Literature summary for 3.1.26.5 extracted from

Takagi, H.; Watanabe, M.; Kakuta, Y.; Kamachi, R.; Numata, T.; Tanaka, I.; Kimura, M.
Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3 (2004), Biochem. Biophys. Res. Commun., 319, 787-794.

Search for more literature for 3.1.26.5

Cloned(Commentary)

Cloned (Comment)	Organism
overexpression of native and selenomethionine-containing wild-type protein subunit Ph1877p, and mutant protein subunits Ph1788p in Escherichia coli	Pyrococcus horikoshii

Crystallization (Commentary)

Crystallization (Comment)	Organism
10 mg/ml purified recombinant selenomethionine labeled protein subunit Ph1877p, vapour diffusion against 22.5% PEG 6000 and 0.1 M HEPES, pH 7.5, hanging drop method, crystals are suspended on a loop in a thin liquid film of stabilizing solution and frozen directly for X-ray diffraction structure determination and analysis at 1.8 A resolution	Pyrococcus horikoshii

Protein Variants

Protein Variants	Comment	Organism
D180A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
D98A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
H114A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
K123A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
K158A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
K196A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
K42A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
R107A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
R176A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in 78% reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
R68A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in slightly reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
R87A	site-directed mutagenesis, activity of the holoenzyme reconstituted with the recombinant mutant protein subunit Ph1877p is unaltered compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii
R90A	site-directed mutagenesis, reconstitution of the holoenzyme with the recombinant mutant protein subunit Ph1877p results in reduced activity compared to holoenzyme reconstituted with recombinant wild-type Ph1877p	Pyrococcus horikoshii

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
tRNA precursor + H2O	Pyrococcus horikoshii	tRNA processing	mature tRNA + 5'-oligonucleotide	-	?
tRNA precursor + H2O	Pyrococcus horikoshii OT-3	tRNA processing	mature tRNA + 5'-oligonucleotide	-	?

Organism

Organism	UniProt	Comment	Textmining
Pyrococcus horikoshii	O59543	strain OT3	-
Pyrococcus horikoshii OT-3	O59543	strain OT3	-

Posttranslational Modification

Posttranslational Modification	Comment	Organism
ribonucleoprotein	-	Pyrococcus horikoshii

Purification (Commentary)

Purification (Comment)	Organism
recombinant wild-type and mutant protein subunits from Escherichia coli	Pyrococcus horikoshii

Reaction

Reaction	Comment	Organism	Reaction ID
endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor	an RNA-containing enzyme, essential for tRNA processing, generates 5'-termini or mature tRNA molecules, amino acids residues Arg90, Arg107, Lys123, Arg176, and Lys196 are involved in interaction with enzyme RNA or with the pre-tRNA	Pyrococcus horikoshii	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
pre-tRNATyr + H2O	substrate from Pyrococcus horikoshii OT3, cleavage of 5'-terminal oligonucleotide	Pyrococcus horikoshii	mature tRNATyr + 5'-oligoribonucleotide	generates 5'-phosphate,3'-hydroxyl-product	?
pre-tRNATyr + H2O	substrate from Pyrococcus horikoshii OT3, cleavage of 5'-terminal oligonucleotide	Pyrococcus horikoshii OT-3	mature tRNATyr + 5'-oligoribonucleotide	generates 5'-phosphate,3'-hydroxyl-product	?
tRNA precursor + H2O	tRNA processing	Pyrococcus horikoshii	mature tRNA + 5'-oligonucleotide	-	?
tRNA precursor + H2O	tRNA processing	Pyrococcus horikoshii OT-3	mature tRNA + 5'-oligonucleotide	-	?

Subunits

Subunits	Comment	Organism
More	protein Ph1877p is one of the essential protein components of the ribozyme and forms a TIM barrel structure consisting of 10 alpha-helices and 7 beta-strands, the protein shows a cluster of positively charged amino acid residues on the molecule surface	Pyrococcus horikoshii

Synonyms

Synonyms	Comment	Organism
RNase P	-	Pyrococcus horikoshii

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Release 2023.1 (January 2023)