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Information on EC 3.1.13.3 - oligonucleotidase and Organism(s) Escherichia coli and UniProt Accession P0A784

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.13 Exoribonucleases producing 5′-phosphomonoesters
                3.1.13.3 oligonucleotidase
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This record set is specific for:
Escherichia coli
UNIPROT: P0A784 not found.
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
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exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates
Synonyms
rnase t, oligoribonuclease, rexo2, nanornase, cpsorn, small fragment nuclease, oligonucleotidase, xc847, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oligoribonuclease
-
nucleotidase, oligo-
-
-
-
-
oligoribonuclease
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY hide
37288-23-6
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,N6-etheno-2'-dApG + H2O
1,N6-etheno-2'-deoxyadenosine + GMP
show the reaction diagram
-
-
-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
show the reaction diagram
i.e. pGpG
-
-
?
dApG + H2O
2'-deoxyadenosine + GMP
show the reaction diagram
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
hydrolyzes oligodeoxyribonucleotides and oligoribonucleotides
-
-
?
(Ap)2 + H2O
?
show the reaction diagram
-
-
-
-
?
(Ap)3 + H2O
?
show the reaction diagram
-
-
-
-
?
(Ap)4 + H2O
?
show the reaction diagram
-
-
-
-
?
(Ap)6 + H2O
?
show the reaction diagram
-
-
-
-
?
5'-p-nitrophenyl-TMP + H2O
p-nitrophenol + TMP
show the reaction diagram
-
-
-
-
?
CpC + H2O
5'-CMP + cytidine
show the reaction diagram
-
-
-
-
?
CpU + H2O
3'-CMP + uridine
show the reaction diagram
-
-
-
-
?
DNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
mRNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
required for for degradation of mRNA to mononucleotides
-
-
?
NAD+ + H2O
NMN + AMP
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
RNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
active after dissociation from a ribonucleoprotein
-
-
?
UpC + H2O
5'-CMP + 5'-UMP
show the reaction diagram
-
-
-
-
?
UpU + H2O
5'-UMP
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
show the reaction diagram
i.e. pGpG
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
no stimulation
K+
-
no effect
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
complete inhibition at 50 mM
Ni2+
-
effective competitive inhibitor
UTP
-
slight
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25
(Ap)2
-
-
0.05
(Ap)3
-
-
0.021
(Ap)4
-
-
0.017
(Ap)6
-
-
0.54 - 1.9
5'-p-nitrophenyl-TMP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.15 - 2.3
5'-p-nitrophenyl-TMP
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.039
Ni2+
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.77
-
purified enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9.5
-
pH 7.0: 50% of maximum activity, pH 9.5: 70% of maximum activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
supernatant fraction
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20000
-
2 * 20000, amino acid analysis, SDS-PAGE
21638
-
2 * 21638, electrospray ionisation mass spectrometry
38000
-
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
homodimer
tetramer
-
crystallization data
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
belongs to space group I422, with unit cell parameters a = 213.1, b = 213.1, c = 149.2, 90.0, 90.0, 90.0, to 30.0-3.1 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
both native and selenomethionine-labeled enzyme
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
ORN mutant, shows growth defect, YtqI from Bacillus subtilis is able to complement the mutant
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100
-
half-life: 2.5 min
65
-
half-life: 10 min
70
-
half-life: 10 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-25°C, 50% glycerol
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
copurifies with polynucleotide phosphorylase
-
on Ni-NTA column and by gel filtration, more than 95% pure
-
to homogeneity
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed as N-terminal His6-tagged ORN enzyme under control of the bacteriophage T7 promoter in Escherichia coli BL21(kDE3)/pLysS using derivatives of the expression vector pETMCSI
-
overexpression of the orn gene in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Niyogi, S.K.; Datta, A.K.
A novel oligoribonuclease of Escherichia coli. I. Isolation and properties
J. Biol. Chem.
250
7307-7312
1975
Escherichia coli
Manually annotated by BRENDA team
Datta, A.K.; Niyogi, S.N.
A novel oligoribonuclease of Escherichia coli. II. Mechanism of action
J. Biol. Chem.
250
7313-7319
1975
Escherichia coli
Manually annotated by BRENDA team
Elson,D.
Latent enzymic activity of a ribonucleoprotein isolated from Escherichia coli
Biochim. Biophys. Acta
36
372-386
1959
Escherichia coli
Manually annotated by BRENDA team
Yu, D.; Deutscher, M.P.
Oligoribonuclease is distinct from the other known exoribonucleases of Escherichia coli
J. Bacteriol.
177
4137-4139
1995
Escherichia coli
Manually annotated by BRENDA team
Zhang, X.; Zhu, L.; Deutscher, M.P.
Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily
J. Bacteriol.
180
2779-2781
1998
Escherichia coli
Manually annotated by BRENDA team
Ghosh, S.; Deutscher, M.P.
Oligoribonuclease is an essential component of the mRNA decay pathway
Proc. Natl. Acad. Sci. USA
96
4372-4377
1999
Escherichia coli
Manually annotated by BRENDA team
Fiedler, T.J.; Vincent, H.A.; Zuo, Y.; Gavrialov, O.; Malhotra, A.
Purification and crystallization of Escherichia coli oligoribonuclease
Acta Crystallogr. Sect. D
60
736-739
2004
Escherichia coli
Manually annotated by BRENDA team
Mechold, U.; Ogryzko, V.; Ngo, S.; Danchin, A.
Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
Nucleic Acids Res.
34
2364-2373
2006
Escherichia coli (P0A784), Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Mechold, U.; Fang, G.; Ngo, S.; Ogryzko, V.; Danchin, A.
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
Nucleic Acids Res.
35
4552-4561
2007
Bacillus subtilis, Escherichia coli
Manually annotated by BRENDA team
Young Park, A.; Elvin, C.M.; Hamdan, S.M.; Wood, R.J.; Liyou, N.E.; Hamwood, T.E.; Jennings, P.A.; Dixon, N.E.
Hydrolysis of the 5-p-nitrophenyl ester of TMP by oligoribonucleases (ORN) from Escherichia coli, Mycobacterium smegmatis, and human
Protein Expr. Purif.
57
180-187
2008
Escherichia coli, Homo sapiens, Mycolicibacterium smegmatis
Manually annotated by BRENDA team
Zuo, Y.; Zheng, H.; Wang, Y.; Chruszcz, M.; Cymborowski, M.; Skarina, T.; Savchenko, A.; Malhotra, A.; Minor, W.
Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover
Structure
15
417-428
2007
Escherichia coli (P30014), Escherichia coli, Pseudomonas aeruginosa (Q9HY82), Pseudomonas aeruginosa
Manually annotated by BRENDA team
Zhou, J.; Zheng, Y.; Roembke, B.; Robinson, S.; Opoku-Temeng, C.; Sayre, D.; Sintim, H.
Fluorescent analogs of cyclic and linear dinucleotides as phosphodiesterase and oligoribonuclease activity probes
RSC Adv.
7
5421-5426
2017
Pseudomonas aeruginosa (A0A069Q255), Mycolicibacterium smegmatis (A0A8B4R3D6), Escherichia coli (P0A784)
-
Manually annotated by BRENDA team