Modification Summary

5-methyluridine

[show modification pathway]
m5U

Summary

Full name5-methyluridine
Short namem5U
New Nomenclature5U
RNAMods abbreviationT
HTML abbreviationT
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 phylogenyArchaea, Eubacteria, Eukaryota
Found in RNArRNA, tRNA
PubChem ID445408
SMILES codeC3(OC(CO)C(O)C(O)3)N1C=C(C)C(=O)NC1(=O)

LC-MS Information

Sum formulaC10O6N2H14
Monoisotopic mass258.085186
Average mass258.231306
HRMS mass258.084637
Normalized LC elution time *1 (Kellner 2014, Kellner 2014)
LC elution order/characteristicsco-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 PubMed Id DOI
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 groupmethyl 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.