3.1.26.12: ribonuclease E
This is an abbreviated version!
For detailed information about ribonuclease E, go to the full flat file.
Word Map on EC 3.1.26.12
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3.1.26.12
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degradosome
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polynucleotide
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phosphorylase
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pnpase
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srnas
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endonuclease
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hfq
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helicase
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endonucleolytic
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exoribonuclease
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single-stranded
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enolase
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stem-loops
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polya
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rna-binding
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polycistronic
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ribonucleolytic
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e-dependent
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base-pairing
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dead-box
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autoregulation
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e-mediated
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e-like
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ompa
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endoribonucleolytic
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5'-terminal
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intercistronic
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cole1-type
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monophosphorylated
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5'-monophosphorylated
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shine-dalgarno
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rho-independent
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hfq-dependent
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glucosamine-6-phosphate
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riboswitches
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au-rich
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glm
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rna-processing
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crescentus
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analysis
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medicine
- 3.1.26.12
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degradosome
- polynucleotide
- phosphorylase
- pnpase
- srnas
- endonuclease
- hfq
- helicase
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endonucleolytic
- exoribonuclease
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single-stranded
- enolase
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stem-loops
- polya
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rna-binding
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polycistronic
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ribonucleolytic
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e-dependent
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base-pairing
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dead-box
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autoregulation
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e-mediated
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e-like
- ompa
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endoribonucleolytic
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5'-terminal
-
intercistronic
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cole1-type
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monophosphorylated
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5'-monophosphorylated
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shine-dalgarno
-
rho-independent
-
hfq-dependent
- glucosamine-6-phosphate
- riboswitches
-
au-rich
- glm
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rna-processing
- crescentus
- analysis
- medicine
Reaction
endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions =
Synonyms
Ams/Rne/Hmp1 polypeptide, AqaRng, endoribonuclease E, endoribonuclease RNase E, More, NCgl2281, ribonuclease E, RNase E, RNase E/G, RNase E/G-type endoribonuclease, RNase ES, RNase EV, RNaseE, Rne, Rne protein, RneC, Rng, SSO1404, SynRne
ECTree
3.1.26.12 ribonuclease EAdvanced search results
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results (Engineering
Engineering on EC 3.1.26.12 - ribonuclease E
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PROTEIN VARIANTS 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
A326T
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
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
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
D303C
mutation results in nearly full loss of activity regardless of metal ion
D303N
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
D346C
the mutation leads to almost complete loss of activity dependent on Mg2+. The activity of the mutant enzyme is fully restored by the presence of Mn2+ with kinetic parameters fully equivalent to those of wild-type enzyme
D346N
E R169Q
mutant protein is strongly overexpressed with accumulation of proteolytic fragments
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
F57A
F67A
G172A
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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
G66S
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
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
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
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
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
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
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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
R48A
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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
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
D303C
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mutation results in nearly full loss of activity regardless of metal ion
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D346C
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the mutation leads to almost complete loss of activity dependent on Mg2+. The activity of the mutant enzyme is fully restored by the presence of Mn2+ with kinetic parameters fully equivalent to those of wild-type enzyme
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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
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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
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G172A
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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
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R187L
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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
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A327P
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
I207N
I207S
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
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
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
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
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
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
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the mutant can cleave a 5'-triphosphorylated transcript efficiently at E3 or E5, but not both
T170V
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the mutant shows considerably reduced activity compared to the wild type enzyme
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
G66C
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site-directed mutagensis, temperature-sensitive mutant, 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
I207N
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site-directed mutagensis, temperature-sensitive mutant, the mutation reduces the nonpolar contacts in the core, which may lead to a less stable protein
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
I207S
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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
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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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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functional analysis of enzyme domains by using deletion mutants of RNase E, interaction with degradosome components, overview
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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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 is an essential gene, its overexpression interferes with cell growth and viability
additional information
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computational molecular modelling of mutation suppression, overview
additional information
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construction of truncated enzyme forms comprising residues 628-843 and 694-790
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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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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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 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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the half-life of cspA mRNA is nearly twofold longer in rne-1 knockout strains KCB1008 and SK5665
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
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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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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
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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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 698762, the enolase binding site, residues 833-850, or the PNPase binding site, residues 1021-1061, are viable, too
additional information
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 698762, the enolase binding site, residues 833-850, or the PNPase binding site, residues 1021-1061, are viable, too
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
additional information
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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
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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
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generation of RNase E-defective mutants and of RNase E/RNase P double mutants, inactivation leads to accumulation of uncleaved tRNA precursors, overview
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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
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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
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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
additional information
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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
