Information on EC 3.5.4.13 - dCTP deaminase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.5.4.13
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RECOMMENDED NAME
GeneOntology No.
dCTP deaminase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
dCTP + H2O = dUTP + NH3
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Deamination
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
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pyrimidine deoxyribonucleotides de novo biosynthesis II
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pyrimidine metabolism
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Pyrimidine metabolism
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superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)
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SYSTEMATIC NAME
IUBMB Comments
dCTP aminohydrolase
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CAS REGISTRY NUMBER
COMMENTARY hide
37289-18-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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UniProt
Manually annotated by BRENDA team
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UniProt
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
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Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-methyl-dCMP + H2O
5-methyl-dCyd
show the reaction diagram
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-
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?
5-methyl-dCTP + H2O
5-methyl-dTTP
show the reaction diagram
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-
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?
5-methyl-dCTP + H2O
dTTP + NH3
show the reaction diagram
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-
-
?
dCMP + H2O
dUMP + NH3
show the reaction diagram
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dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
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?
dCTP + H2O
dUTP + NH3
show the reaction diagram
ddCTP + H2O
ddUTP + NH3
show the reaction diagram
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deamination at the same rate as dCTP
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?
dUTP + 2 H2O
dUMP + 2 phosphate
show the reaction diagram
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?
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
dCMP + H2O
dUMP + NH3
show the reaction diagram
O41078
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dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
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?
dCTP + H2O
dUTP + NH3
show the reaction diagram
additional information
?
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bifunctionality of enzyme avoids release of toxic UTP within cells
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
can partially substitute for Mg2+
Zn2+
the enzyme contains a zinc binding site, but shows less than 6% of maximal activity with Zn2+ as divalent cation
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
H4dUMP
inhibits both dCTP and dCMP deaminase activities
p-hydroxymercuribenzoate
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PDRP
inhibits both dCTP and dCMP deaminase activities
phosphate
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.76
dCMP
pH 9.5, 42C, in presence of 0.1 mM dCTP
0.05 - 0.64
dCTP
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
24.9
dCMP
Paramecium bursaria Chlorella virus 1
O41078
pH 9.5, 42C, in presence of 0.1 mM dCTP
1.24 - 5.7
dCTP
additional information
additional information
Escherichia coli
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1
dTTP
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pH 6.8, 25C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.7 - 6.9
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
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 hide
LITERATURE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 23400, deduced from gene sequence, x * 23300, mass spectrometry
hexamer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complex with dTTP, hanging drop vapor diffusion method, using 200 mM lithium citrate and 20% (w/v) polyethylene glycol 4000
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
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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
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wild-type and mutant E138A, in complex with Mg2+ and dUTP, and dCTP
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apoenzyme in complex with dCTP and with dUTP
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ethylene glycol
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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
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation and DE-52 anion-exchange column chromatography
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity chromatography, the protein quickly precipitates at concentration higher than 2 mg/ml
recombinant protein
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
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ORF A596R, DNA and amino acid sequence determination and analysis, expression of the His6-tagged enzyme in Escherichia coli strain DH5MCR, phylogenetic analysis
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E138D
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site-directed mutagenesis, the mutant enzyme shows a 140fold reduction in kcat and altered dTTP inhibition compared to the wild-type enzyme
E138Q
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no enzymic activity, no change in overall structure compared to wild-type
H121A
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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
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no enzymic activity, no change in overall structure compared to wild-type
R115Q
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site-directed mutagenesis, inactive mutant
S111C
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site-directed mutagenesis, inactive mutant
S111T
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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
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site-directed mutagenesis, inactive mutant
E138A
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no enzymic activity, no change in overall structure compared to wild-type
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E138Q
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no enzymic activity, no change in overall structure compared to wild-type
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R115A
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no enzymic activity, no change in overall structure compared to wild-type
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