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Literature summary for 3.1.13.1 extracted from

  • Vincent, H.A.; Deutscher, M.P.
    The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA (2009), J. Biol. Chem., 284, 486-494.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.1.13.1

Application

Application Comment Organism
degradation RNA-binding domains of RNase II play a more important role in its exoribonuclease activity than they do in the activity of RNase R Escherichia coli

Cloned(Commentary)

Cloned (Comment) Organism
RNase R and RNase II constructs cloned into vector pET44R and overexpressed in Escherichia coli BL21II-R-(DE3)pLysS Escherichia coli

Protein Variants

Protein Variants Comment Organism
D155M truncated RNase II protein pETIIDELTACSD1DELTAS1 consisting of the nuclease domain alone, but lacking any part of CSD2. Removal of the RNA-binding domains does allow RNase II to proceed further Escherichia coli
D278N mutation at the catalytic center of RNase R, is inactive on A(4), but retains 4% activity of wild-type RNase R on poly(A) and A(17) Escherichia coli
additional information RNase RDELTACSDs is missing the first 221 amino acids of RNase R, which include CSD1 and CSD2. RNase RDELTABasic lacks the 83 amino acids from the C terminus, which comprise the low complexity, highly basic region. RNase RDELTAS1 is truncated 170 amino acids from the C-terminus to remove both the S1 domain and the low complexity, highly basic region. RNase RDELTACSDsDELTAS1 consists of the nuclease domain alone, and, therefore, lacks all of the putative RNA-binding domains. Decrease in affinity upon deletion of either the CSDs or the S1 domain. RNase RDELTABasic displays 2fold higher activity than full-length wild-type RNase R. RNase RDELTACSDs looses 30% of the activity of full-length RNase R on poly(A) 90% on the shorter A(17) substrate. The RNase RDELTACSDsDELTAS1 truncated protein retains only 0.5% activity of the full-length protein on poly(A), and only 0.02% activity on A(17). All of the RNase R-truncated proteins have comparable activity on A(4) Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ is important for substrate binding of RNase R in the channel as well as for catalysis. Asp278 is predicted to coordinate a Mg2+ at the catalytic center of RNase R Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli
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-
-

Purification (Commentary)

Purification (Comment) Organism
RNase R and RNase II constructs, full-length wild-type RNase R and RNase R mutant D278N Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
A(17) + H2O full-length RNase R has similar activity on both poly(A) and A(17) substrates. Full-length RNase II is 20fold more active on A(17) than full-length RNase R Escherichia coli AMP + ?
-
 ?
A(4) + H2O poor substrate, is degraded by RNase R 400fold more slowly than A(17) Escherichia coli AMP + ?
-
 ?
dsRNA + H2O
-
 Escherichia coli ?
-
 ?
additional information cold-shock domains of RNase R appear to play a role in substrate recruitment, whereas the S1 domain is most likely required to position substrates for efficient catalysis. The nuclease domain alone, devoid of the cold-shock and S1 domains, is sufficient for RNase R to bind and degrade structured RNAs. RNase R binds RNA more tightly than the nuclease domain of RNase II Escherichia coli ?
-
 ?
poly(A) + H2O full-length RNase R has similar activity on both poly(A) and A(17) substrates Escherichia coli 5'-AMP + oligo(A)
-
 ?

Synonyms

Synonyms Comment Organism
RNase II
-
 Escherichia coli
RNase R
-
 Escherichia coli