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Information on EC 4.6.1.16 - tRNA-intron lyase
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EC Tree
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
-
home
- endonucleases
-
laglidadg
-
inteins
- pre-trnas
-
ribozyme
-
i-crei
-
intron-containing
-
self-splicing
-
i-ppoi
-
selfish
-
intronless
-
giy-yig
-
pi-scei
-
mitogenome
-
pontocerebellar
-
endas
-
meganuclease
-
endonucleolytic
-
overhang
-
free-standing
-
mini-inteins
- molecular biology
-
maturase
- iridis
- physarum
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
=
+
+
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, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
EC 3.1.27.9
-
-
formerly
-
EndA
HEAB
-
human homologue to a hypothetical Caenorhabditis elegans ATP/GTP-binding protein
nuclease, transfer ribonucleate intron endoribo-
-
-
-
-
pre-tRNA splicing endonuclease
RNA splicing endonuclease
RNA-splicing endonuclease
splicing endonuclease
ssol_1416
STK_03580
transfer ribonucleate intron endoribonuclease
-
-
-
-
transfer splicing endonuclease
-
-
-
-
tRNA endonuclease
tRNA intron endonuclease
-
-
-
-
tRNA splicing endonuclease
tRNA-intron endonuclease
-
-
-
-
tRNA-splicing endonuclease
tRNATRPintron endonuclease
-
-
-
-
additional information
fourth type of archaeal tRNA splicing endonuclease
splicing endonuclease
-
-
-
-
tRNA splicing endonuclease
-
-
-
-
tRNA-splicing endonuclease
-
mutations cause pontocerebellar hypoplasia (Homo sapiens)
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REACTION
REACTION DIAGRAM
COMMENTARY
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
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
mechanism
-
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
mechanism
-
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
structural requirements of substrate
-
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
structural requirements of substrate
-
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
mechanism of substrate recognition
-
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
mechanism of substrate recognition
-
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
mechanism of substrate recognition
-
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
mechanism of substrate recognition
-
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
active site structure, the catalytic triad is formed by His257, Lys287, and Tyr246
-
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
substrate recognition and binding structure and mechanism, catalytic mechanism, the catalytic triad is formed by His257, Lys287, and Tyr246, overview
-
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
substrate recognition mechanism
-
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
-
-
-
-
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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.
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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
pre-tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
-
-
-
?
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
siRNA + H2O
?
-
RNA kinase responsible for the phosphorylation at the 5' position of tRNA 3' exons
-
-
?
tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
-
The enzyme is responsible for the excision of introns from nuclear transfer RNA (tRNA) and all archaeal RNAs.
-
-
?
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
pre-t-RNAarcheuka + H2O
?
-
hybrid pre-tRNA molecule derived from yeast and archaea
-
-
?
pre-t-RNAarcheuka + H2O
?
-
hybrid pre-tRNA molecule derived from yeast and archaea
-
-
?
pre-t-RNAarcheuka + H2O
?
-
hybrid pre-tRNA molecule derived from yeast and archaea
-
-
?
pre-tRNA
?
-
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
-
-
?
pre-tRNA
?
-
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
-
-
?
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
-
-
-
-
?
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
-
-
-
?
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
-
-
-
-
?
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
-
-
-
?
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
-
-
-
?
tRNA + H2O
?
-
enzymatically active component of the tRNA splicing endonuclease
-
-
?
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
-
-
-
-
?
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
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
substrate recognition at the exon-intron boundary region
-
-
?
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
-
precise and accurate excision of the intron from halobacterial tRNATrp precursor
-
-
?
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
-
specific for halobacterial tRNATrp substrates, does not remove the intron from a yeast pre-tRNAPhe substrate
-
-
?
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
-
does not require intact mature tRNA structure in the substrate
-
-
?
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
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini
-
-
?
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
-
-
-
-
?
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
-
differences in distance and relative helical orientation of the splice sites in plant pre-tRNAs versus pre-tRNAs from other organisms are tolerated by the vertebrate splicing endonuclease, but not at all by the plant enzyme
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
cleaves pre-tRNA in a random order creating two routes for removal of the introns from pre-tRNA
-
-
?
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
-
cleaves both 3'- and 5'-nicked pre-tRNAPhe
-
-
?
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
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini
-
-
?
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
-
specifically removing the intron
-
-
?
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
-
-
-
-
?
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
-
cleaves pre-tRNA in a random order creating two routes for removal of the introns from pre-tRNA
-
-
?
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
-
cleaves both 3'- and 5'-nicked pre-tRNAPhe
-
-
?
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
-
-
-
-
?
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
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini
-
-
?
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
-
specifically removing the intron
-
-
?
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
-
-
-
-
?
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
-
differences in distance and relative helical orientation of the splice sites in plant pre-tRNAs versus pre-tRNAs from other organisms are tolerated by the vertebrate splicing endonuclease, but not at all by the plant enzyme
-
-
?
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
-
-
-
-
?
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
-
participation of the intron in the splicing reaction
-
-
?
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
-
structural alterations in mutant precursors of yeast tRNALeu which behave as defective substrates
-
-
?
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
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini
-
-
?
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
-
-
?
additional information
?
-
Sulfolobus tokodaii tRNATrp precursor as a substrate
-
-
?
additional information
?
-
-
Sulfolobus tokodaii tRNATrp precursor as a substrate
-
-
?
additional information
?
-
-
the enzyme cleaves tRNA substrates containing bulge-helix-bulge, BHB, motifs, but not bulge-helix-loop, BHL, motifs, specificity for noncanonical and canonical motifs, cis and trans splicing motifs, overview
-
-
?
additional information
?
-
-
the enzyme cleaves two phosphodiester bonds within folded precursor RNAs during intron removal producing functional RNAs required for protein synthesis, the enzyme binds to bulge-helix-bulge motifs of RNA containing a noncleaved and a cleaved splice site, the enzyme the dimer recognizes cooperatively a flipped-out bulge base and stabilizes sharply bent bulge backbones that are poised for an in-line cleavage reaction
-
-
?
additional information
?
-
-
the enzyme recognizes a unique RNA motif that consists of two three-nucleotide bulges separated by a four base-pair helix, known as the bulge-helix-bulge motif, BHB motif
-
-
?
additional information
?
-
-
AFU-EndA has narrow substrate specificity, overview
-
-
?
additional information
?
-
the enzyme recognizes a bulge-helix-bulge motif
-
-
?
additional information
?
-
epsilon2 endonuclease cleaves both canonical and noncanonical bulge-helix-bulge motifs, BHB motif, both strict and relaxed
-
-
?
additional information
?
-
-
epsilon2 endonuclease cleaves both canonical and noncanonical bulge-helix-bulge motifs, BHB motif, both strict and relaxed
-
-
?
additional information
?
-
-
the enzyme cleaves tRNA substrates containing bulge-helix-bulge, BHB, motifs, but not bulge-helix-loop, BHL, motifs, specificity for noncanonical and canonical motifs, cis and trans splicing motifs, overview
-
-
?
additional information
?
-
the enzyme recognizes a bulge-helix-bulge motif
-
-
?
additional information
?
-
-
the enzyme is required for tRNA maturation removing an intervening sequence element from the tRNA precursor
-
-
?
additional information
?
-
-
the enzyme cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves, e.g. of tRNAGlu, tRNAGln, and tRNALys, and removes an intervening sequence element from the tRNA precursor, cleavage pattern determination, overview
-
-
?
additional information
?
-
-
the enzyme is responsible for recognition and excision of nuclear tRNA and all archeal introns
-
-
?
additional information
?
-
-
the enzyme cleaves tRNA substrates containing bulge-helix-bulge, BHB, motifs and bulge-helix-loop, BHL, motifs, specificity for noncanonical and canonical motifs, cis and trans splicing motifs, overview
-
-
?
additional information
?
-
-
the enzyme of Sulfolobus solfataricus shows a broader substrate specificity
-
-
?
additional information
?
-
the enzyme recognizes a bulge-helix-bulge motif
-
-
?
additional information
?
-
the enzyme recognizes a bulge-helix-bulge motif
-
-
?
additional information
?
-
-
enzyme contains two functionally independent active sites for 5 and 3 splicing
-
-
?
additional information
?
-
-
the enzyme recognizes a bulge-helix-bulge motif
-
-
?
additional information
?
-
-
the heteromeric enzyme complex is composed of two components which are both required for catalytic activity, analysis of reaction products with synthetic tRNA substrate, overview
-
-
?
additional information
?
-
-
the heteromeric enzyme complex is composed of two components which are both required for catalytic activity, analysis of reaction products with synthetic tRNA substrate, overview
-
-
?
additional information
?
-
-
enzyme contains two functionally independent active sites for 5 and 3 splicing
-
-
?
additional information
?
-
-
the enzyme cleaves tRNA substrates containing bulge-helix-bulge, BHB, motifs, but not bulge-helix-loop, BHL, motifs, specificity for noncanonical and canonical motifs, cis and trans splicing motifs, overview
-
-
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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
pre-tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
-
-
-
?
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
siRNA + H2O
?
-
RNA kinase responsible for the phosphorylation at the 5' position of tRNA 3' exons
-
-
?
tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
-
The enzyme is responsible for the excision of introns from nuclear transfer RNA (tRNA) and all archaeal RNAs.
-
-
?
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
pre-tRNA
?
-
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
-
-
?
pre-tRNA
?
-
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
-
-
?
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
-
-
-
-
?
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
-
-
-
?
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
-
-
-
-
?
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
-
-
-
?
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
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
?
additional information
?
-
-
AFU-EndA has narrow substrate specificity, overview
-
-
?
additional information
?
-
-
the enzyme is required for tRNA maturation removing an intervening sequence element from the tRNA precursor
-
-
?
additional information
?
-
-
the enzyme is responsible for recognition and excision of nuclear tRNA and all archeal introns
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
nonionic detergents
-
stimulate activity of the endonuclease in the membrane fraction
-
spermine
-
or spermidine required, enhances extent and accuracy of cleavage, degree of stimulation varies with the pre-tRNA substrate
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Carcinoma, Hepatocellular
Autophagy restricts mitochondrial DNA damage-induced release of ENDOG (endonuclease G) to regulate genome stability.
Carcinoma, Hepatocellular
Genomic DNA double-strand breaks are targets for hepadnaviral DNA integration.
Choriocarcinoma
HSPC117 is regulated by epigenetic modification and is involved in the migration of JEG-3 cells.
Coinfection
Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.
Decompression Sickness
Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.
Fetal Death
HSPC117 deficiency in cloned embryos causes placental abnormality and fetal death.
Hepatitis B
Autophagy restricts mitochondrial DNA damage-induced release of ENDOG (endonuclease G) to regulate genome stability.
Infections
Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron.
Infertility
Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations.
Leprosy
Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease.
Malaria
A synthetic homing endonuclease-based gene drive system in the human malaria mosquito.
Malaria
A synthetic sex ratio distortion system for the control of the human malaria mosquito.
Microcephaly
Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly.
Nervous System Diseases
CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.
Retinitis Pigmentosa
Toward genome editing in X-linked RP-development of a mouse model with specific treatment relevant features.
trna-intron lyase deficiency
HSPC117 deficiency in cloned embryos causes placental abnormality and fetal death.
Tuberculosis
In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions.
Tuberculosis
Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn(2+) and DNA-dependent ATPase activity.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00025
pretRNA
-
wild-type protein, substrate: 5'-AAGCGACCGACC*AUA*GCUGCA-3' or 5'-AAUGCAGCGGUC*AAA*GGUCGC-3'
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
65
70
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
P16658: subunit Sen2, P39707: subunit Sen34, Q04675: subunit Sen15, Q02825: subunit 54
SwissProt
brenda
Q8NCE0: subunit Sen2, Q9BSV6: subunit Sen34, Q8WW01: subunit Sen15, Q7Z6J9: subunit 54
SwissProt
brenda
-
-
-
brenda
P16658: subunit Sen2, P39707: subunit Sen34, Q04675: subunit Sen15, Q02825: subunit 54
SwissProt
brenda
heteromeric enzyme complex is composed of two components which are both required for catalytic activity
Q975R3; F9VMU0
UniProt
brenda
heteromeric enzyme complex is composed of two components which are both required for catalytic activity
Q975R3; F9VMU0
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
in Archaea, three types of splicing endonuclease are produced, homotetrameric: alpha4, homodimeric: alpha2, and heterotetrameric: (alphabeta)2. epsilon2 endonuclease represents a fourth type: epsilon2. The presence of an epsilon2 endonuclease in an archaeon deeply branched within Euryarchaeota represents an example of the coevolution of tRNA and their processing enzymes. The ancestral alpha4 endonuclease is assumed to have undergone two independent gene duplication events giving rise to alpha2 and (alphabeta)2 architecture via subfunctionalization, while most of the (alphabeta)2 endonucleases and korarchaeal a2 endonuclease have acquired extra insertion sequences that interact with BHB motif to broaden their substrate specificity. Transition of splicing endonuclease from alpha4 to epsilon2 type, overview
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
malfunction
Tequatrovirus T4
-
deleted key control elements to deregulate I-TevI expression at early and middle times post T4 infection. Deregulation of I-TevI, or of a catalytically inactive variant, generates a thymidine-dependent phenotype that is caused by a reduction in td intron splicing, deregulated I-TevI expression results in defective td intron splicing and overproduction of a truncated thymidylate synthase protein. Prematurely terminating I-TevI translation restores td splicing, full-length TS synthesis, and rescues the thymidine-dependent phenotype, overview
malfunction
-
epleting HSPC117 by RNA interference abolishes interstrand ligation and impaires processing of pre-tRNA transcripts into mature tRNA in cell extracts
malfunction
mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly
physiological function
Tequatrovirus T4
-
the td group I intron interrupting the thymidylate synthase gene of phage T4 is a mobile intron that encodes the homing endonuclease I-TevI. Efficient RNA splicing of the intron is required to restore function of the thymidylate synthase gene, while expression of I-TevI from within the intron is required to initiate intron mobility. Stringent translational control of I-TevI evolved to prevent the ribosome from disrupting key structural elements of the td intron that are required for splicing and thymidylate synthase function at early and middle times post T4 infection
physiological function
tRNA splicing endonucleases are involved in the processing of pre-tRNA molecules
physiological function
EndA function is required for brain development in humans. Human EndA complex (TSen2, TSen15, TSen34, and TSen54) cleaves introns from pre-tRNAs, and the TSen2 subunit is involved in pre-mRNA'3 end formation
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
-
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
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
-
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
-
introduction of the Crenarchaea specific loop, CSL, eg.e from Aeropyrum pernix EndA, into AFU-EndA enhances its intron-cleaving activity irrespective of the position or motif of the intron
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
100000
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
15000
-
alphabetagammadelta, 1 * 54000, 1 * 44000, 1* 34000, 1 * 15000, SDS-PAGE
29500
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
40700
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
44000
-
alphabetagammadelta, 1 * 54000, 1 * 44000, 1* 34000, 1 * 15000, SDS-PAGE
52500
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
54000
-
alphabetagammadelta, 1 * 54000, 1 * 44000, 1* 34000, 1 * 15000, SDS-PAGE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
heterodimer
heterotetramer
homodimer
homotetramer
multimer
oligomer
tetramer
additional information
dimer
-
structure of the enzyme-BHB RNA complex, PDB code 2A9L, the dimer recognizes cooperatively a flipped-out bulge base and stabilizes sharply bent bulge backbones that are poised for an in-line cleavage reaction
dimer
-
heterodimeric enzyme with subunit encoded by genes endo1 and endo2, analysis of the quarternary structure, structure of catalytic subunit, overview
dimer
-
alpha-subunit possesses the catalytic residues and beta-subunit has weakhomology to the alpha-subunit, and contains no catalyticresidues
dimer
-
heteromeric enzyme complex, both enzyme components are required for catalytic activity
dimer
-
heteromeric enzyme complex, both enzyme components are required for catalytic activity
-
homodimer
the enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a three-unit architecture, the conserved L10-pocket interaction between catalytic and structural unit is necessary for the assembly, protein domain structure, overview
multimer
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
multimer
-
x * 100000, polypeptide A, + y * 52500, polypeptide B, + z * 40700, polypeptide C, + v * 29500, polypeptide D, + 4 minor polypeptides of MW 140000, 120000, 90000 and 70000 are detected in SDS-PAGE of most highly purified fraction, probably polypeptides B, C, and D exist as a trimeric complex and represent the tRNA splicing endonuclease
-
oligomer
human EndA complex: 53247 (subunit TSen2) + 18641 (subunit TSen15) + 33652 (subunit TSen34) + 58819 (subunit TSen54), calculated from sequence
oligomer
Q975R3; F9VMU0
heteromeric enzyme complex is composed of two components which are both required for catalytic activity
oligomer
-
heteromeric enzyme complex is composed of two components which are both required for catalytic activity
-
tetramer
-
homotetramer, alpha4 enzyme architecture, structure overview
tetramer
-
heterotetramer, alpha2beta2 enzyme architecture, structure overview
tetramer
-
alphabetagammadelta, 1 * 54000, 1 * 44000, 1* 34000, 1 * 15000, SDS-PAGE
additional information
structure comparisons of EndA from Aeropyrum pernix and from Archaeaoglobus fulgidus, overview
additional information
-
structure comparisons of EndA from Aeropyrum pernix and from Archaeaoglobus fulgidus, overview
additional information
-
structure comparisons of EndA from Aeropyrum pernix and from Archaeaoglobus fulgidus, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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 AFU-EndA, hanging-drop vapor diffusion method, 10 mg/ml protein solution is mixed in equal volumes with reservoir solution containing 2.2 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate and 0.1 M sodium citrate, pH 5.6, several days, equilibration over 0.5 ml reservoir solution, 22°C, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement
-
truncated active dimeric enzyme form lacking the N-terminal domain, hanging drop vapour diffusion method, 60 mg/ml protein is mixed with reservoir solution conatining 0.1 M sodium cacodylate, pH 6.5-6.8, 20 mM ammonium sulfate, and 0.3-0.4 M sodium acetate, approximately 30 days, X-ray diffraction structure determination and analysis at 2.0 A resolution
-
catalytic subunit, X-ray diffraction structure determination and analysis at 3.1 A resolution
-
Crystallization was performed at 44°C by the sitting-drop method using a Hydra II Plus One crystallization robot (Matrix Technology) with approximately 1500 conditions and a ratio of 200 nl precipitants to 200 nl protein solution.
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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
K44A
P45A
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
R46A
K179A
-
site-directed mutagenesis, the mutant removes the BHB intron from the anticodon loop and the D-loop. However, AFU-CSL K179A can not remove the BHL intron correctly
K287E
-
residue of the catalytic triad, no activity in absence of divalent metal ions, activity observed in the presence of specific divalent metal ions
H136A
-
site-directed mutagenesis of the catalytically essential residue results in an inactive mutant
additional information
H133A
site-directed mutagenesis, a catalytic site mutant, crystal structure determination
K44A
site-directed mutagenesis, the mutant shows a severe loss of enzyme activity, crystal structure determination
K44A
site-directed mutagenesis, the mutant shows almost no enzyme activity
R46A
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
R46A
site-directed mutagenesis, the substitution of R46 residue with alanine does not affect its substrate selectivity significantly, crystal structure determination
additional information
-
construction of a truncated fully active dimeric enzyme form lacking the N-terminal domain
additional information
-
introduction of the Crenarchaea specific loop, CSL, into AFU-EndA enhances its intron-cleaving activity irrespective of the position or motif of the intron
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
copurification of recombinant His-tagged SULSO alpha-subunit and untagged beta-subunit from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant EndA from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70°C for 30 min, followed by heparin affinity chromatography and gel filtration
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant His-tagged subunits by nickel affinity chromatography
-
recombinant truncated fully active dimeric enzyme form lacking the N-terminal domain from Escherichia coli strain BLR(DE3) to homogeneity
-
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
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 His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
epsilon2 endonuclease, DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression of C-terminally His6-tagged wild-type and mutant enzyme
expression of genes NEQ205 and NEQ261 in Escherichia coli strain BL21(DE3), phylogenetic analysis
-
expression of His6-tagged wild-type and mutant EndAs in Escherichi coli strain Rosetta 2(DE3)
gene AFN, expression of truncated fully active dimeric enzyme form lacking the N-terminal domain in Escherichia coli strain BLR(DE3)
-
gene ARCFU, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
gene METJA, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
gene SULSO, DNA and amino acid sequence determination and analysis, coexpression of His-tagged SULSO alpha-subunit and untagged beta-subunit in Escherichia coli strain BL21(DE3)
-
gene XENLA, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
genes endo1 and endo2, expression as His-tagged subunits forming the heterocomplex
-
overexpression of wild-type and mutant EndAs in Escherichia coli strain Rosetta 2(DE3)
two distinct genes endA, ORFs ST0358 and STS047, DNA and amino acid sequence determination and analysis of two ORFs encoding the enzyme, one ORF lacks the putative catalytic amino acid residue, individual expression in Escherichia coli reveals that both are components of an enzyme complex
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
molecular biology
-
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
molecular biology
-
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
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Attardi, D.G.; Margarit, I.; Tocchini-Valentini, G.P.
Structural alterations in mutant precursors of the yeast tRNALeu3 gene which behave as defective substrates for a highly purified splicing endoribonuclease
EMBO J.
4
3289-3297
1985
Xenopus laevis
brenda
Peebles, C.L.; Gegenheimer, P.; Abelson, J.
Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease
Cell
32
525-536
1983
Saccharomyces cerevisiae, Saccharomyces cerevisiae M304
brenda
Thompson, L.D.; Brandon, L.D.; Nieuwlandt, D.T.; Daniels, C.J.
Transfer RNA intron processing in the halophilic archaebacteria
Can. J. Microbiol.
35
36-42
1989
Haloferax volcanii
brenda
Thompson, L.D.; Daniels, C.J.
A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties
J. Biol. Chem.
263
17951-17959
1988
Haloferax volcanii
brenda
Green, P.R.; Abelson, J.N.
Highly purified transfer RNA splicing endonuclease from Saccharomyces cerevisiae
Methods Enzymol.
181
471-480
1990
Saccharomyces cerevisiae, Saccharomyces cerevisiae 20B-12-1
brenda
Gandini-Attardi, D.; Baldi, I.M.; Mattoccia, E.; Tocchini-Valentini, G.P.
Transfer RNA splicing endonuclease from Xenopus laevis
Methods Enzymol.
181
510-517
1990
Xenopus laevis
brenda
Thompson, L.D.; Daniels, C.J.
Recognition of exon-intron boundaries by the Halobacterium volcanii tRNA intron endonuclease
J. Biol. Chem.
265
18104-18111
1990
Haloferax volcanii
brenda
Miao, F.; Abelson, J.
Yeast tRNA-splicing endonuclease cleaves precursor tRNA in a random pathway
J. Biol. Chem.
268
672-677
1993
Saccharomyces cerevisiae, Saccharomyces cerevisiae 20B-12-1
brenda
Stange, N.; Gross, H.J.; Beier, H.
Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs
EMBO J.
7
3823-3828
1988
Homo sapiens, Triticum aestivum
brenda
Baldi, M.I.; Mattoccia, E.; Bufardeci, E.; Fabri, S.; Tocchini-Valentini, G.P.
Participation of the intron in the reaction catalyzed by the Xenopus tRNA splicing endonuclease
Science
255
1404-1408
1992
Xenopus laevis
brenda
Li, H.; Trotta, C.R.; Abelson, J.
Crystal structure and evolution of a transfer RNA splicing enzyme
Science
280
279-284
1998
Methanocaldococcus jannaschii
brenda
Fabbri, S.; Fruscoloni, P.; Bufardeci, E.; Di Nicola Negri, E.; Baldi, M.I.; Attardi, D.G.; Mattoccia, E.; Tocchini-Valentini, G.P.
Conservation of substrate recognition mechanisms by tRNA splicing endonucleases
Science
280
284-286
1998
Saccharomyces cerevisiae, Saccharolobus solfataricus, Xenopus laevis
brenda
Abelson, J.; Trotta, C.R.; Li, H.
tRNA splicing
J. Biol. Chem.
273
12685-12688
1998
Saccharomyces cerevisiae, Haloferax volcanii, Methanocaldococcus jannaschii, Xenopus laevis
brenda
Kleman-Leyer, K.; Armbruster, D.W.; Daniels, C.J.
Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems
Cell
89
839-847
1997
Haloferax volcanii
brenda
Trotta, C.R.; Miao, F.; Arn, E.A.; Stevens, S.W.; Ho, C.K.; Rauhut, R.; Abelson, J.N.
The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases
Cell
89
849-858
1997
Saccharomyces cerevisiae
brenda
Yoshihisa, T.; Yunoki-Esaki, K.; Ohshima, C.; Tanaka, N.; Endo, T.
Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria
Mol. Biol. Cell
14
3266-3279
2003
Saccharomyces cerevisiae
brenda
Fruscoloni, P.; Baldi, M.I.; Tocchini-Valentini, G.P.
Cleavage of non-tRNA substrates by eukaryal tRNA splicing endonucleases
EMBO Rep.
2
217-221
2001
Xenopus laevis
brenda
Di Nicola Negri, E.; Fabbri, S.; Bufardeci, E.; Baldi, M.I.; Gandini Attardi, D.; Mattoccia, E.; Tocchini-Valentini, G.P.
The eucaryal tRNA splicing endonuclease recognizes a tripartite set of RNA elements
Cell
89
859-866
1997
Xenopus laevis
brenda
Akama, K.; Junker, V.; Beier, H.
Identification of two catalytic subunits of tRNA splicing endonuclease from Arabidopsis thaliana
Gene
257
177-185
2000
Arabidopsis thaliana (Q9M1E8), Arabidopsis thaliana
brenda
Li, H.; Abelson, J.
Crystal structure of a dimeric archaeal splicing endonuclease
J. Mol. Biol.
302
639-648
2000
Archaeoglobus fulgidus
brenda
Stephens, K.M.; Monnat, R.J., Jr.; Heath, P.J.; Stoddard, B.L.
Crystallization and preliminary X-ray studies of I-CreI: a group I intron-encoded endonuclease from C. reinhardtii
Proteins
28
137-139
1997
Chlamydomonas reinhardtii
brenda
Akama, K.; Junker, V.; Yukawa, Y.; Sugiura, M.; Beier, H.
Splicing of arabidopsis tRNA(Met) precursors in tobacco cell and wheat germ extracts
Plant Mol. Biol.
44
155-165
2000
Arabidopsis thaliana, Triticum aestivum
brenda
Zhang, Y.; Li, H.
Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2
Acta Crystallogr. Sect. D
60
447-452
2004
Archaeoglobus fulgidus
brenda
Yoshinari, S.; Fujita, S.; Masui, R.; Kuramitsu, S.; Yokobori, S.; Kita, K.; Watanabe, Y.
Functional reconstitution of a crenarchaeal splicing endonuclease in vitro
Biochem. Biophys. Res. Commun.
334
1254-1259
2005
Sulfurisphaera tokodaii, Sulfurisphaera tokodaii 7
brenda
Calvin, K.; Hall, M.D.; Xu, F.; Xue, S.; Li, H.
Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease
J. Mol. Biol.
353
952-960
2005
Saccharolobus solfataricus
brenda
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
brenda
Randau, L.; Calvin, K.; Hall, M.; Yuan, J.; Podar, M.; Li, H.; Soll, D.
The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves
Proc. Natl. Acad. Sci. USA
102
17934-17939
2005
Nanoarchaeum equitans
brenda
Xue, S.; Calvin, K.; Li, H.
RNA recognition and cleavage by a splicing endonuclease
Science
312
906-910
2006
Archaeoglobus fulgidus
brenda
Lu, J.; Esberg, A.; Huang, B.; Bystroem, A.S.
Kluyveromyces lactis gamma-toxin, a ribonuclease that recognizes the anticodon stem loop of tRNA
Nucleic Acids Res.
36
1072-1080
2008
Escherichia coli
brenda
Calvin, K.; Xue, S.; Ellis, C.; Mitchell, M.H.; Li, H.
Probing the catalytic triad of an archaeal RNA splicing endonuclease
Biochemistry
47
13659-13665
2008
Archaeoglobus fulgidus
brenda
Budde, B.S.; Namavar, Y.; Barth, P.G.; Poll-The, B.T.; Nuernberg, G.; Becker, C.; van Ruissen, F.; Weterman, M.A.; Fluiter, K.; te Beek, E.T.; et al.
tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia
Nat. Genet.
40
1113-1118
2008
Homo sapiens
brenda
Weitzer, S.; Martinez, J.
hClp1: a novel kinase revitalizes RNA metabolism
Cell Cycle
6
2133-2137
2007
Homo sapiens
brenda
Calvin, K.; Li, H.
RNA-splicing endonuclease structure and function
Cell. Mol. Life Sci.
65
1176-1185
2008
Saccharomyces cerevisiae
brenda
Yoshihisa, T.; Ohshima, C.; Yunoki-Esaki, K.; Endo, T.
Cytoplasmic splicing of tRNA in Saccharomyces cerevisiae
Genes Cells
12
285-297
2007
Saccharomyces cerevisiae
brenda
Kim, Y.K.; Mizutani, K.; Rhee, K.H.; Nam, K.H.; Lee, W.H.; Lee, E.H.; Kim, E.E.; Park, S.Y.; Hwang, K.Y.
Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: catalytic mechanism of tRNA intron-splicing endonucleases
J. Bacteriol.
189
8339-8346
2007
Thermoplasma acidophilum (Q9HIY5)
brenda
Calvin, K.; Li, H.
Achieving specific RNA cleavage activity by an inactive splicing endonuclease subunit through engineered oligomerization
J. Mol. Biol.
366
642-649
2007
Saccharolobus solfataricus
brenda
Weitzer, S.; Martinez, J.
The human RNA kinase hClp1 is active on 3 transfer RNA exons and short interfering RNAs
Nature
447
222-226
2007
Homo sapiens
brenda
Tocchini-Valentini, G.D.; Fruscoloni, P.; Tocchini-Valentini, G.P.
The dawn of dominance by the mature domain in tRNA splicing
Proc. Natl. Acad. Sci. USA
104
12300-12305
2007
Archaeoglobus fulgidus (O29362)
brenda
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
brenda
Gibb, E.A.; Edgell, D.R.
Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron
Mol. Microbiol.
78
35-46
2010
Tequatrovirus T4
brenda
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
Aeropyrum pernix (Q9YE85), Aeropyrum pernix, Archaeoglobus fulgidus
brenda
Fujishima, K.; Sugahara, J.; Miller, C.S.; Baker, B.J.; Di Giulio, M.; Takesue, K.; Sato, A.; Tomita, M.; Banfield, J.F.; Kanai, A.
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity
Nucleic Acids Res.
39
9695-9704
2011
Candidatus Micrarchaeum acidiphilum (C7DIA5), Candidatus Micrarchaeum acidiphilum
brenda
Yoshinari, S.; Fujita, S.; Masui, R.; Kuramitsu, S.; Yokobori, S.; Kita, K.; Watanabe, Y.
Functional reconstitution of an archaeal splicing endonuclease in vitro
Nucleic Acids Symp. Ser.
49
103-104
2005
Sulfurisphaera tokodaii (Q975R3 and F9VMU0), Sulfurisphaera tokodaii 7 (Q975R3 and F9VMU0)
brenda
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
brenda
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
brenda
Dhungel, N.; Hopper, A.K.
Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing
Genes Dev.
26
503-514
2012
Saccharomyces cerevisiae
brenda
Hirata, A.; Fujishima, K.; Yamagami, R.; Kawamura, T.; Banfield, J.F.; Kanai, A.; Hori, H.
X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity
Nucleic Acids Res.
40
10554-10566
2012
Candidatus Micrarchaeum acidiphilum (C7DIA5), Candidatus Micrarchaeum acidiphilum
brenda
Yamazaki, S.; Yoshinari, S.; Kita, K.; Watanabe, Y.; Kawarabayasi, Y.
Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7
Gene
489
103-110
2011
Sulfurisphaera tokodaii (Q975R3), Sulfurisphaera tokodaii, Sulfurisphaera tokodaii 7 (Q975R3)
brenda
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)
brenda
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)
brenda
Popow, J.; Englert, M.; Weitzer, S.; Schleiffer, A.; Mierzwa, B.; Mechtler, K.; Trowitzsch, S.; Will, C.L.; Luehrmann, R.; Soell, D.; Martinez, J.
HSPC117 is the essential subunit of a human tRNA splicing ligase complex
Science
331
760-764
2011
Homo sapiens
brenda
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)
brenda
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