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Information on EC 3.1.26.11 - tRNase Z and Organism(s) Bacillus subtilis and UniProt Accession P54548

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.26 Endoribonucleases producing 5'-phosphomonoesters
                3.1.26.11 tRNase Z
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Bacillus subtilis
UNIPROT: P54548 not found.
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The taxonomic range for the selected organisms is: Bacillus subtilis
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
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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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 tRNase
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-
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3'-tRNA processing endoribonuclease
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-
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nuclease, transfer ribonucleate maturation 3'-endoribo-(9CI)
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-
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pre-tRNA processing endoribonuclease
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-
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precursor tRNA 3'-end processing endoribonuclease
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-
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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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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
hydrolysis of phosphoric ester
CAS REGISTRY NUMBER
COMMENTARY hide
98148-84-6
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Bacillus subtilis tRNACys + H2O
?
show the reaction diagram
efficient cleavage
-
-
?
human pre-tRNAArg + H2O
?
show the reaction diagram
efficient cleavage
-
-
?
pre-tRNAAla + H2O
?
show the reaction diagram
-
-
-
?
pre-tRNACys + H2O
?
show the reaction diagram
-
-
-
?
pre-tRNATyr + H2O
?
show the reaction diagram
-
-
-
?
Thermotoga maritima pre-tRNAArg(GUG) + H2O
?
show the reaction diagram
efficient cleavage
-
-
?
pre-tRNA + H2O
?
show the reaction diagram
-
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
-
-
?
pTyrI + H2O
?
show the reaction diagram
-
pre-tRNATyr from Oenothera berteriana
-
-
?
trnB-THr + H2O
?
show the reaction diagram
-
pre-tRNATHr with a 47 nucleotide 3' trailing sequence and CCA motif, no cleavage
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-
?
trnI-Thr + H2O
?
show the reaction diagram
-
pre-tRNAThr with a 83 nucleotide 3' trailing sequence, cleavage at one or two bases downstream the discriminator base
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-
?
trnI-Thr-CAAATG-trailer + H2O
?
show the reaction diagram
-
-
-
-
?
trnI-Thr-CCAATG-trailer + H2O
?
show the reaction diagram
-
-
-
-
?
trnI-Thr-TAAATG-trailer + H2O
?
show the reaction diagram
-
native trailer sequence
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-
?
trnI-Thr-TCAATG-trailer + H2O
?
show the reaction diagram
-
-
-
-
?
usRNA1 + H2O
?
show the reaction diagram
-
24 nt unstructured RNA
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-
?
usRNA10 + H2O
?
show the reaction diagram
-
40 nt unstructured RNA
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-
?
usRNA2 + H2O
?
show the reaction diagram
-
24 nt unstructured RNA
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-
?
usRNA3 + H2O
?
show the reaction diagram
-
28 nt unstructured RNA
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-
?
usRNA4 + H2O
?
show the reaction diagram
-
39 nt unstructured RNA
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-
?
usRNA5 + H2O
?
show the reaction diagram
-
26 nt unstructured RNA
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-
?
usRNA6 + H2O
?
show the reaction diagram
-
26 nt unstructured RNA
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-
?
usRNA7 + H2O
?
show the reaction diagram
-
24 nt unstructured RNA
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-
?
usRNA8 + H2O
?
show the reaction diagram
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43 nt unstructured RNA
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?
usRNA9 + H2O
?
show the reaction diagram
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22 nt unstructured RNA
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?
additional information
?
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cannot cleave substrates carrying a 3'-CCA motif
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
Bacillus subtilis pre-tRNACys is cleaved in the presence of Mn2+ but not in the presence of Mg2+
Mn2+
Bacillus subtilis pre-tRNACys is cleaved in the presence of Mn2+ but not in the presence of Mg2+
MgCl2
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most active at 0-0.2 mM, weak activity above 3 mM
MnCl2
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most active at 1-5 mM
Zn2+
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the catalytic core of monomer A contains two Zn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
a distortion of one metal-binding site inhibits Zn2+ binding to both metal binding sites in monomer B. 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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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0022
trnI-Thr-CAAATG-trailer
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the first cytosine is the primary anti-determinant for RNaseZ
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0.0024
trnI-Thr-CCAATG-trailer
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CCA motif inhibits RNaseZ cleavage
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0.00097
trnI-Thr-TAAATG-trailer
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native trailer sequence
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0.00058
trnI-Thr-TCAATG-trailer
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-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
in vitro processing activities of different recombinant tRNase Z enzymes with respect to CCA-containing and CCA-less pre-tRNAs reviewed, involvement in potential futile cycles in tRNA 3'-processing shown
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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in a mutant strain, the chromosomal tRNase Z gene is put under control of an IPTG-dependent promoter. Removal of IPTG from the culture medium results in complete growth inhibition, tRNase Z is essential for the organism. Downregulation of Trz expression leads to an accumulation of CCA-less pre-tRNAs in vivo
physiological function
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is required for maturation of pre-tRNAs lacking a CCA motif and is thus essential for cell viability
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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homodimer, crystal structure
homodimer
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crystallography
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cocrystallization with tRNAThr
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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the enzyme bears significant similarity to Zn-dependent metallo-beta-lactamases, two Zn2+ in the active site are complexed by H63, H65, D67, H68, H140, D211 and H269
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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 hide
LITERATURE
H65A
the mutation was introduced at the central histidine to slow down hydrolysis of precursor tRNA during cocrystallization
D211A
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Asp(II), active site residue
D67A
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Asp(I), active site residue
H140A
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His(IV), active site residue
H247A
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His(V), active site residue
H269A
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His(VI), active site residue
H63A
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His(I), active site residue
H65A
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His(II), active site residue
H68A
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His(III), active site residue
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
His-tag fusion, Ni-affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Pellegrini, O.; Nezzar, J.; Marchfelder, A.; Putzer, H.; Condon, C.
Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis
EMBO J.
22
4534-4543
2003
Bacillus subtilis
Manually annotated by BRENDA team
Li de la Sierra-Gallay, I.; Mathy, N.; Pellegrini, O.; Condon, C.
Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA
Nat. Struct. Mol. Biol.
13
376-377
2006
Bacillus subtilis (P54548), Bacillus subtilis
Manually annotated by BRENDA team
de la Sierra-Gallay, I.L.; Pellegrini, O.; Condon, C.
Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z
Nature
433
657-661
2005
Bacillus subtilis
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Dutta, T.; Malhotra, A.; Deutscher, M.P.
Exoribonuclease and endoribonuclease activities of RNase BN/RNase Z both function in vivo
J. Biol. Chem.
287
35747-35755
2012
Bacillus subtilis (P54548), Bacillus subtilis, Bacillus subtilis 168 (P54548)
Manually annotated by BRENDA team
Minagawa, A.; Takaku, H.; Shibata, H.; Ishii, R.; Takagi, M.; Yokoyama, S.; Nashimoto, M.
Substrate recognition ability differs among various prokaryotic tRNase Zs
Biochem. Biophys. Res. Commun.
345
385-393
2006
Bacillus subtilis (P54548), Bacillus subtilis, Bacillus subtilis 168 (P54548), Pyrobaculum aerophilum (Q8ZTJ7), Pyrobaculum aerophilum, Pyrobaculum aerophilum DSM 7523 (Q8ZTJ7), Thermoplasma acidophilum (Q9HJ19), Thermoplasma acidophilum, Thermotoga maritima (Q9WY50), Thermotoga maritima, Thermotoga maritima DSM 3109 (Q9WY50), Thermus thermophilus (Q53W74), Thermus thermophilus, Thermus thermophilus DSM 579 (Q53W74)
Manually annotated by BRENDA team