Pyrimidine metabolism and related diseases (WP4225)

Homo sapiens

Overview of pyrimidine metabolism and related diseases

Authors

Roel Hacking , Denise Slenter , Egon Willighagen , Martina Summer-Kutmon , Irene Hemel , Friederike Ehrhart , Finterly Hu , and Eric Weitz

Activity

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Organisms

Homo sapiens

Communities

Inherited Metabolic Disorders (IMD) Pathways Rare Diseases

Annotations

Disease Ontology

pyrimidine metabolic disorder dihydropyrimidine dehydrogenase deficiency orotic aciduria

Pathway Ontology

dihydropyrimidine dehydrogenase deficiency pathway beta-ureidopropionase deficiency pathway orotic aciduria 1 pathway pyrimidine metabolic pathway inborn error of purine-pyrimidine metabolism pathway disease pathway

Participants

Label Type Compact URI Comment
(S)-Beta-aminoisobutyrate Metabolite chebi:57731 aka (R)-3-amino-2-methylpropanoate; myokine, β-aminoisobutyric acid (BAIBA); D form of β-aminoisobutyric acid (D-BAIBA)
Zwitterion needed for conversion to take place
Glutamine Metabolite chebi:58359 Zwitterion needed for conversion to take place
Orotate Metabolite chebi:30839
UTP Metabolite chebi:46398 (4-) charge needed for conversion to take place
Carbamoyl-phosphate Metabolite chebi:58228 (2-) charge needed for conversion to take place
L-Valine Metabolite chebi:57762
CoQ10 Metabolite chebi:46245
Thymidine Metabolite chebi:17748
OMP Metabolite chebi:57538 Orotidylic acid
(3-) charge needed for conversion to take place
Acetyl-CoA Metabolite chebi:15351
Aspartate Metabolite chebi:29991 (1-) charge needed for conversion to take place
Carbamoylaspartate Metabolite chebi:32814 aka N-carbamoyl-L-aspartate
(2-) charge needed for conversion to take place
CDP Metabolite chebi:58069 (3-) charge needed for conversion to take place
N-Carbamoyl-beta-alanine Metabolite chebi:11892 aka 3-(carbamoylamino)propanoate
Uridine Metabolite chebi:16704
CoQ10 - H2 (reduced) Metabolite chebi:64183
Ornithine Metabolite chebi:46911 (1) charge needed for conversion to take place
Dihydrouracil Metabolite chebi:15901
Cytidine Metabolite chebi:17562
Dihydrothymine Metabolite chebi:27468
UMP Metabolite chebi:57865 (2-) charge needed for conversion to take place
Citrulline Metabolite chebi:57743 Zwitterion needed for conversion to take place
dUDP Metabolite chebi:60471 (3-) charge needed for conversion to take place
Malonate semialdehyde Metabolite chebi:57700 AKA Beta-ketopropionate
Annotated without knowledge of R/S configuration
dUMP Metabolite chebi:246422 (2-) charge needed for conversion to take place
D-methylmalonatesemialdehyde Metabolite chebi:141212 methylmalonate semialdehyde aka 2-Methyl-3-oxopropanoic acid aka 2-methyl-3-oxopropanoate
D configuration == R-annotation in ChEBI
Uracil Metabolite chebi:17568
CMP Metabolite chebi:60377 (2-) charge needed for conversion to take place
Orotidine Metabolite chebi:25722
N-Carbamyl-beta-aminoisobutyric acid Metabolite chebi:74414 aka 3-(carbamoylamino)-2-methylpropanoate
(1-) charge needed for conversion to take place
CTP Metabolite chebi:37563 (4-) charge needed for conversion to take place
Beta-alanine Metabolite chebi:57966 Zwitterion needed for conversion to take place
PRPP Metabolite chebi:17111
UDP Metabolite chebi:58223 (3-) charge needed for conversion to take place
Uridine Metabolite chebi:16704
Thymine Metabolite chebi:17821
HCO3- Metabolite chebi:17544
2-Deoxyuridine Metabolite chebi:16450
dTMP Metabolite chebi:63528 (2-) charge needed for conversion to take place
Orotate Metabolite chebi:30839
Dihydroorotate Metabolite chebi:30864
Carbamoyl-phosphate Metabolite chebi:58228 (2-) charge needed for conversion to take place
Glutamine Metabolite chebi:58359 Zwitterion needed for conversion to take place
HCO3- Metabolite chebi:17544
+ PRPP Metabolite chebi:17111
Glutamate Metabolite chebi:29985 (1-) charge needed for conversion to take place
NH4+ Metabolite chebi:28938
Dihydroorotate Metabolite chebi:30864
L-BAIBA Metabolite chebi:58655 L form of β-aminoisobutyric acid (BAIBA)
L-methylmalonatesemialdehyde Metabolite chebi:62413 methylmalonate semialdehyde aka 2-Methyl-3-oxopropanoic acid aka 2-methyl-3-oxopropanoate
L configuration == S-annotation in ChEBI
Propionyl-CoA Metabolite chebi:57392
UMPS-complex GeneProduct uniprot:P11172
CAD-complex GeneProduct uniprot:P27708
RRM1 Protein uniprot:P23921
RRM2 Protein uniprot:P31350
MMSDH Protein uniprot:Q02252
RRM2B Protein uniprot:Q7LG56
TK2 Protein uniprot:O00142
OTC Protein uniprot:P00480
DPD Protein uniprot:Q12882 AKA DPYD
DHO Protein eccode:3.5.2.3
GLS2 Protein uniprot:Q9UI32
RRM2B Protein uniprot:Q7LG56
UMPH1 Protein uniprot:Q9H0P0 aka P5N1
Enzymes and reactions added with info from https://www.omim.org/entry/606224
UP Protein uniprot:Q9UBR1 aka UPB1
CPS1 Protein uniprot:P31327
TS Protein uniprot:P04818
OPRT Protein eccode:2.4.2.10
OMPDC Protein eccode:4.1.1.23
AGXT2 Protein uniprot:Q9BYV1
TP Protein uniprot:P19971
DHODH Protein uniprot:Q02127
ACT Protein eccode:2.1.3.2
beta-alanine-pyruvate transaminase Protein eccode:2.6.1.18
CPS2 Protein eccode:6.3.5.5
RR Protein eccode:1.17.4.1
DHP Protein uniprot:Q14117 AKA DPYS
CPS2 Protein eccode:6.3.5.5
DHO Protein eccode:3.5.2.3
ACT Protein kegg.genes:2.1.3.2
OPRT Protein eccode:2.4.2.10
OMPDC Protein eccode:4.1.1.23
UMPH2 Protein uniprot:Q8TCD5 aka NT5C
Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPH Protein eccode:3.1.3.5 aka P5N
Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPH1 Protein uniprot:Q9H0P0 aka P5N1
Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPH2 Protein uniprot:Q8TCD5 aka NT5C
Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPH Protein eccode:3.1.3.5 aka P5N
Enzymes and reactions added with info from https://www.omim.org/entry/606224
RRM1 Protein uniprot:P23921
ABAT Protein uniprot:P80404

References

  1. Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases [Internet]. Blau N, Duran M, Gibson KM, Dionisi-Vici C. Springer; 2014. 0 p. Available from: https://books.google.com/books/about/Physician_s_Guide_to_the_Diagnosis_Treat.html?hl=&id=wJRBnwEACAAJ OpenLibrary Worldcat
  2. Pyridoxine-responsive hyper-beta-alaninemia associated with Cohen’s syndrome. Higgins JJ, Kaneski CR, Bernardini I, Brady RO, Barton NW. Neurology. 1994 Sep;44(9):1728–32. PubMed Europe PMC Scholia
  3. Mammalian methylmalonate-semialdehyde dehydrogenase. Kedishvili NY, Goodwin GW, Popov KM, Harris RA. Methods Enzymol. 2000;324:207–18. PubMed Europe PMC Scholia
  4. Dihydropyrimidine dehydrogenase and the efficacy and toxicity of 5-fluorouracil. van Kuilenburg ABP. Eur J Cancer. 2004 May;40(7):939–50. PubMed Europe PMC Scholia
  5. Characterization of enzymatic properties of human ribonucleotide reductase holoenzyme reconstituted in vitro from hRRM1, hRRM2, and p53R2 subunits. Qiu W, Zhou B, Darwish D, Shao J, Yen Y. Biochem Biophys Res Commun. 2006 Feb 10;340(2):428–34. PubMed Europe PMC Scholia
  6. Clinical findings and a therapeutic trial in the first patient with beta-ureidopropionase deficiency. Assmann B, Göhlich G, Baethmann M, Wevers RA, Van Gennip AH, Van Kuilenburg ABP, et al. Neuropediatrics. 2006 Feb;37(1):20–5. PubMed Europe PMC Scholia
  7. Inborn errors of pyrimidine metabolism: clinical update and therapy. Balasubramaniam S, Duley JA, Christodoulou J. J Inherit Metab Dis. 2014 Sep;37(5):687–98. PubMed Europe PMC Scholia
  8. Beta-Aminoisobutyric Acid as a Novel Regulator of Carbohydrate and Lipid Metabolism. Tanianskii DA, Jarzebska N, Birkenfeld AL, O’Sullivan JF, Rodionov RN. Nutrients. 2019 Feb 28;11(3):524. PubMed Europe PMC Scholia
  9. Mevalonate Pathway Provides Ubiquinone to Maintain Pyrimidine Synthesis and Survival in p53-Deficient Cancer Cells Exposed to Metabolic Stress. Kaymak I, Maier CR, Schmitz W, Campbell AD, Dankworth B, Ade CP, et al. Cancer Res. 2020 Jan 15;80(2):189–203. PubMed Europe PMC Scholia