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Information on EC 3.5.4.13 - dCTP deaminase
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3.5.4.13 dCTP deaminaseSpecify your search results
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- 3.5.4.13
- dttp
-
deamination
- thymidylate
- jannaschii
- uracil
- thymine
-
methanocaldococcus
-
bifunctionality
The enzyme appears in viruses and cellular organisms
Synonyms
dcd:dut, deoxycytidine triphosphate deaminase, dctp deaminase:dutpase, 5-methyl-dctp deaminase, dctp deaminase:deoxyuridine triphosphatase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5-methyl-dCTP deaminase
-
-
-
-
DCD:DUT
dcdB
dCTP deaminase
-
-
-
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deoxycytidine triphosphate deaminase
DCD:DUT
bifunctional enzyme with dCTP deaminase and dUTPase activities
DCD:DUT
bifunctional enzyme with dCTP deaminase and dUTPase activities
-
deoxycytidine triphosphate deaminase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dCTP + H2O = dUTP + NH3
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-
-
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dCTP + H2O = dUTP + NH3
mechanism of bifunctional enzyme activity and feedback inhibition by dTTP
dCTP + H2O = dUTP + NH3
reaction involves S111, A124, E138 and two water molecules
-
dCTP + H2O = dUTP + NH3
the mechanism for the deamination of dCTP involves the four residues Ser102, Arg106, Ala115 and Glu129, structure-function relationship of the bifunctional enzyme, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Deamination
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
dCTP aminohydrolase
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CAS REGISTRY NUMBER
COMMENTARY
37289-18-2
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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
dCMP + H2O
dUMP + NH3
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dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
-
?
ddCTP + H2O
ddUTP + NH3
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deamination at the same rate as dCTP
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?
dCTP + H2O
dUTP + NH3
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dUMP is required for dTMP synthesis via hydrolysis of UTP by dUTPase to dUMP
-
?
additional information
?
-
-
bifunctionality of enzyme avoids release of toxic UTP within cells
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?
additional information
?
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the enzyme is a bifunctional dCTP deaminase:dUTPase
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-
-
additional information
?
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the enzyme is a bifunctional dCTP deaminase:dUTPase
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-
-
additional information
?
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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
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-
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additional information
?
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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
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NATURAL SUBSTRATE
NATURAL 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
dCMP + H2O
dUMP + NH3
O41078
-
dUMP is a key intermediate in the synthesis of dTTP and subsequently of DNA synthesis
-
?
additional information
?
-
-
bifunctionality of enzyme avoids release of toxic UTP within cells
-
?
dCTP + H2O
dUTP + NH3
-
-
dUMP is required for dTMP synthesis via hydrolysis of UTP by dUTPase to dUMP
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Mg2+
Mn2+
Zn2+
the enzyme contains a zinc binding site, but shows less than 6% of maximal activity with Zn2+ as divalent cation
Mg2+
the enzyme depends on divalent cations, Mg2+ is preferred , but can partially be substituted by Ca2+, Ni2+, or Mn2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
H4dUMP
inhibits both dCTP and dCMP deaminase activities
PDRP
inhibits both dCTP and dCMP deaminase activities
dTTP
-
inhibits by increasing the kcat several fold, mutants S111T and E138D are less sensitive to dTTP, overview
dTTP
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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
the inhibitor has a regukatory function for the bifunctional enzyme, mechanism of regulation by conformational changes, overview
dTTP
inhibits dCMP deamination, feedback inhibition
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dCTP
activates dCMP deamination about 7fold at 0.005-0.1 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.76
dCMP
pH 9.5, 42°C, in presence of 0.1 mM dCTP
additional information
additional information
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for dUTP, Km-value in millimolar range
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additional information
additional information
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enzyme kinetics and equilibrium binding
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additional information
additional information
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steady-state kinetic analysis
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additional information
additional information
steady-state kinetic analysis
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
24.9
dCMP
pH 9.5, 42°C, in presence of 0.1 mM dCTP
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Ki 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
6.8
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
i.e. PBCV-1 , a chlorovirus from host Chlorella sp. strain NC64A
SwissProt
brenda
bifunctional enzyme dCTP deaminase-dUTP nucleotidohydrolase
SwissProt
brenda
bifunctional enzyme dCTP deaminase-dUTP nucleotidohydrolase
-
-
brenda
Show AA Sequence and Transmembrane Helices (8011 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)
Escherichia coli (strain K12)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
23300
-
x * 23400, deduced from gene sequence, x * 23300, mass spectrometry
23400
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x * 23400, deduced from gene sequence, x * 23300, mass spectrometry
82000
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gel filtration
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 23400, deduced from gene sequence, x * 23300, mass spectrometry
hexamer
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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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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E138A
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
-
no enzymic activity, no change in overall structure compared to wild-type
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
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
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
-50
-
stable for at least two months
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ethylene glycol
-
stable in 20% for several weeks at 0°C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
the purified recombinant His-tagged enzyme in stable without precipitation for more than 1 year in 50% glycerol
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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
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
ORF A596R, DNA and amino acid sequence determination and analysis, expression of the His6-tagged enzyme in Escherichia coli strain DH5MCR, phylogenetic analysis
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, R.Y.H.; Ehrlich, M.
5-Methyl-dCTP deaminase induced by bacteriophage XP-12
J. Virol.
42
42-48
1982
Xanthomonas oryzae
brenda
Neuhard, J.
dCTP Deaminase from Salmonella typhimurium
Methods Enzymol.
55
418-423
1978
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Beck, C.F.; Eisenhardt, A.R.; Neuhard, J.
Deoxycytidine triphosphate deaminase of Salmonella typhimurium
J. Biol. Chem.
250
609-616
1975
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Price, A.R.
Bacteriophage PBS2-induced deoxycytidine triphosphate deaminase in Bacillus subtilis
J. Virol.
14
1314-1317
1974
Bacillus subtilis
brenda
Tomita, F.; Takahashi, I.
A novel enzyme, dCTP deaminase, found in Bacillus subtilis infected with phage PBS1
Biochim. Biophys. Acta
179
18-27
1969
Bacillus subtilis
brenda
Wang, L.; Weiss, B.
Dcd (dCTP deaminase) gene of Escherichia coli: Mapping, cloning, sequencing, and identification as a locus of suppressors of lethal dut (dUTPase) mutations
J. Bacteriol.
174
5647-5653
1992
Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Speed, R.R.; Winkler, H.H.
Deamination of deoxycytidine nucleotides by the obligate intracytopplasmic bacterium Rickettsia prowazekii
J. Bacteriol.
173
4902-4903
1991
Escherichia coli, Rickettsia prowazekii, Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Weiss, B.; Wang, L.
De novo synthesis of thymidylate via deoxycytidine in dcd (dCTP deaminase) mutants of Escherichia coli
J. Bacteriol.
176
2194-2199
1994
Escherichia coli
brenda
Estevenon, A.M.; Kooistra, J.; Sicard, N.
An Escherichia coli strain deficient for both exonuclease V and deoxycytidine triphosphate deaminase shows enhanced sensitivity to ionizing radiation
Mol. Gen. Genet.
246
514-518
1995
Escherichia coli
brenda
Huffman, J.L.; Li, H.; White, R.H.; Tainer, J.A.
Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii
J. Mol. Biol.
331
885-896
2003
Methanocaldococcus jannaschii, Methanocaldococcus jannaschii (Q57872)
brenda
Bjornberg, O.; Neuhard, J.; Nyman, P.O.
A bifunctional dCTP deaminase-dUTP nucleotidohydrolase from the hyperthermophilic archaeon Methanocaldococcus jannaschii
J. Biol. Chem.
278
20667-20672
2003
Methanocaldococcus jannaschii
brenda
Johansson, E.; Fan?, M.; Bynck, J.H.; Neuhard, J.; Larsen, S.; Sigurskjold, B.W.; Christensen, U.; Willemoes, M.
Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes
J. Biol. Chem.
280
3051-3059
2005
Escherichia coli, Escherichia coli (P28248)
brenda
Thymark, M.; Johansson, E.; Larsen, S.; Willemoes, M.
Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase
Arch. Biochem. Biophys.
470
20-26
2008
Escherichia coli, Escherichia coli (P28248)
brenda
Johansson, E.; Thymark, M.; Bynck, J.H.; Fanoe, M.; Larsen, S.; Willemoes, M.
Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme
FEBS J.
274
4188-4198
2007
Escherichia coli, Escherichia coli (P28248)
brenda
Helt, S.S.; Thymark, M.; Harris, P.; Aagaard, C.; Dietrich, J.; Larsen, S.; Willemoes, M.
Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis
J. Mol. Biol.
376
554-569
2008
Mycobacterium tuberculosis, Mycobacterium tuberculosis (P9WP17), Mycobacterium tuberculosis H37Rv (P9WP17)
brenda
Zhang, Y.; Maley, F.; Maley, G.F.; Duncan, G.; Dunigan, D.D.; Van Etten, J.L.
Chloroviruses encode a bifunctional dCMP-dCTP deaminase that produces two key intermediates in dTTP formation
J. Virol.
81
7662-7671
2007
Paramecium bursaria Chlorella virus 1 (O41078), Paramecium bursaria Chlorella virus 1
brenda
Oehlenschlaeger, C.B.; L?vgreen, M.N.; Reinauer, E.; Lehtinen, E.; Pind, M.L.; Harris, P.; Martinussen, J.; Willemoes, M.
Bacillus halodurans strain C125 encodes and synthesizes enzymes from both known pathways to form dump directly from cytosine deoxyribonucleotides
Appl. Environ. Microbiol.
81
3395-3404
2015
Bacillus halodurans, Bacillus halodurans (Q9KFV3), Bacillus halodurans C-125 (Q9KFV3)
brenda
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