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Information on EC 1.3.1.2 - dihydropyrimidine dehydrogenase (NADP+) and Organism(s) Sus scrofa and UniProt Accession Q28943
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1.3.1.2 dihydropyrimidine dehydrogenase (NADP+)IUBMB Comments
Also acts on dihydrothymine.
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Word Map
- 1.3.1.2
- 5-fluorouracil
- thymidine
- phosphorylase
- uridine
- medicine
-
phosphoribosyltransferase
- orotate
-
2.4.2.4
- thymidylate
-
fluoropyrimidine
-
fdurd
-
2.7.1.21
- beta-ureidopropionase
- urdpase
- dihydropyrimidinase
- beta-alanine
- drug development
- analysis
The taxonomic range for the selected organisms is: Sus scrofa
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
dihydrouracil dehydrogenase, dhpdhase, dhpdh, dhu dehydrogenase, dihydrouracil dehydrogenase (nadp+), 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
4,5-dihydrothymine: oxidoreductase
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dehydrogenase, dihydrouracil (nicotinamide adenine dinucleotide phosphate)
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DHPDH
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DHPDHase
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DHU dehydrogenase
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dihydrothymine dehydrogenase
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Dihydrouracil dehydrogenase
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dihydrouracil dehydrogenase (NADP)
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dihydrouracil dehydrogenase (NADP+)
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DPD
hydropyrimidine dehydrogenase
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DPD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
abstraction of pro-S hydrogen of NADPH and thus B-side stereospecific class dehydrogenase
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5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
mechanism, rate-determining half-reaction for reduction of flavin by NADPH has minor rate limitation, while the following protonation of flavin at N-1 is slow
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5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
nonclassical ping-pong mechanism
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5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
comparison of substrate and cofactor binding to wild-type and mutant enzyme
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
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oxidation
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reduction
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PATHWAY SOURCE
PATHWAYS
KEGG
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-, -
SYSTEMATIC NAME
IUBMB Comments
5,6-dihydrouracil:NADP+ 5-oxidoreductase
Also acts on dihydrothymine.
CAS REGISTRY NUMBER
COMMENTARY
9029-01-0
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
the first FeS cluster, with unusual coordination, cannot be reduced and displays no activity when Q156 is mutated to glutamate. The active site loop comprising residues 670-683 are observed in open and closed conformational states, overview
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?
dihydrofluorouracil + NADP+
5-fluorouracil + NADPH + H+
dihydrofluorouracil is further metabolized to 2'-fluoro-beta-alanine
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-
?
dihydrofluorouracil + NADP+
5-fluorouracil + NADPH + H+
pyrimidine binding to this enzyme is accompanied by active site loop closure that positions a catalytically crucial cysteine 671 residue. The deprotonation of the loop residue H673 is required for active site closure, while S670 is important for substrate recognition. R235 is crucial for FAD binding
dihydrofluorouracil is further metabolized to 2'-fluoro-beta-alanine
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?
5,6-dihydrouracil + NADP+
uracil + NADPH
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C671A mutant only forms complex with dihydrouracil nearly without oxidizing it
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r
5,6-dihydrouracil + NADP+
uracil + NADPH
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first and rate-limiting enzyme in the three-step pathway for the degradation of uracil
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?
uracil + NADPH
5,6-dihydrouracil + NADP+
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rate limiting enzyme in pyrimidine degradation
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?
uracil + NADPH
5,6-dihydrouracil + NADP+
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rate limiting enzyme in pyrimidine degradation
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
dihydrofluorouracil + NADP+
5-fluorouracil + NADPH + H+
dihydrofluorouracil is further metabolized to 2'-fluoro-beta-alanine
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-
?
5,6-dihydrouracil + NADP+
uracil + NADPH
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first and rate-limiting enzyme in the three-step pathway for the degradation of uracil
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-
?
uracil + NADPH
5,6-dihydrouracil + NADP+
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rate limiting enzyme in pyrimidine degradation
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?
uracil + NADPH
5,6-dihydrouracil + NADP+
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rate limiting enzyme in pyrimidine degradation
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
flavin
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contains 2 mol FMN and 2 mol FAD per mol of enzyme, tightly associated
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Iron
Iron
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2 * 2 [4Fe-4S] clusters close in space with 16 atoms of non-heme iron, structure
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5-Ethynyluracil
covalently inactivates DPD by cross-linking with the active-site general acid cysteine in the pyrimidine binding site. This reaction is dependent on the simultaneous binding of 5-ethynyluracil and NADPH. The ternary complex induces DPD to become activated by taking up two electrons from the NADPH. The covalent inactivation of DPD by 5-ethynyluracil occurs concomitantly with this reductive activation with a rate constant of about 0.2 per s. This kinact value is correlated with the rate of reduction of one of the two flavin cofactors and the localization of a mobile loop in the pyrimidine active site
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
pH dependence and kinetics of recombinant wild-type and mutant enzymes, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
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inhibitory reactions between uracil, NADP+ and dihydrouracil
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additional information
additional information
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inhibitory reactions between uracil, NADP+ and dihydrouracil
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
pH dependence and kinetics of recombinant wild-type and mutant enzymes, overview
additional information
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investigation of pH-dependency of the reaction and inhibition by 2,6-dihydrouracil and ATP-ribose, kinetics
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
additional information
the N-terminal half of DPD is a member of a family of FAD-containing NADPH oxidoreductases, which transfer electrons to an acceptor protein or domain through [4Fe-4S] clusters of low to very low potential
metabolism
in mammals, the pyrimidines uracil and thymine are metabolised by a three-step reductive degradation pathway. Dihydropyrimidine dehydrogenase catalyses its first and rate-limiting step, reducing uracil and thymine to the corresponding 5,6-dihydropyrimidines in an NADPH-dependent reaction
metabolism
the rate of turnover is not controlled by the protonation state of the general acid, cysteine 671. The initial phase results in the accumulation of charge transfer absorption added to the binding difference spectrum for NADPH. The second phase results in reduction of one of the two flavins. The presumed activated form of the enzyme has the FMN cofactor reduced. Charge transfer arises from the proximity of the NADPH and FAD bases and the ensuing flavin is a result of rapid transfer of electrons to the FMN without accumulation of reduced forms of the FAD or Fe4-S4 centers. The slow rate of turnover of DPD is governed by the movement of a mobile structural feature that carries the C671 residue
metabolism
the reductive activation of DPD results in the reduction of one flavin per dimer consistent with alternating site behavior. During pyrimidine reduction, electron transfer across the flavins and Fe4S4 centers is rapid relative to the other process. The net rate of transmission of electrons from NADPH to the pyrimidine (kcat) must be determined exclusively by the rate of proton transfer from general acid cysteine 671
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). DPYD_PIG
1025
0
111424
Swiss-Prot
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant C671S, to 1.69 A resolution. The thymine substrate is positioned over the FMNH2 cofactor with the 6-methyne carbon 3.3 A from flavin N5
cocrystallization with 5-iodouracil 1 mM and NADPH 5 mM, ternary complex in 100 mM HEPES, pH 7.5, 22% polyethylene glycol 6000, uracil-4-acetic acid 1 mM, structure determination at different pH-values
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C126A
site-directed mutagenesis, a potential [4Fe-4S]-cluster binding residue, the mutant shows slightly increased activity compared to the wild-type enzyme
C671A
mutation eliminates the proton-coupled electron transfer required to reduce pyrimidine substrates
C671S
H673N
site-directed mutagenesis, active site loop residue, the mutant shows reduced activity compared to the wild-type enzyme
H673Q
site-directed mutagenesis, active site loop residue, the mutant shows reduced activity compared to the wild-type enzyme
Q156E
site-directed mutagenesis, [4Fe-4S]-cluster binding residue, inactive mutant
S670A
site-directed mutagenesis, active site loop residue, the mutant shows reduced activity compared to the wild-type enzyme
A551T
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natural mutation identified in a human with complete loss of enzymic activity. Crystallization data of Sus scrofa recombinant mutant, mutation might prevent binding of the prosthetic group FMN and affect folding of the enzyme protein
E244V
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natural mutation identified in a human with complete loss of enzymic activity. Crystallization data of Sus scrofa recombinant mutant, mutation interferes with the electron flow between NADPH and the pyrimidine binding site of the enzyme
C671S
mutation of the pyrimidine site candidate general acid, slows the turnover of the enzyme by approximately 60fold for uracil and 1600fold for thymine
C671S
variant exhibits both delineation of reductive activation into two phases at low pH values and exceptionally slow turnover with thymine
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, protein concentration 0.5-1 mg/ml, 1 mM dithiothreitol, stable for several months
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli by affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain Tuner(DE3)
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
the enzyme is an adjunct target in cancer therapy since it rapidly breaks down the anti-cancer drug 5-fluorouracil and related compounds
medicine
medicine
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target for inhibitor design to enhance the cytotoxical effect of 5-fluorouracil in tumor cells by inhibiting the DPD activity with 5-fluorouracil as substrate
medicine
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rate limiting enzyme for detoxification of exogenous fluoropyrimidines, antitumor drug design
medicine
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rate limiting enzyme in catabolic degradation of pyrimidine derivatives, selective inhibition is strategy for design of antitumor, antimicrobial and potentially antiparasitic agents
medicine
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identification of mutations E244V and A551T and splice site mutation IVS11+1G to T in patients with complete loss of enzymic activity
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Podschun, B.; Wahler, G.; Schnackerz, K.D.
Purification and characterization of dihydropyrimidine dehydrogenase from pig liver
Eur. J. Biochem.
185
219-224
1989
Sus scrofa
Podschun, B.; Cook, P.F.; Schnackerz, K.D.
Kinetic mechanism of dihydropyrimidine dehydrogenase from pig liver
J. Biol. Chem.
265
12966-12972
1990
Sus scrofa
Podschun, B.
Stereochemistry of NADPH oxidation by dihydropyrimidine dehydrogenase from pig liver
Biochem. Biophys. Res. Commun.
182
609-616
1992
Sus scrofa
Rosenbaum, K.; Jahnke, K.; Curti, B.; Hagen, W.R.; Schnackerz, K.D.; Vanoni, M.A.
Porcine Recombinant Dihydropyrimidine Dehydrogenase: Comparison of the spectroscopic and catalytic properties of the wild-type and C671A mutant enzymes
Biochemistry
37
17598-17609
1998
Sus scrofa
Lu, Z.H.; Zhang, R.; Diasio, R.B.
Comparison of dihydropyrimidine dehydrogenase from human, rat, pig and cow liver. Biochemical and immunological properties
Biochem. Pharmacol.
46
945-952
1993
Bos taurus, Homo sapiens, Rattus norvegicus, Sus scrofa
Rosenbaum, K.; Schaffrath, B.; Hagen, W.R.; Jahnke, K.; Gonzalez, F.J.; Cook, P.F.; Schnackerz, K.D.
Purification, characterization, and kinetics of porcine recombinant dihydropyrimidine dehydrogenase
Protein Expr. Purif.
10
185-191
1997
Sus scrofa
Hagen, W.R.; Vanoni, M.A.; Rosenbaum, K.; Schnackerz, K.D.
On the iron-sulfur clusters in the complex redox enzyme dihydropyrimidine dehydrogenase
Eur. J. Biochem.
267
3640-3646
2000
Sus scrofa
Dobritzsch, D.; Ricagno, S.; Schneider, G.; Schnackerz, K.D.; Lindqvist, Y.
Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer
J. Biol. Chem.
277
13155-13166
2002
Sus scrofa
Podschun, B.; Jahnke, K.; Schnackerz, K.D.; Cook, P.F.
Acid base catalytic mechanism of the dihydropyrimidine dehydrogenase from pH studies
J. Biol. Chem.
268
3407-3413
1993
Sus scrofa
Schnackerz, K.D.; Dobritzsch, D.; Lindqvist, Y.; Cook, P.F.
Dihydropyrimidine dehydrogenase: a flavoprotein with four iron-sulfur clusters
Biochim. Biophys. Acta
1701
61-74
2004
Bos taurus, Cupriavidus necator, Homo sapiens, Rattus norvegicus, Sus scrofa
Van Kuilenburg, A.B.; Meinsma, R.; Beke, E.; Bobba, B.; Boffi, P.; Enns, G.M.; Witt, D.R.; Dobritzsch, D.
Identification of three novel mutations in the dihydropyrimidine dehydrogenase gene associated with altered pre-mRNA splicing or protein function
Biol. Chem.
386
319-324
2005
Homo sapiens (Q12882), Sus scrofa
Lohkamp, B.; Voevodskaya, N.; Lindqvist, Y.; Dobritzsch, D.
Insights into the mechanism of dihydropyrimidine dehydrogenase from site-directed mutagenesis targeting the active site loop and redox cofactor coordination
Biochim. Biophys. Acta
1804
2198-2206
2010
Sus scrofa (Q28943)
Beaupre, B.A.; Forouzesh, D.C.; Moran, G.R.
Transient-state analysis of porcine dihydropyrimidine dehydrogenase reveals reductive activation by NADPH
Biochemistry
59
2419-2431
2020
Sus scrofa (Q28943)
Forouzesh, D.C.; Beaupre, B.A.; Butrin, A.; Wawrzak, Z.; Liu, D.; Moran, G.R.
The interaction of porcine dihydropyrimidine dehydrogenase with the chemotherapy sensitizer 5-ethynyluracil
Biochemistry
60
1120-1132
2021
Sus scrofa (Q28943)
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