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Enzyme Nomenclature
Information on EC 3.1.26.12 - ribonuclease E
for references in articles please use BRENDA:EC3.1.26.12
Word Map on EC 3.1.26.12
- 3.1.26.12
-
degradosome
-
phosphorylase
- polynucleotide
- pnpase
-
endonuclease
-
helicase
-
endonucleolytic
-
stem-loops
- enolase
- exoribonuclease
-
srnas
- polya
-
single-stranded
-
rna-binding
-
e-dependent
-
ribonucleolytic
-
polycistronic
-
autoregulation
- ompa
-
dead-box
-
e-mediated
-
base-pairing
-
endoribonucleolytic
-
5'-terminal
-
e-like
-
monophosphorylated
-
intercistronic
-
cole1-type
-
shine-dalgarno
-
rho-independent
-
5'-monophosphorylated
-
rna-processing
-
au-rich
-
hfq-dependent
- glm
- medicine
- analysis
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Specify your search results
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
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EC NUMBER 
COMMENTARY 
3.1.26.12
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RECOMMENDED NAME
GeneOntology No.
ribonuclease E
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
-
-
-
-
endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
catalytic mechanism, the 10-mer and 13-mer RNAs are bound entirely by one tetramer, while the 15-mer RNA is long enough for it to be shared between two different tetramers in the crystal lattice, and this RNA extends from the 5' sensing pocket of one tetramer into the binding channel and catalytic site of a symmetry-related tetramer. Two molecules of 15-mer RNA pass each other in antiparallel orientations and form a highly distorted duplex, Asp 303 and Asp 346 might act as general bases to activate the attacking water
-
endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
molecular mechanism, residues A326 and L385 are involved in substrate binding
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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CAS REGISTRY NUMBER
COMMENTARY
76106-82-6
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
667576, 669073, 669186, 669202, 669862, 670301, 670423, 670424, 670667, 688345, 691958, 693689, 694008, 694009, 694243, 694247, 708928, 710335, 713614, 716262, 716266, 729757, 729924, 730503, 730512, 730699, 730781, 730815
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-
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UniProt
strains CJ1827 and CJ1828 derived from strain MC1061, gene rne or ams
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
malfunction
-
RNAI signals of the DELTA225 mutant lacking the PNPase binding region are similar to those of the wild-type strain. RNAI degradation intermediate accumulates in the DELTA374 mutant lacking the PNPase binding region and protein scaffold domain, which binds to RhlB and enolase, as compared with that in the wild-type strain
malfunction
-
an NCgl2281 knockout mutant accumulates 5S rRNA precursor molecules. The processing of 16S and 23S rRNA, tRNA, and tmRNA is normal in the mutant cells. Primer extension analysis reveals that the RNase E/G orthologue cleaves at the -1 site of the 5' end of 5S rRNA. Mapping of the 5' and 3' ends of 5S rRNA precursors in NCgl2281 knockout mutant, overview
malfunction
-
absence of RNase E differentially affects the decay of specific mRNAs. Neither the native nor N-terminal extended form of RNase G can restore the growth defect associated with either the rne-1 or rneD1018 alleles even when expressed at very high protein levels. In contrast, two distinct spontaneously derived single amino acid substitutions within the predicted RNase H domain of RNase G, generating the rng-219 and rng-248 alleles, result in complementation of the growth defect associated with various RNase E mutants
malfunction
-
mutations in endoribonucleases RNase E reduce Salmonella virulence capacity. Mutants display an impaired motility, by forming a barely detectable motility ring after 8 h of incubation that remains much smaller than the one formed by the wild type after 24 h of incubation
malfunction
-
RNase E deletion or inactivation of temperature-sensitive RNase E protein precludes normal initiation of the SOS response. RNase E-deficient cells remain able to produce RNA and protein during the period when SOS response is inhibited by lack of the enzyme
malfunction
-
an NCgl2281 knockout mutant accumulates 5S rRNA precursor molecules. The processing of 16S and 23S rRNA, tRNA, and tmRNA is normal in the mutant cells. Primer extension analysis reveals that the RNase E/G orthologue cleaves at the -1 site of the 5' end of 5S rRNA. Mapping of the 5' and 3' ends of 5S rRNA precursors in NCgl2281 knockout mutant, overview
-
metabolism
-
the endoribonuclease RNase E of Escherichia coli is an essential enzyme that plays a major role in all aspects of RNA metabolism
metabolism
-
RNase E-dependent degradation of sinI mRNA from the 5'-end is one of the steps mediating a high turnover of sinI mRNA, which allows the Sin quorum-sensing system to respond rapidly to changes in transcriptional control of N-acyl-homoserine lactone production. RNase E acts on the 5'-untranslated region of sinI independently of the posttranscriptional regulator Hfq
metabolism
-
direct entry by RNase E has a major role in bacterial RNA metabolism. Direct entry is mediated by specific unpaired regions that are adjacent to, but not contiguous with, segments cleaved by RNase E. A 5'-monophosphate is not required to activate the catalytic step
metabolism
-
RNase E-dependent degradation of sinI mRNA from the 5'-end is one of the steps mediating a high turnover of sinI mRNA, which allows the Sin quorum-sensing system to respond rapidly to changes in transcriptional control of N-acyl-homoserine lactone production. RNase E acts on the 5'-untranslated region of sinI independently of the posttranscriptional regulator Hfq
-
physiological function
-
RNase E is involved in the post-transcriptional regulation of NifA expression. Host factor required-dependent RNase E cleavage is essential for NifA translation, probably by making ribosome-binding sites accessible
physiological function
RNase E microdomain sequences are well-conserved with those described in Escherichia coli. The RNase E C-terminal half is less conserved and structured than its N-terminal half. RNase E is a hub protein with multiple interaction interfaces that are under different evolutionary pressures. RNase E can rescue the temperature sensitive rne-1 phenotype of Escherichia coli
physiological function
-
knockout mutant cells accumulate 5S rRNA precursor molecules. The processing of 16S and 23S rRNA, tRNA, and tmRNA is normal. RNase E/G cleaves at the -1 site of the 5' end of 5S rRNA. 3' maturation is essentially unaffected; NCgl2281 endoribonuclease is involved in the 5' maturation of 5S rRNA
physiological function
both the full-length and the N-terminal part of RNase EV functionally complement Escherichia coli RNase E and their expression consequently supports normal growth of RNase E-depleted Escherichia coli cells. Escherichia coli cells expressing N-RneV show copy numbers of ColE1-type plasmid similar to that of Escherichia coli cells expressing N-Rne
physiological function
-
RNase E is a key component of the RNA degradosome, a multienzyme complex hat plays a central role in mRNA turnover and the processing of stable RNA in eubacteria. The degradosome is composed of a tetramer of RNase E molecules interacting via their N-terminal regions, with the C-terminal end of each RNase E molecule complexed with a monomer of RhlB, a dimer of enolase, and a trimer of PNPase
physiological function
-
RNase E is responsible for the functional interaction with Hfq to cause the sRNA-mediated destabilization of target mRNAs. the RNA chaperon Hfq along with Hfq-binding sRNAs stably binds to RNase E in Escherichia coli. The role of the Hfq-RNase E interaction is to recruit RNase E to target mRNAs of sRNAs resulting in the rapid degradation of the mRNA-sRNA hybrid. The C-terminal scaffold region of RNase E is responsible for the interaction with Hfq. Mutational interaction analysis, overview
physiological function
-
the phosphate sensor domain in the enzyme is required for efficient autoregulation of RNase E synthesis. Impact of the 5'-sensor on mRNA stability, overview; viable mutations affecting the 5'-phosphate sensor of RNase E, including R169Q or T170A, become lethal when combined with deletions removing part of the non-catalytic C-terminal domain of RNase E. The phosphate sensor is required for efficient autoregulation of RNase E synthesis as RNase E R169Q is strongly overexpressed with accumulation of proteolytic fragments. In addition, mutation of the phosphate sensorstabilizes the rpsT P1 mRNA as much as sixfold and slows the maturation of 16S rRNA. The decay of other model mRNAs and the processing of several tRNA precursors are unaffected by mutations in the phosphate sensor
physiological function
-
extraordinarily long antisense RNAs of 3.5 and 7 kb protect a set of mRNAs from RNase E degradation that accumulate during phage infection. These antisense RNA-mRNA duplex formations mask single-stranded recognition sites of RNase E, leading to increased stability of the mRNAs. The interactions directly modulate RNA stability and provide an explanation for enhanced transcript abundance of certain mRNAs during phage infection
physiological function
-
neither the native nor N-terminal extended form of RNase G can restore the growth defect associated with RNase E deletion mutants even when expressed at very high protein levels. In contrast, two distinct spontaneously derived single amino acid substitutions within the predicted RNase H domain of RNase G, generating the rng-219 and rng-248 alleles, result in complementation of the growth defect associated with various RNase E mutants, suggesting that this region of the two proteins may help distinguish their in vivo biological activities; RNase E is essential for cell viability and plays a major role in mRNA decay, rRNA maturation, tRNA processing, and a variety of other aspects of RNA metabolism. Maturation of tRNACys, tRNAHis, and tRNAPro but not tRNAAsn is completely dependent on RNase E
physiological function
the role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs
physiological function
-
Escherichia coli cells normally require RNase E activity to form colonies
physiological function
-
RNase E function is required to mount a normal SOS response
physiological function
-
knockout mutant cells accumulate 5S rRNA precursor molecules. The processing of 16S and 23S rRNA, tRNA, and tmRNA is normal. RNase E/G cleaves at the -1 site of the 5' end of 5S rRNA. 3' maturation is essentially unaffected; NCgl2281 endoribonuclease is involved in the 5' maturation of 5S rRNA
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physiological function
-
Escherichia coli cells normally require RNase E activity to form colonies
-
physiological function
-
extraordinarily long antisense RNAs of 3.5 and 7 kb protect a set of mRNAs from RNase E degradation that accumulate during phage infection. These antisense RNA-mRNA duplex formations mask single-stranded recognition sites of RNase E, leading to increased stability of the mRNAs. The interactions directly modulate RNA stability and provide an explanation for enhanced transcript abundance of certain mRNAs during phage infection
-
physiological function
-
RNase E is involved in the post-transcriptional regulation of NifA expression. Host factor required-dependent RNase E cleavage is essential for NifA translation, probably by making ribosome-binding sites accessible
-
physiological function
-
the role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs
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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
13mer nucleotide sequence of RNAI + H2O
?
-
endonucleolytic cleavage, a synthetic 13-nt oligoribonucleotide, representing the cleavage site of RNAI, from the 5' end, with the canonical RNase E cleavage site located between U5 and A6
-
-
?
5' monophosphorylated RNA oligonucleotides + H2O
?
-
several synthetic substrates, overview
-
-
?
5'-capped RNA I.26 + H2O
?
-
low activity, cleavage of the 5' substrate end
-
-
?
5'-GAGACAGUAUUUG + H2O
5'-GAGACAGU + AUUUG
-
LU13 substrate, LU13 is a BR13 derivative that has the central G of the 5' triplet replaced with an A. 5'-biotinylated LU13 is cleaved more rapidly when conjugated to streptavidin prior to incubation with N-terminal half-RNase E. In the absence of streptavidin conjugation, 5'-biotinylated LU13 is cleaved as poorly as its 5' hydroxylated equivalent
-
-
?
5'-GGGACAGUAUUUG + H2O
5'-GGGACAGU + AUUUG
-
BR13 substrate, RNase E can cleave certain RNAs rapidly without requiring a 5'-monophosphorylated end. Cleavage of 5'-hydroxylated oligonucleotide substrate by the N-terminal half of RNase E. RNase E can bind with higher affinity to a 5'-hydroxylated substrate with multiple single-stranded regions than to a 5'-monophosphorylated substrate with one single-stranded site
-
-
?
5'-labeled RNA oligonucleotides + H2O
?
-
synthetic RNA substrate variants based on known enzyme RNA substrate sequences, recombinant Rne498 catalytic domain, cleavage site specificity, overview
-
-
?
5'-triphosphorylated cspA mRNA + H2O
?
-
RNase E recognizes multiple single-stranded regions in cspA mRNA
-
-
?
5'-triphosphorylated epd-pgk RNA + H2O
?
-
RNase E cleavage of 5'-triphosphorylated epd-pgkRNA is faster than 5'-triphosphorylated 9S RNA and RNAi, but not as fast as the rate of cleavage of 5'-triphosphorylated cspA mRNA
-
-
?
5'ACAGUAUUUG-fluorescein + H2O
5'ACAGU + AUUUG-fluorescein
-
5' monophosphorylated, 3' fluorescein-labeled synthetic substrate with protective 2'-O-methyl groups at all positions based on the 5' cleavage site of pBR322 RNA I
-
-
?
5'AUCAAAGAAA + H2O
5'AUCAAAGA + AA
-
5'-labeled synthetic RNA substrate, modified 9S RNA sequence, recombinant Rne498 catalytic domain, no activity with the wild-type 9S RNA sequence 5'AUCAAAUAAA and with modified sequence 5'AUCAGAUAAA
-
-
?
5'AUCAAGUAAA + H2O
5'AUCAAGU + AAA
-
low activity, 5'-labeled synthetic RNA substrate, modified 9S RNA sequence, recombinant Rne498 catalytic domain, no activity with the wild-type 9S RNA sequence 5'AUCAAAUAAA and with modified sequence 5'AUCAGAUAAA
-
-
?
5'AUCGAAUAAA + H2O
5'AUCGA + AUAAA
-
5'-labeled synthetic RNA substrate, modified 9S RNA sequence, recombinant Rne498 catalytic domain, no activity with the wild-type 9S RNA sequence 5'AUCAAAUAAA and with modified sequence 5'AUCAGAUAAA
-
-
?
5'GGGA(D-dT)CAGUAUUU-fluorescein + H2O
?
-
5' monophosphorylated, 3' fluorescein-labeled synthetic substrate with protective 2'-O-methyl groups at all positions based on the 5' cleavage site of RNA I
-
-
?
Bacillus subtilis aprE leader-lacZ mRNA + H2O
?
-
wild-type and mutant substrate, the latter with an exchange of a G and an A at +31 and +32, respectively, cleavage of the Bacillus subtilis transcript in a structure-dependent manner at the 5' end to the U residue at +12 within a double-stranded segment of an AU-rich sequence, which is part of the stem-loop structure at the 5' end of the transcript
-
-
?
bacteriophage T4 gene 32 mRNA + H2O
?
-
processing at the -71 site, which forms a stem-loop essential for enzyme activity of RNase E, the putative consensus sequence is RAUUW, mutational disruption of the stem-loop leads to loss of activity, mechanism, overview
-
-
?
BR13N RNA + H2O
?
-
synthetic RNA substrate, the cleavage site is GGGACAGUCUGUG
-
-
?
endonulceolytic cleavage of sodB mRNA
?
-
the enzyme cleaves within the sodB 5'-untranslated region in vitro, thereby removing the 5' stem-loop structure that facilitates Hfq and ribosome binding, RNase E cleavage can also occur at a cryptic site that becomes available upon sodB 5'-UTR/RyhB base pairing
-
-
?
fluorogenic oligonucleotides + H2O
?
-
5' monophosphorylated or 5' hydroxylated substrates, P-BR14-FD or OH-BR14-FD
-
-
?
MicX + H2O
?
-
endonucleolytic cleavage, wild-type substrate, RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA
-
-
?
MicX_DELTA196-263 mutant + H2O
?
-
endonucleolytic cleavage, a truncated Vibrio cholerae sRNA
-
-
?
pppRNA I.26 + H2O
?
-
low activity, cleavage of the 5' substrate end
-
-
?
pRNA I.26 + H2O
?
-
a monophosphate at the 5' end of the RNA I substrate stimulates the enzyme 25-30fold, cleavage of the 5' substrate end
-
-
?
Rep mRNA + H2O
?
-
the arginine-rich RNA binding domain and the protein scaffold domain of RNase E are dispensable for degradation of the replication initiator protein (Rep) mRNA of the ColE2 plasmid
-
-
?
rne mRNA + H2O
?
-
the enzyme autoregulates its expression by cleavage and processing of its own rne mRNA
-
-
?
S20 mRNA + H2O
?
-
mRNA encoding ribosomal proteins, a single cleavage site at residues 300/301 is preceded by variable 5' extensions
-
-
?
S20 mRNA t175D + H2O
?
-
ribosomal protein encoding RNA, structure mapping, secondary structure modeling, overview
-
-
?
S20 mRNA t194D + H2O
?
-
ribosomal protein encoding RNA, structure mapping, secondary structure modeling, overview
-
-
?
S20 mRNA t84D + H2O
?
-
ribosomal protein encoding RNA, contains a 5' stem loop with three noncanonical A-G pairs, structure mapping, secondary structure modeling, overview
-
-
?
sodB mRNA + H2O
?
-
RNase E and RNase III are required for sodB RNA decay in vivo
-
-
?
sodB192 mRNA + H2O
?
-
cleavage of the 5'-untranslated region in vitro thereby removing the stem loop structure that facilitates Hfq and ribosome binding, additional cleavage at a cryptic site, that becomes available upon sodB5'-UTR/RyhB base pairing, RyhB is a small regulatory RNA involved in sodB translation control, overview
-
-
?
tRNA precursors + H2O
?
-
the enzyme, cuts intercistronic regions of putative tRNA precursors, overview
-
-
?
tRNATyrsu3+ + H2O
tRNATyrsu3+ + ?
-
a construct of 404 nucleotides containing a leader sequence and the amber suppressor form of tRNATyr
-
-
?
UAUUU-containing RNA oligonucleotide + H2O
?
-
G378 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
UUUUU-containing RNA oligonucleotide + H2O
?
-
G378/A379 mutant substrate, p23 RNA variant derived from linearized DraI DN1 or DN34 plasmids, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
16s rRNA + H2O
?
RNase E completely suppresses the accumulation of the 16.5S RNA intermediate in the Escherichia coli rne-1 strain
-
-
?
23S rRNA + H2O
5.8S-like rRNA + ?
-
5'-end processing, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
5.8S-like rRNA + ?
-
5'-end processing, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
5.8S-like rRNA + ?
-
5'-end processing, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
82 nt of the NifA mRNA + H2O
?
-
host factor required-dependent RNase E cleavage of NifA mRNA is essential for NifA translation. Cleavage site is located at 32 nucleotides upstream of the NifA translational start codon
-
-
?
82 nt of the NifA mRNA + H2O
?
-
host factor required-dependent RNase E cleavage of NifA mRNA is essential for NifA translation. Cleavage site is located at 32 nucleotides upstream of the NifA translational start codon
-
-
?
9S rRNA precursor + H2O
5S rRNA + ?
-
very low activity with a covalently closed circular variant of the substrate compared to the linear one, overview
-
-
?
9S rRNA precursor + H2O
5S rRNA + ?
-
very low activity with a covalently closed circular variant of the substrate compared to the linear one, overview
-
-
?
9SA RNA + H2O
?
-
9Sa is a fragment of the 9S precursor of 5S rRNA
-
-
?
AAUUU-containing RNA oligonucleotide + H2O
?
-
G378 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
AAUUU-containing RNA oligonucleotide + H2O
?
-
G378 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
BR13 + H2O
?
-
endonucleolytic cleavage, BR13 is an oligoribonucleotide that contains the RNase E-cleaved sequence of RNA I
-
-
?
BR13 + H2O
?
i.e. an oligonucleotide that contains the RNase E target site of RNA I. The N-terminal part of the enzyme from Vibrio vulnificus shows the cleavage specificity and activity of the enzyme from Escherichia coli
-
-
?
BR13 RNA + H2O
?
-
i.e. 5'GGGACAGUAUUUG3', 3' fluorescein-labeled substrate
-
-
?
BR13 RNA + H2O
?
-
synthetic RNA substrate, the cleavage site is GGGACAGUAUUUG
-
-
?
BR30M + H2O
?
-
endonucleolytic cleavage, a synthetic 30-mer oligoribonucleotide substrate containing 2'-O-methylated nucleotides at positions 16 and 17
-
-
?
BR30M + H2O
?
endonucleolytic cleavage, a synthetic 30-mer oligoribonucleotide substrate containing 2'-O-methylated nucleotides at positions 16 and 17
-
-
?
CAUUU-containing RNA oligonucleotide + H2O
?
-
G378 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
CAUUU-containing RNA oligonucleotide + H2O
?
-
G378 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
cspA mRNA + H2O
?
-
degradation of the cspA mRNA in vivo is very rapid at temperatures greater than 30°C, overview
-
-
?
cspA mRNA + H2O
?
-
cleavage at a single site in vitro between two stem-loops about 24 residues 3' to the termination codon and about 31 residues from the 3' end. The site of cleavage is independent of the temperature and largely independent of the phosphorylation status of the 5' end of cspA mRNA, overview
-
-
?
GAUUU-containing RNA oligonucleotide + H2O
?
-
wild-type substrate, best substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
GAUUU-containing RNA oligonucleotide + H2O
?
-
wild-type substrate, best substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
GUUUU-containing RNA oligonucleotide + H2O
?
-
A379 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
GUUUU-containing RNA oligonucleotide + H2O
?
-
A379 mutant substrate, p23 RNA variant derived from linearized DraI plasmid, in vitro substrate synthesis by SP6 RNA poylmerase
-
-
?
immature 16S rRNA + H2O
mature 16S rRNA
-
RNase G, i.e. CafA protein, and RNase E are both required for the 5' maturation of 16S ribosomal RNA
-
-
?
immature 16S rRNA + H2O
mature 16S rRNA
-
secondary processing for formation of the mature 5' terminus
-
-
?
ompA mRNA + H2O
?
-
ompA at a site which is rate determining for degradation and also cleaved by RNase K
-
-
?
pSu3 + H2O
?
-
endonucleolytic cleavage, the precursor of the Escherichia coli tRNATyrSu3, cleavage upstream of the RNase P cleavage site in vitro and in vivo
-
-
?
pSu3 + H2O
?
-
endonucleolytic cleavage, the precursor of the Escherichia coli tRNATyrSu3, cleavage upstream of the RNase P cleavage site in vitro and in vivo, cleavage site mapping, overview, very low activity with the substrate mutants K546A and K552A, lack of Mg2+ leads to unspecific cleavage of pSu3 RNA to small oligoribonucleotides
-
-
?
puf mRNA + H2O
?
-
initiation of degradation of the 5' pufQ mRNA segment, expressed from plasmids pBPT8 or pBRMOD11 using the bla promoter of plasmid pBR322, the enzyme discriminates between the two sequences GGCUUU and GAUUUU preferring AU-rich sequences
-
-
?
puf mRNA + H2O
?
-
initiation of degradation of the 5' pufQ mRNA segment, expressed from plasmids pBPT8 or pBRMOD11 using the bla promoter of plasmid pBR322, the enzyme discriminates between the two sequences GGCUUU and GAUUUU preferring AU-rich sequences
-
-
?
puf mRNA + H2O
?
-
initiation of degradation of the pufLMX segment, the enzyme does not discriminate between the two sequences GGCUUU and GAUUUU
-
-
?
RNA + H2O
?
-
the enzyme is required for RNA processing and degradation
-
-
?
RNA + H2O
?
-
cleavage site specificity is not affected by temperature, selective cleavage at the 5' end of internucleotide bonds in 3' to 5' direction, cleavage pattern, overview
-
-
?
RNA + H2O
?
-
endonucleolytic cleavage, the Arabidopsis enzyme uses single-stranded oligoribonucleotide and chloroplast RNA as substrates, and depends on the number of phosphates at the 5' end, is inhibited by structured RNA, and preferentially cleaves A/U-rich sequences, catalytic domain structure, overview
-
-
?
RNA + H2O
?
-
-
-
-
?
RNA + H2O
?
-
the enzyme or its isolated N-terminal catalytic domain cleave poly(A) tails on the 3' end of RNA substrates, the RNA degradosome cleaves 3' poly(A) tails of RNA irrespective of the 5' phosphorylation status, while the purified RNase E shows high preference for 5'-monophosphorylated RNA substrates, and low activity with 5'-triphosphate RNA, N-terminal ribonucleolytic domain RTD-RNase E is the catalytic domain and sufficient for activity
-
-
?
RNA + H2O
?
-
the enzyme or its isolated N-terminal catalytic domain cleave poly(A) tails on the 3' end of RNA substrates, the RNA degradosome cleaves 3' poly(A) tails of RNA irrespective of the 5' phosphorylation status, while the purified RNase E shows high preference for 5'-monophosphorylated RNA substrates, and low activity with 5'-triphosphate RNA, N-terminal ribonucleolytic domain RTD-RNase E is the catalytic domain and sufficient for activity
-
-
?
RNA + H2O
?
-
the enzyme plays a key role in processing and degradation of RNA in Escherichia coli
-
-
?
RNA + H2O
?
-
Mg2+ targets the mgtA transcript which encodes a Mg2+ transporter, for degradation by RNase E
-
-
?
RNA I + H2O
?
-
full-length RNA I by plasmids pBR322 or pACY184, cleavage site specificity, overview
-
-
?
RNA I + H2O
?
-
the arginine-rich RNA binding domain of RNase E and the protein scaffold domain of RNase E is important for successive exoribonucleolytic degradation of RNAI, suggesting involvement of RhlB. RNase E-PNPase complex formation is not essential for RNAI degradation
-
-
?
RNA I + H2O
?
-
full-length RNA I and GGGRNA I encoded by plasmids pBR322, pCML103, or pCML108, RNA binding domain structure, secondary structure of the substrate RNA, complex formation and mechanism, multiple cleavage sites, overview
several fragments, product mapping, overview
-
?
RNA I.26 + H2O
?
-
5' mono- or triphosphorylated, or 5' hydroxylated substrate
-
-
?
rpsT mRNA + H2O
?
-
the substrate encodes the ribosomal protein S20, very low activity with a covalently closed circular variant of the substrate compared to the linear one, overview
-
-
?
rpsT mRNA + H2O
?
-
the substrate encodes the ribosomal protein S20
-
-
?
rpsT mRNA + H2O
?
-
the substrate encodes the ribosomal protein S20, very low activity with a covalently closed circular variant of the substrate compared to the linear one, overview
-
-
?
single-stranded RNA + H2O
?
-
RhlB is an ATP-dependent motor that unfolds structured RNA for destruction by partner ribonucleases, RhlB associates with the essential endoribonuclease RNase E as part of the multi-enzyme RNA degradosome assembly, RNase E activates RhlB severalfold, determination and analysis of the specific protein interaction sites using limited protease digestion, domain cross-linking and homology modelling. The stoichiometry for RhlB-CTD/RNase E, residues 628-843, complex is 1:1, overview
-
-
?
single-stranded RNA + H2O
?
-
RNA substrate specificity of full-length and truncated RNase E in complex with RhlB, overview
-
-
?
single-stranded RNA + H2O
?
preferentially cleaves single-stranded RNAs within U-rich regions. Most cleavage sites contained one or two U. It cleaves the phosphodiester linkage on the 3'-side and generates 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The enzyme cleaves these substrates only in close proximity to the 5'- or 3'-ends suggesting that it requires the presence of a free RNA end. Oligoribonucleotides as short as 10 nt can serve as SSO1404 substrates. Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37 are important for enzymatic activity. Asp-10 might be the principal catalytic residue. No cleavage of dsRNA substrates prepared by annealing ssRNA substrates. No nuclease activity against either of the DNA substrates. The 39 nucleotide ssRNA substrate AAAUACG-/-U-/-U-/-UUCUCCAUUGUCAUAUUGCGCAUAAGUUGA shows the highest activity among the ssRNA substrates tested
-
-
?
single-stranded RNA + H2O
?
preferentially cleaves single-stranded RNAs within U-rich regions. Most cleavage sites contained one or two U. It cleaves the phosphodiester linkage on the 3'-side and generates 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The enzyme cleaves these substrates only in close proximity to the 5'- or 3'-ends suggesting that it requires the presence of a free RNA end. Oligoribonucleotides as short as 10 nt can serve as SSO1404 substrates. Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37 are important for enzymatic activity. Asp-10 might be the principal catalytic residue. No cleavage of dsRNA substrates prepared by annealing ssRNA substrates. No nuclease activity against either of the DNA substrates. The 39 nucleotide ssRNA substrate AAAUACG-/-U-/-U-/-UUCUCCAUUGUCAUAUUGCGCAUAAGUUGA shows the highest activity among the ssRNA substrates tested
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation, overview
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation, overview
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA, overview
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA, overview
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA
-
-
?
tRNATyr precursor + H2O
tRNATyr + ?
-
maturation, cleavage of the tyrT transcript, containing two tRNATyr1 sequences separated by a 209-nt spacer region plus a downstream mRNA, at three sites in the speacer region, overview
-
-
?
tRNATyr precursor + H2O
tRNATyr + ?
-
maturation, cleavage of the tyrT transcript, containing two tRNATyr1 sequences separated by a 209-nt spacer region plus a downstream mRNA, at three sites in the spacer region
-
-
?
tRNATyrSu3 precursor + H2O
?
-
cleavage in the 5' leader sequence, the enzyme is involved in regulation of cellular tRNA levels
-
-
?
tRNATyrSu3 precursor + H2O
?
-
cleavage in the 5' leader sequence, cleavage sites and activity using wild-type and deletion mutant substrates, overview
-
-
?
unc mRNA + H2O
?
-
the unc operon encodes the eight subunits of the Escherichia coli F1F0-ATPase, processing of the unc mRNAs by the RNase E, overview, RNase E is essential for uncC processing
-
-
?
unc mRNA + H2O
?
-
the unc operon encodes the eight subunits of the Escherichia coli F1F0-ATPase, processing of the unc mRNAs by the RNase E, overview
-
-
?
upRNA + H2O
?
-
RNase E is a processing enzyme involved in 3' end formation of M1 RNA, and plays a dual role in processing and degradation to achieve tight control of M1 RNA biosynthesis
-
-
-
upRNA + H2O
?
-
M1 RNA, the gene product of rnpB, is the catalytic subunit of RNase P in Escherichia coli, M1 RNA is transcribed from a proximal promoter as pM1 RNA, a precursor M1 RNA, and then is processed at its 3' end by RNase E, the M1 RNA structural sequence in upRNA is much more vulnerable to the enzyme than the sequence in pM1 RNA, full-length enzyme and N-terminal domain of RNase E, cleavage patterns, overview
-
-
-
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
additional information
?
-
-
the enzyme prefers 5' monophosphorylated RNA substrates compared to nonphosphorylated or 5' triphosphorylated RNA substrates
-
-
-
additional information
?
-
-
Aquifex aeolicus RNase E/G is able to selectively cleave internucleotide bonds in the 3'-5' direction, and to cut in intercistronic regions of putative tRNA precursors
-
-
-
additional information
?
-
-
the bifunctional enzyme, exhibiting RNase E and RNase G activities, is involved in rRNA processing and maturation of tRNAs, that originated from polycistronic transcripts encoded by the Aquifex aeolicus tufA2 and rRNA operons, overview
-
-
-
additional information
?
-
-
site-specific RNase E/G cleavage of RNA using 5'-end-labelled substrates, e.g. L1 RNA, RNAI, and 9S RNA, overview. RNase E/G has a temperature-dependent, endoribonucleolytic activity that is dependent on the 5'-phosphorylation status of RNA. The enzyme site-specifically cleaves oligonucleotides and structured RNAs at locations that are partly overlapping or completely different when compared to the positions of Escherichia coli RNase E and RNase G cleavage sites, RNase E/G shows 3'-5' directionality in cleavage site selection, overview, the cleavage site selection of RNase E/G is temperature-dependent, overview
-
-
-
additional information
?
-
-
RNA degradation in the chloroplast occurs via the polyadenylation-assisted degradation pathway, plant RNase E participates in the initial endonucleolytic cleavage of the polyadenylation-stimulated RNA degradation process in the chloroplast, perhaps in collaboration with the two other chloroplast endonucleases, RNase J and CSP41, overview
-
-
-
additional information
?
-
-
initiation of tRNA 5' maturation by RNase E is essential for cell viability, the enzyme initiates the processing of polycistronic RNA of several operons, e.g. of glyW cysT leuZ, argX hisR leuT proM, or lysT valT lysW valZ lysY lysZlysQ, as well as of monocistronic transcripts such as pheU, pheV, asnT, asnU, asnV, or asnW, mapping of cleavage sites at the 3' end within tRNA precursors, overview, the enzyme is essential for degradation of many mRNAs, e.g. of rpsO
-
-
-
additional information
?
-
-
RNase E is involved in and interacts with functionally and physically polynucleotide phosphorylase, and also with other enzymes implicated in the processing and degradation of RNA, polynuclease phosphorylase, PNPase, degrades the reaction products generated by RNase E
-
-
-
additional information
?
-
-
the enzyme autoregulates its expression by cleavage and processing of its own rne mRNA
-
-
-
additional information
?
-
-
the enzyme is essential for regulation of mRNA turnover by specific processing and degradation and is involved in regulation of cell homeostasis, growth and development
-
-
-
additional information
?
-
-
the enzyme is part of the RNA degradosome, a large multiprotein machine to process and degrade RNA
-
-
-
additional information
?
-
-
the enzyme is required for rapid decay and correct hydrolytic processing of RNA
-
-
-
additional information
?
-
-
the enzyme is the major endoribonuclease participating in mRNA turnover in Escherichia coli
-
-
-
additional information
?
-
-
the enzyme plays an important role in the processing and degradation of bacteriophage T4 and Escherichia coli mRNAs, mutational processing site analysis, overview
-
-
-
additional information
?
-
-
the enzyme, especially its catalytic N-terminal domain, is essential for RNA processing and degradation, and for cell growth and feedback regulation of RNase E synthesis
-
-
-
additional information
?
-
-
cleavage site recognition mechanism, effect on substrate structure alteration by different treatments on cleavage site recognition, overview
-
-
-
additional information
?
-
-
identification of specific sequence determinants that either facilitate or impede the recognition and cleavage of RNA by the enzyme, RNA-enzyme interactions, overview
-
-
-
additional information
?
-
nucleic acid binding structure, structure-function relationship, overview
-
-
-
additional information
?
-
-
ribonuclease E is a 5'-end-dependent, single-strand-specific endonuclease that initiates the selective decay of mRNA having regulatory function, regulation of mRNA levels in response to environment, the enzyme proceeds in a 5' to 3' direction, the enzyme shows high activity with 5' monophosphorylated RNA, but low activity with 5' triphosphorylated RNA, poor activity with circular RNA substrates, overview
-
-
-
additional information
?
-
-
RNA processing reaction mechanism and involved functional groups, activity depends on protonated and unprotonated groups, the recognition of a guanosine sequence determinant upstream of the scissile bond via interaction with the exocyclic 2-amino group, the 7N of the nucleobase, and the imino proton or 6-keto group, overview
-
-
-
additional information
?
-
-
RNase E acts via a scanning mechanism in processing and degradation of RNA
-
-
-
additional information
?
-
-
RNase E shows preference for 5' monophosphorylated RNA substrates rather than RNA with a triphosphate or hydroxyl at the 5' end, the enzyme needs to be in a multimeric state for activation by 5' monophosphorylated RNA substrates
-
-
-
additional information
?
-
-
structural features required for RNA turnover, the enzyme attacks the 5' terminus of RNA substrates, RNA recognition mechanism, RNA-binding channel formed by the catalytic domain tetramer, cleavage site structure, and reaction mechanism, overview
-
-
-
additional information
?
-
-
the catalytic domain of the multifunctional endoribonuclease determines inherent 3' to 5' directionality in cleavage site selection, cleavage site sequences overview
-
-
-
additional information
?
-
-
the enzyme shows similar cleavage site specificity as RNase G
-
-
-
additional information
?
-
-
the N-terminal catalytic domain is sufficient for catalytic activity, the enzyme shows high RNA binding ability, and cleavage of mRNA and rRNA, RNase E interacts with polynucleotide phosphorylase and other enzymes implicated in the processing and degradation of RNA, cleavage site specificity, overview, RNase E requires the stem loop structure in RNA substrates, altering of the substrate secondary structure alters substrate specificity, overview, the enzymes' arginine-rich RNA-binding site is not essential for activity but allows the degradosome to move progressively along the transcript during degradation
-
-
-
additional information
?
-
-
both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB, iron-dependent variations in the steady-state concentration and translatability of sodB mRNA are modulated by the small regulatory RNA RyhB, the RNA chaperone Hfq, and RNase E, decay of sodB mRNA is retarded upon inactivation of RNaseE in vivo, mechanism, modelling, overview
-
-
-
additional information
?
-
-
ribonuclease E is an essential hydrolytic endonuclease in Escherichia coli, and it plays a central role in maintaining the balance and composition of the messenger RNA population
-
-
-
additional information
?
-
-
RNase E is an essential bacterial endoribonuclease involved in the turnover of messenger RNA and the maturation of structured RNA precursors in Escherichia coli, RNA degradation mechanism, overview
-
-
-
additional information
?
-
-
RNase E is an essential endonuclease involved in the regulatory processing and/or degradation of tRNAs, rRNAs, and non-coding small RNAs as well as many mRNAs, the enzyme is regulated by an RNA-binding protein Hfq. RNase is required for induction of the glutamate-dependent acid resistance system in a RpoS-independent manner
-
-
-
additional information
?
-
-
RNase E is an essential Escherichia coli endoribonuclease that plays a major role in the decay and processing of a large fraction of RNAs in the cell, overview
-
-
-
additional information
?
-
-
RNaseE, as the main component of the RNA degradosome of Escherichia coli, plays an essential role in RNA processing and decay
-
-
-
additional information
?
-
-
the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors
-
-
-
additional information
?
-
-
endonucleolytic cleavage as selective processing via allosteric intermediates of RNA substrates, the catalytic activity is influenced by the 5'-end of the substrate, four subunits of RNase E catalytic domain are organized in an interwoven quaternary structure required for catalytic activity, catalytic site structure, overview
-
-
-
additional information
?
-
the enzyme is active on mRNA and tRNA substrates, overview
-
-
-
additional information
?
-
-
a proportion of PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E
-
-
-
additional information
?
-
-
RNase E autoregulates its production by governing the decay rate of RNase E mRNA by binding directly to a stem-loop in the rne gene 5' untranslated region
-
-
-
additional information
?
-
-
RNase E preferres substrates possessing a 5'-monophosphate
-
-
-
additional information
?
-
-
the C-terminus of this enzyme serves as a scaffold to which other components of the RNA degradosome bind including the phosphorolytic 3'-exonuclease, polynucleotide phosphorylase, the DEAD-box RNA helicase RhlB, and the glycolytic enzyme enolase. The DEAD-box RNA helicases CsdA and RhlE and the RNA binding protein Hfq may bind to RNase E in place of one or more of the prototypical components.
-
-
-
additional information
?
-
-
upon catalytic activation, RNase E undergoes a marked conformational change characterized by the coupled movement of two RNA-binding domains to organize the active site
-
-
-
additional information
?
-
-
Escherichia coli enolase and its RNase E enolase-binding site demonstrate positive interactions. PNPase-binding site of RNase E interacts with Vibrio angustum S14 or Escherichia coli PNPase
-
-
-
additional information
?
-
-
RNase E cleaves the 217-nt RNAs at internal sites in an arginine-rich RNA binding domain-independent manner and about 180-nt degradation intermediates are formed
-
-
-
additional information
?
-
-
RNA chaperon Hfq along with Hfq-binding sRNAs stably binds to RNase E in Escherichia coli. The role of the Hfq-RNase E interaction is to recruit RNase E to target mRNAs of sRNAs resulting in the rapid degradation of the mRNA-sRNA hybrid. The scaffold region of RNase E can be deleted up to residue 750 without losing the ability to cause the rapid degradation of target mRNAs mediated by Hfq/sRNAs. The truncated RNase E750 can still bind to Hfq although the truncation significantly reduces the Hfq-binding ability. Deletion of the 702-50 region greatly impairs the ability of RNase E to cause the degradation of ptsG mRNA. A polypeptide corresponding to the scaffold region binds to Hfq without the help of RNA. Overexpression of RhlB partially inhibits the Hfq binding to RNase E and the rapid degradation of ptsG mRNA
-
-
-
additional information
?
-
-
RNase PH interacts with the carboxy-terminal end of RNase E
-
-
-
additional information
?
-
-
the enzyme is the major endoribonuclease participating in mRNA turnover in Escherichia coli
-
-
-
additional information
?
-
-
the enzyme binds RNA with high affinity
-
-
-
additional information
?
-
-
RNase PH interacts with the carboxy-terminal end of RNase E
-
-
-
additional information
?
-
-
ribonuclease E is a 5'-end-dependent, single-strand-specific endonuclease that initiates the selective decay of mRNA having regulatory function, regulation of mRNA levels in response to environment, the enzyme proceeds in a 5' to 3' direction, the enzyme shows high activity with 5' monophosphorylated RNA, but low activity with 5' triphosphorylated RNA, poor activity with circular RNA substrates, overview
-
-
-
additional information
?
-
-
the C-terminus of this enzyme serves as a scaffold to which other components of the RNA degradosome bind including the phosphorolytic 3'-exonuclease, polynucleotide phosphorylase, the DEAD-box RNA helicase RhlB, and the glycolytic enzyme enolase. The DEAD-box RNA helicases CsdA and RhlE and the RNA binding protein Hfq may bind to RNase E in place of one or more of the prototypical components.
-
-
-
additional information
?
-
-
analysis of cleavage site specficity
-
-
-
additional information
?
-
-
RNase E plays an essential role in the maturation of tRNA precursors, cleavage site and maturation process modeling, overview
-
-
-
additional information
?
-
-
the enzyme can cleave internucleotide bonds in the bubble regions of duplex RNA segments and in single-stranded regions, mechanism
-
-
-
additional information
?
-
-
RNase E plays an essential role in the maturation of tRNA precursors, cleavage site and maturation process modeling, overview
-
-
-
additional information
?
-
the enzyme is active on mRNA and tRNA substrates, overview
-
-
-
additional information
?
-
-
RNase E enolase-binding site interacts with enolase from both Vibrio angustum S14 and Escherichia coli. The C-terminal half of RNase E interacts with Vibrio angustum S14 or Escherichia coli PNPase. C-terminal half of RNase E is capable of self-interaction
-
-
-
additional information
?
-
RNase E enolase-binding site interacts with enolase from both Vibrio angustum S14 and Escherichia coli. The C-terminal half of RNase E interacts with Vibrio angustum S14 or Escherichia coli PNPase. C-terminal half of RNase E is capable of self-interaction
-
-
-
additional information
?
-
-
substrate specificity, the enzyme shows high activity with 5' monophosphorylated RNA, but low activity with 5' triphosphorylated RNA, overview
-
-
-
additional information
?
-
-
cleavage site specificity, overview
-
-
-
additional information
?
-
-
substrate specificity, the enzyme shows high activity with 5' monophosphorylated RNA, but low activity with 5' triphosphorylated RNA, overview
-
-
-
additional information
?
-
-
substrate specificity, the enzyme shows high activity with 5' monophosphorylated RNA, but low activity with 5' triphosphorylated RNA, overview
-
-
-
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
additional information
?
-
N-RneV has cleavage activity and specificity of RNase E on RNase E-targeted sequence of RNA I (BR13)
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATES
NATURAL PRODUCTS
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
Bacillus subtilis aprE leader-lacZ mRNA + H2O
?
-
wild-type and mutant substrate, the latter with an exchange of a G and an A at +31 and +32, respectively, cleavage of the Bacillus subtilis transcript in a structure-dependent manner at the 5' end to the U residue at +12 within a double-stranded segment of an AU-rich sequence, which is part of the stem-loop structure at the 5' end of the transcript
-
-
?
BR13 + H2O
?
-
endonucleolytic cleavage, BR13 is an oligoribonucleotide that contains the RNase E-cleaved sequence of RNA I
-
-
?
cspA mRNA + H2O
?
-
degradation of the cspA mRNA in vivo is very rapid at temperatures greater than 30°C, overview
-
-
?
immature 16S rRNA + H2O
mature 16S rRNA
-
RNase G, i.e. CafA protein, and RNase E are both required for the 5' maturation of 16S ribosomal RNA
-
-
?
ompA mRNA + H2O
?
-
ompA at a site which is rate determining for degradation and also cleaved by RNase K
-
-
?
pSu3 + H2O
?
-
endonucleolytic cleavage, the precursor of the Escherichia coli tRNATyrSu3, cleavage upstream of the RNase P cleavage site in vitro and in vivo
-
-
?
rne mRNA + H2O
?
-
the enzyme autoregulates its expression by cleavage and processing of its own rne mRNA
-
-
?
single-stranded RNA + H2O
?
-
RhlB is an ATP-dependent motor that unfolds structured RNA for destruction by partner ribonucleases, RhlB associates with the essential endoribonuclease RNase E as part of the multi-enzyme RNA degradosome assembly, RNase E activates RhlB severalfold, determination and analysis of the specific protein interaction sites using limited protease digestion, domain cross-linking and homology modelling. The stoichiometry for RhlB-CTD/RNase E, residues 628-843, complex is 1:1, overview
-
-
?
sodB mRNA + H2O
?
-
RNase E and RNase III are required for sodB RNA decay in vivo
-
-
?
tRNATyr precursor + H2O
tRNATyr + ?
-
maturation, cleavage of the tyrT transcript, containing two tRNATyr1 sequences separated by a 209-nt spacer region plus a downstream mRNA, at three sites in the speacer region, overview
-
-
?
tRNATyrSu3 precursor + H2O
?
-
cleavage in the 5' leader sequence, the enzyme is involved in regulation of cellular tRNA levels
-
-
?
unc mRNA + H2O
?
-
the unc operon encodes the eight subunits of the Escherichia coli F1F0-ATPase, processing of the unc mRNAs by the RNase E, overview, RNase E is essential for uncC processing
-
-
?
upRNA + H2O
?
-
RNase E is a processing enzyme involved in 3' end formation of M1 RNA, and plays a dual role in processing and degradation to achieve tight control of M1 RNA biosynthesis
-
-
-
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
23S rRNA + H2O
?
-
RNase E is involved in 5'-end 23S rRNA processing, schematic overview, removal of an internal, transcribed spacer consisting of helices 9 and 10, RNase E is responsible for helix 10 processing, while helix 9 is excised by RNase III
-
-
?
RNA + H2O
?
-
the enzyme is required for RNA processing and degradation
-
-
?
RNA + H2O
?
-
the enzyme plays a key role in processing and degradation of RNA in Escherichia coli
-
-
?
rpsT mRNA + H2O
?
-
the substrate encodes the ribosomal protein S20
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation, overview
-
-
?
tRNAArgHisLeuPro precursor + H2O
tRNAArg + tRNAHis + tRNALeu + tRNAPro + ?
-
polycistronic transcript, maturation, overview
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA, overview
-
-
?
tRNAGlyCysLeu precursor + H2O
tRNAGly + tRNACys + tRNALeu + ?
-
polycistronic transcript, maturation, cleavage downstream of each tRNA, overview
-
-
?
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
additional information
?
-
-
Aquifex aeolicus RNase E/G is able to selectively cleave internucleotide bonds in the 3'-5' direction, and to cut in intercistronic regions of putative tRNA precursors
-
-
-
additional information
?
-
-
the bifunctional enzyme, exhibiting RNase E and RNase G activities, is involved in rRNA processing and maturation of tRNAs, that originated from polycistronic transcripts encoded by the Aquifex aeolicus tufA2 and rRNA operons, overview
-
-
-
additional information
?
-
-
RNA degradation in the chloroplast occurs via the polyadenylation-assisted degradation pathway, plant RNase E participates in the initial endonucleolytic cleavage of the polyadenylation-stimulated RNA degradation process in the chloroplast, perhaps in collaboration with the two other chloroplast endonucleases, RNase J and CSP41, overview
-
-
-
additional information
?
-
-
initiation of tRNA 5' maturation by RNase E is essential for cell viability, the enzyme initiates the processing of polycistronic RNA of several operons, e.g. of glyW cysT leuZ, argX hisR leuT proM, or lysT valT lysW valZ lysY lysZlysQ, as well as of monocistronic transcripts such as pheU, pheV, asnT, asnU, asnV, or asnW, mapping of cleavage sites at the 3' end within tRNA precursors, overview, the enzyme is essential for degradation of many mRNAs, e.g. of rpsO
-
-
-
additional information
?
-
-
RNase E is involved in and interacts with functionally and physically polynucleotide phosphorylase, and also with other enzymes implicated in the processing and degradation of RNA, polynuclease phosphorylase, PNPase, degrades the reaction products generated by RNase E
-
-
-
additional information
?
-
-
the enzyme is essential for regulation of mRNA turnover by specific processing and degradation and is involved in regulation of cell homeostasis, growth and development
-
-
-
additional information
?
-
-
the enzyme is part of the RNA degradosome, a large multiprotein machine to process and degrade RNA
-
-
-
additional information
?
-
-
the enzyme is required for rapid decay and correct hydrolytic processing of RNA
-
-
-
additional information
?
-
-
the enzyme is the major endoribonuclease participating in mRNA turnover in Escherichia coli
-
-
-
additional information
?
-
-
the enzyme plays an important role in the processing and degradation of bacteriophage T4 and Escherichia coli mRNAs, mutational processing site analysis, overview
-
-
-
additional information
?
-
-
the enzyme, especially its catalytic N-terminal domain, is essential for RNA processing and degradation, and for cell growth and feedback regulation of RNase E synthesis
-
-
-
additional information
?
-
-
both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB, iron-dependent variations in the steady-state concentration and translatability of sodB mRNA are modulated by the small regulatory RNA RyhB, the RNA chaperone Hfq, and RNase E, decay of sodB mRNA is retarded upon inactivation of RNaseE in vivo, mechanism, modelling, overview
-
-
-
additional information
?
-
-
ribonuclease E is an essential hydrolytic endonuclease in Escherichia coli, and it plays a central role in maintaining the balance and composition of the messenger RNA population
-
-
-
additional information
?
-
-
RNase E is an essential bacterial endoribonuclease involved in the turnover of messenger RNA and the maturation of structured RNA precursors in Escherichia coli, RNA degradation mechanism, overview
-
-
-
additional information
?
-
-
RNase E is an essential endonuclease involved in the regulatory processing and/or degradation of tRNAs, rRNAs, and non-coding small RNAs as well as many mRNAs, the enzyme is regulated by an RNA-binding protein Hfq. RNase is required for induction of the glutamate-dependent acid resistance system in a RpoS-independent manner
-
-
-
additional information
?
-
-
RNase E is an essential Escherichia coli endoribonuclease that plays a major role in the decay and processing of a large fraction of RNAs in the cell, overview
-
-
-
additional information
?
-
-
RNaseE, as the main component of the RNA degradosome of Escherichia coli, plays an essential role in RNA processing and decay
-
-
-
additional information
?
-
-
the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors
-
-
-
additional information
?
-
-
the enzyme is the major endoribonuclease participating in mRNA turnover in Escherichia coli
-
-
-
additional information
?
-
-
RNase E plays an essential role in the maturation of tRNA precursors, cleavage site and maturation process modeling, overview
-
-
-
additional information
?
-
-
RNase E plays an essential role in the maturation of tRNA precursors, cleavage site and maturation process modeling, overview
-
-
-
additional information
?
-
-
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region
-
-
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
NaCl
NH4+
NH4Cl
Zn2+
Mg2+
-
dependent on, lack of Mg2+ leads to unspecific cleavage of pSu3 RNA to small oligoribonucleotides
Mg2+
-
required, optimal at 20 mM in a buffer containing 100 mM NaCl and 0.1% v/v Triton X-100
Mg2+
-
; required, optimal at 15-25 mM in a buffer containing 100 mM NaCl, bound by ligands D346, N305, and D303, one ion bound per catalytic domain dimer, two ions per catalytic domain tetramer, three-dimensional structure model
Zn2+
-
one ion bound per catalytic domain dimer, two ions per catalytic domain tetramer, three-dimensional structure model
Zn2+
-
catalytic activity does not require zinc directly but does require the quaternary structure, for which the metal is essential, binding and coordination site structure, overview
Zn2+
-
conformation and activity of apo- and holoenzyme, modelling, overview; the enzyme contains Zn2+
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Diamide
-
treatment of the N-terminal catalytic domain with diamide causes complete loss of the zinc, but only slightly reduced activity as tetramer
ribosomal protein L4
-
L4 interacts with a site outside of the catalytic domain at the C-terminal domain of RNase E to regulate the endoribonucleolytic functions of the enzyme thus inhibiting RNase E-specific cleavage in vitro
-
RraAV1
-
the coexpression of RraAV1 more efficiently inhibits RNase E action than coexpression of RraA
-
RraB
-
in vitro cleavage of p23 RNA by 70 ng RNAse ES is inhibited by 20.3% by RraB
-
RraA
-
in vitro cleavage of p23 RNA by 70 ng RNAse ES is inhibited by 38.9% by RraA
-
additional information
-
sequences sequestering the -71 site of bacteriophage T4 gene 32 mRNA inhibit the enzyme
-
additional information
-
anti-sense deoxynucleotide constructs complementary to the 5' end sequences of RNA substrates reduce the enzyme activity
-
additional information
-
the enzyme is not inhibitable by commercially available RNase A inhibitor
-
additional information
-
2'-O-methyl nucleotide substitutions in the synthetic RNA substrate, e.g. in RNA BR13-13M, inhibit the enzyme
-
additional information
-
RraB binds to the C-terminal region of RNase E, thus affecting both the protein composition of the degradosome and the endonucleolytic activity of RNase E. The glmS852::Tn5 allele results in an approximately 50% lower intracellular concentration of uridine 5'-diphospho-N-acetyl-glucosamine and confers a 5fold increase in the level of rraB mRNA, thereby lowering the RNase E activity. Reduction in cellular concentration of uridine 5'-diphospho-N-acetyl-glucosamine by the glmS852::Tn5 allele mediating a 2fold increase in beta-galactosidase activity from a chromosomal fusion of the 5' untranslated region of the rne gene to lacZ, results in increased expression of RraB, which may modulate the action of RNase E
-
additional information
-
overexpression of RhlB partially inhibits the Hfq binding to RNase E and the rapid degradation of ptsG mRNA
-
additional information
-
RNase E complex loses cleavage activity in the absence of host factor required
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
chaperone Hfq
-
plays an important role in facilitating the interaction ofRyhB with sodB mRNA, Hfq is not tightly retained by the RyhB-sodB mRNA complex and can be released from it through interaction with other RNAs added in trans
-
Hfq
-
a factor binding to the sodB RNA and facilitating cleavage due to induced conformational changes within the 5'-UTR, overview
-
additional information
-
5' monphosphorylation of RNA substrates increases the enzyme activity
-
additional information
-
5' monophosphorylation increases the enzyme activity via altered binding of the catalytic domain N-Rne
-
additional information
-
a monophosphate at the 5' end of the RNA substrate stimulates the enzyme
-
additional information
-
host factor required is essential for the cleavage activity of the RNase E complex
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00033
5' hydroxylated fluorogenic oligonucleotide
-
pH 7.5, 25°C, recombinant N-terminal domain
-
0.00023
5' monophosphorylated fluorogenic oligonucleotide
-
pH 7.5, 25°C, recombinant N-terminal domain
-
0.00207
5'-GGGACAGUAUUUG-3'
-
in 25 mM bis-Tris-propane (pH 8.3), 15 mM MgCl2, 100 mM NaCl, 0.1% (v/v) Triton X-100, and 1 mM dithiothreitol
0.00073
AAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00046
CAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00124
GAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00037
GUUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00081
UAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00028
UUUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00032
UUUUU-DN34-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.00013
5'-GGGACAGUAUUUG
-
5'-hydroxylated BR13 with multiple single-stranded regions
0.0036
5'-GGGACAGUAUUUG
-
5'-monophosphorylated BR13 with one single-stranded site
additional information
additional information
-
kinetics of tRNA precursor cleavage at 37°C and 44°C
-
additional information
additional information
-
kinetics, purified recombinant His-tagged N-terminal catalytic domain
-
additional information
additional information
-
kinetics of the reaction with 5' monophosphorylated RNA substrates
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.015
5' hydroxylated fluorogenic oligonucleotide
-
pH 7.5, 25°C, recombinant N-terminal domain
-
0.014
5' monophosphorylated fluorogenic oligonucleotide
-
pH 7.5, 25°C, recombinant N-terminal domain
-
1.4
5'-GGGACAGUAUUUG-3'
-
in 25 mM bis-Tris-propane (pH 8.3), 15 mM MgCl2, 100 mM NaCl, 0.1% (v/v) Triton X-100, and 1 mM dithiothreitol
0.192
AAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.15
CAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.765
GAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.121
GUUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.209
UAUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.015
UUUUU-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
0.023
UUUUU-DN34-containing RNA oligonucleotide
-
recombinant enzyme N-terminal half, pH 7.5, 30°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
wild-type and mutant substrate half-lives in vivo in Escherichia coli cells
additional information
-
RNA degradation activity in wild-type and mutant strains, overview
additional information
-
feedback regulation activity of wild-type and mutant enzymes, overview
additional information
-
validation of an oligonucleotide-based assay method, overview
additional information
-
development of a highly sensitive quantitative assay method using fluorescent 5' monophosphorylated RNA substrates
additional information
-
relative activity of different strains, comparison of wild-type RNase E and mutant N-RNase E to SynRne of Synechocystis sp., overview
additional information
-
relative activity of SynRne expressed in Escherichia coli compared to the Escherichia coli enzyme, overview
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
8.3
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
32
37
45 - 75
-
assay at, the cleavage site selection of RNase E/G is temperature-dependent, overview
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
enzyme membrane binding induces changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for ist substrate
-
-
RNase E and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton, degradosome components, i.e. RNase E, helicase B, polynucleotide hosphorylase, and enolase, are organized as helical filamentous structures that coil around the length of the cell. Formation of the RNaseE cytoskeletal-like structure requires an internal domain of the protein that does not include the domains required for any of its known interactions or the minimal domain required for endonuclease activity, but is independent of MreB and MinD cytoskeletal structures, mechanism of assembly, overview
additional information
-
localized to the inner cytoplasmic membrane, segment-A is necessary and sufficient for RNase E binding to membranes
-
localized to the inner cytoplasmic membrane, segment-A is necessary and sufficient for RNase E binding to membranes
-
additional information
-
the enzyme is part of the RNA degradosome, a large multiprotein machine to process and degrade RNA
-
additional information
-
the enzyme is also part of a high-molecular-weight degradosome, which also contains polynucleotide phosphorylase, but lacks RNase P and RNase III
-
additional information
-
the enzyme is localized in a multi-protein complex, the RNA degradosome
-
additional information
-
the enzyme is part of the RNA degradosome multi-protein complex, which also contains enolase, RhlB, and PNPase
-
additional information
-
the enzyme is the main part of the RNA degradosome
-
additional information
-
the enzyme is part of the RNA degradosome multi-protein complex, which also contains enolase, RhlB, and PNPase
-
-
additional information
-
the enzyme is localized in a multi-protein complex, the RNA degradosome
-
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Q9A749
Caulobacter vibrioides (strain ATCC 19089 / CB15);
Escherichia coli (strain K12);
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
115000
-
x * 115000, about, sequence calculation, x * 150000-160000, SDS-PAGE
124000 - 132000
-
MW of recombinant dimeric ribonuclease E N-terminal catalytic domains of mutants C404A and C407A by mass spectrometry, gel filtration, and sequence calculations, overview
180000
247500
-
tetrameric wild-type ribonuclease E N-terminal catalytic domain, sequence calculation
248800
-
tetrameric wild-type ribonuclease E N-terminal catalytic domain, mass spectrometry
270000
-
about, tetrameric wild-type ribonuclease E N-terminal catalytic domain, gel filtration
300000
-
N-terminal catalytic domain homotetramer, analytical ultracentrifugation
680000
-
gel filtration, the 680 kDa complex is resistant to a high salt concentration of up to 2 M KCl , but is disrupted by 10 mM EDTA
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
oligomer
-
x * 115000, about, sequence calculation, x * 150000-160000, SDS-PAGE
tetramer
additional information
tetramer
-
dimer composed of two dimers, tertiary and quarternary structure, overview
tetramer
-
the catalytic domain of RNase E forms a homotetramer with a molecular mass of roughly 260 kDa
tetramer
-
a pair of dimers, the quaternary organization of RNase E is flexible, modelling, apoprotein formation leads to a conformational change in which the 5' sensor and S1 subdomains move as a single unit through an angle between the apoprotein and holoprotein state, overview; RNase E holoenzyme, X-ray crystallography
additional information
-
catalytic domain structure, homology-based modelling, overview
additional information
-
the enzymes' conserved N-terminal catalytic domain forms homotetramers binding up to four molecules of specific RNA substrate, the tetramers forms a D2 dihedral symmetry, X-ray scattering, analytical ultracentrifugation, mass spectrometry, and circular dichroism used for structure analysis, overview
additional information
-
the enzyme is part of the RNA degradosome, a large multiprotein machine to process and degrade RNA, organization, overview, the enzymes' C-terminal half contains the binding sites for the three other degradosome protein components DEAD-box RNA helicase RhlB, enolase, and polynucleotide phosphorylase PNPase, the C-terminal half of RNase E acts as a scaffold upon which the other components of the complex are assembled, functional analysis of enzyme domains by using deletion mutants of RNase E, overview
additional information
-
structural characterization of the RNase E S1 domain, residues 25-125, by NMR, and identification of its oligonucleotide-binding and dimerization interfaces, overview, isolated S1 domain, which shows an OB fold, undergoes a specific monomer-dimer equilibrium in solution with a KD in the millimolar range
additional information
-
the Rne protein is composed of an N-terminal catalytic domain, two proline-rich segments, an arginine-rich RNA-binding site ARRBS segment, and a proline-rich and acidic domain, domain organization, overview
additional information
-
three-dimensional enzyme structure with an essential N-terminal RNase E domain of the S1 family RNA-binding domain fold, the residues involved in cell growth and feedback regulation of RNase E synthesis form two cluster, e.g. Phe57, Phe67, and Tyr112, or Lys37 and Tyr60, overview, structural modeling of the S1 domain
additional information
-
the enzyme is localized in a multi-protein complex, the RNA degradosome
additional information
-
the enzyme is localized in a multi-protein complex, the RNA degradosome, RNase E S1 catalytic domain structure analysis, structure-function relationship, 4 catalytic domains associate in an interwoven quarternary structure, the catalytic domain structure is structurally congruent to a deoxyribonuclease, the N-terminal half harbors the catalytic domain, while the C-terminal half is involved in interaction with the other protein components of the degradosome, i.e. RNA helicase, enolase, and PNPase
additional information
-
N-terminal ribonucleolytic domain RTD-RNase E is the catalytic domain and sufficient for activity
additional information
-
the enzyme needs to be in a multimeric state for activation by 5' monophosphorylated RNA substrates, possible multimerization mechanism dependent on 5' activation, overview
additional information
-
the N-terminal region N-Rne contains the catalytic domain
additional information
-
RNase E is divided into domains of defined function and structure, the tetramer has two nonequivalent subunit interfaces, one of which is mediated by a single, tetrathiol-zinc complex, which we refer to as a Zn-link motif. One or both interfaces organize the active site, which is distinct from the primary site of RNA binding
additional information
-
N-terminal ribonucleolytic domain RTD-RNase E is the catalytic domain and sufficient for activity
-
additional information
-
the enzyme is localized in a multi-protein complex, the RNA degradosome
-
additional information
-
the catalytic site is located at the N-terminus, residues 1-413
additional information
-
the catalytic site is located at the N-terminus, residues 1-406
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
-
the recombinant enzyme is cleaved from an active 180 kDa form to active about 70 kDa and 60 kDa fragments during purification
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
apoprotein, X-ray diffraction structure determination and analysis at 3.3 resolution, modelling using molecular replacement; RNase E catalytic domain in the apo-state, molecular replacement
-
enolase bound to its cognate site from RNase E, residues 823-850, X-ray diffraction structure determination and analysis at 1.9 A resolution; the crystal structure of enolase bound to its cognate site from RNase E, residues 823-850, at 1.9 A resolution. The structure suggests that enolase may help to organize an adjacent conserved RNA-binding motif in RNase E
-
PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA, hanging drop vapour diffusion method, using 0.2 M ammonium nitrate and 20% w/v PEG 3350 or 0.2 M diammonium hydrogen citrate and 17% PEG 3350
-
purified recombinant detagged isolated S1 domain, residues 35-125, large crystals grow within 4 weeks in 1.65 mM protein containing solution of 20 mM phosphate, pH 6.5, 50 mM NaCl, and 0.05% w/v NaN3 at 4°C, isomorphous crystals are grown by hanging drop vapour diffusion method at 18°C, 1.3 mM protein in 20 mM HEPES, p 6.5, 50 mM NaCl, is mixed with a well solution containing 0.17 M sodium acetate, pH 6.5, 85 mM sodium cacodylate, 50% w/v PEG 8000, and 15% glycerol, X-ray diffraction structure determination and analysis at 2.0 A resolution using single anomalous dispersion or trimethyl lead(IV) acetate derivatives
-
purified recombinant His-tagged N-terminal RNaseE catalytic N domain, vapour diffusion method, 7 mg/ml protein in solution is mixed in a 1:1 ratio with precipitation solution containing 0.18 M Li2SO4, 0.09 M Tris-HCl, pH 8.5, 27% w/v PEG 4000, and 10% v/v glycerol, X-ray diffraction structure determination and analysis at 3.4 A resolution
-
X-ray diffraction structure determination and analysis at 2.9 A resolution
-
hanging drop vapor diffusion method. The crystal structure of SSO1404 is solved at 1.6 A resolution revealing the first ribonuclease with a ferredoxin-like fold
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
85
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
liposome binding stabilizes protein folding and prevents protein structure changes during thermal denaturation
-
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 20 mM Tris-HCl buffer, pH 7.6, 500 mM NaCl, 10 mM MgCl2, 10 mM DTT, 0.5 mM EDTA, and 5% (v/v) glycerol
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, Toyopearl column filtration chromatography, and Affi-Gel blue column chromatography
-
by ammonium sulfate precipitation and cation-exchange chromatography
-
native and recombinant ribonuclease E N-terminal catalytic domains from transformed Escherichia coli
-
native degradosomes from strain CF881, which lacks RNase I, further electrophoretically purification of Rne protein
-
native RNA degradosome from strain BRL2288, recombinant His-tagged full-length wild-type RNase E and His-tagged N-terminal ribonucleolytic domain RTD-RNase E from strain BL21(DE3) by metal affinity chromatography
-
Ni-NTA column chromatography
partially about 100fold by ammonium chloride precipitation, ultracentrifugation, ammonium sulfate fractionation, and gel filtration
-
recombinant active His- and Myc-tagged truncated enzyme from strain BL21(DE3) by affinity chromatography
-
recombinant C-terminally His6- and Myc-tagged N-terminal enzyme half and maltose-binding protein-fused N-terminal half from strain BL21(DE3) by affinity chromatography on a metal chelating resin and an amylose resin, respectively
-
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
-
recombinant His-tagged N-terminal catalytic domain from strain BL21(DE3) by nickel affinity chromatography and gel filtration to over 95% purity
-
recombinant His-tagged N-terminal RNaseE catalytic N domain from strain BL21(DE3) by metal affinity chromatography and gel filtration to homogeneity
-
recombinant His-tagged truncated enzyme mutants from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis and gel filtration
recombinant His-tagged truncated enzyme mutants from strain BL21(DE3) by nickel affinity chromatography, dialysis and gel filtration
-
recombinant His-tagged wild-type and mutant catalytic domains by nickel affinity chromatography
-
recombinant His10-tagged enzyme from Escherichia coli strain BL21(DE3) by His-trap chromatography with or without cleavage of the His-tag by factor Xa; recombinant His10-tagged RNase E/G from Escherichia coli strain BL21(DE3) by metal affinity chromatography, removal of the His-tag by factorXa and dialysis
-
recombinant isolated, His-tagged catalytic domain Rne498 from strain BL21(DE3) by metal affinity chromatography and dialysis to homogeneity
-
recombinant N-terminally His6-tagged wild-type and mutant full-length enzymes, and isolated N-terminally His6-tagged S1 domain by nickel affinity chromatography, removal of the His-tags by thrombin
-
recombinant wild-type and mutant enzymes, purification involves denaturation and renaturation steps due to the poor solubility of the full-length enzyme
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, sequence comparisons, expression in Escherichia coli
-
expressed as a fusion with an N-terminal His6 tag in Escherichia coli strain BL21 (DE3)
expressed in Escherichia coli BL21(DE3) cells
expression in wild-type rne cells and in thermosensitive mutant rne-50 and rne-3071 cells, overexpression of truncated 110 kDa mutant enzyme in rne50 cells
-
expression of His-tagged full-length wild-type RNase E and His-tagged N-terminal ribonucleolytic domain RTD-RNase E, residues 1-498, in strain BL21(DE3)
-
expression of His-tagged truncated enzyme mutants in Escherichia coli strain BL21(DE3), complementation of rne null mutation of Escherichia coli strain KSL2000
expression of His-tagged truncated enzyme mutants in strain BL21(DE3), complementation of rne null mutation of strain KSL2000
-
expression of N-terminal enzyme half, comprising residues 1-499, as C-terminally His6- and Myc-tagged or maltose-binding protein-fused protein in strain BL21(DE3)
-
expression of N-terminally His6-tagged wild-type and mutant full-length enzymes, and of isolated N-terminally His6-tagged S1 domain comprising residues 35-125
-
expression of the His-tagged N-terminal RNaseE catalytic N domain, comprising residues 1-529, in strain BL21(DE3)
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expression of wild-type and mutant enzyme and N-terminal catalytic domains in Escherichia coli
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expression of wild-type and mutant enzymes in different modified strains, cell growth curves, overview
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fragments of RNase E, either containing the enolase-binding microdomain (residues 833-851), the PNPase-binding site (residues 844-1061) or both (residues 734-1061)
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gene rne, expression of His-tagged N-terminal half of RNase E in strain BL21(DE3)
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gene rne, expression of the isolated, His-tagged catalytic domain Rne498, comprising residues 1-498, in strain BL21(DE3)
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gene rne, expression of wild-type and mutant enzymes in Escherichia coli and in the Saccharomyces cerevisiae two-hybrid system
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gene rne, overexpression in Escherichia coli, functional complementation of the RNase E-deficient strain CJ1832 of Escherichia coli
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gene rng, overexpression of His10-tagged RNase E/G, Rng, in Escherichia coli strain BL21(DE3); overexpression of His10-tagged enzyme in Escherichia coli strain BL21(DE3)
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oligohistidine-tagged polypeptides corresponding to the N-terminal half of RNase E with wild-type or mutant sequences
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overexpression of active His- and Myc-tagged truncated enzyme in strain BL21(DE3)
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overexpression of plasmid-encoded rne gene increases cell doubling time and can lead to plasmid loss or aquisition of mutations that reduce RNase E activity
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overexpression of wild-type and truncation mutant enzymes in strain Bl21(DE3), expression in the yeast two-hybrid system, overview
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recombinant overexpression of the His-tagged enzyme in Escherichia coli
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rne gene amplified and subcloned into pCR-BluntII-TOPO vector to generate pTOPOS14Rne. Expression plasmid pBADS14Rne constructed by excising the rne gene as a 3.3 kb gene Nco I-Pme I fragment from pTOPOS14Rne and inserting the fragment into the medium copy number plasmid pBADlacZ, putting RNase E expression under the control of the arabinose inducible promoter PBAD, and transformed into Escherichia coli AC23 (rne-1). RNase E putative enolase-binding microdomain (residues 885-909) and the putative PNPase-binding microdomain from S14 RNase E (residues 1015-1094) cloned
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A326T
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random mutagenesis, mutation in the DNase I subdomain, the mutant shows no detectable binding to p23 RNA due to a reduction in the substrate-binding ability
C404A
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site-directed mutagenesis, mutation of a zinc binding residue, the mutant shows 200fold decreased activity relative to that of the wild-type enzyme for cleaving a 10-mer RNA substrate, and forms a dimer instead of a tetramer
C407A
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site-directed mutagenesis, mutation of a zinc binding residue, the mutant shows 200fold decreased activity relative to that of the wild-type enzyme for cleaving a 10-mer RNA substrate, and forms a dimer instead of a tetramer
D303N
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site-directed mutagenesis of a residue located on the surface of the subdomain of RNase E, the mutant shows about 25fold reduced catalytic activity but almost unaltered RNA binding compared to the wild-type enzyme
D346N
E R169Q
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mutant protein is strongly overexpressed with accumulation of proteolytic fragments
F186C
site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
F57A
F67A
G172A
site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
G66S
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site-directed mutagenesis, the mutation leads to a dramatic destabilization of the OB fold of the S1 domain and leads to increased temperature sensitivity of the mutant compared to the wild-type enzyme
I41N
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random mutagenesis, mutation in the SI subdomain, the mutant shows no detectable binding to p23 RNA due to a reduction in the substrate-binding ability
K106A
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site-directed mutagenesis, 60% reduced feedback regulation activity compared to the wild-type enzyme
K112A
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site-directed mutagenesis, 94% reduced feedback regulation activity compared to the wild-type enzyme
K37A
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site-directed mutagenesis, 94% reduced feedback regulation activity compared to the wild-type enzyme
K38A
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site-directed mutagenesis, 49% reduced feedback regulation activity compared to the wild-type enzyme
K43A
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site-directed mutagenesis, 33% reduced feedback regulation activity compared to the wild-type enzyme
K71A
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site-directed mutagenesis, 56% reduced feedback regulation activity compared to the wild-type enzyme
L112A
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site-directed mutagenesis of a residue located at the hydrophobic pocket on the surface of the S1 domain, the mutant shows about 50fold reduced catalytic activity compared to the wild-type enzyme
L385P
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random mutagenesis, mutation in the DNase I subdomain, the mutant shows no detectable binding to p23 RNA due to a reduction in the substrate-binding ability
N305D
N305L
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site-directed mutagenesis of a residue located on the surface of the subdomain of RNase E, the mutant shows reduced catalytic activity compared to the wild-type enzyme
Q36R
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the mutant is hyperactive in comparison to wild type enzyme. The mutation enhances the RNA binding to the catalytic site of the enzyme
R109A
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site-directed mutagenesis, 78% reduced feedback regulation activity compared to the wild-type enzyme
R169Q
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site-directed mutagensis, the viable mutation in the 5'-phosphate sensor of RNase E, becomes lethal in combination with deletions removing part of the non-catalytic C-terminal domain of RNase E. Loss of autoregulation in R169Q
R187L
site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
R48A
-
site-directed mutagenesis, 49% reduced feedback regulation activity compared to the wild-type enzyme
R64A
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site-directed mutagenesis, 77% reduced feedback regulation activity compared to the wild-type enzyme
R87A
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site-directed mutagenesis, 16% increased feedback regulation activity compared to the wild-type enzyme
R95A
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site-directed mutagenesis, 19% increased feedback regulation activity compared to the wild-type enzyme
T170A
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site-directed mutagensis, the viable mutation in the 5'-phosphate sensor of RNase E, becomes lethal in combination with deletions removing part of the non-catalytic C-terminal domain of RNase E
T170V
Y25A
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the mutant is hypoactive in comparison to wild type enzyme. The mutation increases the RNA binding to the multimer formation interface between amino acid residues 427 and 433
Y42A
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site-directed mutagenesis, 48% reduced feedback regulation activity compared to the wild-type enzyme
Y60A
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site-directed mutagenesis, 99% reduced feedback regulation activity compared to the wild-type enzyme
Y77A
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site-directed mutagenesis, 19% reduced feedback regulation activity compared to the wild-type enzyme
Q36R
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the mutant is hyperactive in comparison to wild type enzyme. The mutation enhances the RNA binding to the catalytic site of the enzyme
-
Y25A
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the mutant is hypoactive in comparison to wild type enzyme. The mutation increases the RNA binding to the multimer formation interface between amino acid residues 427 and 433
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F186C
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site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
-
G172A
-
site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
-
R187L
-
site-directed mutagenesis of a point mutation in the S1 RNA-binding domain of RNase E, which leads to temperature-sensitive growth along with defects in 5S rRNA processing, mRNA decay, and tRNA maturation, intragenic suppressors, rne-172, rne-186 and rne-187 alleles, of the temperature-sensitive rne mutant allele cause the dissociation of RNase E activity on mRNA and tRNA or rRNA substrates in Escherichia coli. Specifically, tRNA maturation and 9S rRNA processing are restored to wild-type levels in suppressor mutants, while mRNA decay remains defective, phenotypes, overview
-
A327P
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mutation in N-terminal part of enzyme, temperature-sensitive mutation that is able to suppress the slow growth caused by the mutation tufA499 at permissive temperatures. In addition, mutation causes a large increase 503 in rne mRNA steady state levels; site-directed mutagensis, temperature-sensitive mutant
A448V
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site-directed mutagensis, the mutation causes steric problemes and leads to conformational changes
C471Y
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site-directed mutagensis, the mutation causes steric problemes and leads to conformational changes
G113D
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site-directed mutagensis, the mutation causes steric problemes and leads to conformational changes
G66C
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mutation in N-terminal part of enzyme, temperature-sensitive mutation that is able to suppress the slow growth caused by the mutation tufA499 at permissive temperatures. In addition, mutation causes a large increase 503 in rne mRNA steady state levels; site-directed mutagensis, temperature-sensitive mutant, the mutation causes steric problemes and leads to conformational changes
I207N
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mutation in N-terminal part of enzyme, temperature-sensitive mutation that is able to suppress the slow growth caused by the mutation tufA499 at permissive temperatures. In addition, mutation causes a large increase 503 in rne mRNA steady state levels; site-directed mutagensis, temperature-sensitive mutant, the mutation reduces the nonpolar contacts in the core, which may lead to a less stable protein
I207S
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mutation in N-terminal part of enzyme, temperature-sensitive mutation that is able to suppress the slow growth caused by the mutation tufA499 at permissive temperatures. In addition, mutation causes a large increase 503 in rne mRNA steady state levels; site-directed mutagensis, temperature-sensitive mutant, the mutation reduces the nonpolar contacts in the core, which may lead to a less stable protein
L424R
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site-directed mutagensis, the mutation reduces the nonpolar contacts in the core, which may lead to a less stable protein
V459G
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site-directed mutagensis, the mutation reduces the nonpolar contacts in the core, which may lead to a less stable protein
additional information
D346N
-
site-directed mutagenesis of a residue located on the surface of the subdomain of RNase E, the mutant shows about 25fold reduced catalytic activity but almost unaltered RNA binding compared to the wild-type enzyme
D346N
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N-terminal half-RNase E mutant, at micromolar concentrations of enzyme, cleavage of cspA mRNA occurs to a detectable level: at several positions the primer extension reactions terminate independent of acylation
F57A
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site-directed mutagenesis, 91% reduced feedback regulation activity compared to the wild-type enzyme
F57A
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site-directed mutagenesis of a residue located at the hydrophobic pocket on the surface of the S1 domain, the mutant shows about 50fold reduced catalytic activity compared to the wild-type enzyme
F67A
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site-directed mutagenesis, 94% reduced feedback regulation activity compared to the wild-type enzyme
F67A
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site-directed mutagenesis of a residue located at the hydrophobic pocket on the surface of the S1 domain, the mutant shows about 50fold reduced catalytic activity compared to the wild-type enzyme
N305D
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site-directed mutagenesis of a residue located on the surface of the subdomain of RNase E, the mutant shows reduced catalytic activity compared to the wild-type enzyme
T170V
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5'-end-sensing mutant of N-terminal half-RNase E, mRNA of cspA is still cleaved rapidly when incubated with the mutant. Relative to wild-type, the mutant cleaves 5'-monophosphorylated BR13 more than 15fold slower, without an obvious effect on the rate of cleavage of the 5'-hydroxylated equivalent
T170V
-
the mutant shows considerably reduced activity compared to the wild type enzyme
T170V
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the mutant can cleave a 5'-triphosphorylated transcript efficiently at E3 or E5, but not both
additional information
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16S rRNA 5' maturation is reduced in an rne mutant, altered in a cafA mutant and completely blocked in an rne/cafA double mutant, phenotype, overview
additional information
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functional analysis of enzyme domains by using deletion mutants of RNase E, interaction with degradosome components, overview
additional information
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construction of the rneDELTA645 allele with an introduced stop codon, the mutant strain shows reduced mRNA decay compared to rne wild-type or overexpressing strains
additional information
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modification of the RNase E recognition sequence at position 1205 within pufL affects the enzyme activity with substrate puf mRNA, overview
additional information
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rne is an essential gene, its overexpression interferes with cell growth and viability
additional information
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mutation of gene rne affect the rate of mRNA decay in vivo, construction of a truncated 110 kDa mutant enzyme
additional information
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rne-1 mutants show abolished regulatory protein GadY expression at 42°C, but normal RpoS expression, phenotypes of rne-1 and rne-1/hfq mutant strains, overview
additional information
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the half-life of cspA mRNA is nearly twofold longer in rne-1 knockout strains KCB1008 and SK5665
additional information
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retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation, RNase E derivatives that are as short as 395 amino acid residues and that lack the Zn-link region shown previously to be essential for tetramer formation, residues 400-415, are catalytically active enzymes that retain the 5' to 3' scanning ability and cleavage site specificity characteristic of full-length RNase E and that also confer colony forming ability on rne null mutant bacteria. Further truncation leads to loss of these properties. A minimal catalytically active RNase E sequence proofs that a tetrameric quaternary structure is not required for RNase E to carry out its core enzymatic functions
additional information
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construction of truncated enzyme forms comprising residues 628-843 and 694-790
additional information
computational molecular modelling of mutation suppression, overview
additional information
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the constructed rne mutant strains AT8, i.e. Prne-rne1-417, and AT14, i.e. Prne-rne1-659, show loss of the helical protein organization and reduced activity, AT8 cells grow slowly and show a defect in cell division as shown by a mixed population ranging from normal-length cells to long filaments, AT8 cells exhibit a chromosome segregation defect, phenotypes, overview
additional information
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genetic screen with a Tn5 transposon library to identify Escherichia coli functions involved in retromobility of the Lactobacillus lactis LtrB intron, i.e. a group II intron recruiting cellular polymerases, nucleases, and DNA ligase to complete the retromobility process in Escherichia coli, isolation of an rne promoter region mutant with elevated retrohoming and retrotransposition levels, overview
additional information
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The scaffold region of RNase E can be deleted up to residue 750 without losing the ability to cause the rapid degradation of target mRNAs mediated by Hfq/sRNAs. The truncated RNase E750 can still bind to Hfq although the truncation significantly reduces the Hfq-binding ability. Deletion of the 702-750 region greatly impairs the ability of RNase E to cause the degradation of ptsG mRNA. A polypeptide corresponding to the scaffold region binds to Hfq without the help of RNA. Overexpression of RhlB partially inhibits the Hfq binding to RNase E and the rapid degradation of ptsG mRNA; the scaffold region of RNase E to bind Hfq can be deleted up to residue 750 without losing the ability to cause the rapid degradation of target mRNAs mediated by Hfq/sRNAs. The truncated RNase E750 can still bind to Hfq although the truncation significantly reduces the Hfq-binding ability. Deletion of the 702-750 region greatly impairs the ability of RNase E to cause the degradation of ptsG mRNA
additional information
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deletion of residues C-terminal to position 529 in the absence of other mutations still permit growth of cells. Deletion strain exhibits smaller colony size and reduced growth rates in liquid media. Additional shorter deletions spanning individual microdomains in the C-terminal scaffold region including the Arg-rich region, residues 608-644, the extended Arg-rich region with a putative coil-coil domain, residues 589-723, the RhlB binding site, residues 698–762, the enolase binding site, residues 833-850, or the PNPase binding site, residues 1021-1061, are viable, too; viable mutations affecting the 5'-phosphate sensor of RNase E, including R169Q or T170A, become lethal when combined with deletions removing part of the non-catalytic C-terminal domain of RNase E. Mutation of the phosphate sensor stabilizes the rpsT P1 mRNA as much as sixfold and slows the maturation of 16S rRNA. In contrast, the decay of other model mRNAs and the processing of several tRNA precursors are unaffected by mutations in the phosphate sensor
additional information
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neither the native nor N-terminal extended form of RNase G can restore the growth defect associated with either the rne-1 or rneD1018 alleles even when expressed at very high protein levels. In contrast, two distinct spontaneously derived single amino acid substitutions within the predicted RNase H domain of RNase G, generating the rng-219 and rng-248 alleles, result in complementation of the growth defect associated with various RNase E mutants. Construction of rneD1018/rng-219 and rneD1018/rng-248 double mutants. Domain swaps between RNase E and RNase G generate proteins that do not complement RNase E deficiency
additional information
-
construction of the truncated mutant enzyme N-RNase E consisting of the N-terminal catalytic site, residues 1-498, an enzyme-deficient strain CJ1832 can be complemented by expression of SynRne of Synechocystis sp., but not by Escherichia coli CafA, i.e. RNase G
additional information
-
generation of RNase E-defective mutants and of RNase E/RNase P double mutants, inactivation leads to accumulation of uncleaved tRNA precursors, overview
additional information
-
generation of RNase E-defective mutants and of RNase E/RNase P double mutants, inactivation leads to accumulation of uncleaved tRNA precursors, overview
-
additional information
-
computational molecular modelling of mutation suppression, overview
-
additional information
-
modification of the RNase E recognition sequence at position 1205 within pufL affects the enzyme activity with substrate puf mRNA, overview
-
additional information
-
retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation, RNase E derivatives that are as short as 395 amino acid residues and that lack the Zn-link region shown previously to be essential for tetramer formation, residues 400-415, are catalytically active enzymes that retain the 5' to 3' scanning ability and cleavage site specificity characteristic of full-length RNase E and that also confer colony forming ability on rne null mutant bacteria. Further truncation leads to loss of these properties. A minimal catalytically active RNase E sequence proofs that a tetrameric quaternary structure is not required for RNase E to carry out its core enzymatic functions
additional information
retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation, RNase E derivatives that are as short as 395 amino acid residues and that lack the Zn-link region shown previously to be essential for tetramer formation, residues 400-415, are catalytically active enzymes that retain the 5' to 3' scanning ability and cleavage site specificity characteristic of full-length RNase E and that also confer colony forming ability on rne null mutant bacteria. Further truncation leads to loss of these properties. A minimal catalytically active RNase E sequence proofs that a tetrameric quaternary structure is not required for RNase E to carry out its core enzymatic functions
additional information
-
modification of the RNase E recognition sequence at position 1205 within pufL only slightly affects the enzyme activity with substrate puf mRNA, overview
additional information
-
identification of the EF-Tu mutation, tufA499, with a slow-groth phenotype, structural basis of properties of suppressors of the mutation, overview. Isolation and identification of temperature-sensitive mutations in RNase E that suppress the slow growth of tufA499. Mutations in rne affect the steady-state level of RNase E mRNA. The rne ts and ts suppressor mutations affect 9S to 5S rRNA processing, growrh profiles, overview. The ts mutations in RNase E affect the maturation of hisR tRNAHis
additional information
both the full-length and the N-terminal part of RNase EV (N-RneV) functionally complement Escherichia coli RNase E and their expression consequently supports normal growth of RNase E-depleted Escherichia coli cells
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes, purification involves denaturation and renaturation steps due to the poor solubility of the full-length enzyme
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RNase E is renatured on the Ni-NTA resin by decreasing the concentration of urea to 0.8 M
-
the diluted Rne is dialyzed against two changes of 100 volumes each of 60 mM NH4Cl, 0.1 mM dithiothreitol, and 10% (v/v) glycerol at 4°C for at least 20 h
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
the enzyme can be a model for investigation of the action of site specific nucleases
medicine
medicine
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extraordinarily long antisense RNAs of 3.5 and 7 kb protect a set of mRNAs from RNase E degradation that accumulate during phage infection. These antisense RNA-mRNA duplex formations mask single-stranded recognition sites of RNase E, leading to increased stability of the mRNAs. The interactions directly modulate RNA stability and provide an explanation for enhanced transcript abundance of certain mRNAs during phage infection
medicine
-
extraordinarily long antisense RNAs of 3.5 and 7 kb protect a set of mRNAs from RNase E degradation that accumulate during phage infection. These antisense RNA-mRNA duplex formations mask single-stranded recognition sites of RNase E, leading to increased stability of the mRNAs. The interactions directly modulate RNA stability and provide an explanation for enhanced transcript abundance of certain mRNAs during phage infection
-
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