Modification Summary

5-methylcytidine

[show modification pathway]
m5C

Summary

Full name5-methylcytidine
Short namem5C
New Nomenclature5C
RNAMods abbreviation?
HTML abbreviation?
Enzymes Dnmt2 (Homo sapiens)
Dnmt2 (Geobacter sulfurreducens)
EfmM (Enterococcus faecium)
Nop2 (Saccharomyces cerevisiae)
Rcm1 (Saccharomyces cerevisiae)
RlmI (Escherichia coli)
RlmO (Thermus thermophilus)
RsmB (Escherichia coli)
RsmF (Escherichia coli)
RsmF (Thermus thermophilus)
Trm4 (Saccharomyces cerevisiae)
Trm4 (Homo sapiens)
Trm4 (Pyrococcus abyssi)
Found in phylogenyEubacteria, Eukaryota
Found in RNAmRNA, other, pre-tRNA, rRNA, tRNA
PubChem ID92918
SMILES codeC3(OC(CO)C(O)C(O)3)N1C=C(C)C(N)=NC1(=O)

LC-MS Information

Sum formulaC10O5N3H15
Monoisotopic mass257.1012
Average mass257.2467
[M+H]+258.109
Product ions126
Normalized LC elution time *0,82 (Kellner 2014); 0,84 (Kellner 2014)
LC elution order/characteristicsbetween U and 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 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 m5C]

Chemical groups contained

methyl groupmethyl at aromatic C

Reactions producing 5-methylcytidine

Name
C:m5C

Reactions starting from 5-methylcytidine

Name
m5C:m5Cm

Occurrence in PDB structures

PDB-ID chain residue
1asy R 5MC /649
1asy S 5MC /649
1asz R 5MC /649
1asz S 5MC /649
1c2w B 5MC /2498
1ehz A 5MC /40
1ehz A 5MC /49
1evv A 5MC /40
1evv A 5MC /49
1f7u B 5MC /949
1f7v B 5MC /949
1fcw A 5MC /40
1fcw A 5MC /49
1fcw B 5MC /40
1fcw B 5MC /49
1fcw C 5MC /40
1fcw C 5MC /49
1fcw D 5MC /40
1fcw D 5MC /49
1fcw E 5MC /40
1fcw E 5MC /49
1fir A 5MC /48
1fir A 5MC /49
1gix B 5MC /40
1gix B 5MC /49
1gix C 5MC /40
1gix C 5MC /49
1gix D 5MC /49
1il2 C 5MC /949
1il2 D 5MC /1949
1jgo B 5MC /40
1jgo B 5MC /49
1jgo C 5MC /40
1jgo C 5MC /49
1jgo D 5MC /49
1jgp B 5MC /40
1jgp B 5MC /49
1jgp C 5MC /40
1jgp C 5MC /49
1jgp D 5MC /49
1jgq B 5MC /40
1jgq B 5MC /49
1jgq C 5MC /40
1jgq C 5MC /49
1jgq D 5MC /49
1luu A 5MC /40
1lux A 5MC /40
1mj1 D 5MC /40
1mj1 D 5MC /49
1mj1 C 5MC /40
1mj1 C 5MC /49
1ml5 B 5MC /40
1ml5 B 5MC /49
1ob2 B 5MC /40
1ob2 B 5MC /49
1ob5 B 5MC /40
1ob5 B 5MC /49
1ob5 D 5MC /40
1ob5 D 5MC /49
1ob5 F 5MC /40
1ob5 F 5MC /49
1sz1 E 5MC /40
1sz1 E 5MC /49
1sz1 F 5MC /40
1sz1 F 5MC /49
1tn2 5MC /40
1tn2 5MC /49
1tra 5MC /40
1tra 5MC /49
1ttt D 5MC /40
1ttt D 5MC /49
1ttt E 5MC /40
1ttt E 5MC /49
1ttt F 5MC /40
1ttt F 5MC /49
1xv6 A C2L /1
1xv6 A C2L /3
1xv6 A C2L /9
1xv6 A C2L /11
1yfg 5MC /48
1yfg 5MC /49
2i1c y 5MC /967
2i1c y 5MC /1400
2i1c y 5MC /1404
2i1c y 5MC /1407
2tra 5MC /49
3tra 5MC /49
486d A 5MC /40
486d A 5MC /49
486d C 5MC /49
486d E 5MC /49
4tna 5MC /40
4tna 5MC /49
4tra 5MC /40
4tra 5MC /49
6tna 5MC /40
6tna 5MC /49

Publications

Title Authors Journal Details PubMed Id DOI
A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing. Militello KT, Chen LM, Ackerman SE, Mandarano AH, Valentine EL Mol Biochem Parasitol [details] 24389163 10.1016

Last modification of this entry: 2017-10-06 15:57:39.084547
Edited by a user: pboccaletto
Edited content: Changed mass_prot.