Pyrimidine metabolism and related diseases (Homo sapiens)

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38654759MitochondrionComplexCAD-complexHyperammonaemiaOrticaciduriatype IhypothesizedUrea cycleMitochondrionSubunit ofACTMMSDHAspartateCytidineThymidineL-ValineCoQ10 - H2 (reduced)GlutamineAGXT2malonate semialdehydeOrnithineUridineUPUMPH1Riboflavin and CoQDisordersDHOGLS2CPS2UMPS-complexRRM1UTPdUDP(S)-Beta-aminoisobutyrateDihydrouracilOPRTUMPCoQ10OTCThymineUridineCPS1beta-alanine-pyruvate transaminasemethylmalonate semialdehydedehydrogenaseRRM2BDihydrothymineRRM2TSUracilCarbamoyl-phosphateTransamination andoxidative reactionsdTMPOMPCTPUDPOrotidineTK2dUMPAcetyl-CoACDPCMPBeta-alanineRR2-DeoxyuridineN-Carbamyl-beta-aminoisobutyric acidN-Carbamoyl-beta-alanineCAD-complexDPDRRM2BOMPDCHCO3-AKTD-methylmalonatesemialdehydeDHODHCitrullineCarbamoylaspartateOrotateTPPRPP5555Orotate1, 5DihydroorotateCarbamoyl-phosphateGlutamineDHPHCO3-CPS2DHOACTOPRTOMPDCUMPS-complex+ PRPPOroticaciduriatype IIHyper-beta-alaninemia2Mitochondrialribonucleotide reductasesubunit 2deficiencyType 8AType 8BThymidine phosphorylase deficiencyDihydropyrimidine dehydrogenase deficiencyDihydropyrimidinase deficiencyBeta-ureidopropionase deficiencyUMPH2UMPHUMPH1UMPH2UMPHPyrimidine 5'-nucleotidase I deficiencyPyrimidine 5'-nucleotidase I deficiencyBeta-aminoisobutyric AciduriaDihydroorotate dehydrogenase deficiencyPyrimidine 5'-nucleotidasesuperactivityPyrimidine 5'-nucleotidasesuperactivityGlutamateNH4+RR-complexThe two possible compositionsThymidine kinase 2 deficiencyRRM1DiseaseCatalysisPathwayBindingProteinMetaboliteConversionConnection to diseaseLegendMetabolite markerDihydroorotateL-BAIBAL-methylmalonatesemialdehyde5Propionyl-CoA555555ABAT5


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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Ontology Terms

 

Bibliography

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  1. Natalia Y. Kedishvili, Gary W. Goodwin, Kirill M. Popov, Robert A. Harris; ''Mammalian Methylmalonate-Semialdehyde Dehydrogenase''; Methods Enzymol., 2007 PubMed Europe PMC Scholia
  2. Dmitrii A Tanianskii, Natalia Jarzebska, Andreas L Birkenfeld, John F O'Sullivan, Roman N Rodionov; ''Beta-Aminoisobutyric Acid as a Novel Regulator of Carbohydrate and Lipid Metabolism''; Nutrients, 2019 PubMed Europe PMC Scholia
  3. van Kuilenburg AB; ''Dihydropyrimidine dehydrogenase and the efficacy and toxicity of 5-fluorouracil''; Eur J Cancer, 2004 PubMed Europe PMC Scholia
  4. J J Higgins, C R Kaneski, I Bernardini, R O Brady, N W Barton; ''Pyridoxine-responsive hyper-beta-alaninemia associated with Cohen's syndrome''; Neurology, 1994 PubMed Europe PMC Scholia
  5. 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
  6. 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.''; , 2006 PubMed Europe PMC Scholia
  7. Shanti Balasubramaniam, John A. Duley, John Christodoulou; ''Inborn errors of pyrimidine metabolism: clinical update and therapy''; Journal of Inherited Metabolic Disease, 2014 PubMed Europe PMC Scholia
  8. Assmann B, Gohlich G, Baethmann M, Wevers RA, et al.; ''Clinical findings and a therapeutic trial in the first patient with beta-ureidopropionase deficiency''; Neuropediatrics, 2006 PubMed Europe PMC Scholia
  9. Kaymak I, Maier CR, Schmitz W, Campbell AD, Dankworth B, Ade CP, Walz S, Paauwe M, Kalogirou C, Marouf H, Rosenfeldt MT, Gay DM, McGregor GH, Sansom OJ, Schulze A; ''Mevalonate Pathway Provides Ubiquinone to Maintain Pyrimidine Synthesis and Survival in p53-Deficient Cancer Cells Exposed to Metabolic Stress.''; Cancer Res, 2020 PubMed Europe PMC Scholia

History

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CompareRevisionActionTimeUserComment
128218view03:52, 29 January 2024EweitzSoften disease color; refine case, size
126065view14:18, 31 March 2023DeSlUpdated comment on AKT (not annotated yet)
126064view14:14, 31 March 2023DeSlChanged ACT database annotation to EC number
124955view08:28, 7 January 2023EgonwFixed the OMIM link patterns
124860view13:06, 15 December 2022DeSlAdded conversion of beta-alanine to acetyl-CoA, to support potential connection for hyper-beta-alaninemia
124859view10:48, 15 December 2022DeSlAdded lit. ref and missing propionyl-CoA ID
124858view10:43, 15 December 2022DeSlUpdated connection to Beta-aminoisobutyric Aciduria
124857view09:15, 15 December 2022DeSlUpdated disorder label for easier retrieval of IEMBase data
123685view07:42, 10 August 2022EgonwTyped three translocations
120401view09:09, 30 November 2021Fehrhartboxed pathway nodes
119710view14:45, 5 August 2021DeSlUpdated OMIM URLs
119282view10:44, 23 June 2021FinterlyAdded ISBN for book citation
114338view14:40, 8 January 2021DeSlAdded CoQ PW link and info for interaction with DHODH.
108218view12:35, 29 November 2019FehrhartOntology Term : 'disease pathway' added !
107162view14:24, 17 September 2019MaintBotChEBI identifier normalization
104804view17:43, 18 June 2019IreneHemelAdded legend
104311view07:49, 16 May 2019IreneHemelChanged first letters of text in node to capitals
104157view07:40, 7 May 2019IreneHemelAdded information about metabolite charge to DataNode comments
104043view12:02, 26 April 2019IreneHemelChanged conversion from Glutamine to glutamate and NH4+
103986view08:11, 24 April 2019DeSlModified description
103968view09:19, 18 April 2019IreneHemelChanged sizes of disease nodes
103920view08:04, 16 April 2019IreneHemelChanged urea cycle label to pathway node
103919view08:00, 16 April 2019IreneHemelUpdated OMIM links for several diseases
103918view07:48, 16 April 2019IreneHemelRemoved symbols in names references
103917view07:44, 16 April 2019IreneHemelChanged disease names to primary names in Blau book; Added alternative names diseases
103914view15:05, 15 April 2019IreneHemelModified description
103912view15:00, 15 April 2019IreneHemelModified description
103910view13:52, 15 April 2019IreneHemelModified description
103909view13:51, 15 April 2019IreneHemelModified description
103902view13:46, 15 April 2019IreneHemelChanged basic interaction to mim-conversion for side metabolites; changed lines for 2 diseases to graphical line
103901view13:39, 15 April 2019IreneHemelChanged separate complexes; added different options for RR
103894view07:41, 15 April 2019IreneHemelModified description
103884view12:52, 12 April 2019IreneHemelAdded literature
103858view11:57, 11 April 2019IreneHemelAdded disease and enzyme related to this disease
103853view10:13, 11 April 2019IreneHemelMoved complexes to separate part of pathway, added complex IDs
103852view09:50, 11 April 2019IreneHemelAdded Rhea IDs, split reaction into two parts, added alternative names for some metabolites
103848view06:51, 11 April 2019IreneHemelAdded Rhea IDs
103841view14:57, 10 April 2019IreneHemelAdded more Rhea IDs
103838view14:03, 10 April 2019IreneHemelAdded Rhea IDs for several reactions
103813view08:55, 9 April 2019IreneHemelAdded disease
103812view08:46, 9 April 2019IreneHemelAdded Uniprot IDs
103811view08:22, 9 April 2019IreneHemelChanged datanodes for enzymes from geneproduct to protein
102678view09:28, 17 January 2019DeSlModified description
102677view09:26, 17 January 2019DeSlChanged interactions to graphical lines for diseases.
98925view05:21, 16 October 2018EgonwModified description
98283view11:19, 16 August 2018EgonwReplaced secondary ChEBI IDs with primary IDs.
98262view12:59, 15 August 2018DeSlModified description
98261view12:57, 15 August 2018DeSlAdded IDs
98260view11:58, 15 August 2018DeSlAdded more IDs.
98259view11:49, 15 August 2018DeSlAdded IDs for added metabolites

External references

DataNodes

View all...
NameTypeDatabase referenceComment
(S)-Beta-aminoisobutyrateMetaboliteCHEBI:57731 (ChEBI)
  • 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
+ PRPPMetaboliteCHEBI:17111 (ChEBI)
2-DeoxyuridineMetaboliteCHEBI:16450 (ChEBI)
ABATProteinP80404 (Uniprot-TrEMBL)
ACTProtein2.1.3.2 (Enzyme Nomenclature)
ACTProtein2.1.3.2 (KEGG Genes)
AGXT2ProteinQ9BYV1 (Uniprot-TrEMBL)
AKTProteinAKA beta-alanine-alpha-ketoglutarate transaminase; or beta-alanyl-alpha-ketoglutarate transaminase (AKT) [PMID:7936305]. No annotations found in UniProt related to this name
Acetyl-CoAMetaboliteCHEBI:15351 (ChEBI)
AspartateMetaboliteCHEBI:29991 (ChEBI) (1-) charge needed for conversion to take place
Beta-alanineMetaboliteCHEBI:57966 (ChEBI) Zwitterion needed for conversion to take place
CAD-complexGeneProductP27708 (Uniprot-TrEMBL)
CDPMetaboliteCHEBI:58069 (ChEBI) (3-) charge needed for conversion to take place
CMPMetaboliteCHEBI:60377 (ChEBI) (2-) charge needed for conversion to take place
CPS1ProteinP31327 (Uniprot-TrEMBL)
CPS2Protein6.3.5.5 (Enzyme Nomenclature)
CTPMetaboliteCHEBI:37563 (ChEBI) (4-) charge needed for conversion to take place
Carbamoyl-phosphateMetaboliteCHEBI:58228 (ChEBI) (2-) charge needed for conversion to take place
CarbamoylaspartateMetaboliteCHEBI:32814 (ChEBI)
  • aka N-carbamoyl-L-aspartate
  • (2-) charge needed for conversion to take place
CitrullineMetaboliteCHEBI:57743 (ChEBI) Zwitterion needed for conversion to take place
CoQ10 - H2 (reduced)MetaboliteCHEBI:64183 (ChEBI)
CoQ10MetaboliteCHEBI:46245 (ChEBI)
CytidineMetaboliteCHEBI:17562 (ChEBI)
D-methylmalonate semialdehydeMetaboliteCHEBI:141212 (ChEBI)
  • methylmalonate semialdehyde aka 2-Methyl-3-oxopropanoic acid aka 2-methyl-3-oxopropanoate
  • D configuration == R-annotation in ChEBI
DHOProtein3.5.2.3 (Enzyme Nomenclature)
DHODHProteinQ02127 (Uniprot-TrEMBL)
DHPProteinQ14117 (Uniprot-TrEMBL) AKA DPYS
DPDProteinQ12882 (Uniprot-TrEMBL) AKA DPYD
DihydroorotateMetaboliteCHEBI:30864 (ChEBI)
DihydrothymineMetaboliteCHEBI:27468 (ChEBI)
DihydrouracilMetaboliteCHEBI:15901 (ChEBI)
GLS2ProteinQ9UI32 (Uniprot-TrEMBL)
GlutamateMetaboliteCHEBI:29985 (ChEBI) (1-) charge needed for conversion to take place
GlutamineMetaboliteCHEBI:58359 (ChEBI) Zwitterion needed for conversion to take place
HCO3-MetaboliteCHEBI:17544 (ChEBI)
L-BAIBAMetaboliteCHEBI:58655 (ChEBI) L form of β-aminoisobutyric acid (BAIBA)
L-ValineMetaboliteCHEBI:57762 (ChEBI)
L-methylmalonate semialdehydeMetaboliteCHEBI:62413 (ChEBI)
  • methylmalonate semialdehyde aka 2-Methyl-3-oxopropanoic acid aka 2-methyl-3-oxopropanoate
  • L configuration == S-annotation in ChEBI
MMSDHProteinQ02252 (Uniprot-TrEMBL)
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
NH4+MetaboliteCHEBI:28938 (ChEBI)
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)
OTCProteinP00480 (Uniprot-TrEMBL)
OrnithineMetaboliteCHEBI:46911 (ChEBI) (1) charge needed for conversion to take place
OrotateMetaboliteCHEBI:30839 (ChEBI)
OrotidineMetaboliteCHEBI:25722 (ChEBI)
PRPPMetaboliteCHEBI:17111 (ChEBI)
Propionyl-CoAMetaboliteCHEBI:57392 (ChEBI)
RRProtein1.17.4.1 (Enzyme Nomenclature)
RRM1ProteinP23921 (Uniprot-TrEMBL)
RRM2BProteinQ7LG56 (Uniprot-TrEMBL)
RRM2ProteinP31350 (Uniprot-TrEMBL)
Riboflavin and CoQ DisordersPathwayWP5037 (WikiPathways)
TK2ProteinO00142 (Uniprot-TrEMBL)
TPProteinP19971 (Uniprot-TrEMBL)
TSProteinP04818 (Uniprot-TrEMBL)
ThymidineMetaboliteCHEBI:17748 (ChEBI)
ThymineMetaboliteCHEBI:17821 (ChEBI)
Transamination and oxidative reactionsPathwayWP4686 (WikiPathways)
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
UMPS-complexGeneProductP11172 (Uniprot-TrEMBL)
UPProteinQ9UBR1 (Uniprot-TrEMBL) aka UPB1
UTPMetaboliteCHEBI:46398 (ChEBI) (4-) charge needed for conversion to take place
UracilMetaboliteCHEBI:17568 (ChEBI)
Urea cyclePathwayWP4571 (WikiPathways)
UridineMetaboliteCHEBI:16704 (ChEBI)
beta-alanine-pyruvate transaminaseProtein2.6.1.18 (Enzyme Nomenclature)
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
malonate semialdehydeMetaboliteCHEBI:57700 (ChEBI)
  • AKA Beta-ketopropionate
  • Annotated without knowledge of R/S configuration
methylmalonate semialdehyde dehydrogenaseProtein

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
(S)-Beta-aminoisobutyrateD-methylmalonate semialdehydemim-conversion18394 (Rhea)
2-DeoxyuridineUracilmim-conversion22825 (Rhea)
Aspartatemim-conversion20014 (Rhea)
CDPCMPmim-conversion11602 (Rhea)
CMPCytidinemim-conversion24676 (Rhea)
CTPCDPmim-conversion25239 (Rhea)
Carbamoyl-phosphateCarbamoylaspartatemim-conversion20014 (Rhea)
Carbamoyl-phosphateCitrullinemim-conversion19514 (Rhea)
CarbamoylaspartateDihydroorotatemim-conversion24298 (Rhea)
CytidineUridinemim-conversion16070 (Rhea)
D-methylmalonate semialdehydePropionyl-CoAmim-conversion20805 (Rhea)
DihydroorotateOrotatemim-conversion13514 (Rhea)
DihydroorotateOrotatemim-conversion28692 (Rhea)
DihydrothymineN-Carbamyl-beta-aminoisobutyric acidmim-conversion37336 (Rhea)
DihydrouracilN-Carbamoyl-beta-alaninemim-conversion16122 (Rhea)
GlutamineCarbamoyl-phosphatemim-conversion18634 (Rhea)
GlutamineGlutamatemim-conversion15890 (Rhea)
HCO3-mim-conversion18030 (Rhea)
HCO3-mim-conversion18634 (Rhea)
N-Carbamoyl-beta-alanineBeta-alaninemim-conversion11185 (Rhea)
N-Carbamyl-beta-aminoisobutyric acid(S)-Beta-aminoisobutyratemim-conversion37340 (Rhea)
NH4+Carbamoyl-phosphatemim-conversion18030 (Rhea)
NH4+mim-conversion15890 (Rhea)
OMPUMPmim-conversion11597 (Rhea)
Ornithinemim-conversion19514 (Rhea)
OrotateOMPmim-conversion10382 (Rhea)
ThymidineThyminemim-conversion16038 (Rhea)
ThymidinedTMPmim-conversion19130 (Rhea)
ThymineDihydrothyminemim-conversion28793 (Rhea)
UDPUTPmim-conversion25099 (Rhea)
UDPdUDPmim-conversion28028 (Rhea)
UMPUDPmim-conversion24401 (Rhea)
UMPUridinemim-conversion29360 (Rhea)
UTPCTPmim-conversion30337 (Rhea)
UracilDihydrouracilmim-conversion20191 (Rhea)
UridineUracilmim-conversion24389 (Rhea)
dTMPThymidinemim-conversion19131 (Rhea)
dUMP2-Deoxyuridinemim-conversion28208 (Rhea)
dUMPdTMPmim-conversion12105 (Rhea)
dUMPdUDPmim-conversion30656 (Rhea)
Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP4225"
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