New Nomenclature | 5U |
| RNAMods abbreviation | T |
| HTML abbreviation | T |
| Enzymes |
RlmC (Escherichia coli) RlmC (Pyrococcus abyssi) RlmCD (Bacillus subtilis) RlmD (Escherichia coli) RlmFO (Mycoplasma capricolum) Trm2 (Saccharomyces cerevisiae) TrmA (Escherichia coli) TrmFO (Bacillus subtilis) TrmFO (Thermus thermophilus) TrmU54 (Pyrococcus abyssi) |
| Found in phylogeny | Archaea, Eubacteria, Eukaryota |
| Found in RNA | rRNA, tRNA |
| PubChem ID | 445408 |
| SMILES code | C3(OC(CO)C(O)C(O)3)N1C=C(C)C(=O)NC1(=O) |
LC-MS Informations
| Sum formula | C10O6N2H14 |
| Monoisotopic mass | 258.085186 |
| Average mass | 258.231306 |
| HRMS mass | 258.084637 |
| Normalized LC elution time * | 1 (Kellner 2014, Kellner 2014) |
| LC elution order/characteristics | co-eluting with G (Kellner 2014, Kellner 2014) |
| Mass transition | -132 (Kellner 2014, Kellner 2014, Su 2014) |
* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.
LC-MS Publications
| Title | Authors | Journal | Details | ||
|---|---|---|---|---|---|
| Profiling of RNA modifications by multiplexed stable isotope labelling. | Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. | Chem Commun (Camb). | [details] | 24567952 | - |
| Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. | Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... | Nat Protoc | [details] | 24625781 | - |
| Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. | Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... | Nucleic Acids Res | [details] | 25129236 | - |
Download [.mol file for m5U]
Comments
Alternative name is ribosylthymidine.
Chemical groups contained
| methyl group | methyl at aromatic C |
Reactions producing 5-methyluridine
| Name |
|---|
| U:m5U |
Reactions starting from 5-methyluridine
| Name |
|---|
| m5U:m5Um |
| m5U:m5s2U |
Occurrence in PDB structures
| PDB-ID | chain | residue |
|---|---|---|
| 1c0a | B | 5MU /654 |
| 1c2w | B | 5MU /747 |
| 1c2w | B | 5MU /1915 |
| 1c2w | B | 5MU /1939 |
| 1c2w | B | 5MU /2449 |
| 1efw | C | 5MU /54 |
| 1ehz | A | 5MU /54 |
| 1eqq | M | 5MU /801 |
| 1eqq | M | 5MU /802 |
| 1eqq | M | 5MU /803 |
| 1f7u | B | 5MU /954 |
| 1f7v | B | 5MU /954 |
| 1fcw | A | 5MU /54 |
| 1fcw | B | 5MU /54 |
| 1fcw | C | 5MU /54 |
| 1fcw | D | 5MU /54 |
| 1fcw | E | 5MU /54 |
| 1gix | B | 5MU /54 |
| 1gix | C | 5MU /54 |
| 1gix | D | 5MU /54 |
| 1h3e | B | RT /54 |
| 1h4q | T | 5MU /54 |
| 1i9v | A | 5MU /54 |
| 1il2 | C | 5MU /954 |
| 1il2 | D | 5MU /1954 |
| 1jgo | B | 5MU /54 |
| 1jgo | C | 5MU /54 |
| 1jgo | D | 5MU /54 |
| 1jgp | B | 5MU /54 |
| 1jgp | C | 5MU /54 |
| 1jgp | D | 5MU /54 |
| 1jgq | B | 5MU /54 |
| 1jgq | C | 5MU /54 |
| 1jgq | D | 5MU /54 |
| 1kos | A | 5MU /6 |
| 1mj1 | D | 5MU /54 |
| 1mj1 | C | 5MU /54 |
| 1ml5 | B | 5MU /54 |
| 1n1o | A | TFT /7 |
| 1n1o | B | TFT /119 |
| 1qf6 | B | 5MU /54 |
| 1sz1 | E | 5MU /54 |
| 1sz1 | F | 5MU /54 |
| 1tn2 | 5MU /54 | |
| 1tra | 5MU /54 | |
| 1ttt | E | 5MU /54 |
| 1ttt | F | 5MU /54 |
| 1u6b | D | 5MU /1 |
| 1wv6 | A | 2BT /6 |
| 1wv6 | B | 2BT /16 |
| 1xv6 | A | U2L /7 |
| 1xv6 | A | U2L /8 |
| 1zzn | D | 5MU /1 |
| 2bh2 | C | FMU /1939 |
| 2bh2 | D | FMU /1939 |
| 2i1c | z | 5MU /54 |
| 2tra | 5MU /54 | |
| 3tra | 5MU /54 | |
| 486d | A | 5MU /54 |
| 486d | C | 5MU /54 |
| 486d | E | 5MU /54 |
| 4tna | 5MU /54 | |
| 4tra | 5MU /54 | |
| 6tna | 5MU /54 |
Last modification of this entry: 2017-07-05 15:41:55.697632
Edited by a user: pboccaletto
Edited content: Changed lc_reference.
