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 Information
Sum formula | C10O6N2H14 |
Monoisotopic mass | 258.0852 |
Average mass | 258.2313 |
[M+H]+ | 259.093 |
Product ions | 127 |
Normalized LC elution time * | 1 (Kellner 2014, Kellner 2014) |
LC elution order/characteristics | co-eluting with G (Kellner 2014, Kellner 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: 2017-10-06 16:28:11.198287
Edited by a user: pboccaletto
Edited content: Changed mass_prot.