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Information on EC 3.1.26.3 - ribonuclease III and Organism(s) Aquifex aeolicus and UniProt Accession O67082
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3.1.26.3 ribonuclease IIISpecify your search results
Word Map
- 3.1.26.3
- rnai
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argonaute
- drosophila
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germline
-
rna-induced
- viruses
- duplex
- ovarian
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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
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3'utrs
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cystic
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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
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rnai-based
- goiter
- hamartoma
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microrna-mediated
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let-7a
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exportin
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dead-box
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rna-processing
- pre-rrnas
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mirna-based
The taxonomic range for the selected organisms is: Aquifex aeolicus
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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-
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nuclease, ribo-, D
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p241
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ribonuclease D
RNase D
RNase O
ribonuclease D
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RNase D
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RNase O
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
Endonucleolytic cleavage to a 5'-phosphomonoester
catalytic active site and substrate binding site structure and number determines the classification into classes I to III, overview, mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
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
Aa-[16S[micro-hp]RNA] + H2O
?
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structures of the Aquifex pre-16S and pre-23S rRNA processing stems and corresponding hairpin substrates, overview
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-
?
double-stranded RNA + H2O
?
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RNA 5, a 30 base stem-loop RNA of the sequence 5 '-AUAAAGGUCAUUCGCAAGAGUGGCCUUUAU-3', is cleaved by RNase III (D44N) from Aquifex aeolicus. The products of the reaction include a dinucleotide 5'-AU-3' and a 28 base stem-loop RNA with a two-base 3' overhang (RNA 6). Two RNA 6 molecules and a dimeric mutant enzyme D44N molecule form a product complex
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-
?
double-stranded RNA + H2O
5'-phosphooligonucleotides
responsible for processing of dsRNA
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-
?
dsRNA + H2O
mature RNA
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reshaping of fully or partially double-stranded RNA precursors in to mature RNAs involved in pre-mRNA splicing, RNA modification, translation, gene silencing, and regulation of developmental timing
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?
dsRNA + H2O
mature RNA
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cleavage of fully or partially double-stranded RNA precursors into mature structural and catalytic RNAs such as the snRNAs that splice pre-mRNA, rRNAs, and tRNAs that function in translation, swnoRNAs that guide modification of rRNAs, and individual mRNAs, whose expression they regulate
staggered breaks with 2 nt, 3'-overhanging ends and 5'-phosphate and 3'-hydroxy termini
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?
additional information
?
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cleave internally 32P-labeled R1.1(WC) RNA
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-
?
additional information
?
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cleave internally 32P-labeled R1.1(WC) RNA
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-
?
additional information
?
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small hairpins based on the stem structures associated with the Aquifex 16S and 23S rRNA precursors are cleaved at sites that are consistent with production of the immediate precursors to the mature rRNAs. Substrate reactivity is independent of the distal box sequence, but is strongly dependent on the proximal box sequence. RNase III mechanism of dsRNA cleavage, overview
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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
responsible for processing of dsRNA
-
-
?
dsRNA + H2O
mature RNA
-
reshaping of fully or partially double-stranded RNA precursors in to mature RNAs involved in pre-mRNA splicing, RNA modification, translation, gene silencing, and regulation of developmental timing
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?
additional information
?
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small hairpins based on the stem structures associated with the Aquifex 16S and 23S rRNA precursors are cleaved at sites that are consistent with production of the immediate precursors to the mature rRNAs. Substrate reactivity is independent of the distal box sequence, but is strongly dependent on the proximal box sequence. RNase III mechanism of dsRNA cleavage, overview
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
Mg2+
Mn2+
additional information
Mg2+
two Mg2+ ions are required for the cleavage of each phosphodiester bond
additional information
no activation by Ca2+. The enzyme requires a divalent metal ion for catalysis, catalysis appears to be largely driven by the two metals. The adjacency of the two metal ions and their interaction with the scissile phosphodiester linkage fit the well-studied two-metal-ion catalytic mechanism, wherein one metal binds and activates the water nucleophile, and the second metal facilitates departure of the 3'-oxygen atom. Both metal ions are jointly coordinated to the side chain of a highly conserved, functionally essential glutamic acid E110
additional information
RNase III requires two transition metal ions to stabilize the catalytic valley where it cleaves dsRNAI
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
RNase III activity during various environmental stresses, overview
physiological function
physiological function
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ribonuclease III cleaves double-stranded structures in bacterial RNAs and participates in diverse RNA maturation and decay pathways, RNase III mechanism of dsRNA cleavage, overview
additional information
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
RNase III is a member of the phylogenetically highly conserved endoribonuclease III family
physiological function
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
RNase III activity during various environmental stresses, overview
additional information
structure analysis and comparison to other enzyme family members, overview
additional information
crystallographic and modeling studies of RNase III from Aquifex aeolicus suggest that highly conserved six negatively charged residues, including E40/D44/D107/E110 and E37/E64, create two potential RNA cleavage sites within the catalytic valley
additional information
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Q157 is a conserved glutamine in the Aa-RNase III dsRNA-binding domain
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
12 three-dimensional structures of bacterial RNase III in various forms have been reported
Aquifex aeolicus RNase III also has been cocrystallized with dsRNA or specific hairpin substrates
crystal structure analysis of wild-type enzyme and D44N mutant enzyme
hanging-drop vapour-diffusion method at 19°C. Crystallisation of the mutant enzyme E110Q in complex with dsRNA 2-2 formed by self-complementary sequence 5'-CGAACUUCGCG-3', complex of wild-type enzyme with dsRNA 3-3 formed by self-complementary sequence 5'-AAAUAUAUAUUU-3', complex of wild-type enzyme with dsRNA 4-4 formed by self-complementary sequence 5'-CGCGAAUUCGCG-3' and complex of mutant enzyme E110Q with dsRNA 4-4 formed by self-complementary sequence 5'-CGCGAAUUCGCG-3'
in complex with dsRNA, in the presence of Mg2+ or Mn2+ one metal ion bound per polypeptide chain
three crystal structures of RNase III in complex with double-stranded RNA are solved at resolutions ranging from 1.7 to 2.9 A
crystal structure of Aquifex aeolicus mutant enzyme D44N with double-stranded RNA bound in its catalytic valley
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the structure of Aa-D44N RNase III in complex with a RNA product is determined at a resolution of 2.05 A
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D44N
E110A
uncoupling of the dsRNA-binding and processing abilities of the enzyme
E110K
E110Q
uncoupling of the dsRNA-binding and processing abilities of the enzyme
D44N
E110Q
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mutant enzyme has negligible RNA cleavage activity but retains its RNA binding affinity
Q157A
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is a conserved glutamine in the Aa-RNase III dsRNA-binding domain. Aa-RNase III cleavage of the pre-16S substrate is blocked by the Q157A mutation, which reflects a loss of substrate binding affinity. But the Q157A mutation does not affect folding or structure in a significant manner
D44N
site-directed mutagenesis, the mutation does not fully inactivate the enzyme, and dsRNA cleavage occurs during crystallization of the mutant enzyme
E110K
loss of Mg2+ binding capacity, non-functional, uncoupling of the dsRNA-binding and processing abilities of the enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 85
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Aa-RNase III activity increases from 35°C, reaching a maximum at 70°C, and shows significant activity up to 85°C
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
the full-length Aa-D44N is cloned for overproduction of the enzyme in Escherichia coli BL21DE3 CodonPlus-RIL cells
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zamore, P.D.
Thirty-three years later, a glimpse at the ribonuclease III active site
Mol. Cell
8
1158-1160
2001
Aquifex aeolicus, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Homo sapiens
Gan, J.; Tropea, J.E.; Austin, B.P.; Court, D.L.; Waugh, D.S.; Ji, X.
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III
Cell
124
355-366
2006
Aquifex aeolicus
Gan, J.; Tropea, J.E.; Austin, B.P.; Court, D.L.; Waugh, D.S.; Ji, X.
Intermediate states of ribonuclease III in complex with double-stranded RNA
Structure
13
1435-1442
2005
Aquifex aeolicus (O67082)
Ji, X.
Structural basis for non-catalytic and catalytic activities of ribonuclease III
Acta Crystallogr. Sect. D
62
933-940
2006
Thermotoga maritima, Aquifex aeolicus (O67082), Escherichia coli (P0A7Y0), Saccharomyces cerevisiae (Q02555), Homo sapiens (Q9NRR4), Homo sapiens (Q9UPY3)
MacRae, I.J.; Doudna, J.A.
Ribonuclease revisited: structural insights into ribonuclease III family enzymes
Curr. Opin. Struct. Biol.
17
138-145
2007
Aquifex aeolicus, Saccharomyces cerevisiae, Escherichia coli, Giardia intestinalis, Homo sapiens
Gan, J.; Shaw, G.; Tropea, J.E.; Waugh, D.S.; Court, D.L.; Ji, X.
A stepwise model for double-stranded RNA processing by ribonuclease III
Mol. Microbiol.
67
143-154
2008
Aquifex aeolicus (O67082)
Meng, W.; Nicholson, R.H.; Nathania, L.; Pertzev, A.V.; Nicholson, A.W.
New approaches to understanding double-stranded RNA processing by ribonuclease III purification and assays of homodimeric and heterodimeric forms of RNase III from bacterial extremophiles and mesophiles
Methods Enzymol.
447
119-129
2008
Escherichia coli, Aquifex aeolicus (O67082), Aquifex aeolicus, Thermotoga maritima (Q9X0I6), Thermotoga maritima
Shi, Z.; Nicholson, R.H.; Jaggi, R.; Nicholson, A.W.
Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates
Nucleic Acids Res.
39
2756-2768
2011
Aquifex aeolicus
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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