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Information on EC 3.1.26.11 - tRNase Z and Organism(s) Escherichia coli and UniProt Accession P0A8V0
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3.1.26.11 tRNase ZSpecify your search results
Word Map
- 3.1.26.11
- pre-trnas
- trailer
-
endonucleolytic
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rnasel
- exoribonucleases
- metallo-beta-lactamase
-
pre-trna-like
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two-line
-
3'-trailers
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bisp-nitrophenylphosphate
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trna-like
- analysis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule
Synonyms
elac2, trnase z, rnase z, rnase bn, trnase zl, 3' trnase, 3'-trnase, trnase zs, trna 3' processing endoribonuclease, rnase zs1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3 tRNase
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3'-tRNA processing endoribonuclease
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nuclease, transfer ribonucleate maturation 3'-endoribo-(9CI)
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pre-tRNA processing endoribonuclease
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precursor tRNA 3'-end processing endoribonuclease
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RNase BN
transfer RNA maturation endonuclease
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tRNA 3 endonuclease
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tRNA 3' processing endoribonuclease
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tRNA precursor-processing endoribonuclease
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tRNase Z
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
hydrolysis of phosphoric ester
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CAS REGISTRY NUMBER
COMMENTARY
98148-84-6
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
pre-tRNA + H2O
?
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the glycine/proline-rich ZiPD exosite of tRNase Z takes part in the pre-tRNA binding, it is a flexible arm which protrudes from the main protein body
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?
thymidine-5-p-nitrophenyl phosphate + H2O
p-nitrophenol + TMP
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TpNPP substrate, phosphodiesterase activities of tRNase Z on small chromogenic substrates mentioned, structural features of potential model substrates indicated
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-
?
bis(p-nitrophenyl)phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
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bpNPP substrate, phosphodiesterase activities of tRNase Z on small chromogenic substrates mentioned, structural features of potential model substrates indicated
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?
bis(p-nitrophenyl)phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
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evidences for sigmoidal saturation kinetics with the small chromogenic phosphodiester substrate reviewed
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?
bis(p-nitrophenyl)phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
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displays efficient phosphodiesterase activity against bis(p-nitrophenyl) phosphate, which is unusual among the RNase Z family of enzymes
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?
bis(p-nitrophenyl)phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
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phosphodiesterase activity
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?
additional information
?
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involvement of tRNase Z in mRNA processing
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?
additional information
?
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RNase BN is active on both double- and single-stranded RNA but duplex RNA is preferred. Displays a profound base specificity, showing no activity on runs of C residues. Digestion by RNase BN leads to 3-mers as the limit products, but the rate slows on molecules shorter than 10 nucleotides in length. RNase BN acts as a distributive exoribonuclease on some substrates, releasing mononucleotides and a ladder of digestion products. RNase BN also cleaves endonucleolytically, releasing 3' fragments as short as 4 nucleotides
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cd2+
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with 0.2 mM, at 37°C, pH 7.4, 28% relative activity when compared to Co2+
Cu2+
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with 0.2 mM, at 37°C, pH 7.4, 8% relative activity when compared to Co2+
Fe2+
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with 0.2 mM, at 37°C, pH 7.4, 34% relative activity when compared to Co2+
Mg2+
Mn2+
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with 0.2 mM, at 37°C, pH 7.4, 95% relative activity when compared to Co2+. When the existing metal ion of the apoenzyme is removed with EDTA, with 0.2 mM, at 37°C, pH 7.4, 23% relative activity when compared to Co2+ after 60 min of incubation
Zn2+
additional information
Mg2+
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with 0.2 mM, at 37°C, pH 7.4, 54% relative activity when compared to Co2+. When the existing metal ion of the apoenzyme is removed with EDTA, with 0.2 mM, at 37°C, pH 7.4, 15% relative activity when compared to Co2+ after 60 min of incubation
Zn2+
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shows two fully loaded catalytic sites, which may result from Zn2+ addition during crystallization
Zn2+
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with 0.2 mM, at 37°C, pH 7.4, 28% relative activity when compared to Co2+. When the existing metal ion of the apoenzyme is removed with EDTA, with 0.2 mM, at 37°C, pH 7.4, 26% relative activity when compared to Co2+ after 60 min of incubation
additional information
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metal binding sites in tRNase Z and metallo-beta-lactamases described
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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is inhibited by the presence of the CCA motif, maybe the loop between beta1 and beta2 is responsible for the inhibitory effect of CCA-containing tRNA precursors
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additional information
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RNase BN is strongly inhibited by the presence of a 3'-CCA sequence or a 3'-phosphoryl group
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additional information
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presence of a 3'-terminal CCA sequence inhibits RNase BN
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
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with 0.2 mM, at 37°C, pH 7.4, 11% relative activity when compared to Co2+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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evidences for sigmoidal saturation kinetics discussed
additional information
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in vitro processing activities of different recombinant tRNase Z enzymes with respect to CCA-containing and CCA-less pre-tRNAs reviewed
additional information
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involvement in 3'-end processing of pre-mRNAs, additional roles in 3'-end processing of RNA precursors, DNA repair, V(D)J recombination, and telomere maintenance reviewed
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
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strains with simultanoeus deletion of genes from RNases II, Z, D, T and PH are not viable, but cells survive when only one of these genes is active
physiological function
physiological function
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is not essential for cell viability, role in RNA metabolism. May also work as a backup 3'-maturation enzyme for pre-tRNAs with incorrect nucleotides incorporated into the CCA triplet
physiological function
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in addition to tRNase Z, RNase BN of Escherichia coli can act on tRNA precursors containing or lacking a CCA sequence and that it can do so as either an exoribonuclease or an endoribonuclease, overview. Addition of Co2+ results in higher activity and predominantly exoribonucleolytic activity, whereas in the presence of Mg2+ RNase BN is primarily an endoribonuclease. Certain tRNA precursors are extremely poor substrates, overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of different tRNase Z enzymes with regard to canonical sequence motifs reviewed, overview about substrate recognition and cleavage sites of tRNase Z given
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each monomer exhibits the typical metallo-beta-lactamase fold, 2 Zn2+ ions are complexed at the active site
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structures of free and RNA-bound prokaryotic tRNase Z proteins compared, overview, electrostatic surface representation, catalytic site and cleavage mechanism indicated, overview
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the enzyme forms a homodimer, the monomeric subunits are arranged in head-to-head fashion. The monomers concertedly build an active site cleft which is capable of accommodating single-stranded RNA
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Q44S/Q46T
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double mutant, cleavage of human pre-tRNA(Arg) after U75, very inefficiently
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
Escherichia coli strain BL21I-II-(DE3)/pLys carrying the pET-ElaC(His) plasmid
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shibata, H.S.; Minagawa, A.; Takaku, H.; Takagi, M.; Nashimoto, M.
Unstructured RNA is a substrate for tRNase Z
Biochemistry
45
5486-5492
2006
Bacillus subtilis, Escherichia coli, Homo sapiens, Pyrobaculum aerophilum, Saccharomyces cerevisiae, Sus scrofa, Thermotoga maritima
Vogel, A.; Schilling, O.; Spath, B.; Marchfelder, A.
The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties
Biol. Chem.
386
1253-1264
2005
Arabidopsis thaliana, Arabidopsis thaliana (Q8L633), Arabidopsis thaliana (Q8LGU7), Arabidopsis thaliana (Q8VYS2), Bacillus subtilis (P54548), Caenorhabditis elegans (O44476), Drosophila melanogaster (Q8MKW7), Escherichia coli (P0A8V0), Haloferax volcanii, Homo sapiens (Q9BQ52), Homo sapiens (Q9H777), Methanocaldococcus jannaschii (Q58897), Pyrobaculum aerophilum (Q8ZTJ7), Pyrococcus furiosus (Q8U182), Saccharomyces cerevisiae (P36159), Thermoplasma acidophilum (Q9HJ19), Thermotoga maritima
Kostelecky, B.; Pohl, E.; Vogel, A.; Schilling, O.; Meyer-Klaucke, W.
The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins
J. Bacteriol.
188
1607-1614
2006
Escherichia coli
Dominski, Z.
Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism
Crit. Rev. Biochem. Mol. Biol.
42
67-93
2007
Escherichia coli, Homo sapiens
Redko, Y.; Li de Lasierra-Gallay, I.; Condon, C.
When alls zed and done: the structure and function of RNase Z in prokaryotes
Nat. Rev. Microbiol.
5
278-286
2007
Aspergillus nidulans, Bacillus subtilis (P54548), Bacteroides fragilis, Bombyx mori, Bradyrhizobium japonicum, Caenorhabditis elegans, Chlamydia trachomatis, Clostridium acetobutylicum, Clostridium spp., Deinococcus radiodurans, Drosophila melanogaster, Escherichia coli, Haloquadratum walsbyi, Lacticaseibacillus casei, Listeria monocytogenes, Methanocaldococcus jannaschii, Methanococcoides burtonii, Mycobacterium tuberculosis, Myxococcus xanthus, Nanoarchaeum equitans, Prochlorococcus marinus, Saccharolobus solfataricus, Saccharomyces cerevisiae, Staphylococcus aureus, Streptococcus pneumoniae, Streptomyces coelicolor, Thermotoga maritima, Treponema pallidum, Xenopus laevis
Ceballos, M.; Vioque, A.
tRNase Z
Protein Pept. Lett.
14
137-145
2007
Synechocystis sp., Arabidopsis thaliana, Bacillus subtilis, Escherichia coli, Homo sapiens, Methanocaldococcus jannaschii, Thermotoga maritima
Elbarbary, R.A.; Takaku, H.; Nashimoto, M.
Functional analyses for tRNase Z variants: an aspartate and a histidine in the active site are essential for the catalytic activity
Biochim. Biophys. Acta
1784
2079-2085
2008
Bacillus subtilis, Escherichia coli, Homo sapiens, Mus musculus
Takaku, H.; Nashimoto, M.
Escherichia coli tRNase Z can shut down growth probably by removing amino acids from aminoacyl-tRNAs
Genes Cells
13
1087-1097
2008
Escherichia coli
Minagawa, A.; Ishii, R.; Takaku, H.; Yokoyama, S.; Nashimoto, M.
The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection
J. Mol. Biol.
381
289-299
2008
Bacillus subtilis, Escherichia coli, Pyrobaculum aerophilum, Thermoplasma acidophilum, Thermotoga maritima
Dutta, T.; Deutscher, M.P.
Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease
J. Biol. Chem.
284
15425-15431
2009
Escherichia coli
Hartmann, R.K.; Goessringer, M.; Spaeth, B.; Fischer, S.; Marchfelder, A.
The making of tRNAs and more - RNase P and tRNase Z
Prog. Mol. Biol. Transl. Sci.
85
319-368
2009
Aeropyrum pernix, Archaeoglobus fulgidus, Bacillus subtilis, Borreliella burgdorferi, Chlamydia trachomatis, Clostridium perfringens, Deinococcus radiodurans, Escherichia coli, Halobacterium sp., Haloferax volcanii, Lactococcus lactis, Methanocaldococcus jannaschii, Methanopyrus kandleri, Methanosarcina mazei, Methanothermobacter thermautotrophicus, Nanoarchaeum equitans, Pyrobaculum aerophilum, Pyrococcus abyssi, Pyrococcus furiosus, Saccharolobus solfataricus, Synechocystis sp. PCC 6803, Thermoplasma acidophilum, Thermotoga maritima, Treponema pallidum, Triticum aestivum
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