BRENDA - Enzyme Database
show all sequences of 3.2.2.8

New insight in to the mechanism of nucleoside hydrolases from crystal structure of the Escherichia coli YbeK protein bound to the reaction product

Muzzolini, L.; Versees, W.; Tornaghi, P.; Van Holsbeke, E.; Steyaert, J.; Degano, M.; Biochemistry 45, 773-782 (2006)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene ybeK, expression in strain W6
Escherichia coli K-12
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme in complex with D-ribose, hanging drop vapour diffusion method, 10 mg/ml protein in 10 mM Tris, pH 7.0, 25 mM NaCl, and 500 mM D-ribose, is mixed with an equal volume of precipitant solution containing 24% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 5.0, and 500 mM D-ribose, 20°C, 1 week, X-ray diffraction structure determination and analysis at 1.78 A resolution
Escherichia coli K-12
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.083
-
uridine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.18
-
4-nitrophenyl ribopyranoside
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.239
-
Inosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.363
-
guanosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.524
-
cytidine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.648
-
adenosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Escherichia coli K-12
the enzyme is required for recycling of nitrogenous bases
?
-
-
-
N-ribosylpurine + H2O
Escherichia coli K-12
-
purine + D-ribose
-
-
r
N-ribosylpyrimidine + H2O
Escherichia coli K-12
preferred substrate
pyrimidine + D-ribose
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli K-12
P33022
-
-
Purification (Commentary)
Commentary
Organism
recombinant enzyme from strain W6 by nickel chelate affinity chromatography and gel filtration
Escherichia coli K-12
Reaction
Reaction
Commentary
Organism
a pyrimidine nucleoside + H2O = D-ribose + a pyrimidine base
catalytic mechanism, active site structure, conformational transition between open and closed structure, product release mechanism
Escherichia coli K-12
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl ribopyranoside + H2O
-
664140
Escherichia coli K-12
4-nitrophenol + D-ribose
-
-
-
?
adenosine + H2O
-
664140
Escherichia coli K-12
adenine + D-ribose
-
-
-
?
cytidine + H2O
-
664140
Escherichia coli K-12
cytosine + D-ribose
-
-
-
?
guanosine + H2O
-
664140
Escherichia coli K-12
guanine + D-ribose
-
-
-
?
inosine + H2O
-
664140
Escherichia coli K-12
hypoxanthine + D-ribose
-
-
-
?
additional information
the enzyme is required for recycling of nitrogenous bases
664140
Escherichia coli K-12
?
-
-
-
-
N-ribosylpurine + H2O
-
664140
Escherichia coli K-12
purine + D-ribose
-
-
-
r
N-ribosylpyrimidine + H2O
preferred substrate
664140
Escherichia coli K-12
pyrimidine + D-ribose
-
-
-
r
uridine + H2O
-
664140
Escherichia coli K-12
uracil + D-ribose
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
determination of the quarternary structure
Escherichia coli K-12
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
35
-
assay at
Escherichia coli K-12
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0056
-
guanosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.0154
-
adenosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.043
-
Inosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
11.6
-
cytidine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
13.9
-
uridine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
39
-
4-nitrophenyl ribopyranoside
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Escherichia coli K-12
Cloned(Commentary) (protein specific)
Commentary
Organism
gene ybeK, expression in strain W6
Escherichia coli K-12
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme in complex with D-ribose, hanging drop vapour diffusion method, 10 mg/ml protein in 10 mM Tris, pH 7.0, 25 mM NaCl, and 500 mM D-ribose, is mixed with an equal volume of precipitant solution containing 24% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 5.0, and 500 mM D-ribose, 20°C, 1 week, X-ray diffraction structure determination and analysis at 1.78 A resolution
Escherichia coli K-12
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.083
-
uridine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.18
-
4-nitrophenyl ribopyranoside
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.239
-
Inosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.363
-
guanosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.524
-
cytidine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.648
-
adenosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Escherichia coli K-12
the enzyme is required for recycling of nitrogenous bases
?
-
-
-
N-ribosylpurine + H2O
Escherichia coli K-12
-
purine + D-ribose
-
-
r
N-ribosylpyrimidine + H2O
Escherichia coli K-12
preferred substrate
pyrimidine + D-ribose
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant enzyme from strain W6 by nickel chelate affinity chromatography and gel filtration
Escherichia coli K-12
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl ribopyranoside + H2O
-
664140
Escherichia coli K-12
4-nitrophenol + D-ribose
-
-
-
?
adenosine + H2O
-
664140
Escherichia coli K-12
adenine + D-ribose
-
-
-
?
cytidine + H2O
-
664140
Escherichia coli K-12
cytosine + D-ribose
-
-
-
?
guanosine + H2O
-
664140
Escherichia coli K-12
guanine + D-ribose
-
-
-
?
inosine + H2O
-
664140
Escherichia coli K-12
hypoxanthine + D-ribose
-
-
-
?
additional information
the enzyme is required for recycling of nitrogenous bases
664140
Escherichia coli K-12
?
-
-
-
-
N-ribosylpurine + H2O
-
664140
Escherichia coli K-12
purine + D-ribose
-
-
-
r
N-ribosylpyrimidine + H2O
preferred substrate
664140
Escherichia coli K-12
pyrimidine + D-ribose
-
-
-
r
uridine + H2O
-
664140
Escherichia coli K-12
uracil + D-ribose
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
determination of the quarternary structure
Escherichia coli K-12
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
35
-
assay at
Escherichia coli K-12
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0056
-
guanosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.0154
-
adenosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
0.043
-
Inosine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
11.6
-
cytidine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
13.9
-
uridine
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
39
-
4-nitrophenyl ribopyranoside
pH 7.0, 35°C, recombinant enzyme
Escherichia coli K-12
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Escherichia coli K-12
Other publictions for EC 3.2.2.8
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
751203
Lenz
Structural explanation for th ...
Escherichia coli
J. Comput. Aided Mol. Des.
32
1375-1388
2018
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1
1
1
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3
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751391
Fan
QM/MM and MM MD Simulations o ...
Escherichia coli
J. Phys. Chem. B
122
1121-1131
2018
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752168
Dalberto
-
Thermodynamics, functional an ...
Leishmania braziliensis
RSC Adv.
7
48861-48875
2017
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1
1
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5
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1
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1
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6
1
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5
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5
5
724342
Minici
New determinants in the cataly ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
Biochemistry
51
4590-4599
2012
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1
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726441
Porcelli
Thermal unfolding of nucleosid ...
Saccharolobus solfataricus
Protein Pept. Lett.
19
369-374
2012
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1
3
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716542
Jung
Arabidopsis nucleoside hydrola ...
Arabidopsis thaliana
Plant J.
65
703-711
2011
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1
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6
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6
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2
2
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707897
Garau
Active site plasticity reveale ...
Escherichia coli
BMC Struct. Biol.
10
14
2010
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1
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1
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1
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4
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1
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1
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1
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1
1
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700741
Jung
Uridine-ribohydrolase is a key ...
Arabidopsis thaliana
Plant Cell
21
876-891
2009
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1
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1
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6
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11
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1
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1
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8
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2
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1
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7
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1
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9
1
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8
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679803
Porcelli
Pyrimidine-specific ribonucleo ...
Saccharolobus solfataricus
FEBS J.
275
1900-1914
2008
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2
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1
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2
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1
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696258
Iovane
Structural basis for substrate ...
Escherichia coli
Biochemistry
47
4418-4426
2008
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1
10
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18
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1
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18
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10
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18
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18
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664140
Muzzolini
New insight in to the mechanis ...
Escherichia coli K-12
Biochemistry
45
773-782
2006
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1
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6
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3
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1
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1
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1
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1
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670166
Kim
Genes encoding ribonucleoside ...
Corynebacterium ammoniagenes
Microbiology
152
1169-1177
2006
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654131
Giabbai
Cloning, purification, crystal ...
Escherichia coli
Acta Crystallogr. Sect. D
D60
524-527
2004
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1
1
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1
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1
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1
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657373
Giabbai
Crystal structure to 1.7 ANG o ...
Escherichia coli
Structure
12
739-749
2004
-
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1
1
2
-
-
8
2
-
3
-
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4
-
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1
1
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7
1
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8
-
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1
-
1
2
-
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8
2
-
3
-
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1
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7
1
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8
-
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663495
Giabbai
Cloning, purification, crystal ...
Escherichia coli K-12
Acta Crystallogr. Sect. D
60
524-527
2004
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1
1
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2
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3
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1
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2
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4
2
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137114
Allam
-
Nature of enzymes that catalyz ...
Penicillium chrysogenum
Biochem. Syst. Ecol.
15
515-517
1987
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1
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1
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1
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1
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5
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1
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1
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1
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137115
Krenitsky
-
Purine salvage enzymes in man ...
Leishmania donovani
Adv. Exp. Med. Biol.
122
51-56
1980
-
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1
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1
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1
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7
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1
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1
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7
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137116
Koszalka
Nucleosidases from Leishmania ...
Leishmania donovani
J. Biol. Chem.
254
8185-8193
1979
-
-
-
-
-
-
7
6
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1
1
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1
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1
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1
1
1
10
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1
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1
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7
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6
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1
1
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1
-
1
1
1
10
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1
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1
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4168
Murray
-
Molecular weight estimations o ...
Pisum sativum
Phytochemistry
10
2645-2648
1971
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1
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1
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3
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1
1
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1
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3
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137117
Terada
Purification and properties of ...
Pseudomonas fluorescens
J. Biol. Chem.
242
5578-5585
1967
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16
9
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1
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2
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1
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1
2
16
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3
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5
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16
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9
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1
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1
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1
2
16
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3
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5
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