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Enzyme Nomenclature
Information on EC 3.5.2.3 - dihydroorotase
for references in articles please use BRENDA:EC3.5.2.3
Word Map on EC 3.5.2.3
- 3.5.2.3
- pyrimidine
-
transcarbamoylase
- atcase
- carbamoyl-phosphate
- phosphoribosyltransferase
-
carbamoyltransferase
-
2.1.3.2
- orotidine
- l-dihydroorotate
- cpsase
-
glutamine-dependent
- dihydropyrimidinase
- dihydro-ouabain
- n-phosphonacetyl-l-aspartate
- allantoinase
-
n-carbamyl-l-aspartate
- hydantoinase
-
pyre
- synthesis
- drug development
- medicine
-
6.3.5.5
- 5-fluoroorotate
-
succinate-grown
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
3.5.2.3
-
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RECOMMENDED NAME
GeneOntology No.
dihydroorotase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
-
-
-
-
(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
unique catalytic mechanism
-
(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
complex formation of enzyme with aspartate transcarbamoylase drives reaction in the biosynthetic direction
-
(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
catalytic mechanism, overview
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
formation of cyclic amides
-
-
-
-
hydrolysis of cyclic amides
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
(S)-dihydroorotate amidohydrolase
-
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CAS REGISTRY NUMBER
COMMENTARY
9024-93-5
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain RH lambda Zap II cDNA library, strain PC117 and 5TN; strains RH, PC117, and 5TN
SwissProt
in noncovalent association with aspartate transcarbamoylase, possible model for the mammalian polypeptide chain CPSase/ATCase/DHOase during pyrimidine biosynthesis
UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
-
following pyrimidine limitation of orotidine 5'-monophosphate decarboxylase mutant strain cells, dihydroorotase and dihydroorotate dehydrogenase activities double while aspartate transcarbamoylase and orotate phosphoribosyltransferase activities are slightly elevated compared to their activities in the mutant strain cells grown on excess uracil
additional information
-
the enzyme contains four histidine, one aspartate, and one post-carboxylated lysine residue, which are required for metal binding and catalytic activity
metabolism
third enzyme in the bacterial de novo pyrimidine biosynthesis pathway, overview
metabolism
-
third enzyme in the bacterial de novo pyrimidine biosynthesis pathway, overview
-
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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
dexrazoxane + H2O
ADR-925
-
i.e. ICRF187 or (+)-1,2-bis(3,5-dioxopiperazin-1-yl)propane, cardioprotective agent
i.e. N,N’-[(1S)-1-methyl-1,2-ethanediyl]bis[N-(2-amino-2-oxoethyl)glycine], biologically active form
?
N-(2-amino-2-oxoethyl)-N-[(1S)-2-(3,5-dioxo-1-piperazinyl)-1-methylethyl]glycine + H2O
N,N'-[(1S)-1-methyl-1,2-ethanediyl]bis[N-(2-amino-2-oxoethyl)]glycine
-
-
-
-
ir
N-(2-amino-2-oxoethyl)-N-[(2S)-2-(3,5-dioxo-1-piperazinyl)propyl]glycine + H2O
N,N'-[(1S)-1-methyl-1,2-ethanediyl]bis[N-(2-amino-2-oxoethyl)]glycine
-
-
-
-
ir
(S)-dihydroorotate + H2O
N-carbamoyl-L-aspartate
-
aspartate transcarbamoylase-dihydroorotase complex
-
-
r
(S)-dihydroorotate + H2O
N-carbamoyl-L-aspartate
-
aspartate transcarbamoylase-dihydroorotase complex
-
-
r
(S)-dihydroorotate + H2O
N-carbamoyl-L-aspartate
-
absolute substrate specificity
-
-
?
L-carbamoyl-L-aspartate
L-dihydroorotate + H2O
-
-
-
-
r
L-carbamoylaspartate
L-dihydroorotate + H2O
-
-
-
-
r
additional information
?
-
no substrate: hydantoin, dihydrouracil, phthalimide, and 3-imonoisoindolinone
-
-
-
additional information
?
-
-
no substrate: hydantoin, dihydrouracil, phthalimide, and 3-imonoisoindolinone
-
-
-
additional information
?
-
-
allantoin, hydantoin, and phthalimide are not hydrolyzed by dihydroorotase
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
L-carbamoyl-L-aspartate
L-dihydroorotate + H2O
-
-
-
-
r
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
Zn2+
-
tagged enzyme contains ca. 1.0 zinc atom per subunit measured by atomic absorption spectroscopy
Zn2+
dihydroorotase enzyme is a di-metalloenzyme that is dependent upon two zinc atoms in the active site for activity
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(S)-1,2,3,6-tetrahydro-6-oxopyridine-2-carboxylic acid
-
competitive inhibitor versus dihydroorotate and thio-dihydroorotate
4(R)-hydroxy-6-oxo-piperidine-2(S)-carboxylic acid
-
competitive inhibitor versus dihydroorotate and thio-dihydroorotate
4(S)-hydroxy-6-oxo-piperidine-2(S)-carboxylic acid
-
competitive inhibitor versus dihydroorotate and thio-dihydroorotate
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
most active competitive inhibitor versus dihydroorotate and thio-dihydroorotate
desferrioxamine
-
hypoxia causes a decrease in carbamoyl phosphate synthetase-aspartate carbamoyltransferase-dihydroorotase expression incubated under desferrioxamine-induced HIF-1alpha accumulation detected in A293T, IMR32, colo320DM and HeLa cell lines
diethyl dicarbonate
-
strong inhibition at 1 mM, activity is restored more than 95% when the enzyme is preincubated with both 1 mM diethyl dicarbonate and 5 mM L-carbamoyl-L-aspartate
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
at 37°C or 60°c the enzyme binds 2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid only slightly more strongly than DHO; competitive inhibitor
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
at 37°C or 60°C the enzyme binds 2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid more tightly than DHO
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
competitive inhibitor
additional information
-
hypoxia causes a decrease in carbamoyl phosphate synthetase-aspartate carbamoyltransferase-dihydroorotase expression detected in A293T, IMR32, HeLa cell lines and human endometiral stromal cells
-
additional information
-
binding and inhibition of allantoinase dihydroorotase by flavonols and the substrates of other cyclic amidohydrolases, dissociation constants, docking analysis using three-dimensional structure model, PDB ID 3JZE, overview. Hydantoin and allantoin bind to dihydroorotase, but do not affect its activity, no inhibition by phthalimide
-
additional information
-
EDTA and 1,10-phenanthroline have no effect on the enzyme activity; L-carbamoyl-L-aspartate and L-dihydroorotate have no inhibitory effect on the enzyme at the pH 7.4
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
following pyrimidine limitation of orotidine 5'-monophosphate decarboxylase mutant strain cells, dihydroorotase and dihydroorotate dehydrogenase activities double while aspartate transcarbamoylase and orotate phosphoribosyltransferase activities are slightly elevated compared to their activities in the mutant strain cells grown on excess uracil
-
Dimethylsulfoxide
-
increases the catalytic efficiency on the ring cyclization reaction, but not on the ring hydrolysis
Dimethylsulfoxide
-
increases the catalytic efficiency on the ring cyclization reaction, but not on the ring hydrolysis
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.118
(S)-dihydroorotate
pH 8.3, 25°C, recombinant detagged enzyme
0.167
(S)-dihydroorotate
pH 8.3, 25°C, recombinant tagged enzyme
6
L-carbamoyl-L-aspartate
-
mutant enzyme T109S, at pH 5.8; mutant enzyme T110V, at pH 5.8
0.334
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant tagged enzyme
0.348
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant detagged enzyme
additional information
carbamoyl aspartate
-
mutants D250A, D250H, D250N, R20Q, R20M, N44A, H254N inactive
additional information
additional information
-
Michaelis-Menten kinetics
-
additional information
additional information
forward and reverse kinetic rate constants for both tagged and wild-type enzyme, kinetic analysis, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.55
(S)-dihydroorotate
pH 8.3, 25°C, recombinant detagged enzyme
1.9
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant tagged enzyme
2.48
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant detagged enzyme
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
13.1
(S)-dihydroorotate
pH 8.3, 25°C, recombinant detagged enzyme
5.69
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant tagged enzyme
7.13
N-Carbamoyl-L-aspartate
pH 8.3, 25°C, recombinant detagged enzyme
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.3
(S)-1,2,3,6-tetrahydro-6-oxopyridine-2-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 8.0
1.6
4(R)-hydroxy-6-oxo-piperidine-2(S)-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 8.0
3
4(S)-hydroxy-6-oxo-piperidine-2(S)-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 8.0
3.5
5-iodoorotate
-
Ki above 3.5 mM, for the ring cleavage reaction; Ki above 3.5 mM, for the ring cyclization reaction
0.0045
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
at 37°C
0.083
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
at 37°C
0.102
2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylic acid
-
at 60°C
0.076
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with dihydroorotate as substrate, pH. 7.0
0.096
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 7.0
0.12
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 8.0
0.21
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with dihydroorotate as substrate, pH. 8.0
0.32
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with thio-dihydroorotate as substrate, pH. 9.0
0.44
4,6-dioxo-piperidine-2-(S)-carboxylic acid
-
with dihydroorotate as substrate, pH. 9.0
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
37
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 45
37 - 60
25 - 45
-
; differences in kinetic isotope effects due to temperature change are nonexistent for hDHOase even though both systems are run at suboptimal temperatures
37 - 60
-
; kinetic isotope effects due to temperature change show a very moderate difference in the secondary kinetic isotope effect for BcDHOase even though both systems are run at suboptimal temperatures
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
; maintained by serial passage in the peritoneal cavity of CFW mice
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
38000
40000
42000
45600
gel filtration and laser light scattering; gel filtration, laser light scattering
48090
-
electrospray ionization mass spectroscopy, enzyme with hexahistidine tag; mass spectroscopy, BcDHOase with the hexahistidine tag
49000
498000
-
gel filtration, DHOase in complex with aspartate transcarbamoylase
500000
-
aspartate transcarbamoylase-dihydroorotase complex, gel filtration
49000
-
dihydroorotase, electro-elution, SDS-PAGE and Coomassie staining
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
hexamer
homodimer
homotetramer
-
temperature-dependent conversion to homodimer, crystallization data
monomer
multimer
additional information
homodimer
-
crystallization data, asymmetry between active sites, with N-carbamyl-L-aspartate bound to one site and dihydroorotate bound to the other
homodimer
-
temperature-dependent conversion to homotetramer, crystallization data
monomer
-
1 * 40000, gel filtration, 75% of the total activity is associated with the monomeric form
monomer
1 * 44200, SDS-PAGE; 1 * 45600, gel filtration and laser light scattering
multimer
-
multi-enzyme complex, carbamoyl phosphate synthetase, aspartate transcarbamylase and dihydroorotase, 129000 + 39000 + 44000, SDS-PAGE
additional information
-
recombinant protein lacks catalytic activity, activity is acquired by forming a complex with aspartate transcarbamoylase, complex may be a heterohexamer or dodecamer
additional information
the His-SUMO tag does not interfere with SaPyrC dimerization
additional information
-
the His-SUMO tag does not interfere with SaPyrC dimerization
-
additional information
-
direct intermolecular interactions between carbamoylphosphate synthetase II, aspartate transcarbamoylase, and dihydroorotase, which catalyze the first 3 reaction steps of the de novo pyrimidine biosynthetic pathway
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop method, monoclinic structure has a novel cysteine ligand to the zinc that blocks the active site and functions as a cysteine switch, active site residues are located in disordered loops, which may function as a disorder-to-order entropy switch
to 2.6 A resolution. The overall tertiary structure formed from the TIM-barrel secondary structure motif is conical, with the active site residing at the base of the cone. The active site includes a binuclear Zn center, with two histidine (His59 and His61) and two asparagine (Asp151 and Asp304) residues bound to the more buried first Zn atom and two histidine (178 and231) residues and Asp151 bound to the second Zn atom. The carboxylate side group of Asp151 forms a bridge between the two Zn atoms
crystallized without ligand and in the presence of the inhibitors 2-oxo-1,2,3,6-tetrahydropyrimidine-4,6-dicarboxylate and 5-fluoroorotate, hanging drop vapour diffusion method with 15-20% (w/v) polyethylene glycol 3350, 0.1 M MES (pH 6.0-6.5), 75 mM MgCl2, 150 mM KCl (with ligand) or 20-25% polyethylene glycol 3350, 0.1 M Na HEPES (pH 7) and 0.2 M NaF (without ligand)
-
hanging drop vapour diffusion method with 15-20% polyethylene glycol 3350, 0.1 M MES, pH 6.0-6.5, 75 mM MgCl2, and 150 mM KCl
-
in complex with 5-fluoroorotate, hanging drop vapour diffusion method 14-16% PEG 3350, 0.1 M MES pH 6.25, 25 mM MgCl2, 0.2 M KCl and 30% sucrose
-
in the presence of enantiomerically pure L-dihydroorotate, refined at 1.9 Angstrom resolution
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
stability decreases in the order pH 8 pH pH 6 pH 9
713469
additional information
-
stability decreases in the order pH 8 pH pH 6 pH 9
713469
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
70
99
-
enzyme complex with aspartate transcarbamoylase, both activities are stable
70
-
BcDHOase starts to unfold at temperatures greater than 70°C with a melting temperature of 79.5°C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, under nitrogen, 100 mM Tris phosphate buffer, pH 7, metal free 10 mM N-carbamoyl-DL-aspartate, at least 2 months
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by Ni-NTA chromatography and Poros Q anion-exchange column; Ni-NTA agarose column chromatography, Poros Q column chromatography, and Sephadex G-75 gel filtration
-
DEAE-Sephacel column chromatography; recombinant protein purified to homogeneity
dihydroorotase and aspartate transcarbamoylase copurify, partially purified by anion exchange chromatography, gel filtration, hydrophobic interaction chromatography; HiTrap Q column chromatography, Hiload Superdex gel filtration, and phenyl-Superose HR column chromatography
-
N-linked butylamine-agarose column chromatography and DEAE-Sephacel column chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis
-
recombinant N-terminal His-SUMO-tagged enzyme SaPyrC from Escherichia coli strain BL21(DE3), by nickel affinity chromatography, dialysis, and His-SUMO tag cleavage through HRV 3C protease, another step of nickel affinity chromatography to remove the tag, followed by ultrafiltration, and gel filtration, to about 95% purity, method optimization, the His-SUMO tag affects enzyme activity slightly
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells; overexpression in Escherichia coli BL21(DES/pLysS)
-
expressed in Escherichia coli strain SO1263; overexpression in Escherichia coli strain BL21(DE3)
-
expressed in Escherichia coli strain SO1263; overexpression in Escherichia coli strain SØ1263/pyrC-
-
expressed in Escherichia coli strain X7014; expression in Escherichia coli mutant strain SØ1263 and strain X7014
expression in Escherichia coli
expression in Escherichia colipyrC mutant strain X7014a, genes pyrC(PA3527) and pyrC2(PA5541) can complement DHOase mutant, pyrC constitutively expressed, pyrC2 can only complement the DHOase mutant when expressed from the lacZalpha promotor
expression of yeast-hamster chimeric proteins in Escherichia coli
gene pyrC, DNA and amino acid sequence determination and analysis, sequence comparison, expression of N-terminal His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3) with an HRV 3C protease recognition site inserted between the SUMO tag and SaPyrC to allow for improved cleavage by HRV protease, method optimization
recombinant overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
with a fusion peptide containing six histidine residues at the amino terminus
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C221S/C263S/C265S/C268S
-
this quadruple mutant is relatively stable to oxidation and has kinetic parameters consistent with reported values for wild type DHO
T109S
additional information
additional information
in noncovalent association with aspartate transcarbamoylase, possible model for mammalian polypeptide chain CPSase/ATCase/DHOase during pyrimidine biosynthesis
additional information
-
deletion mutant DELTA107-116 DHOase shows negligible activity
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
medicine
synthesis
-
growth conditions which maintain DHOase overproduction require supplementation of Yeast Carbon Base with asparagines 5 g/l, glucose 20 g/l at pH 5.5. In this medium DHOase activity decreases with time, thus in terms of DHOase yield, the best time for harvesting cells is reached after 30 to 38 h of growth
drug development
the essential enzyme is a target for antibacterial drug design
drug development
-
the essential enzyme is a target for antibacterial drug design
-
medicine
-
activation of the cardioprotective agent dexrazoxane by the enzyme in heart, mechanism
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LINKS TO OTHER DATABASES (specific for EC-Number 3.5.2.3)
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