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Information on EC 3.5.4.5 - cytidine deaminase and Organism(s) Escherichia coli and UniProt Accession P0ABF6

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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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This record set is specific for:
Escherichia coli
UNIPROT: P0ABF6
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The taxonomic range for the selected organisms is: Escherichia coli
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, yeast cytidine deaminase, cytidine aminohydrolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
activation-induced cytidine deaminase
-
-
-
-
AICDA
-
-
-
-
Cytidine aminohydrolase
-
-
-
-
cytosine nucleoside deaminase
-
-
-
-
DCD
-
-
-
-
dCDA
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cytidine + H2O = uridine + NH3
show the reaction diagram
quantum chemical study on mechanism, the extra water molecule from solvent may support catalysis. Proposal of catalytic cycle
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Deamination
-
-
-
-
amidine hydrolysis
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -, -, -
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
-
9025-06-3
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1-beta-D-arabinofuranosylcytosine + H2O
?
show the reaction diagram
-
-
-
-
?
2'-deoxycytidine + H2O
2'-deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
2'-fluoro-2'-deoxy-5-iodocytosine arabinoside + H2O
?
show the reaction diagram
-
-
-
-
?
2'-fluoro-2'-deoxycytidine + H2O
2'-fluoro-2'-deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
2'-O-methylcytidine + H2O
?
show the reaction diagram
-
-
-
-
?
2'-thio-cytidine + H2O
2'-thiouridine + NH3
show the reaction diagram
-
-
-
-
?
5'-fluoro-5'-deoxycytidine + H2O
5'-fluoro-5'-deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
5'-methyl-2'-deoxycytidine + H2O
5'-methyl-2-deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
5,6-dihydrocytidine + H2O
5,6-dihydrouridine + NH3
show the reaction diagram
-
-
-
-
?
5-aza-2'-deoxycytidine + H2O
5-aza-2'-deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
5-azacytidine + H2O
5-azauridine + NH3
show the reaction diagram
-
-
-
-
?
5-methylcytidine + H2O
5-methyluridine + NH3
show the reaction diagram
-
-
-
-
?
5-methyldeoxycytidine + H2O
?
show the reaction diagram
-
-
-
-
?
cytosine + H2O
?
show the reaction diagram
-
-
-
-
?
cytosine arabinoside + H2O
uridine arabinoside + NH3
show the reaction diagram
-
-
-
-
?
cytosine deoxyriboside + H2O
?
show the reaction diagram
-
-
-
-
?
deoxycytidine + H2O
deoxyuridine + NH3
show the reaction diagram
-
-
-
-
?
N4-methylcytidine + H2O
uridine + methylamine
show the reaction diagram
-
-
-
-
r
additional information
?
-
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
1 mM, activity 101%
Mn2+
-
10 mM, activity 106%
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-(beta-D-ribofuranosyl)-2-pyrimidone
-
-
1-(beta-D-ribofuranosyl)-dihydropyrimidine-2-one
-
-
1-methyladenosine
-
competitive inhibition
3,4,5,6,tetrahydrozebularine
-
-
3,4,5,6-Tetrahydrouridine
3,4-dihydrouridine
-
-
3,4-dihydrozebularine
-
-
5,6-Dihydrouridine
5-(Chloromercuri)cytidine
-
-
5-bromodeoxyuridine
5-fluoropyrimidin-2-one ribonucleoside
-
-
5-fluorozebularine
-
-
acetone
-
-
adenosine
deoxyadenosine
deoxyguanosine
deoxyuridine
dihydrothymidine
-
competitive inhibition
guanosine
mercaptoethanol
-
-
Mersalyl acid
-
-
phosphapyrimidine
-
-
phosphapyrimidine nucleoside
-
-
thioglycolic acid
-
0.7 mM 88% relative activity, complete inhibition at 7 mM
thymidine
thymine riboside
uracil arabinoside
-
4.0 mM, 48% inhibition
Urea
-
above 2 M, reversible inactivation
uridine
Zn2+
-
above 10 mM
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytidine
-
-
EDTA
-
10 mM, activity 108%
iodoacetic acid
-
0.10 mM, activity 105%
N-ethylmaleimide
-
0.10-0.20 mM, activity 114%
p-chloromercuribenzoate
-
0.105 mM, activity 112%
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.058
2'-deoxycytidine
-
-
0.07
2'-fluoro-2'-deoxy-5-iodocytosine arabinoside
-
-
0.087
5'-fluoro-5'-deoxycytidine
-
-
0.11 - 0.113
5,6-Dihydrocytidine
2.27
5-azacytidine
-
-
0.95 - 1.25
5-methylcytidine
0.06
5-Methyldeoxycytidine
-
-
0.0167 - 6.6
cytidine
0.089
cytosine
-
-
0.22 - 0.26
cytosine arabinoside
0.089
cytosine deoxyriboside
-
-
0.06 - 8.53
deoxycytidine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23.9
-
amplified gene, 5'-methylcytidine as substrate
31.8
-
amplified gene, ara-cytidine as substrate
3558
-
amplified gene
4
-
amplified gene, 5'-aza-2'-deoxycytidine as substrate
4.9
-
amplified gene, 2'-thiocytidine as substrate
43
-
amplified gene, cytidine as substrate
47.9
-
amplified gene, 5'-methyl-2'-deoxycytidine as substrate
68.4
-
amplified gene, 2'-fluoro-2'-deoxycytidine as substrate
97.6
-
amplified gene, deoxycytidine as substrate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.9 - 7.35
-
deamination rate 50% higher in phosphate buffers with pH 7.25-8.7
6 - 7.5
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.8 - 7.5
-
-
6.5 - 10.7
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
Uniprot
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31540
-
2 * 31540
32000
-
2 * 32000, homodimer, SDS-PAGE
33000
-
2 * 33000, SDS-PAGE
34000
-
2 * 34000, SDS-PAGE
35000
-
2 * 35000, SDS-PAGE
54000
56000
57000
62000
-
gel filtration, native enzyme
66000
-
gel filtration, SDS-PAGE
73000
-
gel filtration, nonhomogenous preparation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
monomer
-
1 * 54000
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
reasonably stable in this range
209660
6.5 - 10.7
-
irreversible loss of activity at pH values below 4
209648
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
-
relatively labile to thermal treatment, complete inactivation by incubation for 30 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
very unstable
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 50 mM phosphate buffer pH7.5 after 1 month pure enzyme retains 70% original activity
-
-20°C, 50 mM Tris-HCl, pH7.5, after 1 month pure enzyme retains 80% original activity
-
-20°C, preparations kept 4 months retains original activity
-
4°C, 50 mM Tris-HCl, pH 7.5, pure enzyme retains 63% original activity after 2 weeks
-
4°C, in presence of 5 mM mercaptoethanol, reasonably stable, retains 47% of its activity after 3 months, freezing inactivates the enzyme, less than 30% recovery of activity after 1 freeze-thaw cycle
-
4°C, reasonably stable, retains 55% of its activity after 3 weeks
-
4°C, stable for several days, may be kept for months without significant loss of activity if frozen
-
4°C,50 mM phosphate buffer pH 7.5, pure enzyme retains 13% original activity after 2 weeks
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cdd gene cloned and amplified with pTK148, cloning vector pBR322, enzyme overexpression in Escherichia coli C600
-
SO268 harboring plasmid pSO143 containing the B. subtilis cytidine deaminase gene
-
yielding plasmid pAA5970
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ipata, P.L.; Cercignani, G.
Cytosine and cytidine deaminase from yeast
Methods Enzymol.
51
394-401
1978
Saccharomyces cerevisiae, Escherichia coli, Mus musculus, Mus musculus BALB/c
Manually annotated by BRENDA team
Taketo, A.; Kuno, S.
Internal localization of nucleoside-catabolic enzymes in Escherichia coli
J. Biochem.
72
1557-1563
1972
Escherichia coli
Manually annotated by BRENDA team
Wang, T.P.; Sable, H.Z.; Lampen, J.O.
Enzymatic deamination of cytosine nucleosides
J. Biol. Chem.
184
17-28
1950
Bos taurus, Saccharomyces cerevisiae, Oryctolagus cuniculus, Escherichia coli, Mus musculus, Escherichia coli 15 (ATCC 9723), Mus musculus BALB/c
Manually annotated by BRENDA team
Cohen, R.M.; Wolfenden, R.
Cytidine deaminase from Escherichia coli. Purification, properties and inhibition by the potential transition state analog 3,4,5,6-tetrahydrouridine
J. Biol. Chem.
246
7561-7565
1971
Escherichia coli, Escherichia coli B / ATCC 11303, Homo sapiens, Mus musculus, Mus musculus BALB/c, Ovis aries, Saccharomyces cerevisiae
Manually annotated by BRENDA team
Betts, L.; Xiang, S.; Short, S.A.; Wolfenden, R.; Carter, C.W.jr.
Cytidine deaminase.The 2.3 A crystal structure of an enzyme: Transition-state analog complex
J. Mol. Biol.
235
635-656
1994
Escherichia coli
Manually annotated by BRENDA team
Hosono, H.; Kuno, S.
The purification and properties of cytidine deaminase from Escherichia coli
J. Biochem.
74
797-803
1973
Bacillus cereus, Saccharomyces cerevisiae, Escherichia coli, Ovis aries, Mus musculus, Mus musculus BALB/c, Escherichia coli Y-70-272
Manually annotated by BRENDA team
Wentworth, D.F.; Wolfenden, R.
On the interaction of 3,4,5,6-tetrahydrouridine with human liver cytidine deaminase
Biochemistry
14
5099-5105
1975
Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Evans, B.E.; Mitchell, G.N.; Wolfenden, R.
The action of bacterial cytidine deaminase on 5,6-dihydrocytidine
Biochemistry
14
621-624
1975
Escherichia coli
Manually annotated by BRENDA team
Wentworth, D.F.; Wolfenden, R.
Cytidine deaminases (from Escherichia coli and human liver)
Methods Enzymol.
51
401-407
1978
Canis lupus familiaris, Cavia porcellus, Columba sp., Escherichia coli, Escherichia coli B / ATCC 11303, Felis catus domesticus, Homo sapiens, Macaca mulatta, Mus musculus, Mus musculus BALB/c, Oryctolagus cuniculus, Rana sp., Rattus norvegicus, Sus scrofa
Manually annotated by BRENDA team
Ashley, G.W.; Bartlett, P.A.
A phosphorus-containing pyrimidine analog as a potent inhibitor of cytidine deaminase
Biochem. Biophys. Res. Commun.
108
1467-1474
1982
Escherichia coli, Escherichia coli B / ATCC 11303
Manually annotated by BRENDA team
Ashley, G.W.; Bartlett, P.A.
Purification and properties of cytidine deaminase from escherichia coli
J. Biol. Chem.
259
13615-13620
1984
Escherichia coli, Escherichia coli B / ATCC 11303, Homo sapiens, Mus musculus, Mus musculus BALB/c, Ovis aries, Saccharomyces cerevisiae, Zea mays
Manually annotated by BRENDA team
Ashley, G.W.; Bartlett, P.A.
Inhibition of Escherichia coli cytidine deaminase by a phosphopyrimidine nucleoside
J. Biol. Chem.
259
13621-13627
1984
Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Vita, A.; Amici, A.; Cacciamani, T.; Lanciotti, M.; Magni, G.
Cytidine deaminase from Escherichia coli B. Purification and enzymatic and molecular properties
Biochemistry
24
6020-6024
1985
Escherichia coli, Escherichia coli B / ATCC 11303
Manually annotated by BRENDA team
Holy, A.; Ludzisa, A.; Votruba, I.; Sediva, K.
Preparation of analogues of cytosine and 2-pyrimidinone nucleosides and their effect on bacterial (Escherichia coli A19) cytidine aminohydrolase
Collect. Czech. Chem. Commun.
50
393-417
1985
Saccharomyces cerevisiae, Escherichia coli, Macaca mulatta, Mus musculus, Mus musculus BALB/c, Escherichia coli A19
-
Manually annotated by BRENDA team
Vita, A.; Amici, A.; Lanciotti, M.; Cacciamani, T.; Magni, G.
Further properties of cytidine deaminase and uridine phosphorylase from E. coli B
Ital. J. Biochem.
35
145A-147A
1986
Escherichia coli, Escherichia coli B / ATCC 11303
-
Manually annotated by BRENDA team
Nygaard, P.
On the role of cytidine deaminase in cellular metabolism
Adv. Exp. Med. Biol.
195B
415-420
1986
Saccharomyces cerevisiae, Escherichia coli, Ovis aries, Homo sapiens, Mus musculus, no activity in Lactobacillus sp., no activity in Moraxella sp., no activity in Pseudomonas sp., Salmonella enterica subsp. enterica serovar Typhimurium, Zea mays, Mus musculus BALB/c
Manually annotated by BRENDA team
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
Cacciamani, T.; Vita, A.; Cristalli, G.; Vincenzetti, S.; Natalini, P.; Ruggieri, S.; Amici, A.; Magni, G.
Purification of human cytidine deaminase: Molecular and enzymatic characterization and inhibition by synthetic pyrimidine analogs
Arch. Biochem. Biophys.
290
285-292
1991
Canis lupus familiaris, Gallus gallus, Escherichia coli, Homo sapiens, Mus musculus, no activity in Lactobacillus sp., no activity in Moraxella sp., no activity in Pseudomonas sp., Mus musculus BALB/c
Manually annotated by BRENDA team
Smith, A.A.; Carlow, D.C.; Wolfenden, R.; Short, S.A.
Mutations affecting transition-state stabilization by residues coordinating zinc at the active site of cytidine deaminase
Biochemistry
33
6468-6474
1994
Escherichia coli
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
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
Matsubara, T.; Ishikura, M.; Aida, M.
A quantum chemical study of the catalysis for cytidine deaminase: contribution of the extra water molecule
J. Chem. Inf. Model.
46
1276-1285
2006
Escherichia coli (P0ABF6)
Manually annotated by BRENDA team