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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:09:17 UTC
HMDB IDHMDB00767
Secondary Accession Numbers
  • HMDB06075
Metabolite Identification
Common NamePseudouridine
DescriptionPseudouridine is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. Pseudouridine is found in all species and in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA (Wikipedia).
Structure
Thumb
Synonyms
  1. 5-(b-D-Ribofuranosyl)uracil
  2. 5-(b-delta-Ribofuranosyl)uracil
  3. 5-b-D-Ribofuranosyl-Uracil
  4. 5-beta-delta-Ribofuranosyl-Uracil
  5. 5-Ribosyluracil
  6. b-D-Pseudouridine
  7. b-Pseudouridine
  8. beta-delta-Pseudouridine
  9. beta-Pseudouridine
  10. Pseudouridine
  11. Pseudouridine C
  12. y-Uridine
Chemical FormulaC9H12N2O6
Average Molecular Weight244.2014
Monoisotopic Molecular Weight244.069536126
IUPAC Name5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Namepseudouridine
CAS Registry Number1445-07-4
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1
InChI KeyPTJWIQPHWPFNBW-GBNDHIKLSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassCarbohydrates and Carbohydrate Conjugates
ClassGlycosyl Compounds
Sub ClassC-glycosyl Compounds
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Carbohydrates and Carbohydrate Conjugates
  • a small molecule(Cyc)
Substituents
  • 1,2 Diol
  • Dialkyl Ether
  • Hydropyrimidine
  • Oxolane
  • Pentose Monosaccharide
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct ParentC-glycosyl Compounds
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
water solubility63.8 g/LALOGPS
logP-2ALOGPS
logP-3.1ChemAxon
logS-0.58ALOGPS
pKa (strongest acidic)9.55ChemAxon
pKa (strongest basic)-3ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count6ChemAxon
hydrogen donor count5ChemAxon
polar surface area128.12ChemAxon
rotatable bond count2ChemAxon
refractivity52.44ChemAxon
polarizability21.81ChemAxon
Spectra
Spectra1D NMR
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
Amniotic FluidDetected and Quantified1.29 +/- 1.07 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified3.18 +/- 0.99 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified63.47 +/- 32.76 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified29.8 (21.8-47.3) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified12.5 (6.5-20.4) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
UrineDetected and Quantified26.02 +/- 4.62 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified25.0 +/- 5.0 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified25.5 +/- 4.8 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified13.467 (8.307-18.627) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified28.9 (13.3-41.3) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified16.70 +/- 3.72 uMAdult (>18 years old)BothCanavan disease details
Associated Disorders and Diseases
Disease References
Canavan disease
  1. Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB014724
KNApSAcK IDC00001508
Chemspider ID14319
KEGG Compound IDC02067
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPseudouridine
NuGOwiki LinkHMDB00767
Metagene LinkHMDB00767
METLIN ID5734
PubChem Compound15047
PDB IDNot Available
ChEBI ID17802
References
Synthesis Referenceanessian, Stephen; Machaalani, Roger. A highly stereo-controlled and efficient synthesis of a- and b-pseudouridines. Tetrahedron Letters (2003), 44(45), 8321-8323.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. Pubmed: 15116424
  2. Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. Pubmed: 2026685
  3. Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. Pubmed: 954194
  4. Bernert JT Jr, Bell CJ, Guntupalli J, Hannon WH: Pseudouridine is unsuitable as an endogenous renal clearance marker. Clin Chem. 1988 Jun;34(6):1011-7. Pubmed: 3378317
  5. Woodcock TM, Chou TC, Tan CT, Sternberg SS, Philips FS, Young CW, Burchenal JH: Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine. Cancer Res. 1980 Nov;40(11):4243-9. Pubmed: 7471064
  6. Colonna A, Russo T, Esposito F, Salvatore F, Cimino F: Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography. Anal Biochem. 1983 Apr 1;130(1):19-26. Pubmed: 6869800
  7. Mak TW, Ho SS, Ho CS, Jones MG, Lai CK, Lam CW: Pleural fluid pseudouridine in malignant and benign pleural effusions. Ann Clin Biochem. 1998 Jan;35 ( Pt 1):94-8. Pubmed: 9463745

Enzymes

General function:
Involved in RNA binding
Specific function:
Converts specific uridines to PSI in a number of tRNA substrates. Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA. Involved in regulation of nuclear receptor activity possibly through pseudouridylation of SRA1 RNA
Gene Name:
PUS1
Uniprot ID:
Q9Y606
Molecular weight:
47469.7
General function:
Involved in RNA processing
Specific function:
Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme
Gene Name:
DKC1
Uniprot ID:
O60832
Molecular weight:
57673.7
General function:
Involved in RNA binding
Specific function:
Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death
Gene Name:
PUS10
Uniprot ID:
Q3MIT2
Molecular weight:
60243.7
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
Q9BZE2
Molecular weight:
55647.0
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUS7
Uniprot ID:
Q96PZ0
Molecular weight:
75034.9
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUS7L
Uniprot ID:
Q9H0K6
Molecular weight:
80699.9
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD1
Uniprot ID:
Q9UJJ7
Molecular weight:
34755.2
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD2
Uniprot ID:
Q8IZ73
Molecular weight:
61311.0
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD3
Uniprot ID:
Q6P087
Molecular weight:
38460.4
General function:
Involved in RNA binding
Specific function:
Not Available
Gene Name:
RPUSD4
Uniprot ID:
Q96CM3
Molecular weight:
42204.9
General function:
Involved in RNA processing
Specific function:
May be responsible for synthesis of pseudouridine from uracil in transfer RNAs
Gene Name:
TRUB1
Uniprot ID:
Q8WWH5
Molecular weight:
37252.4
General function:
Involved in RNA processing
Specific function:
May be responsible for synthesis of pseudouridine from uracil in transfer RNAs
Gene Name:
TRUB2
Uniprot ID:
O95900
Molecular weight:
36694.1
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUSL1
Uniprot ID:
Q8N0Z8
Molecular weight:
33232.5
General function:
Not Available
Specific function:
Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.
Gene Name:
HDHD1
Uniprot ID:
Q08623
Molecular weight:
27572.48
Reactions
pseudouridine 5'-monophosphate + Water → Pseudouridine + Phosphoric aciddetails