BRENDA - Enzyme Database

Crystal structures of Streptococcus mutans 2-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+

Hou, H.F.; Liang, Y.H.; Li, L.F.; Su, X.D.; Dong, Y.H.; J. Mol. Biol. 377, 220-231 (2008)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
3.5.4.12
dCTP
an allosteric activator, in complex with Mg2+
Streptococcus mutans
Cloned(Commentary)
EC Number
Commentary
Organism
3.5.4.12
overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Streptococcus mutans
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.5.4.12
dCMP deaminase in complex with dCTP and an intermediate analogue, X-ray diffraction structure determination and analysis at 1.66-3.0 A resolution, the crystal structure of the free-state enzyme is determined by the zinc multiwavelength anomalous dispersion, MAD, method
Streptococcus mutans
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.12
dTTP
an allosteric inhibitor
Streptococcus mutans
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.12
Ca2+
can partially substitute for Mg2+, 50% of the activity with Mg2+
Streptococcus mutans
3.5.4.12
Mg2+
required for activity, in complex with activator dCTP, can be substituted by Ca2+ or Mn2+, but not by Zn2+, Co2+, Ni2+, and Cu2+
Streptococcus mutans
3.5.4.12
Mn2+
can partially substitute for Mg2+, 26% of the activity with Mg2+
Streptococcus mutans
3.5.4.12
additional information
Co2+, Ni2+, and Cu2+ cannot substitute for Mg2+
Streptococcus mutans
3.5.4.12
Zn2+
two conserved motifs are involved in the binding of Zn2+, Zn2+ cannot substitute for Mg2+
Streptococcus mutans
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
Streptococcus mutans
the regulation signal is transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate binding pocket is involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex, allosteric mechanism for enzyme regulation, regulator binding structure, overview
dUMP + NH3
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.5.4.12
Streptococcus mutans
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
3.5.4.12
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
Streptococcus mutans
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
the regulation signal is transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate binding pocket is involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex, allosteric mechanism for enzyme regulation, regulator binding structure, overview
688405
Streptococcus mutans
dUMP + NH3
-
-
-
?
3.5.4.12
dCMP + H2O
a conserved motif, G43YNG46, is involved in the binding of dCTP, N-terminal Arg4, a key residue located between two monomers, binds strongly to the gamma phosphate group of dCTP, active site structure and substrate binding, overview
688405
Streptococcus mutans
dUMP + NH3
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
3.5.4.12
hexamer
homohexamer, subunits adopt a three-layer alpha/beta/alpha sandwich fold
Streptococcus mutans
3.5.4.12
More
monomeric and quarternary structure analysis, overview
Streptococcus mutans
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
3.5.4.12
30
-
assay at
Streptococcus mutans
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
3.5.4.12
8
-
assay at
Streptococcus mutans
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
3.5.4.12
dCTP
an allosteric activator, in complex with Mg2+
Streptococcus mutans
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.12
overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Streptococcus mutans
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.5.4.12
dCMP deaminase in complex with dCTP and an intermediate analogue, X-ray diffraction structure determination and analysis at 1.66-3.0 A resolution, the crystal structure of the free-state enzyme is determined by the zinc multiwavelength anomalous dispersion, MAD, method
Streptococcus mutans
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.12
dTTP
an allosteric inhibitor
Streptococcus mutans
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.12
Ca2+
can partially substitute for Mg2+, 50% of the activity with Mg2+
Streptococcus mutans
3.5.4.12
Mg2+
required for activity, in complex with activator dCTP, can be substituted by Ca2+ or Mn2+, but not by Zn2+, Co2+, Ni2+, and Cu2+
Streptococcus mutans
3.5.4.12
Mn2+
can partially substitute for Mg2+, 26% of the activity with Mg2+
Streptococcus mutans
3.5.4.12
additional information
Co2+, Ni2+, and Cu2+ cannot substitute for Mg2+
Streptococcus mutans
3.5.4.12
Zn2+
two conserved motifs are involved in the binding of Zn2+, Zn2+ cannot substitute for Mg2+
Streptococcus mutans
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
Streptococcus mutans
the regulation signal is transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate binding pocket is involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex, allosteric mechanism for enzyme regulation, regulator binding structure, overview
dUMP + NH3
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.12
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
Streptococcus mutans
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
the regulation signal is transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate binding pocket is involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex, allosteric mechanism for enzyme regulation, regulator binding structure, overview
688405
Streptococcus mutans
dUMP + NH3
-
-
-
?
3.5.4.12
dCMP + H2O
a conserved motif, G43YNG46, is involved in the binding of dCTP, N-terminal Arg4, a key residue located between two monomers, binds strongly to the gamma phosphate group of dCTP, active site structure and substrate binding, overview
688405
Streptococcus mutans
dUMP + NH3
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
3.5.4.12
hexamer
homohexamer, subunits adopt a three-layer alpha/beta/alpha sandwich fold
Streptococcus mutans
3.5.4.12
More
monomeric and quarternary structure analysis, overview
Streptococcus mutans
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
3.5.4.12
30
-
assay at
Streptococcus mutans
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
3.5.4.12
8
-
assay at
Streptococcus mutans