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Information on EC 2.7.1.160 - 2'-phosphotransferase and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q12272
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2.7.1.160 2'-phosphotransferaseIUBMB Comments
Catalyses the final step of tRNA splicing in the yeast Saccharomyces cerevisiae . The reaction takes place in two steps: in the first step, the 2'-phosphate on the RNA substrate is ADP-ribosylated, causing the relase of nicotinamide and the formation of the reaction intermediate, ADP-ribosylated tRNA . In the second step, dephosphorylated (mature) tRNA is formed along with ADP ribose 1''-2''-cyclic phosphate. Highly specific for oligonucleotide substrates bearing an internal 2'-phosphate. Oligonucleotides with only a terminal 5'- or 3'-phosphate are not substrates .
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Word Map
- 2.7.1.160
-
2'-phosphate
- junction
- adp-ribose
-
adp-ribosylation
-
2.7.1.23
-
phosphodiester
-
2'-phosphorylated
- pre-trnas
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
Synonyms
2'-phosphotransferase, trpt1, rsltpt1, tpt1p, trna 2'-phosphotransferase, human trpt1, yeast 2'-phosphotransferase, nad+-dependent 2'-phosphotransferase, apetpt1, rna 2'-phosphotransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
2'-phospho-[ligated tRNA]:NAD+ phosphotransferase
Catalyses the final step of tRNA splicing in the yeast Saccharomyces cerevisiae [2]. The reaction takes place in two steps: in the first step, the 2'-phosphate on the RNA substrate is ADP-ribosylated, causing the relase of nicotinamide and the formation of the reaction intermediate, ADP-ribosylated tRNA [6]. In the second step, dephosphorylated (mature) tRNA is formed along with ADP ribose 1''-2''-cyclic phosphate. Highly specific for oligonucleotide substrates bearing an internal 2'-phosphate. Oligonucleotides with only a terminal 5'- or 3'-phosphate are not substrates [1].
CAS REGISTRY NUMBER
COMMENTARY
126905-00-8
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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
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
-
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP-ribose 1'',2''-phosphate + nicotinamide
-
-
-
?
18-mer 2' phosphorylated RNA
?
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pACAAGACUCUAA-(2-phosphate)AUCUUG
-
-
?
18-mer 2' phosphorylated RNA + NAD+
?
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ACAAGACUGUAA-(2-phosphate)AUCUUG
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP-ribose 1'',2''-phosphate + nicotinamide
-
-
-
-
?
3-mer 2' phosphorylated RNA
?
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pApA-(2-phosphate)pA, pApU-(2-phosphate)pA, pUpU-(2-phosphate)pU, pApApA-(2-phosphate),pApApA-(2-phosphate)p, pApApA-(2-phosphate)1OCH3
-
-
?
8-mer 2' phosphorylated RNA + NAD+
?
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GUAA-(2-phosphate)AUCU
-
-
?
NAD+ + trinucleotide substrate
ADP-ribosylated RNA
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requires ca. 0.0004 mM Tpt1 K69A/R71S, only 0.0000003 mM Tpt1p is required for similar or greater product formation
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
-
-
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
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minimal substrate is a dinucleotide containing an internal 2'-phosphate
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
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specificity for substrates bearing an internal 2'-phosphate
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
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Tpt1 can catalyze the conversion of the KptA-generated intermediate to both product and the original substrate
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP ribose-1'',2''-phosphate + nicotinamide + H2O
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tRNA_Leu_UAG, tRNA_SER, tRNA_LEU_CAA, tRNA_TYR, tRNA_LYS, tRNA_PRO1, tRNA_PRO2, tRNA_PHE, unidentified tRNA
-
-
?
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
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP-ribose 1'',2''-phosphate + nicotinamide
-
-
-
?
2'-phospho-[ligated tRNA] + NAD+
mature tRNA + ADP-ribose 1'',2''-phosphate + nicotinamide
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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UMP, SAMP, cAMP, UTP, CTP, GTP, ATP and derivatives of NAD+ like NMN, ADP-ribose, ATP-ribose, NADPH, NADP+, NADH do not support dephosphorylation
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ApGpApUpUpUpApC
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oligonucleotide, which lacks secondary structure and has no terminal phosphate
[pre-tRNA]
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intron-containing yeast [pre-tRNA], which has the same structure as mature yeast [tRNA], except in the region of the intron
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[tRNA]
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mature Escherichia coli [tRNA], has canonical tRNA structue
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0000017
18-mer 2' phosphorylated RNA
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pACAAGACUCUAA-(2-phosphate)AUCUUG, 30°C
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0.00002
8-mer 2' phosphorylated RNA
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pGUAA-(2-phosphate)AUCU, 30°C
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0.000325
3-mer 2' phosphorylated RNA
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pUpU-(2-phosphate)pUs, 30°C
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0.00065
3-mer 2' phosphorylated RNA
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pApApA-(2-phosphate)p, 30°C
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0.003
3-mer 2' phosphorylated RNA
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pApApA-(2-phosphate)pOCH3, 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.04
18-mer 2' phosphorylated RNA
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pACAAGACUCUAA-(2-phosphate)AUCUUG, 30°C
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0.317
8-mer 2' phosphorylated RNA
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pGUAA-(2-phosphate)AUCU, 30°C
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1.173
3-mer 2' phosphorylated RNA
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pApApA-(2-phosphate)pOCH3, 30°C
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6.08
3-mer 2' phosphorylated RNA
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pApApA-(2-phosphate)pOCH3, 30°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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200000000 units/mg for recombinant Tpt1 produced in Escherichia coli and 140000000 units/mg for Tpt1 purified from yeast
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
18 - 30
-
F27A, R71Q, TPT1(1-220) and TPT1(1-210) cells failed to grow at 37°C on yeast medium/peptone/dextrose agar, R71Q and TPT1(1-210) strains grew slower than wild-type TPT1
18 - 37
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growth of mutants K16A, K69A, H90A, S91A, H117A, T119A, H142A, R158A and R138K on yeast medium/peptone/dextrose agar, colony sizes were similar to that of wild-type TPT1 cells
25 - 30
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growth of mutants K16A, Y38A, K69A, F72A, H90A, S91A, H117A, T119A, H142A, R158A, TPT1(1-220) and TPT1(1-210) on 5-fluoroorotic acid agar medium
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
wide distribution of Tpt1 enzymes in taxa that have no fungal-type RNA ligase. Whereas all of the Tpt1 enzymes are capable of NAD+-dependent conversion of an internal RNA 2'-PO4 to a 2'-OH (the canonical Tpt1 reaction), a subset of Tpt1 enzymes also catalyze NAD+-dependent ADP-ribosylation of an RNA or DNA 5'-phosphate terminus
malfunction
the essential functions of TRL1 and TPT1 in budding yeast are bypassed by expressing prespliced, intronless versions of the 10 normally intron-containing tRNAs, indicating this repair pathway does not have additional essential functions. Expression of intronless tRNAs fails to rescue the growth of cells with deletions in components of the SEN complex, implying an additional essential role for the splicing endonuclease. The trl1DELTA and tpt1DELTA mutants accumulate tRNA and HAC1 splicing intermediates indicative of RNA repair defects and are hypersensitive to drugs that inhibit translation. RNA repair mutants have defects in translation. tpt1DELTA mutants grow in the presence of tunicamycin despite reduced accumulation of spliced HAC1 mRNA, while failure to induce the unfolded protein response occurs in trl1DELTA cells grown with tunicamycin is lethal owing to their inability to ligate HAC1 after its cleavage by Ire1. Rescued trl1DELTA and tpt1DELTA cells, RNA repair mutants, have unique phenotypes for both tRNA splicing and HAC1 mRNA splicing during the unfolded protein response. The temperature sensitivity of RNA repair mutants at 37°C is not a consequence of tRNA decay pathway (RTD)
metabolism
RNA repair enzymes catalyze rejoining of an RNA molecule after cleavage of phosphodiester linkages. RNA repair in budding yeast is catalyzed by two separate enzymes that process tRNA exons during their splicing and HAC1 mRNA exons during activation of the unfolded protein response (UPR). The RNA ligase Trl1 (EC 6.5.1.3) joins 2',3'-cyclic phosphate and 5'-hydroxyl RNA fragments, creating a phosphodiester linkage with a 2'-phosphate at the junction. The 2'-phosphate is removed by the 2'-phosphotransferase Tpt1 (EC 2.7.1.160)
physiological function
physiological function
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in yeast the NAD-dependent RNA 2'-phosphotransferase KptA is known to participate in tRNA splicing by removing the splice junction 2'-phosphate from ligated tRNA
physiological function
enzyme TPT1 is essential only in the context of the generation of 2'-phosphorylated tRNAs by Trl1
physiological function
the RNA 2'-phosphotransferase Tpt1 converts an internal RNA 2'-phosphate to a 2'-OH via a two-step NAD+-dependent mechanism in which: (i) the 2'-phosphate attacks the C1'' of NAD+ to expel nicotinamide and form a 2'-phospho-ADP-ribosylated RNA intermediate, and (ii) the ADP-ribose O2'' attacks the phosphate of the RNA 2'-phospho-ADPR intermediate to expel the RNA 2'-OH and generate ADP-ribose 1''-2'' cyclic phosphate. Tpt1 is an essential component of the fungal tRNA splicing pathway that generates a unique 2'-phosphate, 3'-5'-phosphodiester splice junction during tRNA ligation. Tpt1 can catalyze reactions other than RNA 2'-phosphate removal. Whereas all of the Tpt1 enzymes are capable of NAD+-dependent conversion of an internal RNA 2'-phosphate to a 2'-hydroxy (the canonical Tpt1 reaction), a subset of Tpt1 enzymes also catalyze NAD+-dependent ADP-ribosylation of an RNA or DNA 5'-phosphate terminus
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H117A
H142A
H90A
K16A
-
colony size indistinguishable from that of wild-type TPT1 strain
K69A
-
colony size indistinguishable from that of wild-type TPT1 strain
K69A/R71S
-
this mutant produces a substantial amount of the reaction intermediate
R138A
R138K
-
colony size indistinguishable from that of wild-type TPT1 strain
R158A
-
colony size indistinguishable from that of wild-type TPT1 strain
S91A
T119A
-
colony size indistinguishable from that of wild-type TPT1 strain
Y38A
-
colony size indistinguishable from that of wild-type TPT1 strain
additional information
generation and analysis of diverse mutant strains derived from Saccharomyces cerevisiae strain W303. The essential functions of TRL1 and TPT1 in budding yeast are bypassed by expressing prespliced, intronless versions of the 10 normally intron-containing tRNAs, indicating this repair pathway does not have additional essential functions. Expression of intronless tRNAs fails to rescue the growth of cells with deletions in components of the SEN complex, implying an additional essential role for the splicing endonuclease. The trl1DELTA and tpt1DELTA mutants accumulate tRNA and HAC1 splicing intermediates indicative of RNA repair defects and are hypersensitive to drugs that inhibit translation. tpt1DELTA mutants grow in the presence of tunicamycin despite reduced accumulation of spliced HAC1 mRNA, while failure to induce the unfolded protein response occurs in trl1DELTA cells grown with tunicamycin is lethal owing to their inability to ligate HAC1 after its cleavage by Ire1. Tpt1DELTA phenotype, overview
H117A
-
colony size indistinguishable from that of wild-type TPT1 strain
H142A
-
colony size indistinguishable from that of wild-type TPT1 strain
H90A
-
colony size indistinguishable from that of wild-type TPT1 strain
S91A
-
colony size indistinguishable from that of wild-type TPT1 strain
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified 28000fold by Orange A Sepharose column, 4fold less pure by streamlined purification procedure
immobilized metal ion affinity chromatography, > 80% purified by SDS-PAGE
-
partially purified, GST-Tpt1 fusion protein purified by glutahthione agarose chromatography
-
Tpt1-His6 50% purified by sonication, immobilized metal ion chromatography, centrifugation
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Saccharomyces cerevisiae tpt1 mutant strain Y2, the wild-type yeast TPT1 could complement this mutation
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Culver, G.M.; McCraith, S.M.; Consaul, S.A.; Stanford, D.R.; Phizicky, E.M.
A 2'-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae
J. Biol. Chem.
272
13203-13210
1997
Escherichia coli, Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Saccharomyces cerevisiae (Q12272), Schizosaccharomyces pombe
Steiger, M.A.; Kierzek, R.; Turner, D.H.; Phizicky, E.M.
Substrate recognition by a yeast 2'-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog
Biochemistry
40
14098-14105
2001
Escherichia coli, Saccharomyces cerevisiae
Hu, Q.D.; Lu, H.; Huo, K.; Ying, K.; Li, J.; Xie, Y.; Mao, Y.; Li, Y.Y.
A human homolog of the yeast gene encoding tRNA 2'-phosphotransferase: cloning, characterization and complementation analysis
Cell. Mol. Life Sci.
60
1725-1732
2003
Arabidopsis thaliana, Archaeoglobus fulgidus, Clostridium perfringens, Escherichia coli, Fusobacterium nucleatum, Homo sapiens, Homo sapiens (Q86TN4), Methanopyrus kandleri, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Streptomyces coelicolor
Mc Craith, S.M.; Phizicky, E.M.
An enzyme from Saccharomyces cerevisiae uses NAD+ to transfer the splice junction 2'-phosphate from ligated tRNA to an acceptor molecule
J. Biol. Chem.
266
11986-11992
1991
Saccharomyces cerevisiae
Zillman, M.; Gorovsky, M.A.; Phizicky, E.M.
HeLa cells contain a 2'-phosphate-specific phosphotransferase similar to a yeast enzyme implicated in tRNA splicing
J. Biol. Chem.
267
10289-10294
1992
Homo sapiens, Saccharomyces cerevisiae
Spinelli, S.L.; Kierzek, R.; Turner, D.H.; Phizicky, E.M.
Transient ADP-ribosylation of a 2'-phosphate implicated in its removal from ligated tRNA during splicing in yeast
J. Biol. Chem.
274
2637-2644
1999
Saccharomyces cerevisiae, Escherichia coli, Mus musculus
Kato-Murayama, M.; Bessho, Y.; Shirouzu, M.; Yokoyama, S.
Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1
J. Mol. Biol.
348
295-305
2005
Aeropyrum pernix, Arabidopsis thaliana, Archaeoglobus fulgidus, Escherichia coli, Homo sapiens, Methanosarcina mazei, Pseudomonas aeruginosa, Pyrococcus horikoshii, Saccharomyces cerevisiae
Kierzek, R.; Steiger, M.A.; Spinelli, S.L.; Turner, D.H.; Phizicky, E.M.
The chemical synthesis of oligoribonucleotides with selectively placed 2'-O-phosphates
Nucleosides Nucleotides Nucleic Acids
19
917-933
2000
Saccharomyces cerevisiae
Spinelli, S.L.; Malik, H.S.; Consaul, S.A.; Phizicky, E.M.
A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli
Proc. Natl. Acad. Sci. USA
95
14136-14141
1998
Arabidopsis thaliana, Archaeoglobus fulgidus, Candida albicans, Escherichia coli, Mus musculus, no activity in Bacillus subtilis, no activity in Haemophilus influenzae, no activity in Helicobacter pylori, no activity in Mycoplasma genitalium, Pseudomonas aeruginosa, Pyrococcus horikoshii, Saccharomyces cerevisiae, Schizosaccharomyces pombe
Sawaya, R.; Schwer, B.; Shuman, S.
Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1
RNA
11
107-113
2005
Aeropyrum pernix, Archaeoglobus fulgidus, Clostridium perfringens, Drosophila melanogaster, Escherichia coli, Homo sapiens, Leishmania major, Nostoc punctiforme, Pyrococcus horikoshii, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma cruzi
Steiger, M.A.; Jackman, J.E.; Phizicky, E.M.
Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism
RNA
11
99-106
2005
Saccharomyces cerevisiae
Spinelli, S.L.; Consaul, S.A.; Phizicky, E.M.
A conditional lethal yeast phosphotransferase (tpt1) mutant accumulates tRNAs with a 2'-phosphate and an undermodified base at the splice junction
RNA
3
1388-1400
1997
Escherichia coli, Saccharomyces cerevisiae
Sorci, L.; Ruggieri, S.; Raffaelli, N.
NAD homeostasis in the bacterial response to DNA/RNA damage
DNA Repair
23
17-26
2014
Agrobacterium tumefaciens (Q8U9Z2), Agrobacterium tumefaciens C58 / ATCC 33970 (Q8U9Z2), Brachyspira hyodysenteriae (A0A3B6VB17), Brachyspira hyodysenteriae ATCC 49526 (A0A3B6VB17), Catenulispora acidiphila (C7QAQ2), Deinococcus deserti (C1CZ01), Deinococcus deserti DSM 17065 (C1CZ01), Deinococcus gobiensis (H8GTD5), Deinococcus gobiensis DSM 21396 (H8GTD5), Deinococcus radiodurans (Q9RRR1), Deinococcus radiodurans ATCC 13939 (Q9RRR1), Delftia acidovorans (A9C0S5), Delftia acidovorans DSM 14801 (A9C0S5), Flavobacterium johnsoniae (A5FLZ4), Fusobacterium nucleatum subsp. nucleatum (Q8R5N7), Fusobacterium nucleatum subsp. nucleatum ATCC 25586 / JCM14847 (Q8R5N7), Herpetosiphon aurantiacus (A9B356), Herpetosiphon aurantiacus DSM 785 (A9B356), Saccharomyces cerevisiae, Sebaldella termitidis (D1APE3), Sebaldella termitidis ATCC 33386 (D1APE3)
Munir, A.; Banerjee, A.; Shuman, S.
NAD+-dependent synthesis of a 5-phospho-ADP-ribosylated RNA/DNA cap by RNA 2-phosphotransferase Tpt1
Nucleic Acids Res.
46
9617-9624
2018
Acetivibrio thermocellus (A3DJX6), Acetivibrio thermocellus ATCC 27405 (A3DJX6), Acetivibrio thermocellus DSM 1237 (A3DJX6), Acetivibrio thermocellus JCM 9322 (A3DJX6), Acetivibrio thermocellus NBRC 103400 (A3DJX6), Acetivibrio thermocellus NCIMB 10682 (A3DJX6), Acetivibrio thermocellus NRRL B-4536 (A3DJX6), Acetivibrio thermocellus VPI 7372 (A3DJX6), Aeropyrum pernix (Q9YFP5), Aeropyrum pernix, Aeropyrum pernix ATCC 700893 (Q9YFP5), Aeropyrum pernix DSM 11879 (Q9YFP5), Aeropyrum pernix JCM 9820 (Q9YFP5), Aeropyrum pernix NBRC 100138 (Q9YFP5), Archaeoglobus fulgidus (O29841), Archaeoglobus fulgidus ATCC 49558 (O29841), Archaeoglobus fulgidus JCM 9628 (O29841), Archaeoglobus fulgidus NBRC 100126 (O29841), Archaeoglobus fulgidus VC-16 (O29841), Homo sapiens (Q86TN4), Pyrococcus horikoshii (O57899), Pyrococcus horikoshii ATCC 700860 (O57899), Pyrococcus horikoshii DSM 12428 (O57899), Pyrococcus horikoshii JCM 9974 (O57899), Pyrococcus horikoshii NBRC 100139 (O57899), Pyrococcus horikoshii OT-3 (O57899), Runella slithyformis, Saccharomyces cerevisiae (Q12272), Thermochaetoides thermophila (G0S5Z5), Thermochaetoides thermophila CBS 144.50 (G0S5Z5), Thermochaetoides thermophila DSM 1495 (G0S5Z5), Thermochaetoides thermophila IMI 039719 (G0S5Z5)
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