DPYD encodes dihydropyrimidine dehydrogenase [NADP(+)] (DPD; EC 1.3.1.2), the initial and rate-limiting enzyme of the reductive catabolism of the pyrimidine bases uracil and thymine. It reduces uracil to 5,6-dihydrouracil and thymine to 5,6-dihydrothymine using NADPH as the electron donor. DPD is a large cytosolic homodimeric flavoprotein; each subunit binds two FAD, two FMN and four [4Fe-4S] clusters that shuttle electrons from NADPH to the pyrimidine substrate. It is the principal enzyme that catabolises the fluoropyrimidine chemotherapeutic 5-fluorouracil (5-FU), and the dihydrouracil it produces is further processed (by dihydropyrimidinase and beta-ureidopropionase) toward beta-alanine. Deficiency of DPD (DPYD deficiency) causes severe, potentially life-threatening toxicity from 5-FU/capecitabine, and more complete deficiency produces thymine-uraciluria with a variable neurological phenotype (seizures, motor and intellectual disability). DPYD is a major pharmacogenetic gene, and DPYD genotyping is used clinically to guide fluoropyrimidine dosing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006210 thymine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation that DPYD is involved in thymine catabolism. This is a core biological process for DPD: it reduces thymine to 5,6-dihydrothymine as the first step of thymine degradation. Concordant with the IDA annotations from PMID:1512248 and PMID:10410956 and with the UniProt catalytic activity. Reason: Correct, well-supported core process. DPD catalyzes the committed first step of thymine catabolism. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Reaction=5,6-dihydrothymine + NADP(+) = thymine + NADPH + H(+); |
| GO:0006212 uracil catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation that DPYD is involved in uracil catabolism. Core process: DPD reduces uracil to 5,6-dihydrouracil as the committed first step of uracil degradation, consistent with the IDA annotations and UniProt. Reason: Correct, well-supported core process representing the first committed step of uracil catabolism. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Reaction=5,6-dihydrouracil + NADP(+) = uracil + NADPH + H(+); |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation of the diagnostic molecular function of DPD. This is the central catalytic activity of the gene product (EC 1.3.1.2) and is independently supported by multiple experimental (IDA/IMP) annotations. Reason: This is the core molecular function of DPYD and is strongly supported by direct experimental characterization of the purified human enzyme. Supporting Evidence: PMID:1512248 Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. |
| GO:0050661 NADP binding | IBA GO_REF:0000033 | ACCEPT | Summary: DPD uses NADPH as the electron donor for pyrimidine reduction and has a defined NADP(+)-binding site; NADP binding is an integral part of its catalytic mechanism. Reason: Supported by the enzyme's use of NADPH (kinetic KM values for NADPH) and the UniProt NADP(+)-binding site features. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt F:NADP binding; ISS:UniProtKB. |
| GO:0002058 uracil binding | IBA GO_REF:0000033 | ACCEPT | Summary: DPD binds its substrate uracil; a defined uracil-binding site is present in the protein. This substrate-binding activity is part of the enzyme's function. Reason: Uracil is a physiological substrate of DPD (KM 4.9 uM) and a discrete uracil-binding region has been identified in the enzyme. Supporting Evidence: PMID:8083224 A sequence encompassing a peptide corresponding to the uracil binding site was found between the NADPH/FAD-containing NH2-terminal portion of the protein and the iron-sulfur binding sites near to the COOH terminus. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: DPD is a cytosolic enzyme. The phylogenetic localization is concordant with the IDA (PMID:1512248), UniProt subcellular location, and Reactome, which all describe a cytosolic activity. Reason: DPD is a soluble cytosolic protein; this is the well-established location. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based electronic annotation to cytoplasm. Correct but less specific than the cytosol annotations; retained as an accurate broader localization. Reason: Consistent with the more specific cytosol annotations; a correct broader parent localization. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0005829 cytosol | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt Subcellular Location keyword mapping to cytosol. Concordant with all other localization evidence. Reason: Correct cytosolic localization, agreeing with IDA and IBA evidence. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0006208 pyrimidine nucleobase catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic annotation to pyrimidine nucleobase catabolic process, the general parent process encompassing both uracil and thymine catabolism. Accurate for DPD as the initiating enzyme of pyrimidine base degradation. Reason: Correct parent process. DPD catalyzes the first committed step of pyrimidine (uracil and thymine) base catabolism. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Catalyzes the reduction of uracil and thymine (PubMed:1512248). |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro-based electronic annotation to the very general term oxidoreductase activity. DPD is an oxidoreductase, but this term is far less informative than the specific GO:0017113 already annotated. Reason: Too general; the specific activity dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113) is established experimentally and should be preferred. Proposed replacements: dihydropyrimidine dehydrogenase (NADP+) activity |
| GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors | IEA GO_REF:0000002 | MODIFY | Summary: InterPro-based electronic annotation to a more specific oxidoreductase parent (DPD reduces the C5=C6 double bond of the pyrimidine ring). Accurate as an ancestor of GO:0017113 but still more general than the specific, experimentally supported term. Reason: Correct branch but intermediate specificity; the leaf term GO:0017113 is experimentally established and should be used. Proposed replacements: dihydropyrimidine dehydrogenase (NADP+) activity |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated (RHEA/EC-based) electronic annotation of the diagnostic DPD activity. Matches the RHEA reactions and EC 1.3.1.2 in the UniProt record and duplicates the experimentally supported molecular function. Reason: Correct EC/RHEA-based mapping to the enzyme's core molecular function; concordant with experimental evidence. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Reaction=5,6-dihydrouracil + NADP(+) = uracil + NADPH + H(+); |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation for iron-sulfur cluster binding. Well supported: each DPD subunit binds four [4Fe-4S] clusters that mediate electron transfer between the FAD and FMN sites. Reason: DPD is an iron-sulfur flavoprotein; [4Fe-4S] binding is documented biochemically and structurally. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Note=Binds 4 [4Fe-4S] clusters. Contains approximately 16 iron atoms |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Two IPI protein-binding annotations from a high-throughput yeast two-hybrid interactome screen (partners LXN, Q9BS40; GOPC, Q9HD26). The generic term "protein binding" is uninformative about DPD's function, and these binary interactome hits have no established biological role for DPD. Reason: Bare "protein binding" from a proteome-scale Y2H screen provides no functional insight; DPD acts as a soluble homodimeric enzyme and no functional consequence of the LXN or GOPC interactions is established. Supporting Evidence: PMID:25416956 we more than doubled the number of high-quality binary PPIs file:human/DPYD/DPYD-uniprot.txt Q12882; Q9BS40: LXN; NbExp=3; IntAct=EBI-2839838, EBI-1044504; |
| GO:0005829 cytosol | IDA PMID:1512248 Purification and characterization of dihydropyrimidine dehyd... | ACCEPT | Summary: Direct assay: DPD was purified as a soluble enzyme from human liver, consistent with a cytosolic localization. Reason: DPD is a cytosolic enzyme; supported by purification of the soluble protein. Supporting Evidence: PMID:1512248 this enzyme was purified 7800-fold to homogeneity from human liver |
| GO:0006210 thymine catabolic process | IDA PMID:1512248 Purification and characterization of dihydropyrimidine dehyd... | ACCEPT | Summary: Direct experimental evidence: the purified human enzyme reduces thymine, the first step of thymine catabolism. Reason: Core process; directly demonstrated with the purified human enzyme. Supporting Evidence: PMID:1512248 Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. |
| GO:0019483 beta-alanine biosynthetic process | IEA GO_REF:0000041 | KEEP AS NON CORE | Summary: UniPathway-based annotation reflecting that pyrimidine (uracil) catabolism ultimately yields beta-alanine. DPD catalyzes only the first step; ring opening and beta-alanine release are performed by the downstream enzymes DPYS and UPB1. This is a pathway-membership annotation rather than DPD's core molecular function. Reason: Accurate at the pathway level (uracil catabolism feeds beta-alanine biosynthesis) but downstream of DPD's direct reaction; retained as a non-core process. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Amino-acid biosynthesis; beta-alanine biosynthesis. |
| GO:0042178 xenobiotic catabolic process | IDA PMID:8083224 cDNA cloning and chromosome mapping of human dihydropyrimidi... | KEEP AS NON CORE | Summary: Captures DPD's role in catabolising the fluoropyrimidine drug 5-fluorouracil, a xenobiotic. This is well established (>80% of administered 5-FU is inactivated by DPD) but represents a drug-metabolism/pharmacological context rather than DPD's endogenous core function. Reason: Real and clinically important (5-FU degradation), but a xenobiotic/drug-metabolism role that is secondary to the enzyme's endogenous pyrimidine-catabolic function. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt involved the degradation of the chemotherapeutic drug 5-fluorouracil |
| GO:0046045 TMP catabolic process | IDA PMID:8083224 cDNA cloning and chromosome mapping of human dihydropyrimidi... | MARK AS OVER ANNOTATED | Summary: DPD acts on the free pyrimidine base thymine, not on the nucleotide dTMP/TMP. TMP catabolic process is upstream of and more specific than DPD's actual reaction and is an over-specific/mis-leveled annotation for this enzyme. Reason: DPD's substrate is the thymine base; TMP catabolism requires prior dephosphorylation/nucleosidase steps not catalyzed by DPD. Better captured by thymine catabolic process (GO:0006210). Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Catalyzes the reduction of uracil and thymine (PubMed:1512248). |
| GO:0046050 UMP catabolic process | IDA PMID:8083224 cDNA cloning and chromosome mapping of human dihydropyrimidi... | MARK AS OVER ANNOTATED | Summary: DPD acts on the free base uracil, not on the nucleotide UMP. UMP catabolic process is upstream of DPD's reaction and is an over-specific/mis-leveled annotation for this enzyme. Reason: DPD's substrate is the uracil base; UMP catabolism requires prior dephosphorylation/nucleosidase steps not catalyzed by DPD. Better captured by uracil catabolic process (GO:0006212). Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Catalyzes the reduction of uracil and thymine (PubMed:1512248). |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IDA PMID:8083224 cDNA cloning and chromosome mapping of human dihydropyrimidi... | ACCEPT | Summary: Direct evidence: the cloned DPD enzyme reduces uracil, thymine and 5-fluorouracil, demonstrating dihydropyrimidine dehydrogenase (NADP+) activity. Reason: Core molecular function, directly demonstrated for the recombinant enzyme. Supporting Evidence: PMID:8083224 catalyzed the reduction of uracil, thymine, and 5-fluorouracil with kinetics approximating those published for the enzyme purified from mammalian liver |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73585 | ACCEPT | Summary: Reactome (TAS) localization of the uracil-reducing reaction to the cytosol. Concordant with all other localization evidence. Reason: Correct cytosolic localization; Reactome describes cytosolic DPD. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73616 | ACCEPT | Summary: Reactome (TAS) localization of the thymine-reducing reaction to the cytosol. Concordant with all other localization evidence. Reason: Correct cytosolic localization; Reactome describes cytosolic DPD. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0006212 uracil catabolic process | IDA PMID:18075467 Genetic regulation of dihydropyrimidinase and its possible i... | ACCEPT | Summary: Uracil catabolic process is a correct core process for DPD. The cited reference (Thomas et al. 2007) primarily concerns dihydropyrimidinase (DHP, gene DPYS), the SECOND enzyme in the pathway, and uses a uracil breath test that reports overall uracil catabolism (in which DPD catalyzes the first step). The process term is appropriate for DPD even though this particular reference is centered on the downstream enzyme. Reason: Correct process for DPD; independently supported by PMID:1512248 and the IBA annotation. Not removed despite the reference being centered on DPYS, since the process assignment for DPD is accurate (see reference_review for the citation caveat). Supporting Evidence: PMID:18075467 alterations of uracil catabolism are not limited to DPD deficiency |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IDA PMID:18075467 Genetic regulation of dihydropyrimidinase and its possible i... | ACCEPT | Summary: This IDA links DPD activity (GO:0017113) to PMID:18075467, but the cached abstract of that paper is about dihydropyrimidinase (DHP, gene DPYS) and a uracil breath test, not a direct assay of DPD (NADP+) dehydrogenase activity. The molecular function itself is correct and definitively established for DPD by PMID:1512248 and PMID:8083224; the concern is only that this particular reference is a poor citation for the DPD activity (recorded in reference_review as MISCITED). Reason: The DPD molecular function is correct and amply supported; the annotation is retained (experimental; full text not read) with the reference-quality caveat captured in reference_review rather than removing the annotation. Supporting Evidence: PMID:18075467 This study investigates the role of DPYS sequence variations in individuals with unexplained molecular basis of altered uracil catabolism. |
| GO:0006210 thymine catabolic process | IDA PMID:10410956 Radiochemical assay for determination of dihydropyrimidinase... | ACCEPT | Summary: Thymine catabolic process for DPD. The cited method paper describes a radiochemical assay for the pathway (dihydropyrimidinase step), consistent with DPD's role in pyrimidine base degradation. The process assignment is correct for DPD. Reason: Correct core process; supported redundantly by PMID:1512248 and the IBA annotation. Supporting Evidence: PMID:10410956 A radiochemical assay was developed to measure the activity of dihydropyrimidinase (DHP) in human liver homogenates. |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IDA PMID:10410956 Radiochemical assay for determination of dihydropyrimidinase... | ACCEPT | Summary: This IDA links DPD activity to a methods paper (Van Kuilenburg et al. 1999) whose cached abstract describes a radiochemical assay for dihydropyrimidinase (DHP), the downstream enzyme, in liver homogenates. The DPD molecular function is correct but this reference does not itself demonstrate DPD (NADP+) dehydrogenase activity; the citation caveat is recorded in reference_review as MISCITED. Reason: Molecular function is correct for DPD and well supported by PMID:1512248 and PMID:8083224; annotation retained with the reference-quality caveat noted rather than removed (experimental; full text not read). Supporting Evidence: PMID:10410956 A radiochemical assay was developed to measure the activity of dihydropyrimidinase (DHP) in human liver homogenates. |
| GO:0006145 purine nucleobase catabolic process | IMP PMID:11988088 Novel disease-causing mutations in the dihydropyrimidine deh... | MARK AS OVER ANNOTATED | Summary: Annotation to PURINE nucleobase catabolic process. DPD is a PYRIMIDINE catabolic enzyme, and the cited paper (van Kuilenburg et al. 2002) concerns DPD deficiency and thymine-uraciluria (pyrimidine metabolism), not purine catabolism. This is almost certainly a term-selection/data-entry error (purine vs pyrimidine); the intended term is the pyrimidine one (GO:0006208), which is separately annotated. Reason: DPD has no role in purine catabolism; the reference is entirely about pyrimidine (uracil/thymine) metabolism. Flagged as an over-annotation/likely mis-selection rather than removed, per the policy of not deleting experimental annotations whose full text has not been read; the correct process is GO:0006208. Supporting Evidence: PMID:11988088 Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disease characterized by thymine-uraciluria in homozygous deficient patients. |
| GO:0006208 pyrimidine nucleobase catabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity annotation to pyrimidine nucleobase catabolic process, the correct parent process for DPD. Concordant with experimental and phylogenetic evidence. Reason: Correct parent process; DPD initiates pyrimidine base catabolism. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Catalyzes the reduction of uracil and thymine (PubMed:1512248). |
| GO:0006208 pyrimidine nucleobase catabolic process | IMP PMID:11988088 Novel disease-causing mutations in the dihydropyrimidine deh... | ACCEPT | Summary: Experimental (IMP) evidence linking DPD variants to impaired pyrimidine base catabolism (DPD deficiency with thymine-uraciluria). This is the correct core process for the enzyme. Reason: Loss-of-function DPD variants cause thymine-uraciluria, directly implicating DPD in pyrimidine nucleobase catabolism. Supporting Evidence: PMID:11988088 Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disease characterized by thymine-uraciluria in homozygous deficient patients. |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity annotation of the diagnostic DPD molecular function. Redundant with the experimentally supported activity. Reason: Correct core molecular function; supported experimentally and phylogenetically. Supporting Evidence: PMID:1512248 Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IMP PMID:11988088 Novel disease-causing mutations in the dihydropyrimidine deh... | ACCEPT | Summary: IMP evidence: disease-causing DPD missense variants reduce or abolish DPD activity (interpreted via the 3D structure as disrupting cofactor binding/electron transport), supporting the assignment of dihydropyrimidine dehydrogenase (NADP+) activity to DPYD. Reason: Loss-of-function variants map onto cofactor/electron-transfer sites and reduce DPD activity, confirming the molecular function. Supporting Evidence: PMID:11988088 interfered directly or indirectly with cofactor binding or electron transport |
| GO:0042803 protein homodimerization activity | ISS GO_REF:0000024 | ACCEPT | Summary: DPD is a homodimer; homodimerization activity is supported by sequence similarity and by direct biochemical evidence that the human enzyme is composed of two subunits. Reason: The functional enzyme is an obligate homodimer, documented biochemically and in UniProt (SUBUNIT: Homodimer). Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt SUBUNIT: Homodimer. |
| GO:0042803 protein homodimerization activity | IDA PMID:1512248 Purification and characterization of dihydropyrimidine dehyd... | ACCEPT | Summary: Direct evidence: the purified ~210 kDa human enzyme is composed of two subunits, demonstrating homodimerization. Reason: The purified native enzyme is a two-subunit homodimer. Supporting Evidence: PMID:1512248 Purified human enzyme has a molecular mass of 210 +/- 5 kDa and appears to be composed of two subunits. |
| GO:0050660 flavin adenine dinucleotide binding | ISS GO_REF:0000024 | ACCEPT | Summary: DPD is a flavoprotein binding two FAD per subunit; FAD accepts electrons from NADPH at the N-terminal FAD/NADPH domain. Supported by sequence similarity and biochemical flavin content. Reason: FAD is an essential cofactor of DPD; the purified enzyme contains FAD and a defined FAD-binding site. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt Binds 2 FAD |
| GO:0050661 NADP binding | ISS GO_REF:0000024 | ACCEPT | Summary: NADP(+)/NADPH binding by DPD, supported by sequence similarity and the defined NADP(+)-binding site; NADPH is the electron donor for pyrimidine reduction. Reason: NADPH is the physiological electron donor and DPD has a defined NADP(+)-binding site. Supporting Evidence: file:human/DPYD/DPYD-uniprot.txt F:NADP binding; ISS:UniProtKB. |
| GO:0006212 uracil catabolic process | IDA PMID:1512248 Purification and characterization of dihydropyrimidine dehyd... | ACCEPT | Summary: Direct experimental evidence: the purified human enzyme reduces uracil, the first step of uracil catabolism. Reason: Core process; directly demonstrated with the purified human enzyme. Supporting Evidence: PMID:1512248 Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. |
| GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity | IDA PMID:1512248 Purification and characterization of dihydropyrimidine dehyd... | ACCEPT | Summary: Direct experimental characterization of the purified human enzyme establishing dihydropyrimidine dehydrogenase (NADP+) activity, with kinetics on uracil, thymine, 5-FU and NADPH. This is the definitive experimental support for the core molecular function. Reason: Gold-standard IDA on the purified human enzyme; the defining molecular function of DPYD. Supporting Evidence: PMID:1512248 Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. |
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Download this section (compressed HTML)Q: Which DPYD interacting partners identified in high-throughput screens (e.g. LXN, GOPC) have a demonstrable effect on DPD activity, stability or localization?
Q: Do the two GO:0017113 IDA annotations attributed to PMID:18075467 and PMID:10410956 (both centered on the downstream enzyme dihydropyrimidinase / DPYS) reflect the full text, or are they mis-attributed to DPYD?
Experiment: Reconstitute recombinant human DPD and measure steady-state kinetics for uracil, thymine and 5-fluorouracil across clinically relevant DPYD variants to correlate genotype with residual activity.
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