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Information on EC 4.6.1.16 - tRNA-intron lyase and Organism(s) Aeropyrum pernix and UniProt Accession Q9YBF1
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4.6.1.16 tRNA-intron lyaseIUBMB Comments
The enzyme catalyses the final stage in the maturation of tRNA molecules.
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Word Map
- 4.6.1.16
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home
- endonucleases
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laglidadg
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inteins
- pre-trnas
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ribozyme
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i-crei
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intron-containing
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self-splicing
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i-ppoi
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selfish
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intronless
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giy-yig
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pi-scei
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mitogenome
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pontocerebellar
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endas
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meganuclease
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endonucleolytic
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overhang
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free-standing
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mini-inteins
- molecular biology
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maturase
- iridis
- physarum
The taxonomic range for the selected organisms is: Aeropyrum pernix
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
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pretRNA
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a 3'-half-tRNA molecule with a 5'-OH end
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a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end
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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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
nuclease, transfer ribonucleate intron endoribo-
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splicing endonuclease
transfer ribonucleate intron endoribonuclease
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transfer splicing 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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splicing endonuclease
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
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
117444-13-0
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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
additional information
?
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Sulfolobus tokodaii tRNATrp precursor as a substrate
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?
additional information
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Sulfolobus tokodaii tRNATrp precursor as a substrate
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?
additional information
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Aeropyrum pernix expresses precursor-tRNAs with canonical or non-canonical introns at various positions. APE splicing endonuclease removes both types of introns, including the non-canonical introns, without any nucleotide modification. E.g. three tRNAThr species are transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them are cleaved from standard and non-standard positions, APE-EndA has broad substrate specificity, overview
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?
additional information
?
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Aeropyrum pernix expresses precursor-tRNAs with canonical or non-canonical introns at various positions. APE splicing endonuclease removes both types of introns, including the non-canonical introns, without any nucleotide modification. E.g. three tRNAThr species are transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them are cleaved from standard and non-standard positions, APE-EndA has broad substrate specificity, overview
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?
NATURAL SUBSTRATE
NATURAL 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
additional information
?
-
Aeropyrum pernix expresses precursor-tRNAs with canonical or non-canonical introns at various positions. APE splicing endonuclease removes both types of introns, including the non-canonical introns, without any nucleotide modification. E.g. three tRNAThr species are transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them are cleaved from standard and non-standard positions, APE-EndA has broad substrate specificity, overview
-
-
?
additional information
?
-
-
Aeropyrum pernix expresses precursor-tRNAs with canonical or non-canonical introns at various positions. APE splicing endonuclease removes both types of introns, including the non-canonical introns, without any nucleotide modification. E.g. three tRNAThr species are transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them are cleaved from standard and non-standard positions, APE-EndA has broad substrate specificity, overview
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the crenarchaeal heterotetrameric EndAs can be further classified into two subfamilies based on the size of the structural subunit. Subfamily A possesses a structural subunit similar in size to the catalytic subunit, whereas subfamily B possesses a structural subunit significantly smaller than the catalytic subunit
additional information
additional information
EndA from Aeropyrum pernix also possesses an extra loop region that is characteristic of crenarchaeal EndAs, the conserved lysine residue Lys44 in the loop is important for endonuclease activity, substrate docking modeling, overview
additional information
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EndA from Aeropyrum pernix also possesses an extra loop region that is characteristic of crenarchaeal EndAs, the conserved lysine residue Lys44 in the loop is important for endonuclease activity, substrate docking modeling, overview
additional information
APE-EndA possesses a Crenarchaea specific loop, which is responsible for the broad substrate specificity of APE-EndA. Lys44 in CSL functions as the RNA recognition site
additional information
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APE-EndA possesses a Crenarchaea specific loop, which is responsible for the broad substrate specificity of APE-EndA. Lys44 in CSL functions as the RNA recognition site
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
structure comparisons of EndA from Aeropyrum pernix and from Archaeaoglobus fulgidus, overview
additional information
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structure comparisons of EndA from Aeropyrum pernix and from Archaeaoglobus fulgidus, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant wild-type and mutant EndAs, method screening, sitting drop vapor diffusion technique, mixing of 0.001 ml protein solution with 0.001 ml reservoir solution containing 0.2 M NaCl, 0.1 M phosphate-citrate, pH 4.2, and 10% w/v PEG 3000, equilibration over 0.1 ml reservoir solution, 22°C, X-ray diffraction structure determmination and analysis at 1.7-2.3 A resolution, molecular replacement
purified recombinant wild-type and mutant APE-EndAs, hanging-drop vapor diffusion method, 10 mg/ml protein solution is mixed in equal volumes with reservoir solution containing 0.25 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, 0.9 M lithium sulfate and 1 mM MgCl2, 1 day, equilibration over 0.5 ml reservoir solution, 22°C, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D49A
site-directed mutagenesis, the mutation does not affect the enzyme activity
E43A
site-directed mutagenesis, the mutation does not affect the enzyme activity
E51A
site-directed mutagenesis, the mutation does not affect the enzyme activity
F50A
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
H133A
site-directed mutagenesis, a catalytic site mutant, crystal structure determination
K44A
site-directed mutagenesis, the mutant shows almost no enzyme activity
P45A
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
R46A
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
K44A
site-directed mutagenesis, the mutant shows a severe loss of enzyme activity, crystal structure determination
R46A
site-directed mutagenesis, the substitution of R46 residue with alanine does not affect its substrate selectivity significantly, crystal structure determination
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant EndAs from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70°C for 30 min, followed by metal affinity chromatography and gel filtration
recombinant wild-type and mutant EndAs from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70°C for 30 min, followed by heparin affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of His6-tagged wild-type and mutant EndAs in Escherichi coli strain Rosetta 2(DE3)
overexpression of wild-type and mutant EndAs in Escherichia coli strain Rosetta 2(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Okuda, M.; Shiba, T.; Inaoka, D.K.; Kita, K.; Kurisu, G.; Mineki, S.; Harada, S.; Watanabe, Y.; Yoshinari, S.
A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity
J. Mol. Biol.
405
92-104
2011
Aeropyrum pernix (Q9YBF1), Aeropyrum pernix
Hirata, A.; Kitajima, T.; Hori, H.
Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop
Nucleic Acids Res.
39
9376-9389
2011
Archaeoglobus fulgidus, Aeropyrum pernix (Q9YE85), Aeropyrum pernix
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)
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