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Literature summary for 3.2.2.8 extracted from

  • Muzzolini, L.; Versees, W.; Tornaghi, P.; Van Holsbeke, E.; Steyaert, J.; Degano, M.
    New insight in to the mechanism of nucleoside hydrolases from crystal structure of the Escherichia coli YbeK protein bound to the reaction product (2006), Biochemistry, 45, 773-782.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene ybeK, expression in strain W6 Escherichia coli K-12

Crystallization (Commentary)

Crystallization (Comment) 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 Comment 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 Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 UniProt Comment Textmining
Escherichia coli K-12 P33022
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant enzyme from strain W6 by nickel chelate affinity chromatography and gel filtration Escherichia coli K-12

Reaction

Reaction Comment Organism Reaction ID
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 Comment Substrates Organism Products Comment (Products) Rev. Reac.
4-nitrophenyl ribopyranoside + H2O
-
Escherichia coli K-12 4-nitrophenol + D-ribose
-
?
adenosine + H2O
-
Escherichia coli K-12 adenine + D-ribose
-
?
cytidine + H2O
-
Escherichia coli K-12 cytosine + D-ribose
-
?
guanosine + H2O
-
Escherichia coli K-12 guanine + D-ribose
-
?
inosine + H2O
-
Escherichia coli K-12 hypoxanthine + D-ribose
-
?
additional information the enzyme is required for recycling of nitrogenous bases Escherichia coli K-12 ?
-
?
N-ribosylpurine + H2O
-
Escherichia coli K-12 purine + D-ribose
-
r
N-ribosylpyrimidine + H2O preferred substrate Escherichia coli K-12 pyrimidine + D-ribose
-
r
uridine + H2O
-
Escherichia coli K-12 uracil + D-ribose
-
?

Subunits

Subunits Comment Organism
More determination of the quarternary structure Escherichia coli K-12

Synonyms

Synonyms Comment Organism
NH
-
Escherichia coli K-12
nucleoside hydrolase
-
Escherichia coli K-12
RihA
-
Escherichia coli K-12
YbeK
-
Escherichia coli K-12

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
35
-
assay at Escherichia coli K-12

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment 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 Comment Organism
7
-
assay at Escherichia coli K-12