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Literature summary extracted from
- The making of tRNAs and more - RNase P and tRNase Z (2009), Prog. Mol. Biol. Transl. Sci., 85, 319-368.
Activating Compound
| EC Number | Activating Compound | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.1.26.11 | additional information | is only active at low salt concentrations | Haloferax volcanii |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 3.1.26.11 | 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 | Bacillus subtilis |
| 3.1.26.11 | 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 | Escherichia coli |
| 3.1.26.11 | 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 | Thermotoga maritima |
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.1.26.11 | 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 | Bacillus subtilis | |
| 3.1.26.11 | additional information | 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 | Escherichia coli | |
| 3.1.26.11 | additional information | tRNase Z activity is not inhibited by the presence of long 5'-extensions | Pyrococcus furiosus |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.1.26.11 | Zn2+ | contains one Zn2+ ion per monomer | Thermotoga maritima |  |
| 3.1.26.11 | Zn2+ | shows two fully loaded catalytic sites, which may result from Zn2+ addition during crystallization | Escherichia coli | |
| 3.1.26.11 | Zn2+ | the catalytic core of monomer A contains two Zn2+ | Bacillus subtilis | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 3.1.26.11 | Aeropyrum pernix | - |
- |
- |
| 3.1.26.11 | Archaeoglobus fulgidus | - |
- |
- |
| 3.1.26.11 | Bacillus subtilis | - |
- |
- |
| 3.1.26.11 | Borreliella burgdorferi | - |
- |
- |
| 3.1.26.11 | Chlamydia trachomatis | - |
- |
- |
| 3.1.26.11 | Clostridium perfringens | - |
- |
- |
| 3.1.26.11 | Deinococcus radiodurans | - |
- |
- |
| 3.1.26.11 | Escherichia coli | - |
- |
- |
| 3.1.26.11 | Halobacterium sp. | - |
- |
- |
| 3.1.26.11 | Haloferax volcanii | - |
- |
- |
| 3.1.26.11 | Lactococcus lactis | - |
- |
- |
| 3.1.26.11 | Methanocaldococcus jannaschii | - |
- |
- |
| 3.1.26.11 | Methanopyrus kandleri | - |
- |
- |
| 3.1.26.11 | Methanosarcina mazei | - |
- |
- |
| 3.1.26.11 | Methanothermobacter thermautotrophicus | - |
- |
- |
| 3.1.26.11 | Nanoarchaeum equitans | - |
- |
- |
| 3.1.26.11 | Pyrobaculum aerophilum | - |
- |
- |
| 3.1.26.11 | Pyrococcus abyssi | - |
- |
- |
| 3.1.26.11 | Pyrococcus furiosus | - |
- |
- |
| 3.1.26.11 | Saccharolobus solfataricus | - |
- |
- |
| 3.1.26.11 | Synechocystis sp. PCC 6803 | - |
- |
- |
| 3.1.26.11 | Thermoplasma acidophilum | - |
- |
- |
| 3.1.26.11 | Thermotoga maritima | - |
- |
- |
| 3.1.26.11 | Treponema pallidum | - |
- |
- |
| 3.1.26.11 | Triticum aestivum | - |
- |
- |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.1.26.11 | bis(p-nitrophenyl)phosphate + H2O | - |
Pyrococcus furiosus | p-nitrophenol + p-nitrophenyl phosphate | - |
? | |
| 3.1.26.11 | bis(p-nitrophenyl)phosphate + H2O | phosphodiesterase activity | Escherichia coli | p-nitrophenol + p-nitrophenyl phosphate | - |
? | |
| 3.1.26.11 | additional information | can cleave 3' to the CCA motif | Thermotoga maritima | ? | - |
? | |
| 3.1.26.11 | additional information | cannot cleave substrates carrying a 3'-CCA motif | Bacillus subtilis | ? | - |
? | |
| 3.1.26.11 | additional information | involvement of tRNase Z in mRNA processing | Escherichia coli | ? | - |
? | |
| 3.1.26.11 | additional information | involvement of tRNase Z in pre-5S rRNA cleavage | Haloferax volcanii | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | cleaves intron-containing tRNA precursors and 5'-extended pre-tRNAs | Pyrococcus furiosus | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | cleaves pre-tRNAs 3' to the discriminator. Pre-tRNA with 3'-trailers harboring partial CCA motifs (C and CC) are cleaved in vitro by Trz 3' to C and CC, respectively, whereas CCA-containing pre-tRNAs are not cleaved, but are bound to the enzyme | Synechocystis sp. PCC 6803 | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | 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 | Bacillus subtilis | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | 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 | Escherichia coli | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | 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 | Methanocaldococcus jannaschii | ? | - |
? | |
| 3.1.26.11 | pre-tRNA + H2O | the TM-type exosite of tRNase Z containing a cluster of 4-5 basic amino acid residues takes part in the pre-tRNA binding, it is a flexible arm which protrudes from the main protein body | Thermotoga maritima | ? | - |
? | |
| 3.1.26.11 | S-D-lactoylglutathione + H2O | is a glyoxalase II substrate, tRNase Z has a broad substrate spectrum, is able to process a substrate belonging to a different subclass of the MBL family | Pyrococcus furiosus | ? | - |
? | |
| 3.1.26.11 | thymidine 5'-p-nitrophenyl phosphate + H2O | - |
Escherichia coli | p-nitrophenol + TMP | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 3.1.26.11 | homodimer | crystallography | Bacillus subtilis |
| 3.1.26.11 | homodimer | crystallography | Escherichia coli |
| 3.1.26.11 | homodimer | crystallography | Thermotoga maritima |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 3.1.26.11 | Elac | - |
Escherichia coli |
| 3.1.26.11 | RNase BN | - |
Escherichia coli |
| 3.1.26.11 | RNase Z | - |
Chlamydia trachomatis |
| 3.1.26.11 | RNase Z | - |
Bacillus subtilis |
| 3.1.26.11 | RNase Z | - |
Escherichia coli |
| 3.1.26.11 | RNase Z | - |
Triticum aestivum |
| 3.1.26.11 | RNase Z | - |
Methanothermobacter thermautotrophicus |
| 3.1.26.11 | RNase Z | - |
Pyrococcus furiosus |
| 3.1.26.11 | RNase Z | - |
Lactococcus lactis |
| 3.1.26.11 | RNase Z | - |
Haloferax volcanii |
| 3.1.26.11 | RNase Z | - |
Thermoplasma acidophilum |
| 3.1.26.11 | RNase Z | - |
Saccharolobus solfataricus |
| 3.1.26.11 | RNase Z | - |
Clostridium perfringens |
| 3.1.26.11 | RNase Z | - |
Methanocaldococcus jannaschii |
| 3.1.26.11 | RNase Z | - |
Archaeoglobus fulgidus |
| 3.1.26.11 | RNase Z | - |
Methanopyrus kandleri |
| 3.1.26.11 | RNase Z | - |
Thermotoga maritima |
| 3.1.26.11 | RNase Z | - |
Deinococcus radiodurans |
| 3.1.26.11 | RNase Z | - |
Treponema pallidum |
| 3.1.26.11 | RNase Z | - |
Methanosarcina mazei |
| 3.1.26.11 | RNase Z | - |
Borreliella burgdorferi |
| 3.1.26.11 | RNase Z | - |
Pyrobaculum aerophilum |
| 3.1.26.11 | RNase Z | - |
Synechocystis sp. PCC 6803 |
| 3.1.26.11 | RNase Z | - |
Halobacterium sp. |
| 3.1.26.11 | RNase Z | - |
Aeropyrum pernix |
| 3.1.26.11 | RNase Z | - |
Pyrococcus abyssi |
| 3.1.26.11 | RNase Z | - |
Nanoarchaeum equitans |
| 3.1.26.11 | tRNase Z | - |
Chlamydia trachomatis |
| 3.1.26.11 | tRNase Z | - |
Bacillus subtilis |
| 3.1.26.11 | tRNase Z | - |
Escherichia coli |
| 3.1.26.11 | tRNase Z | - |
Triticum aestivum |
| 3.1.26.11 | tRNase Z | - |
Methanothermobacter thermautotrophicus |
| 3.1.26.11 | tRNase Z | - |
Pyrococcus furiosus |
| 3.1.26.11 | tRNase Z | - |
Lactococcus lactis |
| 3.1.26.11 | tRNase Z | - |
Haloferax volcanii |
| 3.1.26.11 | tRNase Z | - |
Thermoplasma acidophilum |
| 3.1.26.11 | tRNase Z | - |
Saccharolobus solfataricus |
| 3.1.26.11 | tRNase Z | - |
Clostridium perfringens |
| 3.1.26.11 | tRNase Z | - |
Methanocaldococcus jannaschii |
| 3.1.26.11 | tRNase Z | - |
Archaeoglobus fulgidus |
| 3.1.26.11 | tRNase Z | - |
Methanopyrus kandleri |
| 3.1.26.11 | tRNase Z | - |
Thermotoga maritima |
| 3.1.26.11 | tRNase Z | - |
Deinococcus radiodurans |
| 3.1.26.11 | tRNase Z | - |
Treponema pallidum |
| 3.1.26.11 | tRNase Z | - |
Methanosarcina mazei |
| 3.1.26.11 | tRNase Z | - |
Borreliella burgdorferi |
| 3.1.26.11 | tRNase Z | - |
Pyrobaculum aerophilum |
| 3.1.26.11 | tRNase Z | - |
Synechocystis sp. PCC 6803 |
| 3.1.26.11 | tRNase Z | - |
Halobacterium sp. |
| 3.1.26.11 | tRNase Z | - |
Aeropyrum pernix |
| 3.1.26.11 | tRNase Z | - |
Pyrococcus abyssi |
| 3.1.26.11 | tRNase Z | - |
Nanoarchaeum equitans |
| 3.1.26.11 | Trz | - |
Thermotoga maritima |
| 3.1.26.11 | zinc-dependent phosphodiesterase | - |
Escherichia coli |
| 3.1.26.11 | ZiPD | - |
Escherichia coli |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 3.1.26.11 | malfunction | 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 | Bacillus subtilis |
| 3.1.26.11 | malfunction | 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 | Escherichia coli |
| 3.1.26.11 | physiological function | 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 | Escherichia coli |
| 3.1.26.11 | physiological function | is required for maturation of pre-tRNAs lacking a CCA motif and is thus essential for cell viability | Bacillus subtilis |
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