Information on EC 3.5.4.13 - dCTP deaminase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY
3.5.4.13
-
RECOMMENDED NAME
GeneOntology No.
dCTP deaminase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dCTP + H2O = dUTP + NH3
show the reaction diagram
-
-
-
-
dCTP + H2O = dUTP + NH3
show the reaction diagram
mechanism of bifunctional enzyme activity and feedback inhibition by dTTP
Q57872
dCTP + H2O = dUTP + NH3
show the reaction diagram
reaction involves S111, A124, E138 and two water molecules
-
dCTP + H2O = dUTP + NH3
show the reaction diagram
the mechanism for the deamination of dCTP involves the four residues Ser102, Arg106, Ala115 and Glu129, structure-function relationship of the bifunctional enzyme, overview
P9WP17
dCTP + H2O = dUTP + NH3
show the reaction diagram
reaction involves S111, A124, E138 and two water molecules
Escherichia coli K12
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Deamination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
-
-
pyrimidine deoxyribonucleotides de novo biosynthesis II
-
-
Pyrimidine metabolism
-
-
pyrimidine metabolism
-
-
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)
-
-
SYSTEMATIC NAME
IUBMB Comments
dCTP aminohydrolase
-
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5-methyl-dCTP deaminase
-
-
-
-
dCTP deaminase
-
-
-
-
deoxycytidine triphosphate deaminase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37289-18-2
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
infected by Bacteriophage PBS1
-
-
Manually annotated by BRENDA team
infected by Bacteriophage PBS2
-
-
Manually annotated by BRENDA team
dCTP deaminase-deficient
-
-
Manually annotated by BRENDA team
bifunctional enzyme dCTP deaminase-dUTP nucleotidohydrolase
SwissProt
Manually annotated by BRENDA team
bifunctional enzyme dCTP deaminase-dUTP nucleotidohydrolase
-
-
Manually annotated by BRENDA team
i.e. PBCV-1 , a chlorovirus from host Chlorella sp. strain NC64A
SwissProt
Manually annotated by BRENDA team
infected by Bacteriophage XP-12
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-methyl-dCMP + H2O
5-methyl-dCyd
show the reaction diagram
-
-
-
?
5-methyl-dCTP + H2O
dTTP + NH3
show the reaction diagram
-
-
-
?
5-methyl-dCTP + H2O
5-methyl-dTTP
show the reaction diagram
-
-
-
?
dCMP + H2O
dUMP + NH3
show the reaction diagram
O41078
-
dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
P9WP17
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
O41078
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
dUMP is required for dTMP synthesis via hydrolyzation of UTP by dUTPase to dUMP
-
?
ddCTP + H2O
ddUTP + NH3
show the reaction diagram
-
deamination at the same rate as dCTP
-
?
dUTP + 2 H2O
dUMP + 2 phosphate
show the reaction diagram
-
-
-
?
additional information
?
-
-
bifunctionality of enzyme avoids release of toxic UTP within cells
-
?
additional information
?
-
O41078
the bifunctional dCMP-dCTP deaminase shows dCMP deaminase and dCTP deaminase activities, dCTP serves as a positive heterotropic effector for the dCMP deaminase activity and a positive homotropic effector for the dCTP deaminase activity, and the enzymatic efficiency of the dCMP deaminase activity is about four times higher than that of the dCTP deaminase activity, the same active site is involved in both dCMP and dCTP deaminations
-
-
-
additional information
?
-
P9WP17
the enzyme is a bifunctional dCTP deaminase:dUTPase
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
dCMP + H2O
dUMP + NH3
show the reaction diagram
O41078
-
dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
P9WP17
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
O41078
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
-
-
?
dCTP + H2O
dUTP + NH3
show the reaction diagram
-
-
dUMP is required for dTMP synthesis via hydrolyzation of UTP by dUTPase to dUMP
-
?
additional information
?
-
-
bifunctionality of enzyme avoids release of toxic UTP within cells
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
O41078
can partially substitute for Mg2+
Mg2+
-
absolutely required
Mg2+
O41078
the enzyme depends on divalent cations, Mg2+ is preferred , but can partially be substituted by Ca2+, Ni2+, or Mn2+
Mn2+
O41078
can partially substitute for Mg2+
Ni2+
O41078
can partially substitute for Mg2+
Zn2+
O41078
the enzyme contains a zinc binding site, but shows less than 6% of maximal activity with Zn2+ as divalent cation
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dTTP
-
inhibition of deamination reaction
dTTP
-
inhibits by increasing the kcat several fold, mutants S111T and E138D are less sensitive to dTTP, overview
dTTP
-
inhibits the enzyme in a nonallosterical way, cooperative kinetics are imposed by a dTTP-dependent lag of product formation observed in presteady-state kinetics, the lag may be derived from a slow equilibration between an inactive and an active conformation of dCTP deaminase represented by the dTTP complex and the dUTP/dCTP complex, respectively, steady-state kinetic analysis of dTTP inhibition, overview
dTTP
P9WP17
the inhibitor has a regukatory function for the bifunctional enzyme, mechanism of regulation by conformational changes, overview
dTTP
O41078
inhibits dCMP deamination, feedback inhibition
dUTP
-
inhibition of deamination reaction
H4dUMP
O41078
inhibits both dCTP and dCMP deaminase activities
p-hydroxymercuribenzoate
-
-
PDRP
O41078
inhibits both dCTP and dCMP deaminase activities
phosphate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dCTP
O41078
activates dCMP deamination about 7fold at 0.005-0.1 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.76
dCMP
O41078
pH 9.5, 42C, in presence of 0.1 mM dCTP
0.05 - 0.1
dCTP
-
-
0.36
dCTP
-
-
0.64
dCTP
O41078
pH 9.5, 42C
additional information
additional information
-
for dUTP, Km-value in millimolar range
-
additional information
additional information
-
enzyme kinetics and equilibrium binding
-
additional information
additional information
P9WP17
steady-state kinetic analysis
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
24.9
dCMP
O41078
pH 9.5, 42C, in presence of 0.1 mM dCTP
1.24
dCTP
-
pH 6.8, 37C, recombinant wild-type enzyme
5.7
dCTP
O41078
pH 9.5, 42C
additional information
additional information
-
-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.1
dTTP
-
pH 6.8, 25C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.7 - 6.9
-
-
7
O41078
dCTP deaminase activity
9.5
O41078
dCMP deaminase activity
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 11
O41078
activity range
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PDB
SCOP
CATH
ORGANISM
Anaplasma phagocytophilum (strain HZ)
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
82000
-
gel filtration
209518, 209519, 209522
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 23400, deduced from gene sequence, x * 23300, mass spectrometry
hexamer
Q57872
crystallization data
hexamer
O41078
6 * 17000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
mutant E138A bound to dTTP and mutant H121A bound to dCTP, hanging drop vapour diffusion method, 3.7 mg/ml E138A or 5.1 mg/ml H121A in 20 mM magnesium chloride, 50 mM HEPES, pH 6.8, and 5 mM nucleotide, mixing of 0.002 ml of protein solution with an equal volume of reservoir solution containing 34% PEG 400, 0.2 mM MgCl2, and 0.1 m HEPES, pH 7.5, equilibration against 1 ml of mother liquor, room temperature, 1 week, X-ray diffraction structure determination and analysis at 2.6-2.7 A resolution
-
recombinant mutant E138D in complex with dUTP, hanging drop vapour diffusion method, 0.002 ml of 2 mg/ml protein in solution with 5 mM dUTP and 20 mM MgSO4 is mixed with 0.002 ml reservoir solution containing 27.5% PEG 400, 50 mM MgSO4 and 0.1 M HEPES, pH 7.5, equilibration against 0.5 ml of reservoir solution, room temeprature, crystal X-ray diffraction structure determination and analysis at 2.1 A resolution
-
wild-type and mutant E138A, in complex with Mg2+ and dUTP, and dCTP
-
apoenzyme in complex with dCTP and with dUTP
Q57872
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
-50
-
stable for at least two months
209518, 209519
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ethylene glycol
-
stable in 20% for several weeks at 0C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
the purified recombinant His-tagged enzyme in stable without precipitation for more than 1 year in 50% glycerol
O41078
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant protein
-
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity chromatography, the protein quickly precipitates at concentration higher than 2 mg/ml
O41078
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
ORF A596R, DNA and amino acid sequence determination and analysis, expression of the His6-tagged enzyme in Escherichia coli strain DH5MCR, phylogenetic analysis
O41078
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E138A
-
no enzymic activity, no change in overall structure compared to wild-type
E138A
-
site-directed mutagenesis, inactive mutant, dTTP is bound to the active site of E138A, the region between Val120 and His125 is formed in a new conformation, the C-terminal fold is disordered
E138D
-
site-directed mutagenesis, the mutant enzyme shows a 140fold reduction in kcat and altered dTTP inhibition compared to the wild-type enzyme
E138Q
-
no enzymic activity, no change in overall structure compared to wild-type
H121A
-
site-directed mutagenesis, inactive mutant, dTTP is bound to the active site of E138A, the region between Val120 and His125 is formed in a new conformation, the C-terminal fold is disordered
R115A
-
no enzymic activity, no change in overall structure compared to wild-type
R115Q
-
site-directed mutagenesis, inactive mutant
S111C
-
site-directed mutagenesis, inactive mutant
S111T
-
site-directed mutagenesis, the mutant enzyme shows a 30fold reduction in kcat and altered dTTP inhibition compared to the wild-type enzyme, modeling of the active site of the S111T enzyme, overview
V122G
-
site-directed mutagenesis, inactive mutant
E138A
Escherichia coli K12
-
no enzymic activity, no change in overall structure compared to wild-type
-
E138Q
Escherichia coli K12
-
no enzymic activity, no change in overall structure compared to wild-type
-
R115A
Escherichia coli K12
-
no enzymic activity, no change in overall structure compared to wild-type
-