BRENDA - Enzyme Database
show all sequences of 3.2.2.8

Structural basis for substrate specificity in group I nucleoside hydrolases

Iovane, E.; Giabbai, B.; Muzzolini, L.; Matafora, V.; Fornili, A.; Minici, C.; Giannese, F.; Degano, M.; Biochemistry 47, 4418-4426 (2008)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli BL21(DE3) cells
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
hanging drop vapour diffusion method, using 100 mM Tris (pH 8.5), 200 mM NaCl, and 24% PEG 4000
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
Q227A
the mutation causes an increase of kcat for uridine and inosine
Escherichia coli
Q227F
the mutation causes an increase of kcat for uridine and inosine
Escherichia coli
Q227Y
the mutation has a strong, enhancing effect on the hydrolysis of inosine, and the catalytic efficiency for the purinic substrate is increased by a factor of 7.6
Escherichia coli
T223A
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T223F
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T223F/Q227Y
the mutant shows a 2fold increase in catalytic efficiency toward inosine
Escherichia coli
T223Y
the mutation does not affect the specificity of the enzyme toward inosine or uridine
Escherichia coli
T223Y/Q227Y
the mutant displays a catalytic efficiency toward inosine that is more than 50fold increased compared to that of wild type enzyme
Escherichia coli
T227A
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T227F
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.12
-
uridine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.31
-
uridine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.33
-
uridine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.57
-
uridine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.77
-
uridine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.06
-
uridine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.09
-
uridine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.13
-
uridine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.16
-
Inosine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.19
-
uridine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.77
-
Inosine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.93
-
Inosine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
2.14
-
Inosine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
2.34
-
Inosine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
3.29
-
Inosine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
4.31
-
Inosine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
4.42
-
Inosine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
5.3
-
Inosine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Ca2+
the substrate binds to the Ca2+-containing active site in the catalytic cavity at the C-terminal end of the core beta-sheet
Escherichia coli
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P33022
-
-
Purification (Commentary)
Commentary
Organism
Ni-NTA column chromatography and MonoQ column chromatography
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
inosine + H2O
poor substrate
696258
Escherichia coli
hypoxanthine + D-ribose
-
-
-
?
uridine + H2O
-
696258
Escherichia coli
uracil + D-ribose
-
-
-
?
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.035
-
Inosine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.086
-
Inosine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.109
-
Inosine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.125
-
Inosine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.18
-
Inosine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.182
-
Inosine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.382
-
Inosine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.593
-
Inosine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
3.62
-
Inosine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
5.4
-
uridine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
15.1
-
uridine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
18.8
-
uridine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
39.8
-
uridine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
44.3
-
uridine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
46.9
-
uridine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
52.5
-
uridine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
59.1
-
uridine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
72.9
-
uridine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli BL21(DE3) cells
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
hanging drop vapour diffusion method, using 100 mM Tris (pH 8.5), 200 mM NaCl, and 24% PEG 4000
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
Q227A
the mutation causes an increase of kcat for uridine and inosine
Escherichia coli
Q227F
the mutation causes an increase of kcat for uridine and inosine
Escherichia coli
Q227Y
the mutation has a strong, enhancing effect on the hydrolysis of inosine, and the catalytic efficiency for the purinic substrate is increased by a factor of 7.6
Escherichia coli
T223A
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T223F
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T223F/Q227Y
the mutant shows a 2fold increase in catalytic efficiency toward inosine
Escherichia coli
T223Y
the mutation does not affect the specificity of the enzyme toward inosine or uridine
Escherichia coli
T223Y/Q227Y
the mutant displays a catalytic efficiency toward inosine that is more than 50fold increased compared to that of wild type enzyme
Escherichia coli
T227A
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
T227F
the mutation does not improve significantly the catalytic efficiency of YeiK toward inosine
Escherichia coli
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.12
-
uridine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.31
-
uridine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.33
-
uridine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.57
-
uridine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.77
-
uridine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.06
-
uridine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.09
-
uridine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.13
-
uridine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.16
-
Inosine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.19
-
uridine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.77
-
Inosine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
1.93
-
Inosine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
2.14
-
Inosine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
2.34
-
Inosine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
3.29
-
Inosine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
4.31
-
Inosine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
4.42
-
Inosine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
5.3
-
Inosine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Ca2+
the substrate binds to the Ca2+-containing active site in the catalytic cavity at the C-terminal end of the core beta-sheet
Escherichia coli
Purification (Commentary) (protein specific)
Commentary
Organism
Ni-NTA column chromatography and MonoQ column chromatography
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
inosine + H2O
poor substrate
696258
Escherichia coli
hypoxanthine + D-ribose
-
-
-
?
uridine + H2O
-
696258
Escherichia coli
uracil + D-ribose
-
-
-
?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.035
-
Inosine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.086
-
Inosine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.109
-
Inosine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.125
-
Inosine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.18
-
Inosine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.182
-
Inosine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.382
-
Inosine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
0.593
-
Inosine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
3.62
-
Inosine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
5.4
-
uridine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
15.1
-
uridine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
18.8
-
uridine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
39.8
-
uridine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
44.3
-
uridine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
46.9
-
uridine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
52.5
-
uridine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
59.1
-
uridine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
72.9
-
uridine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37C
Escherichia coli
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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1
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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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1
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5
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5
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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
1
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2
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726441
Porcelli
Thermal unfolding of nucleosid ...
Saccharolobus solfataricus
Protein Pept. Lett.
19
369-374
2012
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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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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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700741
Jung
Uridine-ribohydrolase is a key ...
Arabidopsis thaliana
Plant Cell
21
876-891
2009
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1
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6
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11
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1
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8
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2
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7
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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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1
1
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2
2
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1
3
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3
1
1
1
2
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
1
10
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18
-
1
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2
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1
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2
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18
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1
10
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18
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1
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1
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2
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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
1
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6
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3
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1
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1
1
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9
1
1
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6
1
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1
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