Biomarkers for pyrimidine metabolism disorders (WP4584)

Homo sapiens

Pyrimidine metabolism disorders are caused by enzyme defects in the metabolism of pyrimidine (WP4225). The clinical presentation of pyrimidine disorders is very diverse, because of the diversity in biological function. The severity of the disorder is determined by the severity of the defect and the function of the normal enzyme. The diagnosis of Pyrimidine metabolism disorders is based on altered concentrations of different metabolic biochemical markers. Some of these markers are metabolites in the pyrimidine metabolism, but there are also several other markers, that are either indirectly or not related to pyrimidine metabolism. All metabolic markers used for the diagnosis of at least one Pyrimidine metabolism disorder and their relations are visualized in this pathway. Biochemical markers derived from http://www.iembase.org/, for all diseases pictured in WP4225.

Authors

Irene Hemel , Denise Slenter , Finterly Hu , and Egon Willighagen

Activity

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Organisms

Homo sapiens

Communities

Annotations

Pathway Ontology

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

Disease Ontology

pyrimidine metabolic disorder orotic aciduria dihydropyrimidine dehydrogenase deficiency

Participants

Label Type Compact URI Comment
(S)-Beta-aminoisobutyrate Metabolite chebi:57731 aka (R)-3-amino-2-methylpropanoate
Zwitterion needed for conversion to take place
Orotate Metabolite chebi:30839
UTP Metabolite chebi:46398 (4-) charge needed for conversion to take place
5-OH-Methyluracil Metabolite chebi:16964
Thymidine Metabolite chebi:17748
OMP Metabolite chebi:57538 Orotidylic acid
(3-) charge needed for conversion to take place
Lactate Metabolite chebi:42111
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
Creatine-P Metabolite chebi:58092 (2-) charge needed for conversion to take place
Dihydrouracil Metabolite chebi:15901
Cytidine Metabolite chebi:17562
Dihydrothymine Metabolite wikidata:Q3027885
Cytosine Metabolite chebi:16040
UMP Metabolite chebi:57865 (2-) charge needed for conversion to take place
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
Cysteine Metabolite chebi:17561
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
Thymine Metabolite chebi:17821
Uric acid Metabolite chebi:27226
Creatine Metabolite chebi:57947 Zwitterion needed for conversion to take place
2-Deoxyuridine Metabolite chebi:16450
Glutathione Metabolite chebi:16856
Pseudouridine Metabolite chebi:65314
+ PRPP Metabolite chebi:17111
dUDP Metabolite chebi:60471 (3-) charge needed for conversion to take place
dUMP Metabolite chebi:246422 (2-) charge needed for conversion to take place
dTMP Metabolite chebi:63528 (2-) charge needed for conversion to take place
Dihydroorotate Metabolite chebi:30864
UMPS GeneProduct uniprot:P11172
Creatine kinase Protein uniprot:P12277
DPD Protein uniprot:Q12882
PUS1 Protein uniprot:Q9Y606
UMPH1 Protein uniprot:Q9H0P0 aka P5N1
Enzymes and reactions added with info from https://www.omim.org/entry/606224
TP Protein uniprot:P19971
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
UP Protein uniprot:Q9UBR1
DHP Protein uniprot:Q14117
TK2 Protein uniprot:O00142
TS Protein uniprot:P04818
RR Protein eccode:1.17.4.1
RRM1 Protein uniprot:P23921
RRM2 Protein uniprot:P31350
RRM2B Protein uniprot:Q7LG56
OPRT Protein eccode:2.4.2.10
OMPDC Protein eccode:4.1.1.23
DHODH Protein uniprot:Q02127

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. Creatine and creatinine metabolism. Wyss M, Kaddurah-Daouk R. Physiol Rev. 2000 Jul;80(3):1107–213. PubMed Europe PMC Scholia
  3. 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