Modification Summary

5-methoxycarbonylmethyl-2-thiouridine

[show modification pathway]
mcm5s2U

Summary

Full name5-methoxycarbonylmethyl-2-thiouridine
Short namemcm5s2U
New Nomenclature2521U
RNAMods abbreviation3
HTML abbreviation3
Enzymes ALKBH8 (Homo sapiens)
Ncs6 (Saccharomyces cerevisiae)
Trm9 (Saccharomyces cerevisiae)
Ncs2 (Saccharomyces cerevisiae)
TrmU (Homo sapiens)
Found in phylogenyEukaryota
Found in RNAtRNA
SMILES codeO=C(OC)CC1=CN(C(=S)NC1=O)[C@@H]2O[C@H](CO)[C@H](O)C2O

LC-MS Information

Sum formulaC12O7N2H16S1
Monoisotopic mass332.067821
Average mass332.333024
HRMS mass332.067272
Normalized LC elution time *1,78 (Kellner 2014)
LC elution order/characteristicsbetween A and m6A (Kellner 2014)
Mass transition-132 (Kellner 2014, Su 2014); -164 (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 -

Download [.mol file for mcm5s2U]

Chemical groups contained

heavy atomsulfur
othercarboxymethyl
othermethylester

Reactions producing 5-methoxycarbonylmethyl-2-thiouridine

Name
cm5s2U:mcm5s2U
mcm5U:mcm5s2U

Occurrence in PDB structures

PDB-ID chain residue
1fir A 70U /34

Last modification of this entry: 2017-07-05 16:22:22.727525
Edited by a user: pboccaletto
Edited content: Changed lc_elution_time, lc_elution_comment, lc_reference and mass_trans.