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EC Tree
The taxonomic range for the selected organisms is: Sus scrofa The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
dihydrouracil dehydrogenase, dhpdhase, dhpdh, dhu dehydrogenase, dihydrouracil dehydrogenase (nadp+),
more
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dihydropyrimidine dehydrogenase
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4,5-dihydrothymine: oxidoreductase
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dehydrogenase, dihydrouracil (nicotinamide adenine dinucleotide phosphate)
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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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hydropyrimidine dehydrogenase
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DPD
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5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
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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5,6-dihydrouracil:NADP+ 5-oxidoreductase
Also acts on dihydrothymine.
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5-fluorouracil + NADPH + H+
5-fluoro-5,6-dihydrouracil + NADP+
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-
?
dihydrofluorouracil + NADP+
5-fluorouracil + NADPH + H+
dihydrothymine + NADP+
thymine + NADPH + H+
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-
-
?
dihydrouracil + NADP+
uracil + NADPH + H+
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-
-
?
thymine + NADPH + H+
5,6-dihydrothymine + NADP+
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-
?
uracil + NADPH + H+
5,6-dihydrouracil + NADP+
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-
-
?
5,6-dihydrouracil + NADP+
uracil + NADPH
5-aminouracil + NADPH
?
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-
-
?
5-fluorouracil + NADPH + H+
5-fluoro-5,6-dihydrouracil + NADP+
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-
?
dihydrothymine + NADP+
thymine + NADPH
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-
r
thymine + NADPH
dihydrothymine + NADP+
uracil + NADPH
5,6-dihydrouracil + NADP+
additional information
?
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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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?
5,6-dihydrouracil + NADP+
uracil + NADPH
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r
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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?
thymine + NADPH
dihydrothymine + NADP+
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?
thymine + NADPH
dihydrothymine + NADP+
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?
thymine + NADPH
dihydrothymine + NADP+
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?
thymine + NADPH
dihydrothymine + NADP+
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-
?
thymine + NADPH
dihydrothymine + NADP+
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-
-
?
uracil + NADPH
5,6-dihydrouracil + NADP+
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-
-
-
?
uracil + NADPH
5,6-dihydrouracil + NADP+
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-
-
?
uracil + NADPH
5,6-dihydrouracil + NADP+
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-
-
-
?
uracil + NADPH
5,6-dihydrouracil + NADP+
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r
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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?
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dihydrofluorouracil + NADP+
5-fluorouracil + NADPH + H+
dihydrofluorouracil is further metabolized to 2'-fluoro-beta-alanine
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-
?
dihydrothymine + NADP+
thymine + NADPH + H+
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-
?
dihydrouracil + NADP+
uracil + NADPH + H+
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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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-
?
thymine + NADPH
dihydrothymine + NADP+
uracil + NADPH
5,6-dihydrouracil + NADP+
thymine + NADPH
dihydrothymine + NADP+
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-
?
thymine + NADPH
dihydrothymine + NADP+
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?
thymine + NADPH
dihydrothymine + NADP+
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?
uracil + NADPH
5,6-dihydrouracil + NADP+
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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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?
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FAD
absolutely required, R235 is crucial for FAD binding
flavin
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flavin
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contains 2 mol FMN and 2 mol FAD per mol of enzyme, tightly associated
FMN
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NADPH
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NADPH
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strictly dependent on
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Fe2+
iron-sulfur cluster binding, overview
Iron
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2 [4Fe-4S] clusters per subunit with 9.0 mol iron per mol of subunit
Iron
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2 * 2 [4Fe-4S] clusters close in space with 16 atoms of non-heme iron, structure
Iron
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16 iron atoms per enzyme, wild-type and mutant C671A, [4Fe-4S] clusters
Iron
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iron atoms are probably present in iron-sulfur centers
Iron
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contains 32 iron atoms per 206000 MW protein
Iron
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each subunit contains 16 nonheme-irons in 4 [4Fe-4S] clusters
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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
2,6-Dihydroxypyridine
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competitive vs. uracil
5,6-Dihydropyrimidine
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5-Iodo-uracil
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mechanism-based inactivator
5-Iodouracil
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inhibition mechanism
5,6-dihydrouracil
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5,6-dihydrouracil
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competitive
ATP-ribose
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competitive
ATP-ribose
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dead-end inhibition
NADP+
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NADP+
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competitive versus NADPH
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Sulfide
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Sulfide
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8.0 mol acid-labile sulfide per mol of subunit
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0.0011
5-fluorouracil
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additional information
additional information
pH dependence and kinetics of recombinant wild-type and mutant enzymes, overview
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0.0023
NADPH
wild-type, anaerobic conditions, pH 7.0, 20°C
0.0054
NADPH
wild-type, aerobic conditions, pH 7.0, 20°C
0.0057
NADPH
pH 7.5, 30°C, recombinant wild-type enzyme
0.0061
NADPH
pH 7.5, 30°C, recombinant mutant C126A
0.0062
NADPH
pH 7.5, 30°C, recombinant mutant H673Q
0.0075
NADPH
pH 7.5, 30°C, recombinant mutant H673N
0.0093
NADPH
mutant C671S, anaerobic conditions, pH 7.0, 20°C
0.0188
NADPH
pH 7.5, 30°C, recombinant mutant S670A
0.00079
thymine
wild-type, anaerobic conditions, pH 7.0, 20°C
0.0046
thymine
wild-type, aerobic conditions, pH 7.0, 20°C
0.00087
Uracil
wild-type, anaerobic conditions, pH 7.0, 20°C
0.0011
Uracil
pH 7.5, 30°C, recombinant mutant C126A
0.0012
Uracil
pH 7.5, 30°C, recombinant wild-type enzyme
0.0015
Uracil
mutant C671S, aerobic conditions, pH 7.0, 20°C
0.0042
Uracil
pH 7.5, 30°C, recombinant mutant H673Q
0.0055
Uracil
mutant C671S, anaerobic conditions, pH 7.0, 20°C
0.0063
Uracil
wild-type, aerobic conditions, pH 7.0, 20°C
0.007
Uracil
pH 7.5, 30°C, recombinant mutant H673N
0.0366
Uracil
pH 7.5, 30°C, recombinant mutant S670A
0.006
NADPH
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0.0066
NADPH
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in presence of 2,6-dihydrouracil
0.0082
NADPH
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in presence of 5-fluorouracil
0.0119
NADPH
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in presence of uracil
0.0167
NADPH
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in presence of thymine
0.001
Uracil
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0.023
Uracil
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in presence of 2,6-dihydrouracil
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0.015
NADPH
mutant C671S, anaerobic conditions, pH 7.0, 20°C
0.65
NADPH
wild-type, aerobic conditions, pH 7.0, 20°C
0.85
NADPH
wild-type, anaerobic conditions, pH 7.0, 20°C
0.00024
thymine
mutant C671S, anaerobic conditions, pH 7.0, 20°C
0.39
thymine
wild-type, anaerobic conditions, pH 7.0, 20°C
0.42
thymine
wild-type, aerobic conditions, pH 7.0, 20°C
0.015
Uracil
mutant C671S, anaerobic conditions, pH 7.0, 20°C
0.068
Uracil
pH 7.5, 30°C, recombinant mutant H673N
0.117
Uracil
pH 7.5, 30°C, recombinant mutant H673Q
0.177
Uracil
pH 7.5, 30°C, recombinant mutant S670A
0.242
Uracil
pH 7.5, 30°C, recombinant wild-type enzyme
0.256
Uracil
pH 7.5, 30°C, recombinant mutant C126A
0.3
Uracil
mutant C671S, aerobic conditions, pH 7.0, 20°C
0.73
Uracil
wild-type, aerobic conditions, pH 7.0, 20°C
0.78
Uracil
wild-type, anaerobic conditions, pH 7.0, 20°C
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2
NADPH
mutant C671S, anaerobic conditions, pH 7.0, 20°C
120
NADPH
wild-type, aerobic conditions, pH 7.0, 20°C
360
NADPH
wild-type, anaerobic conditions, pH 7.0, 20°C
9000
NADPH
pH 7.5, 30°C, recombinant mutant H673N
9000
NADPH
pH 7.5, 30°C, recombinant mutant S670A
19000
NADPH
pH 7.5, 30°C, recombinant mutant H673Q
42000
NADPH
pH 7.5, 30°C, recombinant mutant C126A
42000
NADPH
pH 7.5, 30°C, recombinant wild-type enzyme
90
thymine
wild-type, aerobic conditions, pH 7.0, 20°C
500
thymine
wild-type, anaerobic conditions, pH 7.0, 20°C
3
Uracil
mutant C671S, anaerobic conditions, pH 7.0, 20°C
20
Uracil
mutant C671S, aerobic conditions, pH 7.0, 20°C
110
Uracil
wild-type, aerobic conditions, pH 7.0, 20°C
900
Uracil
wild-type, anaerobic conditions, pH 7.0, 20°C
5000
Uracil
pH 7.5, 30°C, recombinant mutant S670A
10000
Uracil
pH 7.5, 30°C, recombinant mutant H673N
28000
Uracil
pH 7.5, 30°C, recombinant mutant H673Q
208000
Uracil
pH 7.5, 30°C, recombinant wild-type enzyme
238000
Uracil
pH 7.5, 30°C, recombinant mutant C126A
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additional information
additional information
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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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0.417 - 0.5
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purified enzyme
14
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recombinant from Escherichia coli
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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
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UniProt
brenda
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brenda
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brenda
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brenda
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brenda
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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
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DPYD_PIG
1025
0
111424
Swiss-Prot
other Location (Reliability: 2 )
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102000
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2 * 102000, SDS-PAGE
107000
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2 * 107000, SDS-PAGE
111000
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2 * 111000, SDS-PAGE
204000
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HPLC gel filtration
214000
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recombinant from E. coli, native PAGE
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dimer
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dimer
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2 * 111000, SDS-PAGE
dimer
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2 * 102000, SDS-PAGE
dimer
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2 * 107000, SDS-PAGE
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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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crystals diffract to 1.9 A
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mutants E244V and A551T
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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
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
R235A
site-directed mutagenesis, FAD binding residue, inactive mutant
R235K
site-directed mutagenesis, FAD 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
C671A
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1% activity compared to that of the wild-type enzyme
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
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-20°C, protein concentration 0.5-1 mg/ml, 1 mM dithiothreitol, stable for several months
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recombinant wild-type and mutant enzymes from Escherichia coli by affinity chromatography and gel filtration
wild-type and mutant enzyme
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expression in Escherichia coli
expression of wild-type and mutant enzymes in Escherichia coli strain Tuner(DE3)
expression in Escherichia coli
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overproduction of wild-type and mutant enzyme in Escherichia coli
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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
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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
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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
brenda
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
brenda
Podschun, B.
Stereochemistry of NADPH oxidation by dihydropyrimidine dehydrogenase from pig liver
Biochem. Biophys. Res. Commun.
182
609-616
1992
Sus scrofa
brenda
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
brenda
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
brenda
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
brenda
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
brenda
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
brenda
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
brenda
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
brenda
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
brenda
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)
brenda
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)
brenda
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)
brenda
Beaupre, B.A.; Forouzesh, D.C.; Butrin, A.; Liu, D.; Moran, G.R.
Perturbing the movement of hydrogens to delineate and assign events in the reductive activation and turnover of porcine dihydropyrimidine dehydrogenase
Biochemistry
60
1764-1775
2021
Sus scrofa (Q28943)
brenda