Information on EC 3.5.4.1 - cytosine deaminase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

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EC NUMBER
COMMENTARY hide
3.5.4.1
-
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RECOMMENDED NAME
GeneOntology No.
cytosine deaminase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cytosine + H2O = uracil + NH3
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
pyrimidine nucleobases salvage II
-
-
pyrimidine ribonucleosides salvage III
-
-
pyrimidine metabolism
-
-
Pyrimidine metabolism
-
-
Arginine and proline metabolism
-
-
Metabolic pathways
-
-
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SYSTEMATIC NAME
IUBMB Comments
cytosine aminohydrolase
Also acts on 5-methylcytosine.
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CAS REGISTRY NUMBER
COMMENTARY hide
9025-05-2
-
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
ssp. denitrificans J9
-
-
Manually annotated by BRENDA team
Achromobacter liquidum
IFO 3084
-
-
Manually annotated by BRENDA team
Achromobacter polymorph
AKU 0122
-
-
Manually annotated by BRENDA team
Achromobacter polymorph AKU 0122
AKU 0122
-
-
Manually annotated by BRENDA team
AKU 0300; IAM 1526
-
-
Manually annotated by BRENDA team
Alcaligenes viscolactis
IAM 1517
-
-
Manually annotated by BRENDA team
Alcaligenes viscolactis IAM 1517
IAM 1517
-
-
Manually annotated by BRENDA team
J11
-
-
Manually annotated by BRENDA team
JH-13
-
-
Manually annotated by BRENDA team
IFO 3329
-
-
Manually annotated by BRENDA team
IFO 3026
-
-
Manually annotated by BRENDA team
ATCC 17759
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Flavobacterium filamentosum
-
-
-
Manually annotated by BRENDA team
IFO 3070
-
-
Manually annotated by BRENDA team
AKU 0502
-
-
Manually annotated by BRENDA team
AKU 0502
-
-
Manually annotated by BRENDA team
IFO 3082
-
-
Manually annotated by BRENDA team
type S
-
-
Manually annotated by BRENDA team
type S
-
-
Manually annotated by BRENDA team
IFO 3458
-
-
Manually annotated by BRENDA team
ATCC 12099
-
-
Manually annotated by BRENDA team
AKU 0820
-
-
Manually annotated by BRENDA team
type S
-
-
Manually annotated by BRENDA team
Pseudomonas schuylkilliensis
Pseudomonas schuylkilliensis type S
type S
-
-
Manually annotated by BRENDA team
IFO 3460
-
-
Manually annotated by BRENDA team
Pseudomonas trifolii
Pseudomonas trifolii type S
type S
-
-
Manually annotated by BRENDA team
Serratia polymuthicum
AKU 0062
-
-
Manually annotated by BRENDA team
Serratia polymuthicum AKU 0062
AKU 0062
-
-
Manually annotated by BRENDA team
pigs express four different A3 mRNAs encoding poA3Z2, poA3Z3, and by read-through transcription and alternatively splicing poA3Z2-Z3 and poA3Z2-Z3 splice variant A (SVA)
-
-
Manually annotated by BRENDA team
IAM 1671
-
-
Manually annotated by BRENDA team
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
-
human mitochondrial and nuclear DNA are edited by APOBEC3A. The degree of editing is much greater in patients lacking the uracil DNA-glycolyase gene
physiological function
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-thiocytosine + H2O
2-thiouracil + NH3
show the reaction diagram
-
-
-
-
?
3-oxauracil + H2O
malonate semialdehyde + CO2 + NH3
show the reaction diagram
-
-
-
-
?
5-azacytosine + H2O
5-azauracil + NH3
show the reaction diagram
-
-
-
-
?
5-bromocytosine + H2O
5-bromouracil + NH3
show the reaction diagram
-
-
-
-
?
5-chlorocytosine + H2O
5-chlorouracil + NH3
show the reaction diagram
-
-
-
-
?
5-fluorocytosine + H2O
5-fluorouracil + NH3
show the reaction diagram
5-iodocytosine + H2O
5-iodouracil + NH3
show the reaction diagram
-
-
-
-
?
5-methylcytosine + H2O
thymine + NH3
show the reaction diagram
6-azacytosine + H2O
6-azauracil + NH3
show the reaction diagram
creatinine + H2O
N-methylhydantoin + NH3
show the reaction diagram
cytidine + H2O
1-beta-D-ribofuranosylpyrimidin-2(1H)-one + NH3
show the reaction diagram
-
-
-
-
?
cytosine + H2O
uracil + NH3
show the reaction diagram
isocytosine + H2O
?
show the reaction diagram
-
-
-
-
?
pyrimidin-2-one + H2O
(4R)-hydroxyl-3,4-dihydropyrimidine + ?
show the reaction diagram
-
stabilization of a transition-state analogue at the active site of cytosine deaminase with importance of proton transfer from the Zn hydroxide group to Glu64 during the nucleophilic attack, quantum mechanical/molecular mechanical molecular dynamics and free energy simulations, active site structure, overview
-
-
?
additional information
?
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5-fluorocytosine + H2O
5-fluorouracil + NH3
show the reaction diagram
5-methylcytosine + H2O
thymine + NH3
show the reaction diagram
-
-
-
-
?
cytosine + H2O
uracil + NH3
show the reaction diagram
additional information
?
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
Mn2+ reconstitutes apoenzyme after removal of Fe2+
Iron
-
the enzyme contains 0.20 equivalents of Fe
KCl
-
1.0 mM, relative activity 116%
NaCl
-
1.0 mM, relative activity 107%
SnCl2
-
1.0 mM, relative activity 122%
Zinc
-
the enzyme contained 0.56 equivalents of Zn
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(1R,2S)-(-)-ephedrine
-
-
(alpha-D-glucopyranosylthio)gold
-
-
(R)-2,10,11-trihydroxy-N-propyl-noraporphine
-
-
(R)-2,10,11-trihydroxyaporphine
-
-
(R)-apomorphine
-
-
(R)-N-allylnorapomorphine
-
-
(R)-propylnorapomorphine
-
-
(S)-carbidopa
-
-
1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
-
-
2,2'-dipyridyl
-
-
2-hydroxypyrimidine
2-pyrimidinone
-
-
2-thiocytosine
-
weak
2-Thiouracil
-
strong
3,4-dihydroxyphenylacetic acid
-
-
4-chloromercuribenzoic acid
-
-
4-[(2-sulfanyl-1H-imidazol-1-yl)methyl]phenol
-
-
5'-guanidinonaltrindole
-
-
5,5'-dithiobis(2-nitrobenzoic acid)
-
-
5-Azacytosine
-
weak
5-bromo-2-pyrimidinone
-
-
5-fluoro-1H-pyrimidin-2-one
-
19F NMR experiments show that binding of the inhibitor 5-fluoro-1H-pyrimidin-2-one (5FPy) to the wild-type yCD causes an upfield shift, indicating that the bound inhibitor is in the hydrated form, mimicking the transition state or the tetrahedral intermediate in the activation of 5FC. Binding of 5FPy to the E64A mutant enzyme causes a downfield shift, indicating that the bound 5FPy remains in an unhydrated form in the complex with the mutant enzyme
5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine
-
mechanism-based inhibitor
6-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene
-
-
6-hydroxy-DL-DOPA
-
-
alpha,alpha'-dipyridyl
-
-
aurintricarboxylic acid
-
-
caffeic acid
-
-
cephapirin
-
-
Chloramine T
chloramine-T
deoxyguanosine
-
-
dephostatin
-
-
diethyldicarbonate
-
-
dihydrexidine
-
-
ebselen
-
-
ganciclovir
-
-
H2O2
-
only Fe2+CDase, Mn2+CDase, Co2+CDase and Zn2+CDase are not inhibited
Hg(CH3COO)2
-
-
hispidin
-
-
hydroquinone
-
-
Iodine
-
complete inhibition, reversed by cytosine
iodoacetamide
-
-
Mersalyl acid
-
-
methyl 3-hydroxy-DL-tyrosinate
-
-
myricetin
-
-
N-acetyldopamine
-
-
N-bromosuccinimide
nordihydroguaiaretic acid
-
-
o-phenanthroline
p-benzoquinone
-
-
p-chloromercuribenzoate
p-chloromercuribenzoic acid
p-Chloromercuriphenylsulfonic acid
-
-
p-hydroxymercuribenzoate
-
-
p-mercuribenzoate
phenylmethylsulfonyl fluoride
phosphonocytosine
-
-
piceatannol
-
-
PPNDS tetrasodium
-
-
pyridoxal 5'-phosphate
-
strong, reversed by cytosine
pyridoxal-5'-phosphate
SCH202676
-
-
SKF-89626
-
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
-
1.0 mM + glycine methyl ester, relative activity 102%
2-mercaptoethanol
-
1 mM, relative activity 108%
alpha,alpha'-dipyridyl
-
1 mM, relative activity 104%
D-alanine
-
1 mM, relative activity 120%
D-threonine
-
1 mM, relative activity 120%
dAMP
-
10.0 mM, relative activity 154%
dGMP
-
1.0 mM, substrate cytosine, relative activity 109%
diethyldicarbonate
-
1.0 mM, relative activity 102%
DL-alpha-amino-n-butyric acid
-
1 mM, relative activity 140%
DL-homoserine
-
1 mM, relative activity 110%
DL-isoleucine
-
1 mM, relative activity 130%
DL-methionine
-
1mM, relative activity 140%
ethylacetoimidate
GDP
-
10.0 mM, relative activity 176%
glycine
-
1 mM, relative activity 130%
IDP
-
10.0 mM, relative activity 152%
L-amino acids
L-asparagine
L-aspartic acid
L-cysteine
L-Glutamic acid
L-glutamine
L-histidine
L-hydroxyproline
L-isoleucine
-
1 mM, relative activity 130%
L-leucine
-
1 mM, relative activity 120%
L-methionine
L-ornithine
-
1 mM, relative activity 120%
L-phenylalanine
-
1 mM, relative activity 140%
L-serine
-
1 mM, relative activity 140%
L-threonine
-
1 mM, relative activity 120%
L-valine
-
1 mM, relative activity 120%
NaCN
-
1 mM, relative activity 104%
phosphate
Sodium azide
-
1 mM, relative activity 101%
sulfate
-
1.0 mM, relative activity 110%
sulfite
-
1.0 mM, relative activity 105%
trichloroacetate
-
1 mM, relative activity 101%
additional information
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 0.109
2-thiocytosine
0.85 - 4.1
3-oxauracil
0.12 - 0.36
5-Azacytosine
0.117
5-bromocytosine
-
-
0.068 - 19
5-fluorocytosine
0.57 - 36
5-Methylcytosine
1.02 - 1.6
6-azacytosine
25
creatinine
-
wild-type, pH 8.5, 30°C
0.19 - 4.9
cytosine
0.46
isocytosine
-
wild-type, pH 8.5, 30°C
additional information
additional information
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.27 - 22.3
2-thiocytosine
0.18 - 2.3
3-oxauracil
0.65 - 2.68
5-Azacytosine
0.00013 - 233
5-fluorocytosine
5.4 - 186
6-azacytosine
5.6
creatinine
-
wild-type, pH 8.5, 30°C
0.0075 - 2286
cytosine
5.1
isocytosine
-
wild-type, pH 8.5, 30°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21 - 0.56
3-oxauracil
0.0000014 - 106
5-fluorocytosine
0.22
creatinine
-
wild-type, pH 8.5, 30°C
0.004 - 140
cytosine
11
isocytosine
-
wild-type, pH 8.5, 30°C
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00086 - 1.06
5-fluoro-1H-pyrimidin-2-one
0.3
p-mercuribenzoate
-
-
0.000052
phosphonocytosine
-
pH 8.5, 30°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0013
(1R,2S)-(-)-ephedrine
Homo sapiens
-
pH 7.4, 37°C
0.00036
(alpha-D-glucopyranosylthio)gold
Homo sapiens
-
pH 7.4, 37°C
0.013
(R)-2,10,11-trihydroxy-N-propyl-noraporphine
Homo sapiens
-
pH 7.4, 37°C
0.0017
(R)-2,10,11-trihydroxyaporphine
Homo sapiens
-
pH 7.4, 37°C
0.0013
(R)-apomorphine
Homo sapiens
-
pH 7.4, 37°C
0.0029
(R)-N-allylnorapomorphine
Homo sapiens
-
pH 7.4, 37°C
0.006
(R)-propylnorapomorphine
Homo sapiens
-
pH 7.4, 37°C
0.0053
(S)-carbidopa
Homo sapiens
-
pH 7.4, 37°C
0.027
1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
Homo sapiens
-
pH 7.4, 37°C
0.019
3,4-dihydroxyphenylacetic acid
Homo sapiens
-
pH 7.4, 37°C
0.00013
4-chloromercuribenzoic acid
Homo sapiens
-
pH 7.4, 37°C
0.0035
4-[(2-sulfanyl-1H-imidazol-1-yl)methyl]phenol
Homo sapiens
-
pH 7.4, 37°C
0.0064
5'-guanidinonaltrindole
Homo sapiens
-
pH 7.4, 37°C
0.0007
6-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene
Homo sapiens
-
pH 7.4, 37°C
0.004
6-hydroxy-DL-DOPA
Homo sapiens
-
pH 7.4, 37°C
0.00049
aurintricarboxylic acid
Homo sapiens
-
pH 7.4, 37°C
0.085
caffeic acid
Homo sapiens
-
pH 7.4, 37°C
0.0075
cephapirin
Homo sapiens
-
pH 7.4, 37°C
0.00043 - 0.0091
dephostatin
0.00059
dihydrexidine
Homo sapiens
-
pH 7.4, 37°C
0.0028
ebselen
Homo sapiens
-
pH 7.4, 37°C
0.6
ganciclovir
Escherichia coli
-
37°C, recombinant fusion protein HSV-1TKglyCD
0.002
hispidin
Homo sapiens
-
pH 7.4, 37°C
0.0026
hydroquinone
Homo sapiens
-
pH 7.4, 37°C
0.003
iodoacetamide
Homo sapiens
-
pH 7.4, 37°C
0.013
methyl 3-hydroxy-DL-tyrosinate
Homo sapiens
-
pH 7.4, 37°C
0.0034
myricetin
Homo sapiens
-
pH 7.4, 37°C
0.00045
N-acetyldopamine
Homo sapiens
-
pH 7.4, 37°C
0.0088
nordihydroguaiaretic acid
Homo sapiens
-
pH 7.4, 37°C
0.00017
p-benzoquinone
Homo sapiens
-
pH 7.4, 37°C
0.0018
piceatannol
Homo sapiens
-
pH 7.4, 37°C
0.0056
PPNDS tetrasodium
Homo sapiens
-
pH 7.4, 37°C
0.029
SCH202676
Homo sapiens
-
pH 7.4, 37°C
0.0013
SKF-89626
Homo sapiens
-
pH 7.4, 37°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.12
-
(NH4)2SO4 as nitrogen source
0.26
-
strain K-1 AKU 0011
0.32
-
strain AKU 0009
1
-
asparagine as nitrogen source
2
-
+ 0.025 mM Cu(C2H3O2)
2.6
-
+ 0.025 mM HgCl2; + 0.025 mM Pb(C2H3O2)
2.9
-
apoCDase, + 0.025 SnCl2
3.2
-
+ 0.025 mM CaCl2
4
-
+ 0.025 mM NiCl2, additional incubation with 0.025 mM Fe2+
5.6
-
+ 0.025 mM NiCl2
8.3
-
+ 0.025 mM Pb(C2H3O2), additional incubation of 0.025 mM Fe2+
11
-
+ 0.025 mM HgCl2, additional incubation with 0.025 mM Fe2+
12
-
+ 0.025 mM Zn(C2H3O2), additional incubation with 0.025 mM Fe2+
13
-
+ 0.025 mM Zn(C2H3O2)
21
-
+ 0.025 mM CoSO4, additional incubation with 0.025 mM Fe2+
26
-
+ 0.025 mM CoSO4
45
-
+ 0.025 mM MnSO4
58
-
wild-type enzyme, substrate 5-fluorocytosine
62
-
+ 0.025 mM MnSO4, additional incubation with 0.025 mM Fe2+
65
-
+ 0.025 mM FeSO4, additional incubation with 0.025 mM Fe2+
87
-
+ 0.025 mM CrCl2, additional incubation with 0.025 mM Fe2+; + 0.025 mM FeSO4; apoCDase, additional incubation with 0.025 mM Fe2+
88
-
+ 0.025 mM CaCl2, additional incubation with 0.025 mM Fe2+
94
-
+ 0.025 SnCl2, additional incubation with 0.025 mM Fe2+
144
-
wild-type enzyme, substrate cytosine
additional information
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
a small fraction of human mitochondrial genomes are edited by APOBEC3 deaminases in the cytoplasm
Manually annotated by BRENDA team
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PDB
SCOP
CATH
ORGANISM
UNIPROT