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Information on EC 3.2.2.8 - ribosylpyrimidine nucleosidase
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3.2.2.8 ribosylpyrimidine nucleosidaseIUBMB Comments
Also hydrolyses purine D-ribonucleosides, but much more slowly. 2'-, 3'- and 5'-deoxynucleosides are not substrates .
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Word Map
- 3.2.2.8
- purine
- leishmania
-
salvage
- inosine
- leishmaniasis
- donovani
- crithidia
- fasciculata
- vivax
-
purine-specific
-
n-glycosidic
- ribonucleosides
-
schramm
-
chaga
-
horenstein
- iminoribitols
-
inosine-adenosine-guanosine
-
ribooxocarbenium
- xanthosine
-
zymodeme
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
nucleoside hydrolase, cu-nh, n-ribohydrolase, pyrimidine-specific nucleoside hydrolase, sscu-nh, pyrimidine nucleoside hydrolase, uridine-ribohydrolase 1, cytidine-uridine nucleoside hydrolase, sso0505, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
N-ribosylpyrimidine nucleosidase
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-
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N-ribosylpyrimidine ribohydrolase
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nucleosidase, pyrimidine
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nucleoside hydrolase
pyrimidine nucleosidase
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pyrimidine-specific nucleoside hydrolase
RihA
SsCU-NH
SSO0505
URH1
URH1 is a member of the inosine-uridine nucleosidase protein family
YeiK
additional information
additional information
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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
additional information
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the enzyme is a member of the nucleoside hydrolase enzyme family
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a pyrimidine nucleoside + H2O = D-ribose + a pyrimidine base
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a pyrimidine nucleoside + H2O = D-ribose + a pyrimidine base
catalytic mechanism, active site structure, conformational transition between open and closed structure, product release mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of N-glycosyl bond
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-
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-
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SYSTEMATIC NAME
IUBMB Comments
pyrimidine-nucleoside ribohydrolase
Also hydrolyses purine D-ribonucleosides, but much more slowly. 2'-, 3'- and 5'-deoxynucleosides are not substrates [3].
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CAS REGISTRY NUMBER
COMMENTARY
37288-60-1
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1-beta-D-ribofuranosylnicotinamide + H2O
nicotinamide + D-ribose
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-
-
?
1-beta-D-ribofuranosylthymine + H2O
D-ribose + thymine
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-
-
?
4-amino-5-imidazolecarboxamide ribonucleotide + H2O
4-amino-5-imidazolecarboxamide + D-ribose
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-
-
?
4-nitrophenyl beta-D-ribofuranoside + H2O
4-nitrophenol + D-ribose
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-
-
?
4-nitrophenyl ribopyranoside + H2O
4-nitrophenol + D-ribose
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-
-
?
6-azauridine + H2O
6-azauracil + D-ribose
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poor substrate
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?
6-mercaptopurine ribonucleoside + H2O
6-mercaptopurine + D-ribose
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-
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?
imidazoleacetic acid ribonucleotide + H2O
imidazoleacetic acid + D-ribose
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?
inosine + H2O
?
catalytic efficiency towards inosine is at least 100-fold below that for uridine
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?
N-ribosylpyrimidine + H2O
pyrimidine + D-ribose
preferred substrate
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r
tubercidin + H2O
1-deazaadenine + D-ribose
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poor substrate
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?
5-fluorouridine + H2O
5-fluorouracil + D-ribose
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detagged recombinant enzyme
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?
purine D-ribonucleosides + H2O
purine + D-ribose
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appreciable substrate activity if a hydroxyl or thio group is present in the 6-position or if a hydroxyl group is present in the 2- and 6-position, preference for oxo versus amino substituents
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?
purine D-ribonucleosides + H2O
purine + D-ribose
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prefers pyrimidines
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?
purine D-ribonucleosides + H2O
purine + D-ribose
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prefers pyrimidines
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?
purine D-ribonucleosides + H2O
purine + D-ribose
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prefers pyrimidines
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?
uridine + H2O
uracil + D-ribose
the pure recombinant protein exhibits highest hydrolase activity for uridine, followed by inosine and adenosine
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?
uridine + H2O
uracil + D-ribose
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cleaves uridine most efficiantly
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?
uridine + H2O
uracil + D-ribose
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cleaves uridine most efficiantly
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?
xanthosine + H2O
xanthine + D-ribose
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high hydrolytic efficiency, xanthosine is a better substrate for isoform NSH1 compared to inosine and adenosine
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-
?
additional information
?
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the pure recombinant protein exhibits highest hydrolase activity for uridine, followed by inosine and adenosine
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?
additional information
?
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the pure recombinant protein exhibits highest hydrolase activity for uridine, followed by inosine and adenosine
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?
additional information
?
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enzyme is pyrimidine specific, purine nucleosides are not hydrolysed, 2'-, 3'- and 5'-deoxynucleosides are no substrates
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?
additional information
?
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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
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?
additional information
?
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the enzyme is required for recycling of nitrogenous bases
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?
additional information
?
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detagged recombinant enzyme: substrate specificity, no activity with purine nucleosides, and with 2'-, 3'-, and 5'-deoxynucleosides
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?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-ribosylpyrimidine + H2O
pyrimidine + D-ribose
preferred substrate
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r
additional information
?
-
the enzyme is required for recycling of nitrogenous bases
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-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Na+
likely bound to the enzyme under physiological conditions
Ca2+
the substrate binds to the Ca2+-containing active site in the catalytic cavity at the C-terminal end of the core beta-sheet
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3,4-diaminophenyl-D-iminoribitol
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competitive, the ligand can bind at the active site in two distinct orientations, binding structure, overview
CdCl2
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
CoCl2
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
FeCl3
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
HgCl2
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
MnSO4
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
ZnCl2
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at 1 mM: inhibition ranging from 40-95%, at 0.01 mM: inhibition less than 10%
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Acanthamoeba Keratitis
Production of a polyclonal antibody against inosine-uridine preferring nucleoside hydrolase of Acanthamoeba castellanii and its access to diagnosis of Acanthamoeba keratitis.
Anthrax
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation.
Anthrax
Combined virtual screening, MMPBSA, molecular docking and dynamics studies against deadly anthrax: An in silico effort to inhibit Bacillus anthracis nucleoside hydrolase.
Anthrax
Design of new chemotherapeutics against the deadly anthrax disease. Docking and molecular dynamics studies of inhibitors containing pyrrolidine and riboamidrazone rings on nucleoside hydrolase from Bacillus anthracis.
Bacterial Infections
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation.
Infections
A Chimera Containing CD4+ and CD8+ T-Cell Epitopes of the Leishmania donovani Nucleoside Hydrolase (NH36) Optimizes Cross-Protection against Leishmania amazonesis Infection.
Infections
Druggability of the guanosine/adenosine/cytidine nucleoside hydrolase from Trichomonas vaginalis.
Infections
Evaluation of immune responses and protection induced by A2 and nucleoside hydrolase (NH) DNA vaccines against Leishmania chagasi and Leishmania amazonensis experimental infections.
Infections
Leishmania donovani Nucleoside Hydrolase Terminal Domains in Cross-Protective Immunotherapy Against Leishmania amazonensis Murine Infection.
Infections
The F1F3 Recombinant Chimera of Leishmania donovani-Nucleoside Hydrolase (NH36) and Its Epitopes Induce Cross-Protection Against Leishmania (V.) braziliensis Infection in Mice.
Leishmaniasis
F1 Domain of the Leishmania (Leishmania) donovani Nucleoside Hydrolase Promotes a Th1 Response in Leishmania (Leishmania) infantum Cured Patients and in Asymptomatic Individuals Living in an Endemic Area of Leishmaniasis.
Leishmaniasis, Cutaneous
Expression, purification, immunogenicity and protective efficacy of a recombinant nucleoside hydrolase from Leishmania donovani, a vaccine candidate for preventing cutaneous leishmaniasis.
Leishmaniasis, Cutaneous
Isoenzyme characterization of Leishmania isolated from human cases with localized cutaneous leishmaniasis from the State of Campeche, Yucatan Peninsula, Mexico.
Leishmaniasis, Visceral
Cross-protective efficacy of a prophylactic Leishmania donovani DNA vaccine against visceral and cutaneous murine leishmaniasis.
Leishmaniasis, Visceral
Expression, purification and spectrophotometric analysis of nucleoside hydrolase from Leishmania chagasi (LcNH).
Leishmaniasis, Visceral
F1 Domain of the Leishmania (Leishmania) donovani Nucleoside Hydrolase Promotes a Th1 Response in Leishmania (Leishmania) infantum Cured Patients and in Asymptomatic Individuals Living in an Endemic Area of Leishmaniasis.
Leishmaniasis, Visceral
Nucleoside hydrolase DNA vaccine against canine visceral leishmaniasis.
Leishmaniasis, Visceral
Nucleoside hydrolase from Leishmania (L.) donovani is an antigen diagnostic for visceral leishmaniasis.
Neoplasms
Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
Neoplasms
Identification of a 2'-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries.
Parasitic Diseases
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation.
Trypanosomiasis, African
Evaluation of nucleoside hydrolase inhibitors for treatment of African trypanosomiasis.
Tuberculosis
Biochemical characterization of recombinant nucleoside hydrolase from Mycobacterium tuberculosis H37Rv.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.18
4-nitrophenyl ribopyranoside
pH 7.0, 35°C, recombinant enzyme
0.4
isopentenyladenine-riboside
recombinant enzyme expressed in Escherichia coli, in 50 mM Tris-HCl, pH 7.5, at 30°C
0.44
methyluridine
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isoform NSH1, pH not specified in the publication, at 30°C
0.7
adenosine
recombinant enzyme expressed in Escherichia coli, in 50 mM Tris-HCl, pH 7.5, at 30°C
0.7
adenosine
-
isoform NSH1, pH not specified in the publication, at 30°C
1.16
Inosine
mutant enzyme T223Y, in 50 mM HEPES buffer (pH 7.3), at 37°C
1.4
Inosine
recombinant enzyme expressed in Escherichia coli, in 50 mM Tris-HCl, pH 7.5, at 30°C
1.4
Inosine
-
isoform NSH1, pH not specified in the publication, at 30°C
1.77
Inosine
mutant enzyme Q227F, in 50 mM HEPES buffer (pH 7.3), at 37°C
1.93
Inosine
mutant enzyme T223Y/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37°C
2.14
Inosine
mutant enzyme Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37°C
2.34
Inosine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37°C
3.29
Inosine
mutant enzyme T223A, in 50 mM HEPES buffer (pH 7.3), at 37°C
4.31
Inosine
mutant enzyme Q227A, in 50 mM HEPES buffer (pH 7.3), at 37°C
4.42
Inosine
mutant enzyme T223F/Q227Y, in 50 mM HEPES buffer (pH 7.3), at 37°C
5.3
Inosine
mutant enzyme T223F, in 50 mM HEPES buffer (pH 7.3), at 37°C
0.12
uridine
wild type enzyme, in 50 mM HEPES buffer (pH 7.3), at 37°C
0.31