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Information on EC 3.5.4.5 - cytidine deaminase and Organism(s) Bacillus subtilis and UniProt Accession P19079

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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.4 In cyclic amidines
                3.5.4.5 cytidine deaminase
IUBMB Comments
Contains zinc. Catalyses the deamination of cytidine and 2'-deoxycytidine with similar efficiencies. The enzyme, which is widely distributed among organisms, is involved in salvage of both exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
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Bacillus subtilis
UNIPROT: P19079
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Word Map
The taxonomic range for the selected organisms is: Bacillus subtilis
The enzyme appears in selected viruses and cellular organisms
Synonyms
cytidine deaminase, activation-induced cytidine deaminase, aicda, deoxycytidine deaminase, cr deaminase, cyd deaminase, t-cda, cytosine nucleoside deaminase, cytidine aminohydrolase, yeast cytidine deaminase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
activation-induced cytidine deaminase
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-
-
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AICDA
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-
-
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Cytidine aminohydrolase
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-
-
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cytosine nucleoside deaminase
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-
-
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DCD
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-
-
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dCDA
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Deamination
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-
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amidine hydrolysis
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-
-
-
PATHWAY SOURCE
PATHWAYS
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-, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
cytidine/2'-deoxycytidine aminohydrolase
Contains zinc. Catalyses the deamination of cytidine and 2'-deoxycytidine with similar efficiencies. The enzyme, which is widely distributed among organisms, is involved in salvage of both exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
CAS REGISTRY NUMBER
COMMENTARY hide
37259-56-6
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9025-06-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
cytidine + H2O
uridine + NH3
show the reaction diagram
-
-
-
?
deoxycytidine + H2O
deoxyuridine + NH3
show the reaction diagram
-
-
-
?
cytidine + H2O
uridine + NH3
show the reaction diagram
-
-
-
-
?
deoxycytidine + H2O
deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
cytidine + H2O
uridine + NH3
show the reaction diagram
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zinc
wild-type enzyme and mutant enzymes R56A, R56Q and C53H/R56Q contain about 1 mol of zinc per subunit. Mutant enzyme R56D contains 0.2 mol of zinc per subunit
Zn2+
contains 4 Zn2+ per tetramer. The role of Zn2+ is to activate a water molecule and thereby generate a hydroxide ion
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-(beta-D-ribofuranosyl)-dihydropyrimidine-2-one
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3,4,5,6,tetrahydrozebularine
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3,4-dihydrouridine
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3,4-dihydrozebularine
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5-fluorozebularine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.14 - 0.267
cytidine
0.0075 - 0.236
deoxycytidine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.8 - 7.5
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-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12 - 66
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12°C: about 55% of maximal activity, 66°C: about 65% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.2
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chromatofocusing
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14000
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4 * 14000, deduced from cdd structural gene nucleotide sequence and mini-cell experiments
14800
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4 * 14800
56000
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calculated from Stokes radius
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of tetrameric cytidine deaminase at 2.0 A resolution, hanging drop vapour-diffusion method
hanging drop vapour diffusion method. R56A and R56Q crystallize in the same space group as the wild-type enzyme with two subunits in the asymmetric unit, whereas C53H/R56Q can not crystallize in this crystal form but is crystallized in another space group, P3(2)21, with a full tetramer in the asymmetric unit
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C53H
attempts to express and purify the mutant enzyme are unsuccessful
C53H/R56Q
mutant enzyme contains the same amount of zinc as the wild-type enzyme. Because of dissociation into its inactive subunits, it is impossible to determine the kinetic parameters for the mutant enzyme
R56A
mutant enzyme contains the same amount of zinc as the wild-type enzyme. Similar KM-value but decreased Vmax-value compared to wild-type enzyme
R56D
zinc-binding capacity of mutant enzyme is reduced
R56Q
mutant enzyme contains the same amount of zinc as the wild-type enzyme. Similar KM-value but decreased Vmax-value compared to wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
72
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30 min, irreversible denaturation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
irreversible denaturation after 30 min at 72°C
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression of wild-type enzyme and mutant enzymes R56A, R56Q and C53H/R56Q in Escherichia coli
cdd genes cloned and characterized
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kwon, T.K.; Lee, S.Y.; Kim, J.G.; Song, B.H.; Hong, S.D.
Purification and properties of Escherichia coli cytidine deaminase by amplification of the cdd gene
Mol. Cells
1
281-286
1991
Geobacillus stearothermophilus, Bacillus subtilis, Saccharomyces cerevisiae, Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium, Escherichia coli JF611
-
Manually annotated by BRENDA team
Vincenzetti, S.; Cambi, A.; Neuhard, J.; Garattini, E.; Vita, A.
Recombinant human cytidine deaminase: Expression, purification, and characterization
Protein Expr. Purif.
8
247-253
1996
Bacillus subtilis, Escherichia coli, Homo sapiens, Escherichia coli DH5-alpha
Manually annotated by BRENDA team
Vincenzetti, S.; Cambi, A.; Balducci, E.; Natalini, P.; Volpini, R.; Vita, A.
Human placenta cytidine deaminase: A zinc metalloprotein
Biochemistry
42
469-476
1997
Bacillus subtilis, Homo sapiens
Manually annotated by BRENDA team
Carlow, D.C.; Carter, C.W.; Mejlhede, N.; Neuhard, J.; Wolfenden, R.
Cytidine deaminases from B. subtilis and E. coli: Compensating effects of changing zinc coordination and quaternary structure
Biochemistry
38
12258-12265
1999
Bacillus subtilis, Escherichia coli, Homo sapiens, Escherichia coli SO268
Manually annotated by BRENDA team
Vincenzetti, S.; Cambi, A.; Neuhard, J.; Schnorr, K.; Grelloni, M.; Vita, A.
Cloning, expression, and purification of cytidine deaminase from Arabidopsis thaliana
Protein Expr. Purif.
15
8-15
1999
Arabidopsis thaliana, Bacillus subtilis, Gallus gallus, Escherichia coli, Haemophilus influenzae, Ovis aries, Mus musculus, Escherichia coli SO5201, Mus musculus BALB/c
Manually annotated by BRENDA team
Faivre-Nitschke, E.; Grienenberger, J.M.; Gualberto, J.M.
A prokaryotic-type cytidine deaminase from Arabidopsis thaliana gene expression and functional characterization
Eur. J. Biochem.
263
896-903
1999
Arabidopsis thaliana, Bacillus subtilis, Saccharomyces cerevisiae, Brugia pahangi, Caenorhabditis elegans, Escherichia coli, Haemophilus influenzae, Homo sapiens, Mycoplasma pneumoniae, Escherichia coli BL21(D3)
Manually annotated by BRENDA team
Johansson, E.; Mejlhede, N.; Neuhard, J.; Larsen, S.
Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution
Biochemistry
41
2563-2570
2002
Bacillus subtilis (P19079), Bacillus subtilis
Manually annotated by BRENDA team
Johansson, E.; Neuhard, J.; Willemoes, M.; Larsen, S.
Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase
Biochemistry
43
6020-6029
2004
Bacillus subtilis (P19079)
Manually annotated by BRENDA team
Cambi, A.; Vincenzetti, S.; De Sanctis, G.; Neuhard, J.; Natalini, P.; Vita, A.
Cytidine deaminase from two extremophilic bacteria: cloning, expression and comparison of their structural stability
Protein Eng.
14
807-813
2001
Bacillus subtilis, [Bacillus] caldolyticus (Q9R2S1), [Bacillus] caldolyticus, Sporosarcina psychrophila (Q9S3M0), Sporosarcina psychrophila
Manually annotated by BRENDA team