BRENDA - Enzyme Database
show all sequences of 3.2.2.8

Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor

Garau, G.; Muzzolini, L.; Tornaghi, P.; Degano, M.; BMC Struct. Biol. 10, 14 (2010)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
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 4C 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
Commentary
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
Commentary
Organism
Structure
Ca2+
dependent on
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
a pyrimidine nucleoside + H2O
Escherichia coli
-
D-ribose + a pyrimidine base
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
a pyrimidine nucleoside + H2O
-
707897
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
707897
Escherichia coli
?
-
-
-
-
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Escherichia coli
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.085
-
3,4-diaminophenyl-D-iminoribitol
pH 7.4, 37C
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
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 4C 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 (protein specific)
Inhibitors
Commentary
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
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
0.085
-
3,4-diaminophenyl-D-iminoribitol
pH 7.4, 37C
Escherichia coli
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Ca2+
dependent on
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
a pyrimidine nucleoside + H2O
Escherichia coli
-
D-ribose + a pyrimidine base
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
a pyrimidine nucleoside + H2O
-
707897
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
707897
Escherichia coli
?
-
-
-
-
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Escherichia coli
General Information
General Information
Commentary
Organism
physiological function
possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
physiological function
possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules
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
-
-
1
1
1
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
751391
Fan
QM/MM and MM MD Simulations o ...
Escherichia coli
J. Phys. Chem. B
122
1121-1131
2018
-
-
-
1
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
752168
Dalberto
-
Thermodynamics, functional an ...
Leishmania braziliensis
RSC Adv.
7
48861-48875
2017
-
-
1
1
-
-
-
5
-
-
1
-
-
1
-
-
-
-
-
-
-
-
6
1
-
-
-
5
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
5
-
-
1
-
-
-
-
-
-
-
-
-
6
1
-
-
-
5
-
-
-
-
-
-
-
-
5
5
724342
Minici
New determinants in the cataly ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
Biochemistry
51
4590-4599
2012
-
-
1
1
-
-
-
-
-
1
-
-
-
2
-
-
1
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
726441
Porcelli
Thermal unfolding of nucleosid ...
Saccharolobus solfataricus
Protein Pept. Lett.
19
369-374
2012
-
-
-
-
-
-
-
-
-
-
-
-
1
3
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
716542
Jung
Arabidopsis nucleoside hydrola ...
Arabidopsis thaliana
Plant J.
65
703-711
2011
-
-
-
-
-
-
-
5
1
-
-
-
-
3
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5
1
-
-
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
707897
Garau
Active site plasticity reveale ...
Escherichia coli
BMC Struct. Biol.
10
14
2010
-
-
-
1
-
-
1
-
-
1
-
1
-
4
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
-
-
-
1
-
-
-
-
-
-
1
-
-
-
1
1
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
-
-
-
-
1
1
-
-
-
700741
Jung
Uridine-ribohydrolase is a key ...
Arabidopsis thaliana
Plant Cell
21
876-891
2009
-
-
1
-
1
-
-
6
-
-
-
-
-
11
-
-
1
-
-
6
1
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
1
-
-
-
-
7
-
-
-
-
-
-
-
1
-
9
1
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
679803
Porcelli
Pyrimidine-specific ribonucleo ...
Saccharolobus solfataricus
FEBS J.
275
1900-1914
2008
-
-
1
-
-
-
-
2
-
1
3
-
-
6
-
-
1
-
-
-
-
-
3
1
1
1
2
2
-
-
-
-
-
1
-
-
-
1
-
-
-
-
-
-
-
2
-
1
3
-
-
-
-
1
-
-
-
-
3
1
1
1
2
2
-
-
-
1
-
-
-
-
-
-
696258
Iovane
Structural basis for substrate ...
Escherichia coli
Biochemistry
47
4418-4426
2008
-
-
1
1
10
-
-
18
-
1
-
-
-
2
-
-
1
-
-
-
-
-
2
-
-
-
-
18
-
-
-
-
-
-
-
-
-
1
-
1
10
-
-
-
-
18
-
1
-
-
-
-
-
1
-
-
-
-
2
-
-
-
-
18
-
-
-
-
-
-
-
-
-
-
664140
Muzzolini
New insight in to the mechanis ...
Escherichia coli K-12
Biochemistry
45
773-782
2006
-
-
1
1
-
-
-
6
-
-
-
3
-
1
-
-
1
1
-
-
-
-
9
1
1
-
-
6
1
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
6
-
-
-
3
-
-
-
1
-
-
-
-
9
1
1
-
-
6
1
-
-
-
-
-
-
-
-
-
670166
Kim
Genes encoding ribonucleoside ...
Corynebacterium ammoniagenes
Microbiology
152
1169-1177
2006
-
-
1
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
654131
Giabbai
Cloning, purification, crystal ...
Escherichia coli
Acta Crystallogr. Sect. D
D60
524-527
2004
-
-
1
1
-
-
-
-
-
-
2
-
-
3
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
1
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
657373
Giabbai
Crystal structure to 1.7 ANG o ...
Escherichia coli
Structure
12
739-749
2004
-
-
1
1
2
-
-
8
2
-
3
-
-
4
-
-
1
1
-
-
-
-
7
1
-
-
-
8
-
-
-
-
-
-
-
-
-
1
-
1
2
-
-
-
-
8
2
-
3
-
-
-
-
1
-
-
-
-
7
1
-
-
-
8
-
-
-
-
-
-
-
-
-
-
663495
Giabbai
Cloning, purification, crystal ...
Escherichia coli K-12
Acta Crystallogr. Sect. D
60
524-527
2004
-
-
1
1
-
-
-
-
-
-
2
-
-
3
-
-
1
-
-
-
-
-
4
2
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
1
-
-
-
-
4
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
137114
Allam
-
Nature of enzymes that catalyz ...
Penicillium chrysogenum
Biochem. Syst. Ecol.
15
515-517
1987
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
5
-
1
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
5
-
1
-
1
-
1
-
-
-
-
-
-
-
-
-
137115
Krenitsky
-
Purine salvage enzymes in man ...
Leishmania donovani
Adv. Exp. Med. Biol.
122
51-56
1980
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
1
-
-
7
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
7
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
137116
Koszalka
Nucleosidases from Leishmania ...
Leishmania donovani
J. Biol. Chem.
254
8185-8193
1979
-
-
-
-
-
-
7
6
-
-
1
1
-
1
-
-
1
-
-
1
1
1
10
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
7
-
6
-
-
1
1
-
-
-
1
-
1
1
1
10
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
4168
Murray
-
Molecular weight estimations o ...
Pisum sativum
Phytochemistry
10
2645-2648
1971
-
-
-
-
-
-
-
-
-
-
1
1
-
1
-
-
-
-
-
1
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
-
-
1
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
137117
Terada
Purification and properties of ...
Pseudomonas fluorescens
J. Biol. Chem.
242
5578-5585
1967
-
-
-
-
-
-
16
9
-
-
-
1
-
2
-
-
1
-
-
-
1
2
16
-
-
-
3
-
5
-
-
-
-
-
-
-
-
-
-
-
-
-
-
16
-
9
-
-
-
1
-
-
-
1
-
-
1
2
16
-
-
-
3
-
5
-
-
-
-
-
-
-
-
-