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Literature summary for 3.2.2.8 extracted from

  • Garau, G.; Muzzolini, L.; Tornaghi, P.; Degano, M.
    Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor (2010), BMC Struct. Biol., 10, 14.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
RihA bound to inhibitor 3,4-diaminophenyl-D-iminoribitol, hanging drop vapour diffusion method, 8 mg/ml RihA in 50 mM HEPES, pH 7.2, 150 mM NaCl is mixed with a 5:1 molar excess of 3,4-diaminophenyl-D-iminoribitol, solubilized in 50 mM HEPES, pH 7.2, and incubated at 4°C for 3 hours, the protein/inhibitor complex is mixed with an equal volume of a precipitant solution containing 25% PEG 4000, 0.1 M sodium acetate, pH 5.0, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement Escherichia coli

Inhibitors

Inhibitors Comment Organism Structure
3,4-diaminophenyl-D-iminoribitol competitive, the ligand can bind at the active site in two distinct orientations, binding structure, overview Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ dependent on Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
a pyrimidine nucleoside + H2O Escherichia coli
-
D-ribose + a pyrimidine base
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
a pyrimidine nucleoside + H2O
-
Escherichia coli D-ribose + a pyrimidine base
-
?
additional information catalytic cycles between the open and closed conformations of RihA, stabilization of two flexible active site regions is pivotal to establish the interactions required for substrate discrimination and catalysis, involvement of the Asp10 as general base in the mechanism, role of the conserved His82 residue in modulating product release, structure-function analysis, detailed overview Escherichia coli ?
-
?

Synonyms

Synonyms Comment Organism
More the enzyme belongs to the pyrimidine-preferring N-ribohydrolases, CU-NHs, a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides Escherichia coli
N-ribohydrolase
-
Escherichia coli
RihA
-
Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
assay at Escherichia coli

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.085
-
3,4-diaminophenyl-D-iminoribitol pH 7.4, 37°C Escherichia coli

General Information

General Information Comment Organism
physiological function possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules Escherichia coli