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Information on EC 3.1.26.3 - ribonuclease III and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q02555
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3.1.26.3 ribonuclease IIISpecify your search results
Word Map
- 3.1.26.3
- rnai
-
argonaute
- drosophila
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germline
-
rna-induced
- viruses
- duplex
- ovarian
-
microprocessor
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pri-mirnas
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single-stranded
- chromatin
- elegans
- helicase
- tumour
- neoplasm
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predisposition
- thyroid
- tumorigenesis
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rna-dependent
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sequence-specific
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stem-loop
-
3'utrs
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cystic
-
hotspot
- rhabdomyosarcoma
- heterochromatin
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dsrna-binding
- snornas
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retrotransposons
- exoribonuclease
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piwi-interacting
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gene-silencing
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endonucleolytic
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rna-directed
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virus-derived
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mirna-mediated
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multinodular
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overhang
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wilms
-
rnai-based
- goiter
- hamartoma
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microrna-mediated
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let-7a
-
exportin
-
dead-box
-
rna-processing
- pre-rrnas
-
mirna-based
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
dicer, dicer1, drosha, dicer-2, rnt1p, ribonuclease iii, dicer-1, rnase d, dcr-1, rnase3, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
HCS protein
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nuclease, ribo-, D
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p241
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ribonuclease D
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RNase D
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RNase III
RNase O
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RNT1
Rnt1p
additional information
-
the enzyme belongs to the double-stranded RNA specific RNase III family of endoribonucleases
RNase III
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Endonucleolytic cleavage to a 5'-phosphomonoester
RNA substrate forms a duplex structure with a terminal four-base loop with the sequence AGNN, being an important determinant of the substrate selectivity in the dsRNA binding domain dsRBD, the N-terminal region is not required for selective cleavage in vitro but required for full function and viability of yeast cells in vivo, substrate binding modeling
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Endonucleolytic cleavage to a 5'-phosphomonoester
catalytic mechanism, overview. The enzyme activates water as a nucleophile to hydrolyze target site phosphodiesters, creating 3'-hydroxyl, 5'-phosphomonoester product termini
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
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CAS REGISTRY NUMBER
COMMENTARY
78413-14-6
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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
double-stranded RNA + H2O
?
2'-hydroxyl groups of nucleotides of the tetraloop or adjacent base pairs are predicted to interact with residues of alpha-helix 1 are important for Rnt1p cleavage in vitro
-
-
?
35S pre-rRNA + H2O
mature 35S rRNA
-
double-stranded RNA regions in the 3'external transcribed spacer capped by terminal AGNN tetraloops determine the cleavage specificity
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-
?
RNA + H2O
?
RNA substrate tested are U5, U2, Mig2, and Yta6. Comparison between the association and dissociation kinetics of Mig2 and U5 products indicated that Mig2 products have a 2fold higher association rate and an 8fold lower dissociation rate. The reactivity of Rnt1p substrates is defined by the basepairing of the cleavage site, substrate specificity, overview
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-
?
synthetic 25S rRNA 3' ETS cleavage site containing RNA + H2O
?
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-
-
-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
the enzymatic activity requires a conserved catalytic domain, while RNA binding requires the double-stranded RNA-binding domain at the C-terminus of the protein. Rnt1p specifically cleaves RNAs that possess short irregular stem-loops containing 1214 base pairs interrupted by internal loops and bulges and capped by conserved AGNN tetraloops. A new carboxy-terminal helix following a canonical ds double-stranded RNA-binding domain structure allows the Rnt1p double-stranded RNA-binding domain to bind to short RNA stem-loops by modulating the conformation of helix a1, a key RNA-recognition element of the double-stranded RNA-binding domain
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-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
the observed interactions between helix alpha1 in the double-stranded RNA binding domain RNA complex in vitro are required for substrate recognition in the context of the entire protein in vivo. The endonuclease domain of Rnt1p is almost immediately N-terminal to the helix alpha1
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?
double-stranded RNA + H2O
5'-phosphooligonucleotides
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cleaves multimeric tRNA precursor at the spacer region, also involved in processing of precursor rRNA, hnRNA and early T7-mRNA. Also cleaves double-stranded DNA and single-stranded RNA
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-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
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involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference, a dsRNA-binding domain recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops
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-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
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involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference, preferred substrate contains NGNN tetraloops
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-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
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a dsRNA-binding domain recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops, new form of Rnt1p substrates identified lacking the conserved AGNN sequence but instead harboring an AAGU tetraloop was found at the 5' end of snoRNA 48 precursor
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?
double-stranded RNA + H2O
5'-phosphooligonucleotides
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new form of Rnt1p substrates identified harboring an AAGU tetraloop at the 5' end of snoRNA 48 precursor, reactions performed under low salt (10 mM KCl) and physiological salt (150 mM KCl) conditions, construction of substrate containing a AAAU or UUGU structure instead of AAGU showed similar efficiency under low salt conditions but strongly reduced efficiency under physiological salt conditions, stem structure is found to partially contribute t the substrate binding efficiency
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?
dsRNA + H2O
mature RNA
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diverse model RNA substreates, enzyme cleaves specifically RNA stems capped with the conserved AGNN tetraloop, the dsRNA sequence adjacent to the tetraloop regulates enzyme activity by interfering with substrate binding, sequences surrounding the cleavage site directly influence the cleavage efficiency, a minimum substrate length is required
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-
?
dsRNA + H2O
mature RNA
-
specific for double-stranded RNA, a dimerization signal within the N-terminal domain is required for efficient cleavage
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-
?
pre-rRNA + H2O
mature rRNA
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enzyme is required for processing
-
-
?
pre-rRNA + H2O
mature rRNA
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double-stranded RNA regions in the 3'external transcribed spacer capped by terminal AGNN tetraloops determine the cleavage specificity
-
-
?
pre-snoRNA + H2O
mature snoRNA
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enzyme is required for processing
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-
?
pre-snoRNA + H2O
mature snoRNA
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i.e. small nucleolar RNA, double-stranded RNA regions in intergenic spacers of polycistronic snoRNA transcription units capped by terminal AGNN tetraloops determine the cleavage specificity
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?
pre-snRNA + H2O
mature snRNA
-
enzyme is required for processing
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?
pre-snRNA + H2O
mature snRNA
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i.e. small nuclear RNA, double-stranded RNA regions in the 5'- or 3'-end flanking sequences capped by terminal AGNN tetraloops determine the cleavage specificity
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?
additional information
?
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the enzyme plays an important role in the maturation of a diverse set of RNAs
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?
additional information
?
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the enzyme plays an important role in the maturation of a diverse set of RNAs
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?
additional information
?
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design of series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate is engineered to carry a single or multiple 2'-O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Introduction of 2'-O-methyl ribonucleotides near the cleavage site increases the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'-O-methyl ribonucleotides inhibits cleavage while single 2'-fluoro ribonucleotide substitutions does not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated
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?
additional information
?
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design of series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate is engineered to carry a single or multiple 2'-O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Introduction of 2'-O-methyl ribonucleotides near the cleavage site increases the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'-O-methyl ribonucleotides inhibits cleavage while single 2'-fluoro ribonucleotide substitutions does not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated
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?
additional information
?
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the enzyme Rnt1p binds to RNA stems capped with an NGNN tetraloop, via specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain and the guanine nucleotide in the second position of the loop
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?
additional information
?
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the enzyme Rnt1p binds to RNA stems capped with an NGNN tetraloop, via specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain and the guanine nucleotide in the second position of the loop
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?
additional information
?
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mode of substrate recognition by the enzyme, which has a unique RNA-binding motif, the enzyme interacts with the RNA stem upstream of the cleavage sites, structure-function analysis, detailed overview. Interaction between the N-terminal domain and RNA increases precision of cleavage site selection
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?
additional information
?
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mode of substrate recognition by the enzyme, which has a unique RNA-binding motif, the enzyme interacts with the RNA stem upstream of the cleavage sites, structure-function analysis, detailed overview. Interaction between the N-terminal domain and RNA increases precision of cleavage site selection
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?
additional information
?
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enzyme is involved in RNA processing and RNA interference, i.e. RNAi, regulation by a combination of primary and tertiary structural elements allowing a substrate-specific binding and cleavage efficiency
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?
additional information
?
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enzyme is required for maturation of pre-rRNAs
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?
additional information
?
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determination and analysis of processing signals within the secondary structure of pre-RNA substrates, comparison with the sequences and structure of RNA from other hemiascomycetes species, overview
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?
additional information
?
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substrate specificity, overview, RNA substrate with introduced sequences stabilizing the RNA helix enhances binding while the turnover rate is reduced, thus substrate binding becomes rate-limiting
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?
additional information
?
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specificity of cleavage by Rnt1p relies on the presence of RNA tetraloop structures with the consensus sequence AGNN at the top of the target dsRNA. Identification of exocyclic groups of purines in the major groove downstream of the tetraloop as a major antideterminant in RNase III activity
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?
additional information
?
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Rnt1p, the major RNase III in Saccharomyces cerevisiae, cleaves RNA substrates containing hairpins capped by A/uGNN tetraloops, using its double-stranded RNA binding domains, dsRBD, to recognize a conserved tetraloop fold. The dsRBD adopts the same conformation in both the AAGU and AGAA complexes
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?
additional information
?
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the AAGU hairpin binds to and is efficiently cleaved by Rnt1p in the context of the snR47 stem sequence
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?
additional information
?
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processing of dsRNA, specific bp sequence elements can modulate substrate reactivity, and a network of hydrogen bonds provides an energetically important contribution to Rnt1p binding, a phylogenetic-based substrate alignment analysis reveals a statistically significant exclusion of the UA bp from the position adjacent to the tetraloop. Rnt1p cleaves hairpin structures in pre-rRNAs, pre-mRNAs, and transcripts containing noncoding RNAs such as snoRNAs, as part of the respective maturation pathways. The enzyme also interacts with Gar1p, a protein involved in pseudouridylation reactions, via its C-terminal portion adjacent to the dsRBD
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?
additional information
?
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the enzyme processes ribosomal RNA, small nucleolar RNA, small nuclear RNA, and messenger RNA
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?
additional information
?
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the catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate. Development of a real-time FRET assay for the detection of dsRNA degradation by yeast RNase III (Rnt1p) and detection of kinetic bottlenecks controlling the reactivity of different substrates. Rnt1p cleavage reaction is not only limited by the rate of catalysis but can also depend on base-pairing of product termini. Cleavage products terminating with paired nucleotides, like the degradation signals found in coding mRNA sequence, were less reactive and more prone to inhibition than products having unpaired nucleotides found in noncoding RNA substrates
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?
additional information
?
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the catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate. Development of a real-time FRET assay for the detection of dsRNA degradation by yeast RNase III (Rnt1p) and detection of kinetic bottlenecks controlling the reactivity of different substrates. Rnt1p cleavage reaction is not only limited by the rate of catalysis but can also depend on base-pairing of product termini. Cleavage products terminating with paired nucleotides, like the degradation signals found in coding mRNA sequence, were less reactive and more prone to inhibition than products having unpaired nucleotides found in noncoding RNA 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
double-stranded RNA + H2O
5'-phosphooligonucleotides
-
cleaves multimeric tRNA precursor at the spacer region, also involved in processing of precursor rRNA, hnRNA and early T7-mRNA. Also cleaves double-stranded DNA and single-stranded RNA
-
-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
-
involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference, a dsRNA-binding domain recognizes its substrate by interacting with stems capped with conserved AGNN tetraloops
-
-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
-
involved in a variety of cellular functions, including the processing of many non-coding RNAs, mRNA decay, and RNA interference, preferred substrate contains NGNN tetraloops
-
-
?
pre-rRNA + H2O
mature rRNA
-
enzyme is required for processing
-
-
?
pre-snoRNA + H2O
mature snoRNA
-
enzyme is required for processing
-
-
?
pre-snRNA + H2O
mature snRNA
-
enzyme is required for processing
-
-
?
additional information
?
-
the enzyme plays an important role in the maturation of a diverse set of RNAs
-
-
?
additional information
?
-
-
the enzyme plays an important role in the maturation of a diverse set of RNAs
-
-
?
additional information
?
-
the enzyme Rnt1p binds to RNA stems capped with an NGNN tetraloop, via specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain and the guanine nucleotide in the second position of the loop
-
-
?
additional information
?
-
-
the enzyme Rnt1p binds to RNA stems capped with an NGNN tetraloop, via specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain and the guanine nucleotide in the second position of the loop
-
-
?
additional information
?
-
-
enzyme is involved in RNA processing and RNA interference, i.e. RNAi, regulation by a combination of primary and tertiary structural elements allowing a substrate-specific binding and cleavage efficiency
-
-
?
additional information
?
-
-
enzyme is required for maturation of pre-rRNAs
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?
additional information
?
-
-
Rnt1p, the major RNase III in Saccharomyces cerevisiae, cleaves RNA substrates containing hairpins capped by A/uGNN tetraloops, using its double-stranded RNA binding domains, dsRBD, to recognize a conserved tetraloop fold. The dsRBD adopts the same conformation in both the AAGU and AGAA complexes
-
-
?
additional information
?
-
-
processing of dsRNA, specific bp sequence elements can modulate substrate reactivity, and a network of hydrogen bonds provides an energetically important contribution to Rnt1p binding, a phylogenetic-based substrate alignment analysis reveals a statistically significant exclusion of the UA bp from the position adjacent to the tetraloop. Rnt1p cleaves hairpin structures in pre-rRNAs, pre-mRNAs, and transcripts containing noncoding RNAs such as snoRNAs, as part of the respective maturation pathways. The enzyme also interacts with Gar1p, a protein involved in pseudouridylation reactions, via its C-terminal portion adjacent to the dsRBD
-
-
?
additional information
?
-
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the enzyme processes ribosomal RNA, small nucleolar RNA, small nuclear RNA, and messenger RNA
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KCl
Mg2+
additional information
-
the enzyme requires a divalent metal ion for catalysis
KCl
-
substrate affinity is enhanced under low-salt (10 mM KCl) conditions
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
substrate binding is inhibited by a specific sequence within the dsRNA stem, overview
-
additional information
product inhibition, presence of 800 nM products reduces the value of the initial phase kcat by 5fold. The reduction of Rnt1p activity by the product is impaired when the reaction is carried out with a buffer containing 500 mM KCl, which reduces the stability of Rnt1p/RNA complex. Addition of Xrn1p, which degrades the reaction products, to the cleavage reaction significantly increases the steady-state catalytic rate of Rnt1p without affecting the initial burst phase
-
additional information
-
product inhibition, presence of 800 nM products reduces the value of the initial phase kcat by 5fold. The reduction of Rnt1p activity by the product is impaired when the reaction is carried out with a buffer containing 500 mM KCl, which reduces the stability of Rnt1p/RNA complex. Addition of Xrn1p, which degrades the reaction products, to the cleavage reaction significantly increases the steady-state catalytic rate of Rnt1p without affecting the initial burst phase
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetics, substrate binding with diverse RNA substrates
-
additional information
additional information
real-time analysis of Rnt1p cleavage kinetics, RNA binding to purified Rnt1p is monitored, Michaelis-Menten kinetics
-
additional information
additional information
-
real-time analysis of Rnt1p cleavage kinetics, RNA binding to purified Rnt1p is monitored, Michaelis-Menten kinetics
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Rnt1p cleavage of bipartite substrates: 0.087 1/s for EL11:TL as a substrate, 0.248 1/s for EL18-EM:TL as a substrate, 0.55 1/s for EL11-EM:TL as a substrate, 0.302 1/s for EL11-EM+1:TL as a substrate, 0.4 1/s for EL11-5'3'M:TL as a substrate, 0.55 1/s for EL11-dT:TL as a substrate, 0.028 1/s for EL11-ES:TL as a substrate, 0.042 1/s for EL11-5'stemM:TL as a substrate, 0.03 1/s for EL11-A6M:TL as a substrate. Rnt1p cleavage of 2'-fluoro-modified substrate: 0.07 1/s for EL11:TL as a substrate, 0.0283 1/s for EL11-A6F:TL as a substrate, 0.026 1/s for EL11-G7F:TL as a substrate, 0.016 1/s for EL11-C10F:TL as a substrate, 0.026 1/s for EL11-AAGU:TL as a substrate, 0.0115 1/s for EL11-AAGU-A6F:TL as a substrate, 0.013 1/s for EL11-AAGU-A7F:TL as a substrate, 0.0078 1/s for EL11-AAGU-C10F:TL as a substrate, 0.0183 1/s for EL11:TL as a substrate. DELTAN-term cleavage of 2'-fluoro-modified substrate: 0.022 1/s for EL11-A6F:TL as a substrate, 0.012 1/s for EL11-G7F:TL as a substrate, 0.012 1/s for EL11-C10F:TL as a substrate, 0.01 1/s for EL11-AAGU:TL as a substrate, 0.0085 1/s for EL11-AAGU-A6F:TL as a substrate, 0.0073 1/s for EL11-AAGU-A7F:TL as a substrate, 0.00783 1/s for EL11-AAGU-C10F:TL as a substrate
-
additional information
additional information
-
Rnt1p cleavage of bipartite substrates: 0.087 1/s for EL11:TL as a substrate, 0.248 1/s for EL18-EM:TL as a substrate, 0.55 1/s for EL11-EM:TL as a substrate, 0.302 1/s for EL11-EM+1:TL as a substrate, 0.4 1/s for EL11-5'3'M:TL as a substrate, 0.55 1/s for EL11-dT:TL as a substrate, 0.028 1/s for EL11-ES:TL as a substrate, 0.042 1/s for EL11-5'stemM:TL as a substrate, 0.03 1/s for EL11-A6M:TL as a substrate. Rnt1p cleavage of 2'-fluoro-modified substrate: 0.07 1/s for EL11:TL as a substrate, 0.0283 1/s for EL11-A6F:TL as a substrate, 0.026 1/s for EL11-G7F:TL as a substrate, 0.016 1/s for EL11-C10F:TL as a substrate, 0.026 1/s for EL11-AAGU:TL as a substrate, 0.0115 1/s for EL11-AAGU-A6F:TL as a substrate, 0.013 1/s for EL11-AAGU-A7F:TL as a substrate, 0.0078 1/s for EL11-AAGU-C10F:TL as a substrate, 0.0183 1/s for EL11:TL as a substrate. DELTAN-term cleavage of 2'-fluoro-modified substrate: 0.022 1/s for EL11-A6F:TL as a substrate, 0.012 1/s for EL11-G7F:TL as a substrate, 0.012 1/s for EL11-C10F:TL as a substrate, 0.01 1/s for EL11-AAGU:TL as a substrate, 0.0085 1/s for EL11-AAGU-A6F:TL as a substrate, 0.0073 1/s for EL11-AAGU-A7F:TL as a substrate, 0.00783 1/s for EL11-AAGU-C10F:TL as a substrate
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme is a member of the ribonuclease III (RNase III) family
evolution
physiological function
additional information
evolution
-
class I enzymes are the simplest, consisting of those found in bacteria and simple eukaryotes, such as Rnt1 in Saccharomyces cerevisiae. These are thought to be the antecedents of the more complex class II Drosha and class III Dicer proteins. Class I enzymes achieve the dimeric catalytic RNase III module by forming dimers, whereas the more complex class II and III members use intramolecular dimerization of their two RNase III domains
evolution
-
the enzyme belongs to the ribonuclease III (RNase III) family of divalent-metal-ion-dependent phosphodiesterases. RNase III family members share a unique fold (RNase III domain) that can dimerize to form a structure that binds dsRNA and cleaves phosphodiesters on each strand, providing the characteristic 2 nt, 3'-overhang product ends. Domain structures of ribonuclease III family polypeptides, overview
evolution
the enzyme is a member of the ribonuclease III (RNase III) family
physiological function
-
Rnt1p, the major RNase III in Saccharomyces cerevisiae, cleaves RNA substrates containing hairpins capped by A/uGNN tetraloops, using its dsRBD to recognize a conserved tetraloop fold
physiological function
-
the enzyme is involved in RNA quality control. Processing of dsRNA by the enzyme is an essential step in the maturation and decay of coding and noncoding RNAs, including miRNAs and siRNAs
physiological function
members of the ribonuclease III (RNase III) family regulate gene expression by triggering the degradation of double stranded RNA (dsRNA)
additional information
the dsRNA-binding domain and N-terminal domains of enzyme Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site, mechanism, overview. Both rulers interact with the NGNN tetraloop: ruler 1 recognizes the Gua16 base, and ruler 2 secures the Gua16 recognition
additional information
-
the dsRNA-binding domain and N-terminal domains of enzyme Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site, mechanism, overview. Both rulers interact with the NGNN tetraloop: ruler 1 recognizes the Gua16 base, and ruler 2 secures the Gua16 recognition
additional information
-
structure of RNase III double-stranded RNA binding domain complex with a noncanonical RNA substrate, analysis of the binding specificity, overview. The dsRBD adopts the same conformation in both the AAGU and AGAA complexes. The AAGU tetraloop in the complex adopts a backbone fold similar to that of the AGAA tetraloop
additional information
-
features of the Rnt1p-substrate interaction contributing to processing reactivity, overview. Structure analysis and comparison to other enzyme family members, overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
additional information
-
deletion mutant RNT1DELTA2-198 also behaves as a dimer
additional information
-
enzyme contains the conserved dsRNA binding and nuclease domains, the dsRBD self-interacts with the N-terminal domain to stabilize the enzyme homodimer
additional information
-
domain structure: the enzyme is composed of N-terminal domain, RNase III domain and dsRNA binding domain, comparison of class I-III enzymes, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K371A
dissociation constant for RNA is 2.1fold higher than the wild-type value
M368A
dissociation constant for RNA is 1.4fold higher than the wild-type value
M368E
dissociation constant for RNA is nearly identical to wild-type value
R372A
dissociation constant for RNA is nearly identical to wild-type value
S376E
dissociation constant for RNA is 1.3fold higher than the wild-type value
additional information
additional information
-
construction of deletion mutants RNT1DELTA2-329 and RNT1DELTA2-198, which are both catalytically active in vitro but do not rescue a growth defective mutant and are not able to retain activity and viability in vivo, construction of a AGNN-loop exchange mutant GNRA-loop shows reduced activity and substrate selectivity
additional information
-
construction of several deletion mutants, lacking parts or total of the C-terminus or N-terminus, deletion of the N-terminal domain leads to slight accumulation of unprocessed 25S pre-rRNA in vivo and reduced enzyme activity in vitro
additional information
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building a class of RNA sensing actuation devices based on direct integration of RNA aptamers into a region of the RNase III Rnt1p hairpin that modulates Rnt1p cleavage rates, design of an Rnt1p switch platform based on direct replacement of the CEB with an aptamer sequence. Integration of a sensor component, DELTATCT-4 aptamer, into the actuator component, R31L-3B4Inv Rnt1p hairpin. Ligand binding to the integrated aptamer domain is associated with a structural change sufficient to inhibit Rnt1p processing, overview. Three tuning strategies based on the incorporation of different functional modules into the Rnt1p switch platform optimize switch dynamics and ligand responsiveness. Application of multiple switch modules decreases theophylline responsiveness and increases fold-change. The tuning modules can be implemented combinatorially in a predictable manner to further improve the regulatory response properties of the switch. The modularity and tunability of the Rnt1p switch platform will allow for rapid optimization and tailoring of this gene control device. Method evaluation and system stabililty, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli
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recombinant His-tagged wild-type and mutant enzymes from Escherichia coli, expression of the mutant enzymes in a two-hybrid system in Saccharomyces strains
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of GFP-tagged Rnt1p in Saccharomyces cerevisiae strain W303 from plasmid pCS321
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expression of N-terminal and dsRNA binding domain in a two-hybrid system, expression of His-tagged wild-type enzyme and deletion mutants in Escherichia coli BL21(DE3)
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expression of wild-type and mutant enzymes in Escherichia coli BL21(DE3) as C-terminally His-tagged proteins
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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101
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Saccharomyces cerevisiae (Q02555), Saccharomyces cerevisiae
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11
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Saccharomyces cerevisiae (Q02555), Saccharomyces cerevisiae
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62
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Thermotoga maritima, Aquifex aeolicus (O67082), Escherichia coli (P0A7Y0), Saccharomyces cerevisiae (Q02555), Homo sapiens (Q9NRR4), Homo sapiens (Q9UPY3)
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Saccharomyces cerevisiae
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17
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Aquifex aeolicus, Saccharomyces cerevisiae, Escherichia coli, Giardia intestinalis, Homo sapiens
Lavoie, M.; Abou Elela, S.
Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage
Biochemistry
47
8514-8526
2008
Saccharomyces cerevisiae (Q02555), Saccharomyces cerevisiae
Babiskin, A.H.; Smolke, C.D.
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39
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Saccharomyces cerevisiae
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Structure
19
999-1010
2011
Saccharomyces cerevisiae
Liang, Y.H.; Lavoie, M.; Comeau, M.A.; Abou Elela, S.; Ji, X.
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Mol. Cell
54
431-444
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Saccharomyces cerevisiae (Q02555), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (Q02555)
Johanson, T.M.; Lew, A.M.; Chong, M.M.
MicroRNA-independent roles of the RNase III enzymes Drosha and Dicer
Open Biology
3
130144
2013
Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Homo sapiens, Mus musculus
Nicholson, A.W.
Ribonuclease III mechanisms of double-stranded RNA cleavage
Wiley Interdiscip. Rev. RNA
5
31-48
2013
Saccharomyces cerevisiae, Escherichia coli, Homo sapiens, Schizosaccharomyces pombe, Giardia intestinalis (A8BQJ3), Aquifex aeolicus (O67082), Mycobacterium tuberculosis (P9WH03), Thermotoga maritima (Q9X0I6), Mycobacterium tuberculosis H37Rv (P9WH03)
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The catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate
Nucleic Acids Res.
44
7911-7921
2016
Saccharomyces cerevisiae (C7GRB2), Saccharomyces cerevisiae, Saccharomyces cerevisiae JAY291 (C7GRB2)
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