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Information on EC 3.1.13.3 - oligonucleotidase and Organism(s) Pseudomonas aeruginosa and UniProt Accession Q9HY82
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3.1.13.3 oligonucleotidaseSpecify your search results
Word Map
- 3.1.13.3
- exoribonuclease
-
exonuclease
- trna
- oligoribonucleotides
- pnpase
- cyclic-di-gmp
-
exonucleolytic
-
phosphoesterase
- c-di-gmp
-
deddh
- 3'-phosphoadenosine
The taxonomic range for the selected organisms is: Pseudomonas aeruginosa
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
rnase t, oligoribonuclease, rexo2, nanornase, cpsorn, small fragment nuclease, oligonucleotidase, xc847, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
nucleotidase, oligo-
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oligoribonuclease
ORN
oligoribonuclease
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
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CAS REGISTRY NUMBER
COMMENTARY
37288-23-6
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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,N6-etheno-2'-dApG + H2O
1,N6-etheno-2'-deoxyadenosine + GMP
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-
-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
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-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
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i.e. pGpG
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-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
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-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
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-
?
additional information
?
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oligoribonuclease (Orn) is an exoribonuclease that hydrolyzes two- to five-nucleotide-long RNAs. Orn degrades short oligoRNAs regardless of sequence
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?
additional information
?
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oligoribonuclease (Orn) is an exoribonuclease that hydrolyzes two- to five-nucleotide-long RNAs. Orn degrades short oligoRNAs regardless of sequence
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?
additional information
?
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poor activity with 4-nitrophenyl phosphate
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?
additional information
?
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recombinant Orn degrades small RNAs in vitro, the enzyme has a proclivity for degrading RNA oligomers comprised of two to five nucleotides (nanoRNAs), including 5'-phosphoguanylyl-(3',5')-guanosine. Orn preferentially degrades purine dinucleotides in vitro. Exonuclease assays are carried out using 33P- and Cy5-labled RNA oligomer substrates. Orn is a calcium-insensitive exoribonuclease that selectively degrades purine rich nanoRNAs. (A) Degradation of the 24-mer 5'-33P-CACACACACA-CACACACACACACA-3'. Orn is a poor degrader of cytosine-rich nanoRNA substrates
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?
additional information
?
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recombinant Orn degrades small RNAs in vitro, the enzyme has a proclivity for degrading RNA oligomers comprised of two to five nucleotides (nanoRNAs), including 5'-phosphoguanylyl-(3',5')-guanosine. Orn preferentially degrades purine dinucleotides in vitro. Exonuclease assays are carried out using 33P- and Cy5-labled RNA oligomer substrates. Orn is a calcium-insensitive exoribonuclease that selectively degrades purine rich nanoRNAs. (A) Degradation of the 24-mer 5'-33P-CACACACACA-CACACACACACACA-3'. Orn is a poor degrader of cytosine-rich nanoRNA substrates
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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
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
-
-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
-
i.e. pGpG
-
-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
-
-
?
5'-phosphoguanylyl-(3',5')-guanosine + H2O
GMP + guanosine
i.e. pGpG
-
-
?
additional information
?
-
oligoribonuclease (Orn) is an exoribonuclease that hydrolyzes two- to five-nucleotide-long RNAs. Orn degrades short oligoRNAs regardless of sequence
-
-
?
additional information
?
-
-
oligoribonuclease (Orn) is an exoribonuclease that hydrolyzes two- to five-nucleotide-long RNAs. Orn degrades short oligoRNAs regardless of sequence
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
Orn is a calcium-insensitive exoribonucleas
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5'-phosphoguanylyl-(3',5')-guanosine
pGpG, product inhibition at elevated levels
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
evolution
Orn is highly conserved among bacteria but is not likely the only nano-RNAse important for cyclic diguanylate signal transduction
malfunction
mutation of gene orn leads to the accumulation of pGpG, which inhibits the function of glutamate-alanine-leucine (EAL) domain-containing enzymes, resulting in increased levels of cyclic-di-GMP and the consequent hyperbiofilm phenotype. EAL domain-containing enzymes hydrolyze cyclic-di-GMP to 5'-phosphoguanylyl-(3',5')-guanosine (pGpG). Mutation of orn drastically increases bacterial susceptibility to quinolones but not to tetracycline, aminoglycoside, or beta-lactam antibiotics. Upregulation of pyocin genes contributes to increased susceptibility to ciprofloxacin in the orn mutant. PrtR stability is reduced by the mutation of orn. Expression levels of prtN and PA0613 in wild-type and DELTAorn mutant strains PA14, phenotypes, overview
malfunction
Pseudomonas aeruginosa DELTAorn mutant has high intracellular cyclic diguanylate (c-di-GMP) levels, causing this strain to overexpress extracellular polymers and overproduce biofilm. Mutant DELTAorn cells possess highly elevated 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) levels
malfunction
the lysates from DELTAorn show 25fold decrease in 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) hydrolysis. Complementation with wild-type, but not active site mutants, restores hydrolysis. Accumulation of pGpG in the DELTAorn strain inhibits PDE-As, increasing cyclic-diguanylate (c-di-GMP) concentration. Increased transcription from the cyclic-diguanylate-regulated pel promoter is observed. Additionally, the cyclic-diguanylate-governed auto-aggregation and biofilm phenotypes are elevated in the DELTAorn strain in a pel-dependent manner. Detection of elevated levels of pGpG and cyclic-diguanylate in the DELTAorn strain. Phenotype, overview
physiological function
bacterial oligoribonuclease (Orn) is a conserved 3'-to-5' exonuclease. In Pseudomonas aeruginosa, Orn plays a major role in the hydrolysis of pGpG, which is required for cyclic-di-GMP homeostasis. Orn is involved in the degradation of nanoRNAs, which can alter global gene expression by serving as transcription initiation primers. And Orn is required for the type III secretion system and pathogenesis of Pseudomonas aeruginosa, indicating a role of Orn in the bacterial response to environmental stimuli. Orn is required for the tolerance of Pseudomonas aeruginosa to ciprofloxacin, role of Orn in bacterial resistance to antibiotics. And role of Orn in genome integrity and bacterial resistance to quinolones. Oligoribonuclease is required for bacterial resistance to fluoroquinolones
physiological function
oligoribonuclease (Orn), an exoribonuclease that hydrolyzes two- to five-nucleotide-long RNAs, is the primary enzyme responsible for degrading 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) in cells. Orn binds to pGpG specifically and can cleave it into GMP. pGpG inhibits RocR phosphodiesterase activity by binding to the active site and competing for cyclic diguanylate binding in the active site, and excess pGpG extends cyclic diguanylate half-life in vitro
physiological function
oligoribonuclease (Orn), which had earlier been established as an essential enzyme in most bacteria involved in the recycling of RNA into ribonucleotides, acts as c-di-GMP PDB-B in Pseudomonas aeruginosa cleaving diguanylate into (pGpG), and pGpG then into GMP
physiological function
the oligoribonuclease (Orn) is a manganese-dependent 3'->5' exonuclease that produces 5'-phosphorylated ribonucleotide monomers from polyribonucleotides, and it is important in providing homeostatic control of intracellular pGpG under native physiological conditions as well as in cyclic diguanylate (c-di-GMP) signaling in Pseudomonas aeruginosa. It is the primary enzyme responsible for 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) degradation in Pseudomonas aeruginosa cells, it degrades pGpG and prevents its accumulation in the bacterial cells. pGpG reduces the rate of c-di-GMP degradation in cell lysates and inhibits the activity of EAL-dependent phosphodiesterases (PA2133, PvrR, and purified recombinant RocR) from Pseudomonas aeruginosa. pGpG-dependent inhibition is alleviated by the addition of Orn. Orn is essential for the viability of Escherichia coli
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
belongs to space group P21, with unit cell parameters a = 49.9, b = 76.6, c = 61.7, 90.0, 93.55, 90.0, to 19.97-2.09 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
construction of an enzyme knockout mutant by gene replacement, Pseudomonas aeruginosa DELTAorn mutant has high intracellular cyclic diguanylate (c-di-GMP) levels, causing this strain to overexpress extracellular polymers and overproduce biofilm. Mutant DELTAorn cells possess highly elevated 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) levels
additional information
-
construction of an enzyme knockout mutant by gene replacement, Pseudomonas aeruginosa DELTAorn mutant has high intracellular cyclic diguanylate (c-di-GMP) levels, causing this strain to overexpress extracellular polymers and overproduce biofilm. Mutant DELTAorn cells possess highly elevated 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) levels
additional information
generation of enzyme mutant DELTAorn, mRNA levels of pyocin biosynthesis genes in the DELTAorn mutant compared to those in wild-type strain PA14. Mutation of orn drastically increases bacterial susceptibility to quinolones but not to tetracycline, aminoglycoside, or beta-lactam antibiotics. Upregulation of pyocin genes contributes to increased susceptibility to ciprofloxacin in the orn mutant. PrtR stability is reduced by the mutation of orn
additional information
-
generation of enzyme mutant DELTAorn, mRNA levels of pyocin biosynthesis genes in the DELTAorn mutant compared to those in wild-type strain PA14. Mutation of orn drastically increases bacterial susceptibility to quinolones but not to tetracycline, aminoglycoside, or beta-lactam antibiotics. Upregulation of pyocin genes contributes to increased susceptibility to ciprofloxacin in the orn mutant. PrtR stability is reduced by the mutation of orn
additional information
generation of enzyme mutant DELTAorn. The lysates from DELTAorn show 25fold decrease in 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) hydrolysis. Complementation with wild-type, but not active site mutants, restores hydrolysis. Accumulation of pGpG in the DELTAorn strain inhibits PDE-As, increasing cyclic-diguanylate (c-di-GMP) concentration. Increased transcription from the cyclic-diguanylate-regulated pel promoter is observed. Additionally, the cyclic-diguanylate-governed auto-aggregation and biofilm phenotypes are elevated in the DELTAorn strain in a pel-dependent manner. Detection of elevated levels of pGpG and cyclic-diguanylate in the DELTAorn strain
additional information
-
generation of enzyme mutant DELTAorn. The lysates from DELTAorn show 25fold decrease in 5'-phosphoguanylyl-(3',5')-guanosine (pGpG) hydrolysis. Complementation with wild-type, but not active site mutants, restores hydrolysis. Accumulation of pGpG in the DELTAorn strain inhibits PDE-As, increasing cyclic-diguanylate (c-di-GMP) concentration. Increased transcription from the cyclic-diguanylate-regulated pel promoter is observed. Additionally, the cyclic-diguanylate-governed auto-aggregation and biofilm phenotypes are elevated in the DELTAorn strain in a pel-dependent manner. Detection of elevated levels of pGpG and cyclic-diguanylate in the DELTAorn strain
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene orn, detailed phylogenetic analysis, recombinant expression of C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
gene orn, quantitative RT-PCR expression analysis
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
requirement of dimerization for RNase T action
additional information
-
requirement of dimerization for RNase T action
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Chen, F.; Chen, G.; Liu, Y.; Jin, Y.; Cheng, Z.; Liu, Y.; Yang, L.; Jin, S.; Wu, W.
Pseudomonas aeruginosa oligoribonuclease contributes to Tolerance to ciprofloxacin by regulating pyocin biosynthesis
Antimicrob. Agents Chemother.
61
e02256-16
2017
Pseudomonas aeruginosa (Q02F67), Pseudomonas aeruginosa
Cohen, D.; Mechold, U.; Nevenzal, H.; Yarmiyhu, Y.; Randall, T.E.; Bay, D.C.; Rich, J.D.; Parsek, M.R.; Kaever, V.; Harrison, J.J.; Banin, E.
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa
Proc. Natl. Acad. Sci. USA
112
11359-11364
2015
Pseudomonas aeruginosa (P57665), Pseudomonas aeruginosa, Pseudomonas aeruginosa 1C (P57665), Pseudomonas aeruginosa ATCC 15692 (P57665), Pseudomonas aeruginosa CIP 104116 (P57665), Pseudomonas aeruginosa DSM 22644 (P57665), Pseudomonas aeruginosa JCM 14847 (P57665), Pseudomonas aeruginosa LMG 12228 (P57665), Pseudomonas aeruginosa PRS 101 (P57665)
Orr, M.W.; Donaldson, G.P.; Severin, G.B.; Wang, J.; Sintim, H.O.; Waters, C.M.; Lee, V.T.
Oligoribonuclease is the primary degradative enzyme for pGpG in Pseudomonas aeruginosa that is required for cyclic-di-GMP turnover
Proc. Natl. Acad. Sci. USA
112
E5048-E5057
2015
Pseudomonas aeruginosa (Q02F67), Pseudomonas aeruginosa
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)
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