Pseudouridine (BioDeep_00000001301)

 

Secondary id: BioDeep_00000229653, BioDeep_00000406168

human metabolite PANOMIX_OTCML-2023 Endogenous blood metabolite natural product


代谢物信息卡片


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

化学式: C9H12N2O6 (244.0695)
中文名称: 假尿苷
谱图信息: 最多检出来源 Homo sapiens(blood) 19.86%

Reviewed

Last reviewed on 2024-07-01.

Cite this Page

Pseudouridine. BioDeep Database v3. PANOMIX ltd, a top metabolomics service provider from China. https://query.biodeep.cn/s/pseudouridine (retrieved 2024-12-22) (BioDeep RN: BioDeep_00000001301). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0).

分子结构信息

SMILES: C1=C(C(=O)NC(=O)N1)C2C(C(C(O2)CO)O)O
InChI: 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

描述信息

Beta-pseudouridine, also known as p or 5-(b-D-ribofuranosyl)uracil, is a member of the class of compounds known as nucleoside and nucleotide analogues. Nucleoside and nucleotide analogues 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. Beta-pseudouridine is soluble (in water) and a very weakly acidic compound (based on its pKa). Beta-pseudouridine can be found in a number of food items such as eggplant, wax gourd, asparagus, and garden cress, which makes beta-pseudouridine a potential biomarker for the consumption of these food products. Beta-pseudouridine can be found primarily in amniotic fluid, blood, feces, and urine. Beta-pseudouridine exists in all living species, ranging from bacteria to humans. Moreover, beta-pseudouridine is found to be associated with canavan disease.
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 specifically has its uracil attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond to the ribofuranose. It is the most prevalent of the over one hundred different modified nucleosides found in RNA (PMID: 17113994). Pseudouridine is a solid that is soluble in water. Pseudouridine exists in all living species, ranging from bacteria to humans, and is in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA.

Pseudouridine. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=1445-07-4 (retrieved 2024-07-01) (CAS RN: 1445-07-4). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0).
Pseudouridine is an isomer of the nucleoside uridine, and the most abundant modified nucleoside in non-coding RNAs. Pseudouridine in rRNA and tRNA can fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation[1][2][3][4].
Pseudouridine is an isomer of the nucleoside uridine, and the most abundant modified nucleoside in non-coding RNAs. Pseudouridine in rRNA and tRNA can fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation[1][2][3][4].

同义名列表

27 个代谢物同义名

5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione; (1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol; 5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione; 5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione; 5-beta-delta-Ribofuranosyl-uracil; 5-(b-delta-Ribofuranosyl)uracil; 5-(beta-D-Ribofuranosyl)uracil; 5-(Β-D-ribofuranosyl)uracil; 5-(b-D-Ribofuranosyl)uracil; 5-b-D-Ribofuranosyl-uracil; beta-delta-Pseudouridine; beta-D-Pseudouridine; beta-Pseudouridine; Β-D-pseudouridine; b-D-Pseudouridine; b-Pseudouridine; 5-Ribosyluracil; Β-pseudouridine; Pseudouridine C; Pseudouridine; .psi.-Uridine; Psi-uridine; Ψ-uridine; Y-uridine; P; Pseudouridine; Pseudouridine



数据库引用编号

28 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(2)

BioCyc(0)

PlantCyc(0)

代谢反应

203 个相关的代谢反应过程信息。

Reactome(64)

BioCyc(12)

WikiPathways(0)

Plant Reactome(0)

INOH(0)

PlantCyc(126)

COVID-19 Disease Map(0)

PathBank(1)

  • Purine Degradation: Adenosine triphosphate + Pseudouridine ⟶ Adenosine diphosphate + Hydrogen Ion + Pseudouridine 5'-phosphate

PharmGKB(0)

26 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有：

  • PubMed: 来源于PubMed文献库中的文献信息，我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表，这个列表按照代谢物同时出现的文献数量降序排序，取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘，得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序，取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中，存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称，可以跳转到相关代谢物的信息页面。

亚细胞结构定位 关联基因列表
Cytoplasm 9 AFP, AKT1, DKC1, EGFR, EMG1, PUS1, PUS10, PUS3, RBMS3
Endosome membrane 1 EGFR
Endoplasmic reticulum membrane 1 EGFR
Nucleus 10 AKT1, DKC1, EGFR, EMG1, PUS1, PUS10, PUS3, PUS7, RBMS3, TRUB1
cytosol 5 AKT1, B2M, PUS3, RBMS3, TRUB1
nuclear body 1 NOP10
nucleoplasm 6 AKT1, DKC1, EMG1, GAR1, NOP10, PUS1
Cell membrane 4 AKT1, B2M, EGFR, SLC19A2
lamellipodium 1 AKT1
ruffle membrane 1 EGFR
Early endosome membrane 2 B2M, EGFR
Multi-pass membrane protein 1 SLC19A2
cell cortex 1 AKT1
cell junction 1 EGFR
cell surface 4 ALPP, B2M, EGFR, EPO
glutamatergic synapse 2 AKT1, EGFR
Golgi apparatus 1 B2M
Golgi membrane 3 B2M, C1GALT1, EGFR
lysosomal membrane 1 B2M
postsynapse 1 AKT1
Cytoplasm, cytosol 1 TRUB1
endosome 1 EGFR
plasma membrane 6 AKT1, ALPP, B2M, EGFR, IFNLR1, SLC19A2
Membrane 6 AKT1, B2M, C1GALT1, EGFR, IFNLR1, SLC19A2
apical plasma membrane 1 EGFR
basolateral plasma membrane 1 EGFR
extracellular exosome 2 B2M, EPO
endoplasmic reticulum 1 B2M
extracellular space 5 AFP, B2M, CRP, EGFR, EPO
perinuclear region of cytoplasm 1 EGFR
mitochondrion 3 PUS1, PUS10, TRUB1
protein-containing complex 2 AKT1, EGFR
intracellular membrane-bounded organelle 1 PUS1
Single-pass type I membrane protein 2 EGFR, IFNLR1
Secreted 4 AFP, B2M, CRP, EPO
extracellular region 3 B2M, CRP, EPO
mitochondrial matrix 1 PUS1
nuclear membrane 1 EGFR
external side of plasma membrane 1 B2M
microtubule cytoskeleton 1 AKT1
nucleolus 2 DKC1, EMG1
cell-cell junction 1 AKT1
Single-pass type II membrane protein 1 C1GALT1
vesicle 1 AKT1
Membrane raft 1 EGFR
focal adhesion 2 B2M, EGFR
spindle 1 AKT1
intracellular vesicle 1 EGFR
Mitochondrion intermembrane space 1 AKT1
mitochondrial intermembrane space 1 AKT1
receptor complex 1 EGFR
ciliary basal body 1 AKT1
Late endosome membrane 1 B2M
phagocytic vesicle membrane 1 B2M
Chromosome 1 EMG1
[Isoform 1]: Mitochondrion 1 PUS1
Nucleus, nucleolus 2 EMG1, NOP10
chromosome, telomeric region 1 GAR1
Lipid-anchor, GPI-anchor 1 ALPP
fibrillar center 2 DKC1, GAR1
Recycling endosome membrane 1 B2M
cell body 1 EPO
side of membrane 1 ALPP
basal plasma membrane 1 EGFR
[Isoform 3]: Cytoplasm 1 DKC1
synaptic membrane 1 EGFR
secretory granule lumen 1 EPO
HFE-transferrin receptor complex 1 B2M
endoplasmic reticulum lumen 2 AFP, B2M
specific granule lumen 1 B2M
tertiary granule lumen 1 B2M
small-subunit processome 1 EMG1
sno(s)RNA-containing ribonucleoprotein complex 1 NOP10
ER to Golgi transport vesicle membrane 1 B2M
telomerase holoenzyme complex 3 DKC1, GAR1, NOP10
clathrin-coated endocytic vesicle membrane 1 EGFR
Cajal body 1 DKC1
ribonucleoprotein complex 2 NOP10, RBMS3
[Isoform 2]: Nucleus 1 PUS1
[Isoform 1]: Nucleus, nucleolus 1 DKC1
MHC class I peptide loading complex 1 B2M
Nucleus, Cajal body 2 DKC1, NOP10
box H/ACA scaRNP complex 3 DKC1, GAR1, NOP10
box H/ACA snoRNP complex 3 DKC1, GAR1, NOP10
box H/ACA telomerase RNP complex 3 DKC1, GAR1, NOP10
multivesicular body, internal vesicle lumen 1 EGFR
Shc-EGFR complex 1 EGFR
MHC class I protein complex 1 B2M
MHC class II protein complex 1 B2M
early endosome lumen 1 B2M
interleukin-28 receptor complex 1 IFNLR1


文献列表

  • Yanli Niu, Lingyun Liu. RNA pseudouridine modification in plants. Journal of experimental botany. 2023 11; 74(21):6431-6447. doi: 10.1093/jxb/erad323. [PMID: 37581601]
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  • Ruijia He, Jing Qiao, Xiaoxia Wang, Wenlian Chen, Tong Yin. A new quantitative method for pseudouridine and uridine in human serum and its clinical application in acute myeloid leukemia. Journal of pharmaceutical and biomedical analysis. 2022 Sep; 219(?):114934. doi: 10.1016/j.jpba.2022.114934. [PMID: 35839582]
  • Zidong Jia, Feilong Meng, Hui Chen, Gao Zhu, Xincheng Li, Yunfan He, Liyao Zhang, Xiao He, Huisen Zhan, Mengquan Chen, Yanchun Ji, Meng Wang, Min-Xin Guan. Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Ψ55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro. Nucleic acids research. 2022 09; 50(16):9368-9381. doi: 10.1093/nar/gkac698. [PMID: 36018806]
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  • Qi Cui, Kailin Yin, Xiaoting Zhang, Peng Ye, Xianwei Chen, Jianfei Chao, Haowei Meng, Jiangbo Wei, Daniel Roeth, Li Li, Yue Qin, Guihua Sun, Mingzi Zhang, Jeremy Klein, Marvin Huynhle, Cheng Wang, Leying Zhang, Behnam Badie, Markus Kalkum, Chuan He, Chengqi Yi, Yanhong Shi. Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. Nature cancer. 2021 09; 2(9):932-949. doi: 10.1038/s43018-021-00238-0. [PMID: 35121864]
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