Modification Summary

pseudouridine

[show modification pathway]
Y

Summary

Full namepseudouridine
Short nameY
New Nomenclature9U
RNAMods abbreviationP
HTML abbreviationP
Enzymes Cbf5 (Saccharomyces cerevisiae)
Pus1 (Saccharomyces cerevisiae)
Pus1 (Homo sapiens)
Pus10 (Pyrococcus furiosus)
Pus2 (Saccharomyces cerevisiae)
Pus3 (Saccharomyces cerevisiae)
Pus4 (Saccharomyces cerevisiae)
Pus5 (Saccharomyces cerevisiae)
Pus6 (Saccharomyces cerevisiae)
Pus7 (Saccharomyces cerevisiae)
Pus8 (Saccharomyces cerevisiae)
Pus9 (Saccharomyces cerevisiae)
RluA (Escherichia coli)
RluB (Escherichia coli)
RluB (Bacillus subtilis)
RluC (Escherichia coli)
RluD (Escherichia coli)
RluE (Escherichia coli)
RluF (Escherichia coli)
RsuA (Escherichia coli)
TruA (Escherichia coli)
TruB (Escherichia coli)
TruC (Escherichia coli)
TruD (Escherichia coli)
Found in phylogenyArchaea, Eubacteria, Eukaryota
Found in RNArRNA, snRNA, snoRNA, tRNA
PubChem ID15047
SMILES codeC3(OC(CO)C(O)C(O)3)C1=CNC(=O)NC1(=O)

LC-MS Information

Sum formulaC9O6N2H12
Monoisotopic mass244.0695
Average mass244.2043
[M+H]+245.0773
Product ions209/179/155
Normalized LC elution time *0,34 (Kellner 2014); 0,37 (Kellner 2014)
LC elution order/characteristicsbefore C (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 Y]

Comments

It is called pseudouridine because the ring structure is the same as in U, just attached by a different atom.

Chemical groups contained

ring modificationpseudouridine

Reactions producing pseudouridine

Name
U:Y

Reactions starting from pseudouridine

Name
Y:m3Y
Y:Ym
Y:m1Y
Y:acp3Y

Occurrence in PDB structures

PDB-ID chain residue
1asy R PSU /613
1asy R PSU /632
1asy R PSU /655
1asy S PSU /613
1asy S PSU /632
1asy S PSU /655
1asz R PSU /613
1asz R PSU /632
1asz R PSU /655
1asz S PSU /613
1asz S PSU /632
1asz S PSU /655
1b23 R PSU /32
1b23 R PSU /39
1b23 R PSU /55
1bzt PSU /39
1bzu PSU /39
1c0a B PSU /655
1c0a B PSU /665
1c2w B PSU /746
1c2w B PSU /1911
1c2w B PSU /1917
1efw C PSU /55
1efw C PSU /65
1efw D PSU /55
1efw D PSU /65
1ehz A PSU /39
1ehz A PSU /55
1evv A PSU /39
1evv A PSU /55
1f7u B PSU /901
1f7u B PSU /927
1f7u B PSU /955
1f7v B PSU /901
1f7v B PSU /927
1f7v B PSU /955
1fcw A PSU /39
1fcw A PSU /55
1fcw B PSU /39
1fcw B PSU /55
1fcw C PSU /39
1fcw C PSU /55
1fcw D PSU /39
1fcw D PSU /55
1fcw E PSU /39
1fcw E PSU /55
1fir A PSU /27
1fir A PSU /39
1fir A PSU /55
1fl8 A PSU /39
1gix B PSU /39
1gix B PSU /55
1gix C PSU /39
1gix C PSU /55
1gix D PSU /55
1h3e B PSU /35
1h3e B PSU /55
1h4q T PSU /55
1il2 C PSU /913
1il2 C PSU /932
1il2 C PSU /955
1il2 D PSU /1913
1il2 D PSU /1932
1il2 D PSU /1955
1jgo B PSU /39
1jgo B PSU /55
1jgo C PSU /39
1jgo C PSU /55
1jgo D PSU /55
1jgp B PSU /39
1jgp B PSU /55
1jgp C PSU /39
1jgp C PSU /55
1jgp D PSU /55
1jgq B PSU /39
1jgq B PSU /55
1jgq C PSU /39
1jgq C PSU /55
1jgq D PSU /55
1k8w B FHU /410
1lpw A PSU /5
1lu3 A PSU /39
1mj1 D PSU /39
1mj1 D PSU /55
1mj1 C PSU /39
1mj1 C PSU /55
1ml5 B PSU /39
1ml5 B PSU /55
1n32 Y PSU /38
1n33 Y PSU /40
1ob2 B PSU /39
1ob2 B PSU /55
1ob5 B PSU /39
1ob5 B PSU /55
1ob5 D PSU /39
1ob5 D PSU /55
1ob5 F PSU /39
1ob5 F PSU /55
1qf6 B PSU /55
1r3e C FHU /410
1s72 0 PSU /2621
1ser T PSU /55
1sz1 E PSU /39
1sz1 E PSU /55
1sz1 F PSU /39
1sz1 F PSU /55
1tn2 PSU /39
1tn2 PSU /55
1tra PSU /39
1tra PSU /55
1ttt D PSU /39
1ttt D PSU /55
1ttt E PSU /39
1ttt E PSU /55
1ttt F PSU /39
1ttt F PSU /55
1vq4 0 PSU /2621
1vq5 0 PSU /2621
1vq6 0 PSU /2621
1vq7 0 PSU /2621
1vq8 0 PSU /2621
1vq9 0 PSU /2621
1vqk 0 PSU /2621
1vql 0 PSU /2621
1vqm 0 PSU /2621
1vqn 0 PSU /2621
1vqo 0 PSU /2621
1vqp 0 PSU /2621
1yhq 0 PSU /2621
1yi2 0 PSU /2621
1yij 0 PSU /2621
1yit 0 PSU /2621
1yj9 0 PSU /2621
1yjn 0 PSU /2621
1yjw 0 PSU /2621
1ze2 C FHU /10
1ze2 D FHU /10
2ab4 B FHU /10
2awq A PSU /6
2b64 W PSU /39
2b64 W PSU /55
2b9m W PSU /39
2b9m W PSU /55
2b9o W PSU /39
2b9o W PSU /55
2fmt C PSU /55
2fmt D PSU /55
2i1c y PSU /516
2i1c z PSU /32
2i1c z PSU /39
2i1c z PSU /55
2tra PSU /13
2tra PSU /32
2tra PSU /55
3tra PSU /13
3tra PSU /32
3tra PSU /55
486d A PSU /13
486d A PSU /55
486d C PSU /32
486d C PSU /55
486d E PSU /13
486d E PSU /32
486d E PSU /55
4tra PSU /39
4tra PSU /55
6tna PSU /39
6tna PSU /55

Last modification of this entry: 2017-10-06 15:52:05.288435
Edited by a user: pboccaletto
Edited content: Changed mass_prot.