Human Metabolome Database: Showing metabocard for Pseudouridine (HMDB0000767)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (14) Show 14 proteins XML

enzymes (14) Show 14 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-10-09 21:00:38 UTC

HMDB ID

HMDB0000767

Secondary Accession Numbers

HMDB0006075
HMDB00767
HMDB06075

Metabolite Identification

Common Name

Pseudouridine

Description

Pseudouridine, also known as psi-uridine or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides such as phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides. Pseudouridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Pseudouridine exists in all living species, ranging from bacteria to humans. It has been detected but not quantified in several different foods, such as cereal products, red bell peppers, sweet rowanberries, bayberries, and cinnamons. This could make pseudouridine a potential biomarker for the consumption of these foods. Pseudouridine 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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol	ChEBI
5-(beta-D-Ribofuranosyl)uracil	ChEBI
beta-Pseudouridine	ChEBI
p	ChEBI
Psi-uridine	ChEBI
5-(b-D-Ribofuranosyl)uracil	Generator
5-(Β-D-ribofuranosyl)uracil	Generator
b-Pseudouridine	Generator
Β-pseudouridine	Generator
5-(b-delta-Ribofuranosyl)uracil	HMDB
5-b-D-Ribofuranosyl-uracil	HMDB
5-beta-delta-Ribofuranosyl-uracil	HMDB
5-Ribosyluracil	HMDB
b-D-Pseudouridine	HMDB
beta-delta-Pseudouridine	HMDB
Pseudouridine C	HMDB
Y-uridine	HMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-β-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
Pseudouridine	HMDB
beta-D-Pseudouridine	HMDB
β-D-Pseudouridine	HMDB
ψ-Uridine	HMDB

Chemical Formula

C₉H₁₂N₂O₆

Average Molecular Weight

244.2014

Monoisotopic Molecular Weight

244.069536126

IUPAC Name

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

β-pseudouridine

CAS Registry Number

1445-07-4

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 Key

PTJWIQPHWPFNBW-GBNDHIKLSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

Not Available

Direct Parent

Nucleoside and nucleotide analogues

Alternative Parents

Substituents

C-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Lactam
Secondary alcohol
Urea
Azacycle
Oxacycle
Ether
Dialkyl ether
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pseudouridines (CHEBI:17802 )

Ontology

Physiological effect

Health effect:

Health condition:

Uremia

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Fabaceae

Biological location:

Tissue and substructures:

Placenta

Subcellular:

Cytoplasm

Biofluid and excreta:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	63.8 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.1	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	8.66	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.44 m³·mol⁻¹	ChemAxon
Polarizability	21.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0unc-7930000000-a1e7f343c88a63ac1976	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0fi0-3494100000-8d726ed412554c1f92f0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , negative	splash10-0udi-0900000000-6ade42aaa885371e176c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, positive	splash10-0a4i-0190000000-129f123affa0ecbf7a59	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 20V, positive	splash10-052f-0910000000-302fbdef606070bd5a67	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 40V, positive	splash10-001i-9300000000-11f5761be16d1b061df5	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0490000000-226d044c24dd80a7c2ca	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0h0s-2980000000-add34ee37b95c102114d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06rm-5900000000-8d66d80928e84e9c93fd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9360000000-3bd8fcdd66c5d245778e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-f551740a13c90ff1d324	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-bf4e4234a47d8aa03828	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Amniotic Fluid
Blood
Feces
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Amniotic Fluid	Detected and Quantified	1.29 +/- 1.07 uM	Adult (>18 years old)	Female	Normal	16139832	details
Blood	Detected and Quantified	2.0492 +/- 23.770 uM	Children (3 months - 6 years old)	Not Specified	Normal	12675874	details
Blood	Detected and Quantified	3.18 +/- 0.99 uM	Adult (>18 years old)	Both	Normal	16139832	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Urine	Detected and Quantified	63.47 +/- 32.76 umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	2026685	details
Urine	Detected and Quantified	29.8 (21.8-47.3) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	12.5 (6.5-20.4) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	26.02 +/- 4.62 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	9129323	details
Urine	Detected and Quantified	25.0 +/- 5.0 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	9129323	details
Urine	Detected and Quantified	25.5 +/- 4.8 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	9129323	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	21389975	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	13.467 (8.307-18.627) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details
Urine	Detected and Quantified	28.9 (13.3-41.3) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	53.689 +/- 87.705 uM	Children (3 months - 6 years old)	Not Specified	Uremia	12675874	details
Blood	Detected and Quantified	16.70 +/- 3.72 uM	Adult (>18 years old)	Both	Canavan disease	16139832	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Epithelial ovarian cancer	23163809	details

Associated Disorders and Diseases

Disease References

Canavan disease
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 ]
Uremia
Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
Colorectal cancer
Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ] Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

271900 (Canavan disease)
114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pseudouridine

METLIN ID

5734

PubChem Compound

15047

PDB ID

Not Available

ChEBI ID

17802

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000249

References

Synthesis Reference

anessian, 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

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 ]
Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. [PubMed:954194 ]
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 ]
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 ]
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 ]
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 ]
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 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Only showing the first 10 proteins. There are 14 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. tRNA pseudouridine synthase A, mitochondrial

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

Enzyme Details

2. H/ACA ribonucleoprotein complex subunit 4

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

Enzyme Details

3. Putative tRNA pseudouridine synthase Pus10

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

Enzyme Details

4. tRNA pseudouridine synthase 3

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

Enzyme Details

5. Pseudouridylate synthase 7 homolog