Biomarkers for pyrimidine metabolism disorders (Homo sapiens)
From WikiPathways
Description
Overview of pyrimidine metabolism and related diseases. Pyrimidine metabolism is important for the synthesis of thymine, cytosine and uracil, some of the building blocks for DNA and RNA and they also have functions in signal transduction and energy transport. The pathway can be split up in 3 parts, one is the de novo synthesis of pyrimidines, starting with glutamine and ending at UMP. From here the UMP can either be used in the nucleic acid synthesis (up) or broken down to Beta-alanine or (S)-beta-aminoisobutyrate.
Disorders in the metabolism of pyrimidine are mostly caused by enzyme defects (highlighted in pink, one disease is depicted in orange, since there appears to be no clinical difference between type 2 and 1 of orotic aciduria, therefore researchers believe that type 2 does not exist officially). 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.
Metabolic markers are highlighted in dark purple. Complexes mentioned in pathway are pictured in bottom left corner. The link to the Urea cycle is depicted for clarity.
This pathway was inspired by Chapter 41 of the book of Blau (ISBN 3642403360 (978-3642403361)).Quality Tags
Ontology Terms
Bibliography
- Wyss M, Kaddurah-Daouk R; ''Creatine and creatinine metabolism.''; Physiol Rev, 2000 PubMed Europe PMC Scholia
- Qiu W, Zhou B, Darwish D, Shao J, Yen Y; ''Characterization of enzymatic properties of human ribonucleotide reductase holoenzyme reconstituted in vitro from hRRM1, hRRM2, and p53R2 subunits.''; Biochem Biophys Res Commun, 2006 PubMed Europe PMC Scholia
- Blau, N., Duran, M., Gibson, K.M., Donisi-Vici, C; ''Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases Chapter 41''; ISBN:978-3-642-40337-8, 2014
History
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External references
DataNodes
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Name | Type | Database reference | Comment |
---|---|---|---|
(S)-beta-aminoisobutyrate | Metabolite | CHEBI:57731 (ChEBI) | aka (R)-3-amino-2-methylpropanoate |
+ PRPP | Metabolite | CHEBI:17111 (ChEBI) | |
2-Deoxyuridine | Metabolite | CHEBI:16450 (ChEBI) | |
5-OH-Methyluracil | Metabolite | CHEBI:16964 (ChEBI) | |
Amino Acid metabolism | Pathway | WP3925 (WikiPathways) | |
Beta-alanine | Metabolite | CHEBI:57966 (ChEBI) | |
CDP | Metabolite | CHEBI:58069 (ChEBI) | CDP 3-, charge needed for conversion can take place |
CMP | Metabolite | CHEBI:60377 (ChEBI) | CMP (2-), charge needed for conversion can take place |
CTP | Metabolite | CHEBI:37563 (ChEBI) | |
Creatine kinase | Protein | P12277 (Uniprot-TrEMBL) | |
Creatine-P | Metabolite | CHEBI:58092 (ChEBI) | |
Creatine | Metabolite | CHEBI:57947 (ChEBI) | |
Cysteine | Metabolite | CHEBI:15356 (ChEBI) | |
Cytosine | Metabolite | CHEBI:16040 (ChEBI) | |
DHP | Protein | Q14117 (Uniprot-TrEMBL) | |
DPD | Protein | Q12882 (Uniprot-TrEMBL) | |
Dihydrouracil | Metabolite | CHEBI:15901 (ChEBI) | |
Glutathione | Metabolite | CHEBI:16856 (ChEBI) | |
Glutathione metabolism | Pathway | WP100 (WikiPathways) | |
Lactate | Metabolite | CHEBI:24996 (ChEBI) | |
N-Carbamoyl-beta-alanine | Metabolite | CHEBI:11892 (ChEBI) | aka 3-(carbamoylamino)propanoate |
N-Carbamyl-beta-aminoisobutyric acid | Metabolite | CHEBI:74414 (ChEBI) | aka 3-(carbamoylamino)-2-methylpropanoate |
OMP | Metabolite | CHEBI:57538 (ChEBI) | Orotidylic acid |
OMPDC | Protein | 4.1.1.23 (Enzyme Nomenclature) | |
OPRT | Protein | 2.4.2.10 (Enzyme Nomenclature) | |
Orotate | Metabolite | CHEBI:30839 (ChEBI) | |
PRPP | Metabolite | CHEBI:17111 (ChEBI) | |
Purine metabolism | Pathway | WP4224 (WikiPathways) | |
Pyrimidine metabolism | Pathway | WP4225 (WikiPathways) | |
RR | Protein | 1.17.4.1 (Enzyme Nomenclature) | |
RRM1 | Protein | P23921 (Uniprot-TrEMBL) | |
RRM2B | Protein | Q7LG56 (Uniprot-TrEMBL) | |
RRM2 | Protein | P31350 (Uniprot-TrEMBL) | |
TK2 | Protein | O00142 (Uniprot-TrEMBL) | |
TP | Protein | P19971 (Uniprot-TrEMBL) | |
TS | Protein | P04818 (Uniprot-TrEMBL) | |
UDP | Metabolite | CHEBI:58223 (ChEBI) | |
UMP | Metabolite | CHEBI:57865 (ChEBI) | |
UMPH1 | Protein | Q9H0P0 (Uniprot-TrEMBL) |
|
UMPH2 | Protein | Q8TCD5 (Uniprot-TrEMBL) |
|
UMPH | Protein | 3.1.3.5 (Enzyme Nomenclature) |
|
UMPS | GeneProduct | P11172 (Uniprot-TrEMBL) | |
UP | Protein | Q9UBR1 (Uniprot-TrEMBL) | |
UTP | Metabolite | CHEBI:46398 (ChEBI) | |
Uric acid | Metabolite | CHEBI:27226 (ChEBI) | |
cytidine | Metabolite | CHEBI:17562 (ChEBI) | |
dTMP | Metabolite | CHEBI:63528 (ChEBI) | |
dUDP | Metabolite | CHEBI:60471 (ChEBI) | |
dUMP | Metabolite | CHEBI:246422 (ChEBI) | |
dihydrothymine | Metabolite | Q3027885 (Wikidata) | |
orotidine | Metabolite | CHEBI:25722 (ChEBI) | |
thymidine | Metabolite | CHEBI:17748 (ChEBI) | |
thymine | Metabolite | CHEBI:17821 (ChEBI) | |
uracil | Metabolite | CHEBI:17568 (ChEBI) | |
uridine | Metabolite | CHEBI:16704 (ChEBI) |
Annotated Interactions
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Source | Target | Type | Database reference | Comment |
---|---|---|---|---|
2-Deoxyuridine | uracil | mim-conversion | 22825 (Rhea) | |
CDP | CMP | mim-conversion | 11602 (Rhea) | |
CMP | cytidine | mim-conversion | 24676 (Rhea) | |
CTP | CDP | mim-conversion | 25239 (Rhea) | |
Creatine | Creatine-P | mim-conversion | 17158 (Rhea) | |
Dihydrouracil | N-Carbamoyl-beta-alanine | mim-conversion | 16122 (Rhea) | |
N-Carbamoyl-beta-alanine | Beta-alanine | mim-conversion | 11185 (Rhea) | |
N-Carbamyl-beta-aminoisobutyric acid | (S)-beta-aminoisobutyrate | mim-conversion | 37340 (Rhea) | |
OMP | UMP | mim-conversion | 11597 (Rhea) | |
Orotate | OMP | mim-conversion | 10382 (Rhea) | |
UDP | UTP | mim-conversion | 25099 (Rhea) | |
UMP | UDP | mim-conversion | 24401 (Rhea) | |
UMP | dUDP | mim-conversion | 28028 (Rhea) | |
UMP | uridine | mim-conversion | 29360 (Rhea) | |
UTP | CTP | mim-conversion | 30337 (Rhea) | |
cytidine | Cytosine | mim-conversion | 27959 (Rhea) | |
dTMP | thymidine | mim-conversion | 19131 (Rhea) | |
dUMP | 2-Deoxyuridine | mim-conversion | 28208 (Rhea) | |
dUMP | dTMP | mim-conversion | 12105 (Rhea) | |
dUMP | dUDP | mim-conversion | 30656 (Rhea) | |
dihydrothymine | N-Carbamyl-beta-aminoisobutyric acid | mim-conversion | 37336 (Rhea) | |
thymidine | dTMP | mim-conversion | 19130 (Rhea) | |
thymidine | thymine | mim-conversion | 16038 (Rhea) | |
thymine | 5-OH-Methyluracil | mim-conversion | 10317 (Rhea) | |
thymine | dihydrothymine | mim-conversion | 28793 (Rhea) | |
uracil | Dihydrouracil | mim-conversion | 20191 (Rhea) | |
uridine | uracil | mim-conversion | 24389 (Rhea) |