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The 1.48 A resolution crystal structure of the homotetrameric cytidine deaminase from mouse

Teh, A.H.; Kimura, M.; Yamamoto, M.; Tanaka, N.; Yamaguchi, I.; Kumasaka, T.; Biochemistry 45, 7825-7833 (2006)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
3.5.4.5
enzyme expression in Escherichia coli strain BL21
Mus musculus
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.5.4.5
in complex with tetrahydrouridine, 3-deazauridine, or cytidine. Two alternate conformations of R68 influence zinc-product interaction; purified recombinant CDA complexed with either tetrahydrouridine, 3-deazauridine, or cytidine, hanging drop vapor diffusion technique, 25°C, protein solution, containing 10-15 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 1 mM DTT, and 5 mM ligand, is mixed with crystallization solution containing 2.0 M ammonium sulfate and 0.1 M Tris-HCl, pH 8.5, crystals appear after a few hours or several days, respectively, X-ray diffraction structure determination and analysis at 1.48-2.36 A resolutions, molecular replacement
Mus musculus
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.5
3-deazauridine
-
Mus musculus
3.5.4.5
tetrahydrouridine
-
Mus musculus
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.5
Zn2+
catalytic ion, coordinated by C65, C99, and C102; dependent on
Mus musculus
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.5.4.5
2'-deoxycytidine + H2O
Mus musculus
-
2'-deoxyuridine + NH3
-
-
?
3.5.4.5
cytidine + H2O
Mus musculus
-
uridine + NH3
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.5.4.5
Mus musculus
P56389
-
-
Purification (Commentary)
EC Number
Commentary
Organism
3.5.4.5
recombinant enzyme from Escherichia coli strain BL21 by two steps of anion exchange chromatography, and gel filtration
Mus musculus
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.4.5
2'-deoxycytidine + H2O
-
667736
Mus musculus
2'-deoxyuridine + NH3
-
-
-
?
3.5.4.5
cytidine + H2O
-
667736
Mus musculus
uridine + NH3
-
-
-
?
3.5.4.5
cytidine + H2O
cytidine is distinguished from uridine by its 4-NH2 group that acts as a hydrogen bond donor, the charge-neutralizing Arg68 of CDA exhibits two alternate conformations I and II, binding structure, overview
667736
Mus musculus
uridine + NH3
-
-
-
?
3.5.4.5
additional information
active site and substrate binding structure, overview
667736
Mus musculus
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
3.5.4.5
tetramer
homotetramer
Mus musculus
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.5
enzyme expression in Escherichia coli strain BL21
Mus musculus
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.5.4.5
in complex with tetrahydrouridine, 3-deazauridine, or cytidine. Two alternate conformations of R68 influence zinc-product interaction; purified recombinant CDA complexed with either tetrahydrouridine, 3-deazauridine, or cytidine, hanging drop vapor diffusion technique, 25°C, protein solution, containing 10-15 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 1 mM DTT, and 5 mM ligand, is mixed with crystallization solution containing 2.0 M ammonium sulfate and 0.1 M Tris-HCl, pH 8.5, crystals appear after a few hours or several days, respectively, X-ray diffraction structure determination and analysis at 1.48-2.36 A resolutions, molecular replacement
Mus musculus
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.4.5
3-deazauridine
-
Mus musculus
3.5.4.5
tetrahydrouridine
-
Mus musculus
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
3.5.4.5
Zn2+
catalytic ion, coordinated by C65, C99, and C102; dependent on
Mus musculus
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3.5.4.5
2'-deoxycytidine + H2O
Mus musculus
-
2'-deoxyuridine + NH3
-
-
?
3.5.4.5
cytidine + H2O
Mus musculus
-
uridine + NH3
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.4.5
recombinant enzyme from Escherichia coli strain BL21 by two steps of anion exchange chromatography, and gel filtration
Mus musculus
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.4.5
2'-deoxycytidine + H2O
-
667736
Mus musculus
2'-deoxyuridine + NH3
-
-
-
?
3.5.4.5
cytidine + H2O
-
667736
Mus musculus
uridine + NH3
-
-
-
?
3.5.4.5
cytidine + H2O
cytidine is distinguished from uridine by its 4-NH2 group that acts as a hydrogen bond donor, the charge-neutralizing Arg68 of CDA exhibits two alternate conformations I and II, binding structure, overview
667736
Mus musculus
uridine + NH3
-
-
-
?
3.5.4.5
additional information
active site and substrate binding structure, overview
667736
Mus musculus
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
3.5.4.5
tetramer
homotetramer
Mus musculus