Modification Summary

dihydrouridine

[show modification pathway]
D

Summary

Full namedihydrouridine
Short nameD
New Nomenclature8U
RNAMods abbreviationD
HTML abbreviationD
Enzymes Dus1 (Saccharomyces cerevisiae)
Dus2 (Saccharomyces cerevisiae)
Dus3 (Saccharomyces cerevisiae)
Dus4 (Saccharomyces cerevisiae)
DusA (Escherichia coli)
DusB (Escherichia coli)
DusC (Escherichia coli)
Found in phylogenyEubacteria, Eukaryota
Found in RNArRNA, tDNA, tRNA
PubChem ID94312
SMILES codeC3(OC(CO)C(O)C(O)3)N1CCC(=O)NC1(=O)

LC-MS Information

Sum formulaC9O6N2H14
Monoisotopic mass246.085186
Average mass246.220269
HRMS mass246.084637
Normalized LC elution time *0,32 (Kellner 2014); 0,35 (Kellner 2014)
LC elution order/characteristicsbefore C (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 D]

Chemical groups contained

ring modificationpartial saturation

Reactions producing dihydrouridine

Name
U:D

Reactions starting from dihydrouridine

Name
D:m5D
D:acp3D

Occurrence in PDB structures

PDB-ID chain residue
1a31 C 5IU /10
1f7u B DHU /916
1f7u B DHU /919
1f7u B DHU /947
1f7v B DHU /916
1f7v B DHU /919
1f7v B DHU /947
1fir A DHU /16
1fir A DHU /20
1fir A DHU /47
1ixy UDP /400
1ixy UDP /401
1k4s B +U /10
1m5r UDP /400
1m5r UDP /401
1n38 U3H /1291
1nh3 B UBB /10
1pnn A IPN /5
1pnn C IPN /5
1qf6 B DHU /16
1qf6 B DHU /17
1qf6 B DHU /20
1ser T DHU /20A
1sxq A UDP /400
1sxq B UDP /400
1y6f UDP /601
1y6g UDP /1101
1y6g UDP /1201
1y8z UDP /1001
1y8z UDP /2001
1ya6 UDP /2001
1zl3 B UD5 /410
2i1c z DHU /16
2i1c z DHU /20

Last modification of this entry: 2017-07-05 14:22:56.499004
Edited by a user: pboccaletto
Edited content: No fields changed.