Literature summary for 3.1.26.3 extracted from

Nicholson, A.W.
Ribonuclease III mechanisms of double-stranded RNA cleavage (2013), Wiley Interdiscip. Rev. RNA, 5, 31-48.

Activating Compound

Activating Compound	Comment	Organism	Structure
additional information	T7-induced catalytic enhancement of the enzyme	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystal structure analysis of wild-type enzyme and D44N mutant enzyme	Aquifex aeolicus
crystal structure analysis, PDB ID 1O0W	Thermotoga maritima
crystal structure analysis, PDB ID 2A11	Mycobacterium tuberculosis
crystal structure analysis, PDB ID 2ffl, crystallographic analysis of the minimal Dicer of Giardia intestinalis, containing the PAZ and tandem RNase III domainsl	Giardia intestinalis

Protein Variants

Protein Variants	Comment	Organism
D44N	site-directed mutagenesis, the mutation does not fully inactivate the enzyme, and dsRNA cleavage occurs during crystallization of the mutant enzyme	Aquifex aeolicus

Inhibitors

Inhibitors	Comment	Organism	Structure
additional information	the RNase III activity in vivo is responsive to osmotic stress	Escherichia coli

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytoplasm	dicer	Homo sapiens	5737	-
nucleus	drosha	Homo sapiens	5634	-

Metals/Ions

Metals/Ions	Comment	Organism
Co2+	activates	Escherichia coli
Co2+	activates	Homo sapiens
Co2+	activates	Saccharomyces cerevisiae
Co2+	activates	Schizosaccharomyces pombe
Co2+	activates	Aquifex aeolicus
Co2+	activates	Thermotoga maritima
Co2+	activates	Mycobacterium tuberculosis
Co2+	activates	Giardia intestinalis
Mg2+	activates	Escherichia coli
Mg2+	activates	Homo sapiens
Mg2+	activates	Saccharomyces cerevisiae
Mg2+	activates	Schizosaccharomyces pombe
Mg2+	activates	Aquifex aeolicus
Mg2+	activates	Thermotoga maritima
Mg2+	activates	Mycobacterium tuberculosis
Mg2+	activates	Giardia intestinalis
Mn2+	activates	Escherichia coli
Mn2+	activates	Homo sapiens
Mn2+	activates	Saccharomyces cerevisiae
Mn2+	activates	Schizosaccharomyces pombe
Mn2+	activates	Aquifex aeolicus
Mn2+	activates	Thermotoga maritima
Mn2+	activates	Mycobacterium tuberculosis
Mn2+	activates	Giardia intestinalis
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	Aquifex aeolicus
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 E117	Escherichia coli
additional information	the enzyme requires a divalent metal ion for catalysis	Homo sapiens
additional information	the enzyme requires a divalent metal ion for catalysis	Saccharomyces cerevisiae
additional information	the enzyme requires a divalent metal ion for catalysis	Schizosaccharomyces pombe
additional information	the enzyme requires a divalent metal ion for catalysis	Thermotoga maritima
additional information	the enzyme requires a divalent metal ion for catalysis	Mycobacterium tuberculosis
additional information	the enzyme requires a divalent metal ion for catalysis	Giardia intestinalis
Ni2+	activates	Escherichia coli
Ni2+	activates	Homo sapiens
Ni2+	activates	Saccharomyces cerevisiae
Ni2+	activates	Schizosaccharomyces pombe
Ni2+	activates	Aquifex aeolicus
Ni2+	activates	Thermotoga maritima
Ni2+	activates	Mycobacterium tuberculosis
Ni2+	activates	Giardia intestinalis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
additional information	Aquifex aeolicus	processing of dsRNA	?	-	?
additional information	Thermotoga maritima	processing of dsRNA	?	-	?
additional information	Mycobacterium tuberculosis	processing of dsRNA	?	-	?
additional information	Saccharomyces cerevisiae	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	Giardia intestinalis	processing of dsRNA, the PAZ domain specifically recognizes the 2-nt, 3'-overhangs of a processed dsRNA terminus	?	-	?
additional information	Homo sapiens	processing of dsRNA. Drosha acts on primary transcripts synthesized by RNA polymerase II that typically contain several miRNAs. Site-specific cleavage within irregular, extended hairpin structures (pri-miRNAs) creates the pre-miRNAs that then are delivered by Exportin5 to the cytoplasm for final maturation by Dicer. Drosha functions within a complex termed the microprocessor that contains a protein, DGCR8, that is required for Drosha action	?	-	?
additional information	Schizosaccharomyces pombe	processing of dsRNA. Pac1p cleaves hairpin structures in pre-rRNAs, pre-mRNAs, and transcripts containing noncoding RNAs such as snoRNAs, as part of the respective maturation pathways	?	-	?
additional information	Escherichia coli	the enzyme cleaves the proU operon transcript reducing its half-life from 65 sec to 4 sec, the rapid degradation ensures efficient inhibition of proU expression and further uptake of osmoprotectants. Processing of dsRNA, product release is the rate-limiting step in the catalytic pathway	?	-	?
additional information	Mycobacterium tuberculosis H37Rv	processing of dsRNA	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Aquifex aeolicus	O67082	-	-
Escherichia coli	-	-	-
Giardia intestinalis	A8BQJ3	-	-
Homo sapiens	-	-	-
Mycobacterium tuberculosis	P9WH03	-	-
Mycobacterium tuberculosis H37Rv	P9WH03	-	-
Saccharomyces cerevisiae	-	-	-
Schizosaccharomyces pombe	-	-	-
Thermotoga maritima	Q9X0I6	-	-

Posttranslational Modification

Posttranslational Modification	Comment	Organism
phosphoprotein	phosphorylation on a serine in the RNase III domain activates the enzyme, the covalent modification facilitates product release, which is the rate-limiting step in the catalytic pathway	Escherichia coli

Reaction

Reaction	Comment	Organism	Reaction ID
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	Homo sapiens	a
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	Saccharomyces cerevisiae	a
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	Schizosaccharomyces pombe	a
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	Aquifex aeolicus	a
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	Thermotoga maritima	a
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	Mycobacterium tuberculosis	a
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	Giardia intestinalis	a
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, essential irreversibility of the hydrolytic step	Escherichia coli	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	processing of dsRNA	Aquifex aeolicus	?	-	?
additional information	processing of dsRNA	Thermotoga maritima	?	-	?
additional information	processing of dsRNA	Mycobacterium tuberculosis	?	-	?
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	Saccharomyces cerevisiae	?	-	?
additional information	processing of dsRNA, the PAZ domain specifically recognizes the 2-nt, 3'-overhangs of a processed dsRNA terminus	Giardia intestinalis	?	-	?
additional information	processing of dsRNA. Drosha acts on primary transcripts synthesized by RNA polymerase II that typically contain several miRNAs. Site-specific cleavage within irregular, extended hairpin structures (pri-miRNAs) creates the pre-miRNAs that then are delivered by Exportin5 to the cytoplasm for final maturation by Dicer. Drosha functions within a complex termed the microprocessor that contains a protein, DGCR8, that is required for Drosha action	Homo sapiens	?	-	?
additional information	processing of dsRNA. Pac1p cleaves hairpin structures in pre-rRNAs, pre-mRNAs, and transcripts containing noncoding RNAs such as snoRNAs, as part of the respective maturation pathways	Schizosaccharomyces pombe	?	-	?
additional information	the enzyme cleaves the proU operon transcript reducing its half-life from 65 sec to 4 sec, the rapid degradation ensures efficient inhibition of proU expression and further uptake of osmoprotectants. Processing of dsRNA, product release is the rate-limiting step in the catalytic pathway	Escherichia coli	?	-	?
additional information	Dicer substrate recognition and specificity, overview	Giardia intestinalis	?	-	?
additional information	Drosha cleavage site analysis, reactivity determinants of a pri-miRNA substrate for Drosha, and a proposed DGCR8-dsRNA interaction, and Dicer substrate recognition and specificity, overview	Homo sapiens	?	-	?
additional information	processing of dsRNA	Mycobacterium tuberculosis H37Rv	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	-	Escherichia coli
homodimer	-	Saccharomyces cerevisiae
homodimer	-	Schizosaccharomyces pombe
homodimer	-	Aquifex aeolicus
homodimer	-	Thermotoga maritima
homodimer	-	Mycobacterium tuberculosis
homodimer	the Drosha polypeptide possesses tandem RNase III domains and a C-terminal dsRBD. The RNase III domains form an intramolecular pseudodimer with two catalytic sites. The Drosha dsRBD structure shows an alpha1-alpha1 loop element with a dynamic, extended structure	Homo sapiens
homodimer	the minimal Dicer of Giardia intestinalis contains the PAZ and tandem RNase III domains, pseudodimeric RNase III domain	Giardia intestinalis
More	inability of the Drosha dsRBD to form a stable complex on its own with dsRNA. Dicer structure analysis, overview	Homo sapiens

Synonyms

Synonyms	Comment	Organism
Dicer	-	Homo sapiens
Dicer	-	Giardia intestinalis
Drosha	-	Homo sapiens
Pac1p	-	Schizosaccharomyces pombe
RNase III	-	Escherichia coli
RNase III	-	Homo sapiens
RNase III	-	Saccharomyces cerevisiae
RNase III	-	Schizosaccharomyces pombe
RNase III	-	Aquifex aeolicus
RNase III	-	Thermotoga maritima
RNase III	-	Mycobacterium tuberculosis
RNase III	-	Giardia intestinalis
Rnt1p	-	Saccharomyces cerevisiae

General Information

General Information	Comment	Organism
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	Escherichia coli
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	Saccharomyces cerevisiae
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	Schizosaccharomyces pombe
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	Aquifex aeolicus
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	Thermotoga maritima
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	Mycobacterium tuberculosis
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	Giardia intestinalis
evolution	the enzyme belongs to the 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	Homo sapiens
additional information	features of the Rnt1p-substrate interaction contributing to processing reactivity, overview. Structure analysis and comparison to other enzyme family members, overview	Saccharomyces cerevisiae
additional information	structure analysis and comparison to other enzyme family members, overview	Escherichia coli
additional information	structure analysis and comparison to other enzyme family members, overview	Schizosaccharomyces pombe
additional information	structure analysis and comparison to other enzyme family members, overview	Aquifex aeolicus
additional information	structure analysis and comparison to other enzyme family members, overview	Thermotoga maritima
additional information	structure analysis and comparison to other enzyme family members, overview	Mycobacterium tuberculosis
additional information	structure analysis and comparison to other enzyme family members, overview. Additional domains, including the dsRNA-binding and PAZ domains, that cooperate with the RNase III domain to select target sites, regulate activity, confer processivity, and support the recognition of structurally diverse substrates	Homo sapiens
additional information	structure analysis and comparison to other enzyme family members, overview. Additional domains, including the dsRNA-binding and PAZ domains, that cooperate with the RNase III domain to select target sites, regulate activity, confer processivity, and support the recognition of structurally diverse substrates	Giardia intestinalis
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	Homo sapiens
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	Aquifex aeolicus
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	Thermotoga maritima
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	Mycobacterium tuberculosis
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	Giardia intestinalis
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. RNase III is negatively regulated by the macrodomain protein, YmdB, and might be dependent upon the direct interaction of the two proteins. The enzyme's catalytic activity is also subject to positive regulation. The T7 bacteriophage expresses a protein kinase that phosphorylates RNase III and enhances catalytic activity about fourfold, as measured in vitro	Escherichia coli
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	Saccharomyces cerevisiae
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	Schizosaccharomyces pombe