Cloned (Comment) | Organism |
---|---|
expression of His-tagged wild-type and mutant catalytic domains | Escherichia coli |
Crystallization (Comment) | Organism |
---|---|
X-ray diffraction structure determination and analysis at 2.9 A resolution | Escherichia coli |
Protein Variants | Comment | Organism |
---|---|---|
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 | Escherichia coli |
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 | Escherichia coli |
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 | Escherichia coli |
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 | Escherichia coli |
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 | Escherichia coli |
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 | Escherichia coli |
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 | Escherichia coli |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
additional information | the enzyme is localized in a multi-protein complex, the RNA degradosome | Escherichia coli | - |
- |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | - |
Escherichia coli | |
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 | Escherichia coli | |
Zn2+ | one ion bound per catalytic domain dimer, two ions per catalytic domain tetramer, three-dimensional structure model | Escherichia coli |
Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
---|---|---|---|
260000 | - |
tetrameric catalytic domains, gel filtration | Escherichia coli |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
additional information | Escherichia coli | 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 | Escherichia coli | 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 | ? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Escherichia coli | - |
gene rne | - |
Escherichia coli | P21513 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant His-tagged wild-type and mutant catalytic domains by nickel affinity chromatography | Escherichia coli |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
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 | Escherichia coli |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
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 | Escherichia coli | ? | - |
? | |
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 | Escherichia coli | ? | - |
? | |
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 | Escherichia coli | ? | - |
? | |
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 | Escherichia coli | ? | - |
? | |
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 | Escherichia coli | ? | - |
? | |
RNA I + H2O | 5' cleavage site | Escherichia coli | ? | - |
? |
Subunits | Comment | Organism |
---|---|---|
More | 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 | Escherichia coli |
tetramer | the catalytic domain of RNase E forms a homotetramer with a molecular mass of roughly 260 kDa | Escherichia coli |
Synonyms | Comment | Organism |
---|---|---|
RNase E | - |
Escherichia coli |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Escherichia coli |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.9 | - |
assay at | Escherichia coli |
8.3 | - |
- |
Escherichia coli |