BRENDA - Enzyme Database

Three-dimensional structure of the R115E mutant of T4-bacteriophage 2-deoxycytidylate deaminase

Almog, R.; Maley, F.; Maley, G.F.; Maccoll, R.; Van Roey, P.; Biochemistry 43, 13715-13723 (2004)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
3.5.4.12
deoxycytidine 5'-triphosphate
allosteric feedback regulation of the enzyme by products of the metabolic pathway, allosteric regulation involved residues 112 and 115
Escherichia virus T4
Application
EC Number
Application
Commentary
Organism
3.5.4.12
medicine
the enzyme is a major target for cancer chemotherapy
Escherichia virus T4
Cloned(Commentary)
EC Number
Commentary
Organism
3.5.4.12
expression of mutant R115E in Escherichia coli
Escherichia virus T4
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.5.4.12
purified mutant R115E free or in complex with active site binding inhibitor pyrimidin-2-one deoxyribotide, the mutant R115E is dimeric in solution, while hexameric in crystals, hanging drop vapour diffusion method, 0.28 mM mutant R115E protein in 20 mM phosphate, pH 7.2, 0.38 mM inhibitor, and 30 mM DTT, is mixed with an equal volume of reservoir solution containing 1.3 M ammonium sulfate, 0.1 M sodium citrate, pH 6.0, and 10 mM DTT, 22C, 3 weeks, X-ray diffraction structure determination and analysis at 2.2 A resolution
Escherichia virus T4
Engineering
EC Number
Amino acid exchange
Commentary
Organism
3.5.4.12
R115E
site-directed mutagenesis, quarternary structure analysis
Escherichia virus T4
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.12
deoxythymidine 5'-triphosphate
allosteric feedback regulation of the enzyme by products of the metabolic pathway, allosteric regulation involved residues 112 and 115
Escherichia virus T4
3.5.4.12
pyrimidin-2-one deoxyribotide
active site binding structure, overview
Escherichia virus T4
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.12
Zn2+
the enzyme shows a zinc ion-based reaction mechanism, binding structure and coordinating residues, two zinc ions per subunit, the first is coordinated by His104, Cys132, and Cys135, the second by Cys19, Cys49, His94, and Glu102, overview
Escherichia virus T4
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.5.4.12
dCMP + H2O
Escherichia virus T4
the enzyme is the major supplier of substrate for the thymidylate synthase important in DNA synthesis
dUMP + NH3
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.5.4.12
Escherichia virus T4
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
3.5.4.12
recombinant mutant R115E from Escherichia coli
Escherichia virus T4
Reaction
EC Number
Reaction
Commentary
Organism
3.5.4.12
dCMP + H2O = dUMP + NH3
zinc ion-based reaction mechanism, substrate binding structure
Escherichia virus T4
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.4.12
dCMP + H2O
-
667587
Escherichia virus T4
dUMP + NH3
-
-
-
?
3.5.4.12
dCMP + H2O
the enzyme is the major supplier of substrate for the thymidylate synthase important in DNA synthesis
667587
Escherichia virus T4
dUMP + NH3
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
3.5.4.12
dimer
the mutant R115E is dimeric in solution, while hexameric in crystals, quarternary structure analysis
Escherichia virus T4
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
3.5.4.12
deoxycytidine 5'-triphosphate
allosteric feedback regulation of the enzyme by products of the metabolic pathway, allosteric regulation involved residues 112 and 115
Escherichia virus T4
Application (protein specific)
EC Number
Application
Commentary
Organism
3.5.4.12
medicine
the enzyme is a major target for cancer chemotherapy
Escherichia virus T4
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.12
expression of mutant R115E in Escherichia coli
Escherichia virus T4
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.5.4.12
purified mutant R115E free or in complex with active site binding inhibitor pyrimidin-2-one deoxyribotide, the mutant R115E is dimeric in solution, while hexameric in crystals, hanging drop vapour diffusion method, 0.28 mM mutant R115E protein in 20 mM phosphate, pH 7.2, 0.38 mM inhibitor, and 30 mM DTT, is mixed with an equal volume of reservoir solution containing 1.3 M ammonium sulfate, 0.1 M sodium citrate, pH 6.0, and 10 mM DTT, 22C, 3 weeks, X-ray diffraction structure determination and analysis at 2.2 A resolution
Escherichia virus T4
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
3.5.4.12
R115E
site-directed mutagenesis, quarternary structure analysis
Escherichia virus T4
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.12
deoxythymidine 5'-triphosphate
allosteric feedback regulation of the enzyme by products of the metabolic pathway, allosteric regulation involved residues 112 and 115
Escherichia virus T4
3.5.4.12
pyrimidin-2-one deoxyribotide
active site binding structure, overview
Escherichia virus T4
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.12
Zn2+
the enzyme shows a zinc ion-based reaction mechanism, binding structure and coordinating residues, two zinc ions per subunit, the first is coordinated by His104, Cys132, and Cys135, the second by Cys19, Cys49, His94, and Glu102, overview
Escherichia virus T4
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.5.4.12
dCMP + H2O
Escherichia virus T4
the enzyme is the major supplier of substrate for the thymidylate synthase important in DNA synthesis
dUMP + NH3
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.12
recombinant mutant R115E from Escherichia coli
Escherichia virus T4
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.4.12
dCMP + H2O
-
667587
Escherichia virus T4
dUMP + NH3
-
-
-
?
3.5.4.12
dCMP + H2O
the enzyme is the major supplier of substrate for the thymidylate synthase important in DNA synthesis
667587
Escherichia virus T4
dUMP + NH3
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
3.5.4.12
dimer
the mutant R115E is dimeric in solution, while hexameric in crystals, quarternary structure analysis
Escherichia virus T4