Literature summary for 3.1.26.12 extracted from

Callaghan, A.J.; Marcaida, M.J.; Stead, J.A.; McDowall, K.J.; Scott, W.G.; Luisi, B.F.
Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover (2005), Nature, 437, 1187-1191.

Search for more literature for 3.1.26.12

Cloned(Commentary)

Cloned (Comment)	Organism
expression of His-tagged wild-type and mutant catalytic domains	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
X-ray diffraction structure determination and analysis at 2.9 A resolution	Escherichia coli

Protein Variants

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

Localization	Comment	Organism	GeneOntology No.	Textmining
additional information	the enzyme is localized in a multi-protein complex, the RNA degradosome	Escherichia coli	-	-

Metals/Ions

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 [Da]	Molecular Weight Maximum [Da]	Comment	Organism
260000	-	tetrameric catalytic domains, gel filtration	Escherichia coli

Natural Substrates/ Products (Substrates)

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

Organism	UniProt	Comment	Textmining
Escherichia coli	-	gene rne	-
Escherichia coli	P21513	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant catalytic domains by nickel affinity chromatography	Escherichia coli

Reaction

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	a

Substrates and Products (Substrate)

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

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

Synonyms	Comment	Organism
RNase E	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Escherichia coli

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.9	-	assay at	Escherichia coli
8.3	-	-	Escherichia coli

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Release 2023.1 (January 2023)