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Information on EC 4.6.1.16 - tRNA-intron lyase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q58819

for references in articles please use BRENDA:EC4.6.1.16
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EC Tree
IUBMB Comments
The enzyme catalyses the final stage in the maturation of tRNA molecules.
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This record set is specific for:
Methanocaldococcus jannaschii
UNIPROT: Q58819
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The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
hide
pretRNA
=
a 3'-half-tRNA molecule with a 5'-OH end
+
a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end
+
an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
pretRNA
=
a 3'-half-tRNA molecule with a 5'-OH end
+
a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end
+
an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
Synonyms
homing endonuclease, i-tevi, splicing endonuclease, trna splicing endonuclease, hspc117, intron-encoded endonuclease, hclp1, trna-splicing endonuclease, af endonuclease, rna splicing endonuclease, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pre-tRNA splicing endonuclease
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tRNA-splicing endonuclease
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nuclease, transfer ribonucleate intron endoribo-
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splicing endonuclease
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transfer ribonucleate intron endoribonuclease
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transfer splicing endonuclease
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tRNA endonuclease
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tRNA intron endonuclease
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tRNA splicing endonuclease
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tRNA-intron endonuclease
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tRNATRPintron endonuclease
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
show the reaction diagram
mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
endoribonuclease reaction
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
pretRNA lyase (intron-removing; cyclic-2',3'-phosphate-forming)
The enzyme catalyses the final stage in the maturation of tRNA molecules.
CAS REGISTRY NUMBER
COMMENTARY hide
117444-13-0
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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
pretRNA
a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
show the reaction diagram
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-
-
?
pre-tRNA
?
show the reaction diagram
tRNA precursor
a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
show the reaction diagram
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?
additional information
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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
pretRNA
a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
show the reaction diagram
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?
pre-tRNA
?
show the reaction diagram
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processing of multiple-intron-containing pretRNA. In these multiple-intron-containing pretRNAs, the introns are nested one inside the other and the pretRNA folds into a conformation that presumably allows the splicing of the last intron only after the splicing of the others. The tRNA splicing endonuclease and the ligase, through a series of cleavages and ligations, should lead to the formation of mature tRNA
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene METJA, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
molecular biology
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controlled RNA splicing in mammalian cells. mRNA modification technology that makes use of tRNA splicing endonuclease and its natural substrate, the bulge-helix-bulge structure. These components can perform both cis- and trans-splicing in cellular and animal models and may provide a convenient way to modulate gene expression using components independent of cellular regulatory networks. To use the Methanocaldococcus jannaschii enzyme in stable expression mammalian systems, variants are developed which are characterized by high efficiency and sustainable in vivo activity. The variants are created by the introduction of proper localization signals followed by mutagenesis and direct selection in mammalian cells. The best endonuclease variant shows 40fold higher activity compared to the parental enzyme and stable processing of 30% of the target mRNA. These variants show complete compatibility with long-term expression in mammalian cells, suggesting that they may be usefully applied in functional genomics and genetically modified animal models
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Li, H.; Trotta, C.R.; Abelson, J.
Crystal structure and evolution of a transfer RNA splicing enzyme
Science
280
279-284
1998
Methanocaldococcus jannaschii
Manually annotated by BRENDA team
Abelson, J.; Trotta, C.R.; Li, H.
tRNA splicing
J. Biol. Chem.
273
12685-12688
1998
Saccharomyces cerevisiae, Haloferax volcanii, Methanocaldococcus jannaschii, Xenopus laevis
Manually annotated by BRENDA team
Tocchini-Valentini, G.D.; Fruscoloni, P.; Tocchini-Valentini, G.P.
Coevolution of tRNA intron motifs and tRNA endonuclease architecture in archaea
Proc. Natl. Acad. Sci. USA
102
15418-15422
2005
Archaeoglobus fulgidus, Methanocaldococcus jannaschii, Saccharolobus solfataricus, Xenopus laevis
Manually annotated by BRENDA team
Tocchini-Valentini, G.D.; Fruscoloni, P.; Tocchini-Valentini, G.P.
Processing of multiple-intron-containing pretRNA
Proc. Natl. Acad. Sci. USA
106
20246-20251
2009
Methanocaldococcus jannaschii, Saccharolobus solfataricus
Manually annotated by BRENDA team
Putti, S.; Calandra, P.; Rossi, N.; Scarabino, D.; Deidda, G.; Tocchini-Valentini, G.P.
Highly efficient, in vivo optimized, archaeal endonuclease for controlled RNA splicing in mammalian cells
FASEB J.
27
3466-3477
2013
Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661
Manually annotated by BRENDA team
Tocchini-Valentini, G.D.; Fruscoloni, P.; Tocchini-Valentini, G.P.
Evolution of introns in the archaeal world
Proc. Natl. Acad. Sci. USA
108
4782-4787
2011
Schizosaccharomyces pombe, Saccharolobus solfataricus (D0KSD0), Archaeoglobus fulgidus (O29362), Methanocaldococcus jannaschii (Q58819), Saccharolobus solfataricus 98/2 (D0KSD0)
Manually annotated by BRENDA team
Tocchini-Valentini, G.D.; Tocchini-Valentini, G.P.
Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes
Proc. Natl. Acad. Sci. USA
109
21325-21329
2012
Schizosaccharomyces pombe, Methanocaldococcus jannaschii (Q58819)
Manually annotated by BRENDA team
Hirata, A.
Recent insights into the structure, function, and evolution of the RNA-splicing endonucleases
Front. Genet.
10
103
2019
Candidatus Micrarchaeum acidiphilum ARMAN-2 (C7DIA5), Archaeoglobus fulgidus (O29362), Saccharomyces cerevisiae (P16658 AND P39707 AND Q04675 AND Q02825), Saccharomyces cerevisiae, Methanocaldococcus jannaschii (Q58819), Nanoarchaeum equitans (Q74MP4), Homo sapiens (Q8NCE0 AND Q9BSV6 AND Q8WW01 AND Q7Z6J9), Homo sapiens, Methanopyrus kandleri (Q8TGZ5), Pyrobaculum aerophilum (Q8ZVI1), Thermoplasma acidophilum (Q9HIY5), Aeropyrum pernix (Q9YE85), Aeropyrum pernix ATCC 700893 (Q9YE85), Archaeoglobus fulgidus ATCC 49558 (O29362), Methanocaldococcus jannaschii ATCC 43067 (Q58819), Saccharomyces cerevisiae ATCC 204508 (P16658 AND P39707 AND Q04675 AND Q02825), Pyrobaculum aerophilum ATCC 51768 (Q8ZVI1), Thermoplasma acidophilum ATCC 25905 (Q9HIY5)
Manually annotated by BRENDA team