Literature summary for 3.1.13.1 extracted from

Barbas, A.; Matos, R.G.; Amblar, M.; L�pez-Vinas, E.; Gomez-Puertas, P.; Arraiano, C.M.
New insights into the mechanism of RNA degradation by ribonuclease II identification of the residue responsible for setting the RNase II end product (2008), J. Biol. Chem., 283, 13070-13076.

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Cloned(Commentary)

Cloned (Comment)	Organism
wild-type and RNase II mutants cloned into plasmid pFCT6.9 and expressed in Escherichia coli BL21(DE3)	Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
D201N	significant loss of activity in degradation of poly(A) (0.2% of that of the wild-type enzyme). Generates a 10-11-nt fragment as a major degradation product, although longer reaction times result in the usual 4-nt fragment as a secondary product	Escherichia coli
D207N	still retains 12% activity	Escherichia coli
D210N	significant loss of activity in degradation of poly(A) (0.3% of that of the wild-type enzyme). Generates a 10-11-nt fragment as a major degradation product, although longer reaction times result in the usual 4-nt fragment as a secondary product	Escherichia coli
F358A	the protein is 2fold more active than the wild-type	Escherichia coli
Y253A	26% of the activity of the enzyme persists, significantly impairs RNA binding	Escherichia coli
Y253A/F358A	12% of the activity of the enzyme persists, whereas RNA binding affinity is not significantly affected	Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	Asp209, but not Asp207, contacting Mg2+ in addition to Asp201, Asp210, and the phosphate group of nt 13	Escherichia coli

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P30850	-	-
Homo sapiens	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
wild-type and RNase II mutants purified by affinity chromatography	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	Tyr253 and Phe358 are not essential for catalysis by RNase II. Tyr253 seems to be a critical residue in setting the smallest product generated by RNase II, thus being important for the stabilization of the 3'-end of the RNA molecule. Tyr253 is highly conserved and equivalent residues are present in many RNase II family members. Phe358 can be preventing a faster degradation of the RNA by stalling its translocation, probably due to the stacking of its aromatic ring between the bases of contiguous nucleotides. Asp201, Asp207, Asp209, and Asp210 are located in the RNase II active site. These residues are not equivalent and their functions in RNA metabolism are distinct, whereby Asp209 is the only residue essential for RNase II activity	Escherichia coli	?	-	?
oligoribonucleotide + H2O	final end product of RNase II is 4-nt, whereas for RNase R it is a 2-nt fragment	Escherichia coli	?	-	?
oligoribonucleotide + H2O	final end product of Rrp44 is 4-nt	Homo sapiens	?	-	?

Subunits

Subunits	Comment	Organism
More	human Rrp44 proteins shows an overall structure similar to that of Escherichia coli RNase II	Homo sapiens

Synonyms

Synonyms	Comment	Organism
Dis3	-	Homo sapiens
ribonuclease II	-	Homo sapiens
ribonuclease II	-	Escherichia coli
RNase II	-	Homo sapiens
RNase II	-	Escherichia coli
RNase R	-	Escherichia coli
Rrp44	-	Homo sapiens

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Release 2023.1 (January 2023)