BRENDA - Enzyme Database
show all sequences of 3.2.2.8

Cloning, purification, crystallization and X-ray analysis of the Escherichia coli pyrimidine nucleoside hydrolase YeiK

Giabbai, B.; Degano, M.; Acta Crystallogr. Sect. D 60, 524-527 (2004)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene yeiK, subcloning in strain DH5alpha, expression of the His6-tagged enzyme in strain BL21(DE3)
Escherichia coli K-12
Crystallization (Commentary)
Crystallization
Organism
purified detagged recombinant enzyme, hanging drop vapour diffusion method, 10 mg/ml protein in 20 mM HEPES, pH 7.4, 150 mM NaCl, is mixed with precipitant solution, 25°C, equilibration versus reservoir solution containing 100 mM Tris-HCl, pH 8.5, 200 mM NaCl, 25% w/v PEG 3350, cryoprotection by 25% glycerol, X-ray diffraction structure determination and analysis at 1.7 A resolution
Escherichia coli K-12
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
36000
-
4 * 36000, detagged recombinant enzyme, SDS-PAGE
Escherichia coli K-12
143000
-
detagged recombinant enzyme, gel filtration
Escherichia coli K-12
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli K-12
-
gene yeiK
-
Purification (Commentary)
Commentary
Organism
recombinant His6-tagged enzyme from strain BL21(DE3) by nickel chelate affinity chromatography and gel filtration, the His-tag is cleaved off by thrombin
Escherichia coli K-12
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5-fluorouridine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
5-fluorouracil + D-ribose
-
-
-
?
cytidine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
cytosine + D-ribose
-
-
-
?
additional information
detagged recombinant enzyme: substrate specificity, no activity with purine nucleosides, and with 2'-, 3'-, and 5'-deoxynucleosides
663495
Escherichia coli K-12
?
-
-
-
-
uridine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
uracil + D-ribose
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
structure analysis by dynamic light scattering
Escherichia coli K-12
tetramer
4 * 36000, detagged recombinant enzyme, SDS-PAGE
Escherichia coli K-12
Cloned(Commentary) (protein specific)
Commentary
Organism
gene yeiK, subcloning in strain DH5alpha, expression of the His6-tagged enzyme in strain BL21(DE3)
Escherichia coli K-12
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified detagged recombinant enzyme, hanging drop vapour diffusion method, 10 mg/ml protein in 20 mM HEPES, pH 7.4, 150 mM NaCl, is mixed with precipitant solution, 25°C, equilibration versus reservoir solution containing 100 mM Tris-HCl, pH 8.5, 200 mM NaCl, 25% w/v PEG 3350, cryoprotection by 25% glycerol, X-ray diffraction structure determination and analysis at 1.7 A resolution
Escherichia coli K-12
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
36000
-
4 * 36000, detagged recombinant enzyme, SDS-PAGE
Escherichia coli K-12
143000
-
detagged recombinant enzyme, gel filtration
Escherichia coli K-12
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged enzyme from strain BL21(DE3) by nickel chelate affinity chromatography and gel filtration, the His-tag is cleaved off by thrombin
Escherichia coli K-12
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5-fluorouridine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
5-fluorouracil + D-ribose
-
-
-
?
cytidine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
cytosine + D-ribose
-
-
-
?
additional information
detagged recombinant enzyme: substrate specificity, no activity with purine nucleosides, and with 2'-, 3'-, and 5'-deoxynucleosides
663495
Escherichia coli K-12
?
-
-
-
-
uridine + H2O
detagged recombinant enzyme
663495
Escherichia coli K-12
uracil + D-ribose
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
structure analysis by dynamic light scattering
Escherichia coli K-12
tetramer
4 * 36000, detagged recombinant enzyme, SDS-PAGE
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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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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5
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724342
Minici
New determinants in the cataly ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
Biochemistry
51
4590-4599
2012
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726441
Porcelli
Thermal unfolding of nucleosid ...
Saccharolobus solfataricus
Protein Pept. Lett.
19
369-374
2012
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716542
Jung
Arabidopsis nucleoside hydrola ...
Arabidopsis thaliana
Plant J.
65
703-711
2011
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707897
Garau
Active site plasticity reveale ...
Escherichia coli
BMC Struct. Biol.
10
14
2010
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700741
Jung
Uridine-ribohydrolase is a key ...
Arabidopsis thaliana
Plant Cell
21
876-891
2009
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679803
Porcelli
Pyrimidine-specific ribonucleo ...
Saccharolobus solfataricus
FEBS J.
275
1900-1914
2008
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696258
Iovane
Structural basis for substrate ...
Escherichia coli
Biochemistry
47
4418-4426
2008
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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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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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657373
Giabbai
Crystal structure to 1.7 ANG o ...
Escherichia coli
Structure
12
739-749
2004
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1
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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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137114
Allam
-
Nature of enzymes that catalyz ...
Penicillium chrysogenum
Biochem. Syst. Ecol.
15
515-517
1987
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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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137116
Koszalka
Nucleosidases from Leishmania ...
Leishmania donovani
J. Biol. Chem.
254
8185-8193
1979
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4168
Murray
-
Molecular weight estimations o ...
Pisum sativum
Phytochemistry
10
2645-2648
1971
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137117
Terada
Purification and properties of ...
Pseudomonas fluorescens
J. Biol. Chem.
242
5578-5585
1967
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