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PseudoUridine 5'-monophosphate - CAS 1157-60-4
A metabolic process has been acknowledged for pseudoUridine, and it involves the pseudoUridine phosphorylation to generate pseudoUridine 5ʹ-monophosphate (ΨMP) catalyzed by the enzyme pseudoUridine kinase and thereafter the C-C glycosidic bond cleavage to give uracil and ribose 5-phosphate which mediated by the pseudoUridine 5ʹ-monophosphate glycosidase.
Catalog Number
1157-60-4
CAS
1157-60-4
Molecular Weight
324.18
Molecular Formula
C9H13N2O9P
Synonyms
Pseudouridylic acid; (1S)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol; pseudouridine 5'-phosphate; 5-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione; 5-b-D-Ribofuranosyluracil 5'-phosphate; Uracil, 5-b-D-ribofuranosyl-, 5'-phosphate
IUPAC Name
[(2R,3S,4R,5S)-5-(2,4-dioxo-1H-pyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate
Canonical SMILES
C1=C(C(=O)NC(=O)N1)C2C(C(C(O2)COP(=O)(O)O)O)O
InChI
InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
InChIKey
MOBMOJGXNHLLIR-GBNDHIKLSA-N
Boiling Point
728.8°C at 760 mmHg
Purity
≥95%
Density
1.833 g/cm3
Higher enzymatic hydrolysis stability of pseudoUridine
In general, the heterocyclic moiety is linked to the ribose portion through its nitrogen atom forming a C-N bond to product nucleoside, which could be called N-nucleoside. Differently, C-nucleosides is referred non-canonical nucleosides where the heterocycle combine with ribose via a C-C bond. These C-nucleosides are naturally occurring and endowed with a higher enzymatic hydrolysis stability of the C-C glycosidic bond compared with the C-N bond of N-nucleosides.
pseudoUridine (Ψ) is an isomer of uridine and belong to the non-canonical C-nucleoside, which is the most abundant modified nucleoside in noncoding RNAs (ncRNAs). Introducing the Ψ into both single-stranded and double-stranded RNAs to provide structural rigidity enhancement, because of an appropriate setting for the co-ordination of a water molecule between the Ψ free imino proton and the 5'-phosphate backbone of the preceding residue when incorporation of Ψ in oligonucleotides. To lead a reduced backbone mobility and a restricted base conformation inducing enhanced bases stacking which is perhaps the major contribution of Ψ toward stabilizing the RNA structure.
Catabolism of pseudoUridine
In Ψ biosynthesis, pseudoUridine synthases introduce Ψ through the isomerization of specific uridine residues via the post-transcriptional modification of the RNA. As early as 1970, it was found that in Escherichia coli, pseudoUridine added to the growth medium could be used as the sole pyrimidine source by pyrimidine auxotrophic mutants. This was later shown to be achieved through the catabolism of pseudoUridine. A metabolic process has been acknowledged for pseudoUridine, and it involves the pseudoUridine phosphorylation to generate pseudoUridine 5'-monophosphate (ΨMP) catalyzed by the enzyme pseudoUridine kinase and thereafter the C-C glycosidic bond cleavage to give uracil and ribose 5-phosphate which mediated by the pseudoUridine 5ʹ-monophosphate glycosidase.
Study reported the crystal structure of pseudoUridine 5'-monophosphate glycosidase, the proposed mechanism of pseudoUridine cleavage contemplates the acid catalyzed ribose ring opening followed by a covalent linkage between the ribose C1' and a pseudoUridine 5'-monophosphate glycosidase active site lysine amino group. This modification leads to a facile C-C glycosidic bond fragmentation following a novel retro aldol-type mechanism. These above two enzymes responsible for pseudoUridine degradation were identified in the uropathogenic Escherichia coli, the principal agent of urinary tract infections in humans, while the genes encoding these enzymes are absent from the genomes of man and other mammals.
pseudoUridine 5'-monophosphate in plant
PseudoUridine is a common nucleoside modification found in ncRNAs and mRNAs. RNA undergoes constant turnover, releasing free pseudoUridine, but the metabolism of pseudoUridine in eukaryotes has not been studied enough. Recently, one research showed that pseudoUridine is catabolized in the peroxisome by a pseudoUridine kinase from the PfkB family that generates ΨMP and a ΨMP glycosylase that hydrolyzes ΨMP to uracil and ribose-5-phosphate in Arabidopsis thaliana. Disruption of pseudoUridine catabolism leads to strong pseudoUridine accumulation and increased ΨMP content. It is worth noting that ΨMP is toxic to this plant, causing delayed germination and growth inhibition. However, experiments have shown that impairing pseudoUridine catabolism does not affect the Ψ/U ratio in RNA. The bipartite peroxisomal pseudoUridine kinase and ΨMP glycosylase are conserved in plants and algae, whereas some fungi and most animals (except mammals) possess a ΨMP glycosylase - pseudoUridine kinase fusion protein, likely in mitochondria.
1.Molecular modeling studies of pseudouridine isoxazolidinyl nucleoside analogues as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase
Chem Biol Drug Des. 2018 Feb;91(2):519-525. doi: 10.1111/cbdd.13113.
In this paper, we investigated the hypothesis that pseudouridine isoxazolidinyl nucleoside analogues could act as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase. This purpose was pursued using molecular modeling and in silico ADME-Tox profiling. From these studies emerged that the isoxazolidinyl derivative 1 5'-monophosphate can be effectively accommodated within the active site of the enzyme with a ligand efficiency higher than that of the natural substrate. In this context, the poor nucleofugality of the N-protonated isoxazolidine prevents or slows down, the first mechanistic step proposed for the degradation of the pseudouridine 5'-monophosphate glycosidase, leading to the enzyme inhibition. Finally, the results of the physicochemical and ADME-Tox informative analysis pointed out that compound 1 is weakly bounded to plasma protein, only moderately permeate the blood-brain barrier, and is non-carcinogen in rat and mouse. To the best of our knowledge, this is the first paper that introduces the possibility of inhibition of pseudouridine 5'-monophosphate glycosidase by a molecule that competing with the natural substrate hinders the glycosidic C-C bond cleavage.
2.Semi-enzymatic synthesis of pseudouridine
Bioorg Med Chem Lett. 2021 Jul 15;44:128105. doi: 10.1016/j.bmcl.2021.128105.
Modifications of RNA molecules have a significant effect on their structure and function. One of the most common modifications is the isomerization from uridine to pseudouridine. Despite its prevalence in natural RNA sequences, organic synthesis of pseudouridine has been challenging because of the stereochemistry requirement and the sensitivity of reaction steps to moisture. Herein, a semi-enzymatic synthetic route is developed for the synthesis of pseudouridine using adenosine 5'-monophosphate and uracil as the starting materials and a reverse reaction catalyzed by the pseudouridine monophosphate glycosidase. This synthetic route has only three steps and the overall yield of β-pseudouridine production was 68.4%.
3.Pseudouridine monophosphate glycosidase: a new glycosidase mechanism
Biochemistry. 2012 Nov 13;51(45):9245-55. doi: 10.1021/bi3006829.
Pseudouridine (Ψ), the most abundant modification in RNA, is synthesized in situ using Ψ synthase. Recently, a pathway for the degradation of Ψ was described [Preumont, A., Snoussi, K., Stroobant, V., Collet, J. F., and Van Schaftingen, E. (2008) J. Biol. Chem. 283, 25238-25246]. In this pathway, Ψ is first converted to Ψ 5'-monophosphate (ΨMP) by Ψ kinase and then ΨMP is degraded by ΨMP glycosidase to uracil and ribose 5-phosphate. ΨMP glycosidase is the first example of a mechanistically characterized enzyme that cleaves a C-C glycosidic bond. Here we report X-ray crystal structures of Escherichia coli ΨMP glycosidase and a complex of the K166A mutant with ΨMP. We also report the structures of a ring-opened ribose 5-phosphate adduct and a ring-opened ribose ΨMP adduct. These structures provide four snapshots along the reaction coordinate. The structural studies suggested that the reaction utilizes a Lys166 adduct during catalysis. Biochemical and mass spectrometry data further confirmed the existence of a lysine adduct. We used site-directed mutagenesis combined with kinetic analysis to identify roles for specific active site residues. Together, these data suggest that ΨMP glycosidase catalyzes the cleavage of the C-C glycosidic bond through a novel ribose ring-opening mechanism.
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