Information on EC 3.1.27.9 - tRNA-intron endonuclease

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY
3.1.27.9
-
RECOMMENDED NAME
GeneOntology No.
tRNA-intron endonuclease
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism of substrate recognition
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism of substrate recognition
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism of substrate recognition
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
mechanism of substrate recognition
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
structural requirements of substrate
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
active site structure, the catalytic triad is formed by His257, Lys287, and Tyr246
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
substrate recognition mechanism
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
substrate recognition and binding structure and mechanism, catalytic mechanism, the catalytic triad is formed by His257, Lys287, and Tyr246, overview
-
endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
endoribonuclease reaction
-
-
-
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
AF endonuclease
-
-
archaeal pre-tRNA splicing endonuclease
-
-
EndA
Q9YBF1
-
EndA
Q9YE85
-
epsilon2 endonuclease
C7DIA5
-
Gamma-toxin
-
-
HEAB
-
human homologue to a hypothetical Caenorhabditis elegans ATP/GTP-binding protein
homing endonuclease
-
-
nuclease, transfer ribonucleate intron endoribo-
-
-
-
-
RNA splicing endonuclease
-
-
RNA splicing endonuclease
-
-
RNA-splicing endonuclease
-
-
RNA-splicing endonuclease
-
-
splicing endonuclease
-
-
-
-
splicing endonuclease
Q9YBF1
-
splicing endonuclease
Q9YE85
-
splicing endonuclease
-
-
splicing endonuclease
-
-
splicing endonuclease
-
-
splicing endonuclease
-
-
splicing endonuclease
Sulfolobus tokodaii 7
-
-
-
three-unit tRNA splicing endonuclease
C7DIA5
-
transfer ribonucleate intron endoribonuclease
-
-
-
-
transfer splicing endonuclease
-
-
-
-
tRNA anticodon nucleases (ACNs)
-
-
tRNA intron endonuclease
-
-
-
-
tRNA intron-splicing endonuclease
Q9HIY5
-
tRNA splicing endonuclease
-
-
-
-
tRNA splicing endonuclease
C7DIA5
-
tRNA splicing endonuclease
-
-
tRNA-intron endonuclease
-
-
-
-
tRNA-splicing endonuclease
-
mutations cause pontocerebellar hypoplasia (Homo sapiens)
tRNATRPintron endonuclease
-
-
-
-
intron-encoded endonuclease
-
-
additional information
C7DIA5
fourth type of archaeal tRNA splicing endonuclease
CAS REGISTRY NUMBER
COMMENTARY
117444-13-0
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
Saccharomyces cerevisiae 20B-12-1
strain 20B-12-1
-
-
Manually annotated by BRENDA team
Saccharomyces cerevisiae M304
strain M304
-
-
Manually annotated by BRENDA team
genes endo1 and endo2
-
-
Manually annotated by BRENDA team
heteromeric enzyme complex composed of two components; strain 7
-
-
Manually annotated by BRENDA team
Sulfolobus tokodaii 7
heteromeric enzyme complex composed of two components; strain 7
-
-
Manually annotated by BRENDA team
gene XENLA
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
evolution
Q9YBF1
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
evolution
C7DIA5
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
physiological function
-
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
C7DIA5
tRNA splicing endonucleases are involved in the processing of pre-tRNA molecules
malfunction
-
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
additional information
Q9YBF1
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
Q9YE85
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
-
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
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5'-AAGCGACCGACC*AUA*GCUGCA-3' + H2O
?
show the reaction diagram
-
-
-
-
-
pre-t-RNAarcheuka + H2O
?
show the reaction diagram
-
-
-
-
?
pre-t-RNAarcheuka + H2O
?
show the reaction diagram
-
hybrid pre-tRNA molecule derived from yeast and archaea
-
-
?
pre-tRNA + H2O
?
show the reaction diagram
O29362
-
-
-
?
pre-tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
show the reaction diagram
Q9HIY5
-
-
-
?
siRNA + H2O
?
show the reaction diagram
-
RNA kinase responsible for the phosphorylation at the 5' position of tRNA 3' exons
-
-
?
tRNA + H2O
?
show the reaction diagram
-
-
-
-
?
tRNA + H2O
?
show the reaction diagram
-
-
-
-
?
tRNA + H2O
?
show the reaction diagram
-
enzymatically active component of the tRNA splicing endonuclease
-
-
?
tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
show the reaction diagram
-
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
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
Q9M1E8
-
-
-
?
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
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
-
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
show the reaction diagram
Saccharomyces cerevisiae M304
-
-, endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, 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
show the reaction diagram
Saccharomyces cerevisiae 20B-12-1
-
-
-
-
?
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
Saccharomyces cerevisiae 20B-12-1
-
cleaves pre-tRNA in a random order creating two routes for removal of the introns from pre-tRNA, cleaves both 3'- and 5'-nicked pre-tRNAPhe
-
-
?
5'-AAUGCAGCGGUC*AAA*GGUCGC-3' + H2O
?
show the reaction diagram
-
-
-
-
-
additional information
?
-
-
enzyme contains two functionally independent active sites for 5 and 3 splicing
-
-
-
additional information
?
-
-
enzyme contains two functionally independent active sites for 5 and 3 splicing
-
-
-
additional information
?
-
-
structural requirements of substrate
-
-
-
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
-
-
-
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 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 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 of Sulfolobus solfataricus shows a broader substrate specificity
-
-
-
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
?
-
-
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
?
-
Q9YE85
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
?
-
C7DIA5
epsilon2 endonuclease cleaves both canonical and noncanonical bulge-helix-bulge motifs, BHB motif, both strict and relaxed
-
-
-
additional information
?
-
Q9YBF1
Sulfolobus tokodaii tRNATrp precursor as a substrate
-
-
-
additional information
?
-
Sulfolobus tokodaii 7
-
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
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
pre-tRNA + H2O
?
show the reaction diagram
O29362
-
-
-
?
pre-tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
show the reaction diagram
Q9HIY5
-
-
-
?
siRNA + H2O
?
show the reaction diagram
-
RNA kinase responsible for the phosphorylation at the 5' position of tRNA 3' exons
-
-
?
tRNA + H2O
?
show the reaction diagram
-
-
-
-
?
tRNA + H2O
?
show the reaction diagram
-
-
-
-
?
tRNA + H2O
tRNA containing 5'hydroxy and 2',3'-cyclic phosphate termini
show the reaction diagram
-
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
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
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
Saccharomyces cerevisiae M304
-
-
-
-
?
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
Saccharomyces cerevisiae 20B-12-1
-
-
-
-
?
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
-
-
-
additional information
?
-
Q9YE85
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
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-
Mg2+ or Ca2+ required
Mg2+
-
required
Mg2+
-
Mg2+ or Ca2+ required; required
Mg2+
Q9YE85
required
Mg2+
-
required
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Mg2+
-
at high concentrations
Monovalent cations
-
at high concentrations
-
Monovalent cations
-
at 50 mM
-
p-hydroxymercuribenzoate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Nonionic detergents
-
stimulate activity of the endonuclease in the membrane fraction
-
spermidine
-
or spermine required
spermidine
-
required
spermine
-
or spermidine required, enhances extent and accuracy of cleavage, degree of stimulation varies with the pre-tRNA substrate
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.00025
-
additional information
-
wild-type protein, substrate: 5'-AAGCGACCGACC*AUA*GCUGCA-3' or 5'-AAUGCAGCGGUC*AAA*GGUCGC-3'
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
-
-
additional information
-
-
-
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
7.5
-
-
assay at
7.5
-
-
assay at
7.5
-
Q9YE85
assay at
7.5
-
-
assay at
8
-
Q9YBF1
assay at
8.5
-
-
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
8
-
active in the range
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
22
-
-
assay at
37
-
-
assay at
65
-
-
assay at
65
-
Q9YE85
assay at
65
-
-
assay at
70
-
-
assay at
70
-
Q9YBF1
assay at
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
soluble and membrane bound
Manually annotated by BRENDA team
Saccharomyces cerevisiae 20B-12-1, Saccharomyces cerevisiae M304
-
integral membrane protein
-
Manually annotated by BRENDA team
-
mitochondrial cytosolic surface
Manually annotated by BRENDA team
-
soluble and membrane bound
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Nanoarchaeum equitans (strain Kin4-M)
Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
21700
-
-
SDS-PAGE
45000
-
-
-
146000
-
-
deduced from gene sequences of subunits
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 37000, SDS-PAGE
dimer
-
homodimer, crystallization data
dimer
-
heteromeric enzyme complex, both enzyme components are required for catalytic activity
dimer
-
heterodimeric enzyme with subunit encoded by genes endo1 and endo2, analysis of the quarternary structure, structure of catalytic subunit, overview
dimer
-
homodimer, alpha'2 enzyme architecture, structure overview
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
-
alpha-subunit possesses the catalytic residues and beta-subunit has weakhomology to the alpha-subunit, and contains no catalyticresidues
dimer
Sulfolobus tokodaii 7
-
heteromeric enzyme complex, both enzyme components are required for catalytic activity
-
homodimer
Q9HIY5
-
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
Saccharomyces cerevisiae 20B-12-1
-
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
-
tetramer
-
alpha4, crystallization data
tetramer
-
alphabetagammadelta, 1 * 54000, 1 * 44000, 1* 34000, 1 * 15000, SDS-PAGE
tetramer
-
homotetramer, alpha4 enzyme architecture, structure overview
tetramer
-
heterotetramer, alpha2beta2 enzyme architecture, structure overview
tetramer
-
homotetramer, alpha4 enzyme architecture, structure overview
tetramer
-
four different subunits alpha, beta, gamma, delta
tetramer
-
Sen54p, Sen2p, Sen34p and Sen15p
homodimer
C7DIA5
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
additional information
-
heteromeric endonuclease type
additional information
Q9YE85
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
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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, 22C, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement
Q9YE85
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, 22C, X-ray diffraction structure determmination and analysis at 1.7-2.3 A resolution, molecular replacement
Q9YBF1
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, 22C, 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 44C 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.
Q9HIY5
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
rapid inactivation above
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-70C, stable for months
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
recombinant wild-type and mutant EndAs from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70C for 30 min, followed by heparin affinity chromatography and gel filtration
Q9YE85
recombinant wild-type and mutant EndAs from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70C for 30 min, followed by metal affinity chromatography and gel filtration
Q9YBF1
recombinant EndA from Escherichia coli strain Rosetta 2(DE3) by heat treatment at 70C for 30 min, followed by heparin affinity chromatography and gel filtration
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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recombinant truncated fully active dimeric enzyme form lacking the N-terminal domain from Escherichia coli strain BLR(DE3) to homogeneity
-
chromatographic methods
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
partial, strain M304
-
copurification of recombinant His-tagged SULSO alpha-subunit and untagged beta-subunit from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His-tagged subunits by nickel affinity chromatography
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression of His6-tagged wild-type and mutant EndAs in Escherichi coli strain Rosetta 2(DE3)
Q9YBF1
overexpression of wild-type and mutant EndAs in Escherichia coli strain Rosetta 2(DE3)
Q9YE85
two genes coding for different subunits
Q9M1E8
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)
-
overexpression of EndA in Escherichia coli strain Rosetta 2(DE3)
-
epsilon2 endonuclease, DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression of C-terminally His6-tagged wild-type and mutant enzyme
C7DIA5
expression in Eschericha coli
-
gene METJA, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
expression of genes NEQ205 and NEQ261 in Escherichia coli strain BL21(DE3), phylogenetic analysis
-
genes of all four subunits, each of them being essential
-
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)
-
genes endo1 and endo2, expression as His-tagged subunits forming the heterocomplex
-
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
-
gene XENLA, DNA and amino acid sequence determination and analysis, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D49A
Q9YBF1
site-directed mutagenesis, the mutation does not affect the enzyme activity
E43A
Q9YBF1
site-directed mutagenesis, the mutation does not affect the enzyme activity
E51A
Q9YBF1
site-directed mutagenesis, the mutation does not affect the enzyme activity
F50A
Q9YBF1
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
H133A
Q9YBF1
site-directed mutagenesis, a catalytic site mutant, crystal structure determination
H133A
Q9YE85
site-directed mutagenesis, crystal structure determination
K44A
Q9YBF1
site-directed mutagenesis, the mutant shows almost no enzyme activity
K44A
Q9YE85
site-directed mutagenesis, the mutant shows a severe loss of enzyme activity, crystal structure determination
P45A
Q9YBF1
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
R46A
Q9YBF1
site-directed mutagenesis, the mutant shows reduced enzyme activity compared to the wild-type enzyme
R46A
Q9YE85
site-directed mutagenesis, the substitution of R46 residue with alanine does not affect its substrate selectivity significantly, crystal structure determination
H257A
-
residue of the catalytic triad, 28-fold reduction in activity
H257C
-
residue of the catalytic triad
H257D
-
residue of the catalytic triad
H257N
-
residue of the catalytic triad
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
K287Q
-
residue of the catalytic triad
Y246F
-
residue of the catalytic triad, 7-fold reduction in activity
Y246F/H257A
-
residues of the catalytic triad, no activity
Y246H
-
residue of the catalytic triad
D357A
C7DIA5
site-directed mutagenesis
K224E
C7DIA5
site-directed mutagenesis
H136A
-
site-directed mutagenesis of the catalytically essential residue results in an inactive mutant
K287R
-
residue of the catalytic triad
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