Biomarkers for pyrimidine metabolism disorders (Homo sapiens)

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312Amino Acid metabolismN-Carbamoyl-beta-alanineTPDPDCreatine-PPyrimidine metabolismDihydrouracilUracilUMPLactatePurine metabolismCDPCysteineUridine2-DeoxyuridinePRPPCTPOrotateDihydrothymineUric acidGlutathioneGlutathione metabolismCytosineCMPBeta-alanine(S)-Beta-aminoisobutyrateOMPUDP5-OH-MethyluracilCytidineThymidinePseudouridineN-Carbamyl-beta-aminoisobutyric acidUMPSCreatineUTPCreatine kinaseUMPH1OrotidineThyminePUS1+ PRPPUMPH2UMPHUMPH1UMPH2UMPHUPDHPTK2TSdUDPdUMPdTMPRRRRM1RRM2RRM2BOPRTOMPDCUMPS-complexRR-complexThe two possible compositionsRRM1DihydroorotateDHODH


Description

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.

Quality Tags

Ontology Terms

 

Bibliography

  1. Wyss M, Kaddurah-Daouk R; ''Creatine and creatinine metabolism.''; Physiol Rev, 2000 PubMed Europe PMC Scholia
  2. 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
  3. 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

View all...
CompareRevisionActionTimeUserComment
104645view12:32, 7 June 2019IreneHemelAdded Dihydroorotate
104312view08:13, 16 May 2019IreneHemelChanged first letters of text in node to capitals
104273view07:06, 15 May 2019IreneHemelAdded Pseudouridine with reaction
104206view08:38, 10 May 2019IreneHemelChanged ID for Lactate
104205view08:27, 10 May 2019IreneHemelChanged ID for Cysteine
104159view10:02, 7 May 2019IreneHemelAdded information about metabolite charge to DataNode comments
104146view13:35, 6 May 2019IreneHemelAdded references
104117view10:09, 6 May 2019DeSlRemoved unnecessary references.
104112view07:16, 6 May 2019IreneHemelFixed interaction
104095view13:22, 3 May 2019IreneHemelModified description
104094view13:17, 3 May 2019IreneHemelNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
(S)-Beta-aminoisobutyrateMetaboliteCHEBI:57731 (ChEBI)
  • aka (R)-3-amino-2-methylpropanoate
  • Zwitterion needed for conversion to take place
+ PRPPMetaboliteCHEBI:17111 (ChEBI)
2-DeoxyuridineMetaboliteCHEBI:16450 (ChEBI)
5-OH-Methyluracil MetaboliteCHEBI:16964 (ChEBI)
Amino Acid metabolismPathwayWP3925 (WikiPathways)
Beta-alanineMetaboliteCHEBI:57966 (ChEBI) Zwitterion needed for conversion to take place
CDPMetaboliteCHEBI:58069 (ChEBI) (3-) charge needed for conversion to take place
CMPMetaboliteCHEBI:60377 (ChEBI) (2-) charge needed for conversion to take place
CTPMetaboliteCHEBI:37563 (ChEBI) (4-) charge needed for conversion to take place
Creatine kinase ProteinP12277 (Uniprot-TrEMBL)
Creatine-PMetaboliteCHEBI:58092 (ChEBI) (2-) charge needed for conversion to take place
CreatineMetaboliteCHEBI:57947 (ChEBI) Zwitterion needed for conversion to take place
CysteineMetaboliteCHEBI:17561 (ChEBI)
CytidineMetaboliteCHEBI:17562 (ChEBI)
CytosineMetaboliteCHEBI:16040 (ChEBI)
DHODHProteinQ02127 (Uniprot-TrEMBL)
DHPProteinQ14117 (Uniprot-TrEMBL)
DPDProteinQ12882 (Uniprot-TrEMBL)
DihydroorotateMetaboliteCHEBI:30864 (ChEBI)
DihydrothymineMetaboliteQ3027885 (Wikidata)
DihydrouracilMetaboliteCHEBI:15901 (ChEBI)
Glutathione MetaboliteCHEBI:16856 (ChEBI)
Glutathione metabolismPathwayWP100 (WikiPathways)
LactateMetaboliteCHEBI:42111 (ChEBI)
N-Carbamoyl-beta-alanineMetaboliteCHEBI:11892 (ChEBI) aka 3-(carbamoylamino)propanoate
N-Carbamyl-beta-aminoisobutyric acidMetaboliteCHEBI:74414 (ChEBI)
  • aka 3-(carbamoylamino)-2-methylpropanoate
  • (1-) charge needed for conversion to take place
OMPMetaboliteCHEBI:57538 (ChEBI)
  • Orotidylic acid
  • (3-) charge needed for conversion to take place
OMPDCProtein4.1.1.23 (Enzyme Nomenclature)
OPRTProtein2.4.2.10 (Enzyme Nomenclature)
OrotateMetaboliteCHEBI:30839 (ChEBI)
OrotidineMetaboliteCHEBI:25722 (ChEBI)
PRPPMetaboliteCHEBI:17111 (ChEBI)
PUS1ProteinQ9Y606 (Uniprot-TrEMBL)
Pseudouridine MetaboliteCHEBI:65314 (ChEBI)
Purine metabolismPathwayWP4224 (WikiPathways)
Pyrimidine metabolismPathwayWP4225 (WikiPathways)
RRProtein1.17.4.1 (Enzyme Nomenclature)
RRM1ProteinP23921 (Uniprot-TrEMBL)
RRM2BProteinQ7LG56 (Uniprot-TrEMBL)
RRM2ProteinP31350 (Uniprot-TrEMBL)
TK2ProteinO00142 (Uniprot-TrEMBL)
TPProteinP19971 (Uniprot-TrEMBL)
TSProteinP04818 (Uniprot-TrEMBL)
ThymidineMetaboliteCHEBI:17748 (ChEBI)
ThymineMetaboliteCHEBI:17821 (ChEBI)
UDPMetaboliteCHEBI:58223 (ChEBI) (3-) charge needed for conversion to take place
UMPMetaboliteCHEBI:57865 (ChEBI) (2-) charge needed for conversion to take place
UMPH1ProteinQ9H0P0 (Uniprot-TrEMBL)
  • aka P5N1
  • Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPH2ProteinQ8TCD5 (Uniprot-TrEMBL)
  • aka NT5C
  • Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPHProtein3.1.3.5 (Enzyme Nomenclature)
  • aka P5N
  • Enzymes and reactions added with info from https://www.omim.org/entry/606224
UMPSGeneProductP11172 (Uniprot-TrEMBL)
UPProteinQ9UBR1 (Uniprot-TrEMBL)
UTPMetaboliteCHEBI:46398 (ChEBI) (4-) charge needed for conversion to take place
UracilMetaboliteCHEBI:17568 (ChEBI)
Uric acid MetaboliteCHEBI:27226 (ChEBI)
UridineMetaboliteCHEBI:16704 (ChEBI)
dTMPMetaboliteCHEBI:63528 (ChEBI) (2-) charge needed for conversion to take place
dUDPMetaboliteCHEBI:60471 (ChEBI) (3-) charge needed for conversion to take place
dUMPMetaboliteCHEBI:246422 (ChEBI) (2-) charge needed for conversion to take place

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
2-DeoxyuridineUracilmim-conversion22825 (Rhea)
CDPCMPmim-conversion11602 (Rhea)
CMPCytidinemim-conversion24676 (Rhea)
CTPCDPmim-conversion25239 (Rhea)
CreatineCreatine-Pmim-conversion17158 (Rhea)
CytidineCytosinemim-conversion27959 (Rhea)
DihydroorotateOrotatemim-conversion13514 (Rhea)
DihydrothymineN-Carbamyl-beta-aminoisobutyric acidmim-conversion37336 (Rhea)
DihydrouracilN-Carbamoyl-beta-alaninemim-conversion16122 (Rhea)
N-Carbamoyl-beta-alanineBeta-alaninemim-conversion11185 (Rhea)
N-Carbamyl-beta-aminoisobutyric acid(S)-Beta-aminoisobutyratemim-conversion37340 (Rhea)
OMPUMPmim-conversion11597 (Rhea)
OrotateOMPmim-conversion10382 (Rhea)
ThymidineThyminemim-conversion16038 (Rhea)
ThymidinedTMPmim-conversion19130 (Rhea)
Thymine5-OH-Methyluracil mim-conversion10317 (Rhea)
ThymineDihydrothyminemim-conversion28793 (Rhea)
UDPUTPmim-conversion25099 (Rhea)
UMPUDPmim-conversion24401 (Rhea)
UMPUridinemim-conversion29360 (Rhea)
UMPdUDPmim-conversion28028 (Rhea)
UTPCTPmim-conversion30337 (Rhea)
UracilDihydrouracilmim-conversion20191 (Rhea)
UridinePseudouridine mim-conversion22377 (Rhea)
UridineUracilmim-conversion24389 (Rhea)
dTMPThymidinemim-conversion19131 (Rhea)
dUMP2-Deoxyuridinemim-conversion28208 (Rhea)
dUMPdTMPmim-conversion12105 (Rhea)
dUMPdUDPmim-conversion30656 (Rhea)
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