Biomarkers for pyrimidine metabolism disorders (Homo sapiens)

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1uracilthymidineorotidinethymineCytosineN-Carbamyl-beta-aminoisobutyric acidCysteineCreatine5-OH-MethyluracilOrotateUDPcytidineGlutathione metabolismTPPyrimidine metabolismCDPCreatine kinase(S)-beta-aminoisobutyrateAmino Acid metabolismBeta-alanineUTPUric acidDPDUMPSPRPP2-DeoxyuridinePurine metabolismLactateDihydrouraciluridineCTPCreatine-PN-Carbamoyl-beta-alanineUMPH1dihydrothymineCMPGlutathioneOMPUMP+ PRPPUMPH2UMPHUMPH1UMPH2UMPHUPDHP23TK2TSdUDPdUMPdTMPRRRRM1RRM2RRM2BOPRTOMPDCUMPS-complexRR-complexThe two possible compositionsRRM1


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)).

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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
123407view06:48, 23 July 2022EgonwMade four pathways clickable
119306view13:09, 23 June 2021FinterlyAdded ISBN for book citation
116762view09:32, 12 May 2021DeSlUpdating ISBN nr for ref
116761view09:30, 12 May 2021DeSlChecking validity in GPML schema
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
+ PRPPMetaboliteCHEBI:17111 (ChEBI)
2-DeoxyuridineMetaboliteCHEBI:16450 (ChEBI)
5-OH-Methyluracil MetaboliteCHEBI:16964 (ChEBI)
Amino Acid metabolismPathwayWP3925 (WikiPathways)
Beta-alanineMetaboliteCHEBI:57966 (ChEBI)
CDPMetaboliteCHEBI:58069 (ChEBI) CDP 3-, charge needed for conversion can take place
CMPMetaboliteCHEBI:60377 (ChEBI) CMP (2-), charge needed for conversion can take place
CTPMetaboliteCHEBI:37563 (ChEBI)
Creatine kinase ProteinP12277 (Uniprot-TrEMBL)
Creatine-PMetaboliteCHEBI:58092 (ChEBI)
CreatineMetaboliteCHEBI:57947 (ChEBI)
CysteineMetaboliteCHEBI:15356 (ChEBI)
CytosineMetaboliteCHEBI:16040 (ChEBI)
DHPProteinQ14117 (Uniprot-TrEMBL)
DPDProteinQ12882 (Uniprot-TrEMBL)
DihydrouracilMetaboliteCHEBI:15901 (ChEBI)
Glutathione MetaboliteCHEBI:16856 (ChEBI)
Glutathione metabolismPathwayWP100 (WikiPathways)
LactateMetaboliteCHEBI:24996 (ChEBI)
N-Carbamoyl-beta-alanineMetaboliteCHEBI:11892 (ChEBI) aka 3-(carbamoylamino)propanoate
N-Carbamyl-beta-aminoisobutyric acidMetaboliteCHEBI:74414 (ChEBI) aka 3-(carbamoylamino)-2-methylpropanoate
OMPMetaboliteCHEBI:57538 (ChEBI) Orotidylic acid
OMPDCProtein4.1.1.23 (Enzyme Nomenclature)
OPRTProtein2.4.2.10 (Enzyme Nomenclature)
OrotateMetaboliteCHEBI:30839 (ChEBI)
PRPPMetaboliteCHEBI:17111 (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)
UDPMetaboliteCHEBI:58223 (ChEBI)
UMPMetaboliteCHEBI:57865 (ChEBI)
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)
Uric acid MetaboliteCHEBI:27226 (ChEBI)
cytidineMetaboliteCHEBI:17562 (ChEBI)
dTMPMetaboliteCHEBI:63528 (ChEBI)
dUDPMetaboliteCHEBI:60471 (ChEBI)
dUMPMetaboliteCHEBI:246422 (ChEBI)
dihydrothymineMetaboliteQ3027885 (Wikidata)
orotidineMetaboliteCHEBI:25722 (ChEBI)
thymidineMetaboliteCHEBI:17748 (ChEBI)
thymineMetaboliteCHEBI:17821 (ChEBI)
uracilMetaboliteCHEBI:17568 (ChEBI)
uridineMetaboliteCHEBI:16704 (ChEBI)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
2-Deoxyuridineuracilmim-conversion22825 (Rhea)
CDPCMPmim-conversion11602 (Rhea)
CMPcytidinemim-conversion24676 (Rhea)
CTPCDPmim-conversion25239 (Rhea)
CreatineCreatine-Pmim-conversion17158 (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)
UDPUTPmim-conversion25099 (Rhea)
UMPUDPmim-conversion24401 (Rhea)
UMPdUDPmim-conversion28028 (Rhea)
UMPuridinemim-conversion29360 (Rhea)
UTPCTPmim-conversion30337 (Rhea)
cytidineCytosinemim-conversion27959 (Rhea)
dTMPthymidinemim-conversion19131 (Rhea)
dUMP2-Deoxyuridinemim-conversion28208 (Rhea)
dUMPdTMPmim-conversion12105 (Rhea)
dUMPdUDPmim-conversion30656 (Rhea)
dihydrothymineN-Carbamyl-beta-aminoisobutyric acidmim-conversion37336 (Rhea)
thymidinedTMPmim-conversion19130 (Rhea)
thymidinethyminemim-conversion16038 (Rhea)
thymine5-OH-Methyluracil mim-conversion10317 (Rhea)
thyminedihydrothyminemim-conversion28793 (Rhea)
uracilDihydrouracilmim-conversion20191 (Rhea)
uridineuracilmim-conversion24389 (Rhea)
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