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Information on EC 3.1.13.1 - exoribonuclease II and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q08162

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.13 Exoribonucleases producing 5′-phosphomonoesters
                3.1.13.1 exoribonuclease II
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Saccharomyces cerevisiae
UNIPROT: Q08162 not found.
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The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
Synonyms
rnase, exoribonuclease, rnase r, rnase ii, rrp44, rnase 2, ribonuclease r, rnaser, ribonuclease 2, exonuclease isg20, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ribonuclease II
-
-
-
-
ribonuclease Q
-
-
-
-
Rrp44
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Exonucleolytic cleavage in the 3'- to 5'- direction to yield nucleoside 5'-phosphates
show the reaction diagram
acts in a processive manner
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-
CAS REGISTRY NUMBER
COMMENTARY hide
37288-24-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
dsRNA + H2O
?
show the reaction diagram
Rrp44 is very efficient in degrading a duplex with a 30 overhang of 14 nucleotides and is inactive with overhangs as short as 2 or 3 nucleotides
-
-
?
ssRNA + H2O
?
show the reaction diagram
50fold higher affinity for ssRNA than for a corresponding ssDNA oligonucleotide
-
-
?
5' end-labeled pre-tRNASer + H2O
?
show the reaction diagram
degradation of pre-tRNASer in a processive manner, leaving a short oligonucleotide (about 3nt) product
-
-
?
mRNA + H2O
5'-phosphomononucleotide
show the reaction diagram
-
-
-
-
?
poly (A)
5'-AMP
show the reaction diagram
-
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
show the reaction diagram
-
-
-
?
poly(A) + H2O
?
show the reaction diagram
-
-
-
-
?
RNA
5'-phosphomononucleotides
show the reaction diagram
-
Tyrosine aminotransferase RNA with 5'-phosphate terminus
-
-
?
rRNA
5'-phosphomononucleotides
show the reaction diagram
-
-
-
-
?
rRNA + H2O
?
show the reaction diagram
-
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
show the reaction diagram
-
-
-
?
tRNAiMet + H2O
?
show the reaction diagram
complete degradation of the hypomodified tRNA requires both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 fails to degrade tRNAi Met, showing this to be a specific Rrp44 substrate
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ss RNA + H2O
5'-phosphomononucleotides
show the reaction diagram
-
-
-
?
tRNAiMet + H2O
?
show the reaction diagram
complete degradation of the hypomodified tRNA requires both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 fails to degrade tRNAi Met, showing this to be a specific Rrp44 substrate
-
-
?
additional information
?
-
-
Dis3 is responsible for exosome core activity
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
required for activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-capped mRNA
-
-
Rna with a terminal 5'-phosphate group
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
970
-
pH 8.0, 37°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
160000
-
SDS-PAGE
175000
-
amino acid sequence
67000
-
1 * 67000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
-
1 * 67000
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Rrp44 in complex with single-stranded RNA, to 2.3 A resolution. Structure of Rrp44 displays CSD1, CSD2, RNB, and S1 domains. The two N-terminal cold shock domains (CSD1, residues 271-399; CSD2, residues 400-475) and the C-terminal S1 domain (residues 911-998) display characteristic OB folds, with five antiparallel beta strands organized in a beta barrel structure. CSD1 is fused to an N-terminal alpha helix (residues 261-268) and the S1 domain has an insertion of three beta strands (between beta3 and beta4) as compared to a standard OB fold. The RNB domain is centered around a core and is surrounded by several alpha helices
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A815F
degrades RNA duplexes with 7 or 14 nucleotides of ssRNA overhang significantly slower (about 4fold) than the wild-type enzyme
A815W
degrades RNA duplexes with 7 or 14 nucleotides of ssRNA overhang significantly slower (about 3fold) than the wild-type enzyme
D551N
abolishes the exonucleolytic activity
D551N
mutation in Rrp44-cat abolishes the exonucleolytic activity of Rrp44 without affecting its ability to bind RNA
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
full-length protein and mutants purified by affinity Ni-NTA chromatography, followed by ion exchange chromatography and gel filtration. 242-1001 construct purified to homogeneity
includes glutathione-Sepharose resin chromatography
-
Rrp44-exosome (RE) architecture suggests an active site sequestration mechanism for strict control of 3' exoribonuclease activity in the RE complex
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
full-length Rrp44 (residues 1-1001) and truncated constructs of Rrp44 expressed from a pETM11 vector in Escherichia coli
expressed in Escherichia coli (XL-1)
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expression in Escherichia coli
-
wild-type Rrp44, Rrp44-20, and Rrp44-cat are expressed in Escherichia coli as GST fusions
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Stevens, A.
An exoribonuclease from Saccharomyces cerevisiae: effect of modifications of 5'-end groups on the hydrolysis of substrates to 5'-mononucleotides
Biochem. Biophys. Res. Commun.
81
656-661
1978
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Stevens, A.
5'-Exoribonuclease 1: Xrn1
Methods Enzymol.
342
251-259
2001
Saccharomyces cerevisiae, Saccharomyces cerevisiae BJ5464
Manually annotated by BRENDA team
Burkard, K.T.D.; Butler, J.S.
A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with poly(A) polymerase and the hnRNA protein Np13p
Mol. Cell. Biol.
20
604-616
2000
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Bollenbach, T.J.; Schuster, G.; Stern, D.B.
Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover
Prog. Nucleic Acid Res. Mol. Biol.
78
305-337
2004
Synechocystis sp., Saccharomyces cerevisiae, Caenorhabditis elegans, Chlamydomonas sp., Drosophila sp. (in: flies), Escherichia coli, Haloferax volcanii, Embryophyta, Homo sapiens, Mammalia, no activity in archaebacteria, Streptomyces coelicolor, uncultured Gammaproteobacteria bacterium
Manually annotated by BRENDA team
Schneider, C.; Anderson, J.T.; Tollervey, D.
The exosome subunit Rrp44 plays a direct role in RNA substrate recognition
Mol. Cell
27
324-331
2007
Saccharomyces cerevisiae (P39112), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Dziembowski, A.; Lorentzen, E.; Conti, E.; Seraphin, B.
A single subunit, Dis3, is essentially responsible for yeast exosome core activity
Nat. Struct. Mol. Biol.
14
15-22
2007
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Wang, H.W.; Wang, J.; Ding, F.; Callahan, K.; Bratkowski, M.A.; Butler, J.S.; Nogales, E.; Ke, A.
Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3 end processing
Proc. Natl. Acad. Sci. USA
104
16844-16849
2007
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Nordick, K.; Hoffman, M.G.; Betz, J.L.; Jaehning, J.A.
Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II
Eukaryot. Cell
7
1158-1167
2008
Saccharomyces cerevisiae, Saccharomyces cerevisiae YJJ
Manually annotated by BRENDA team
Lorentzen, E.; Basquin, J.; Tomecki, R.; Dziembowski, A.; Conti, E.
Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family
Mol. Cell
29
717-728
2008
Saccharomyces cerevisiae (Q08162), Saccharomyces cerevisiae
Manually annotated by BRENDA team