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Information on EC 3.1.13.B1 - 5'-3' exoribonuclease and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q02792

for references in articles please use BRENDA:EC3.1.13.B1
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Saccharomyces cerevisiae
UNIPROT: Q02792
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The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Archaea, Eukaryota
Reaction Schemes
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Synonyms
5'-3' exoribonuclease, 5'-to-3' exoribonuclease, pab-rnase j, 5'-3' exoribonuclease 2, saci-acpsf2, sso-rnase j, tk-rnase j, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5'-3' exoribonuclease 2
UniProt
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
show the reaction diagram
cleavage scheme, Rail/Rat1 mechanism and mechanism of RNAPII termination, overview
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
absolutely required for catalysis
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ATP
ATP significantly enhances Rat1/Rai1-mediated RNAPII termination. The ATP-dependent effect seems to be unique to Rat1/Rai1. ATP addition does not stimulate the processivity of Rat1. Rather, it slightly reduces the exonuclease activity because 1 mM of ATP is sufficient to chelate the Mg2+ ion necessary for the nuclease activity of Rat1, suggesting that ATP affects Rat1-mediated termination in a somewhat different manner
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
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LITERATURE
ORGANISM
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LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
yeast Rat1 is evolutionarily well conserved from yeast to human (Xrn2 in human)
physiological function
yeast Rat1 is an essential nuclear protein. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination. Rat1 forms a complex with Rai1 that stabilizes Rat1 and helps target 5' monophosphate RNA by its diphosphohydrolase activity. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNAPII on protein-coding genes, overview. RNAPII is prone to more effective termination by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, implying that paused RNAPII, which is often found in vivo near termination sites, can adopt a similar configuration to Rat1/Rai1 and trigger termination. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Multiple-mechanistic features contribute to Rat1-mediated termination of RNAPII. NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1, Rat1/Rai1 more effectively terminates RNAPII when a non-cognate NTP (ATP, CTP or UTP), rather than cognate GTP. Exoribonuclease activity is required for Rat1 not only to approach RNAPII but also to accumulate a sufficient driving force to dislodge the polymerase from the DNA template
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E203A/D233A/D235A
site-directed mutagenesis, mutation of three active site residues, mutant rat1EDD does not show 5'-3' exoribonuclease activity, and rat1EDD/Rai1 complex does not degrade RNAs or decrease RNAPII elongation, demonstrating that RNA degradation by exonuclease activity is critical to RNAPII termination
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged Rat1 from Escherichia coli strain BL21 Codon-Plus (DE3) RIL by nickel affinity chromatography and anion exchange chromatography, followed by gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant overexpression of His6-tagged Rat1 in Escherichia coli strain BL21 Codon-Plus(DE3)RIL. The recombinant Rat1/Rai1 cannot terminate Escherichia coli RNAP in vitro and addition of each NTP has no effect either
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Park, J.; Kang, M.; Kim, M.
Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1
Nucleic Acids Res.
43
2625-2637
2015
Saccharomyces cerevisiae (Q02792), Saccharomyces cerevisiae
Manually annotated by BRENDA team