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PubMed1965

THIOL GROUPS IN DEOXYRIBONUCLEIC ACID NUCLEOTIDYLTRANSFERASE.

1. The inhibitory effects of iodoacetate, iodoacetamide, p-hydroxymercuribenzoate and sarkomycin were studied in a partially purified preparation of deoxyribonucleic acid nucleotidyltransferase from Landschutz ascites-tumour cells. All of these agents inhibited the activity of the enzyme, and it was shown that the inhibition exerted by the last three compounds obeyed non-competitive kinetics. 2. Inclusion of glutathione or 2-mercaptoethanol in the enzyme assays did not prevent the inhibition by iodoacetate or iodoacetamide, but did prevent inhibition by p-hydroxymercuribenzoate. Inhibition by sarkomycin could be partially prevented by glutathione or 2-mercaptoethanol. 3. The enzyme fraction also catalysed incorporation in the presence of only one triphosphate (thymidine 5'-triphosphate), and the limited incorporation observed in these circumstances was more resistant to the inhibitory action of iodoacetamide and p-hydroxy-mercuribenzoate than was the standard nucleotidyltransferase reaction (four triphosphates present). Levels of inhibition imposed on the standard reaction were achieved in the limited incorporation reaction with 2.5-fold higher concentrations of the two inhibitors. 4. The addition of certain bivalent cations to the standard system resulted in severe inhibition of the reaction: Zn(2+) ions (10mum) gave 50% inhibition; ethylenediaminetetra-acetate (0.4mm) in the reaction mixture gave essentially complete protection against this inhibitory effect of Zn(2+) ions. 5. Deoxyribonucleic acid-nucleotidyltransferase fractions prepared in the presence of a thiol and ethylenediaminetetra-acetate could be stored without loss of activity for 2 months at 0 degrees or for 1 year at -70 degrees .

Acetates↗

PubMed2000

Isolation and nucleotide sequence of a gene encoding tRNA nucleotidyltransferase from Kluyveromyces lactis.

A gene (KlCCA1) encoding ATP(CTP):tRNA specific tRNA nucleotidyltransferase (EC 2.7.7.25) was isolated from Kluyveromyces lactis by complementation of the Saccharomyces cerevisiae cca1-1 mutation. Sequencing of a 2665 bp EcoRI-SpeI restriction fragment revealed an open reading frame potentially encoding a protein of 489 amino acids with 57% sequence similarity to its S. cerevisiae homologue. Southern hybridization revealed a single copy of KlCCA1 in the K. lactis genome. KlCCA1 was able to complement both the mitochondrial and cytosolic defects in the cca1-1 mutant, suggesting that, as in S. cerevisiae, the K. lactis gene encodes a sorting isozyme that is targeted to mitochondria and the nucleus and/or cytosol. An altered KlCCA1 gene encoding a tRNA nucleotidyltransferase that lacked its first 35 amino acids was able to complement the nuclear/cytosolic but not the mitochondrial defect in the S. cerevisiae cca1-1 mutant, suggesting that the 35 amino-terminal amino acids are necessary for targeting to mitochondria but are not required for enzyme activity. Our results suggest that the mechanisms for production and distribution of mitochondrial and nuclear/cytosolic tRNA nucleotidyltransferase in K. lactis differ from those seen in S. cerevisiae.

Amino Acid Sequence↗

PubMedDate not supplied

COG4849 is a novel family of nucleotidyltransferases.

Only a minority of currently known protein families is characterized structurally. This makes homology-based structure modeling an essential instrument that can be viewed as the first approximation to experimental determination of protein structure. Using sequence similarity searches, we detected a distant similarity between a family of uncharacterized hypothetical proteins, COG4849, and the family of tRNA nucleotidyltransferases. The suggested remote homology between the N-terminal domain of COG4849 and the catalytic domain of tRNA nucleotidyltransferase was further supported by comparison of sequence profiles, methods for fold recognition and structure modeling. The combined multiple alignment of the two families reveals shared conservation of functionally important motifs and suggests the similarity in catalytic mechanisms of the performed reactions. Our results suggest that (i) the N-terminal domain of proteins from COG4849 shares structural similarity with the catalytic domain of tRNA nucleotidyltransferase, and (ii) this domain catalyzes the nucleotidyl transfer reaction involving two metal ions.

Bacterial Proteins↗

PubMed1996

Purification and characterization of a tRNA nucleotidyltransferase from Lupinus albus and functional complementation of a yeast mutation by corresponding cDNA.

ATP (CTP):tRNA nucleotidyltransferase (EC 2.7.7.25) was purified to apparent homogeneity from a crude extract of Lupinus albus seeds. Purification was accomplished using a multistep protocol including ammonium sulfate fractionation and chromatography on anion-exchange, hydroxylapatite and affinity columns. The lupin enzyme exhibited a pH optimum and salt and ion requirements that were similar to those of tRNA nucleotidyltransferases from other sources. Oligonucleotides, based on partial amino acid sequence of the purified protein, were used to isolate the corresponding cDNA. The cDNA potentially encodes a protein of 560 amino acids with a predicted molecular mass of 64 164 Da in good agreement with the apparent molecular mass of the pure protein determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The size and predicted amino acid sequence of the lupin enzyme are more similar to the enzyme from yeast than from Escherichia coli with some blocks of amino acid sequence conserved among all three enzymes. Functionality of the lupin cDNA was shown by complementation of a temperature-sensitive mutation in the yeast tRNA nucleotidyltransferase gene. While the lupin cDNA compensated for the nucleocytoplasmic defect in the yeast mutant it did not enable the mutant strain to grow at the non-permissive temperature on a non-fermentable carbon source.

Amino Acid Sequence↗

PubMed1996

Effects of nucleotide substitutions within the T-loop of precursor tRNAs on interaction with ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and yeast.

Recognition of tRNA and tRNA-like substrates by the enzyme ATP/CTP:tRNA nucleotidyltransferase requires chemically intact nucleotides within the T-loop, especially at positions 57 and 58, which are invariant purines among naturally occurring tRNAs. To test the effects of base substitutions at these positions, which are distant from the site of catalysis, we synthesized mutant tRNA(Glu) molecules. These in vitro-synthesized RNAs also contained an extra 33 bases at the 5' end and lacked post-transcriptionally modified bases. The precursor tRNAs were used as substrates for nucleotidyltransferases from Escherichia coli and yeast. Substitution of cytidines at either position 57 or 58 had dramatic inhibitory effects on recognition by both enzymes, including raising the apparent Km and lowering the apparent Vmax.; substitution of an adenosine at position 57 or a uridine at position 58 inhibited the reaction only slightly by comparison. Our results demonstrate that the identities of nucleotides at positions 57 and 58 are relevant to recognition by nucleotidyltransferase, and that a purine is required at position 57. The extra bases at the 5' end and the lack of post-transcriptionally modified bases did not substantially inhibit interaction with the enzyme, as judged by the wild-type precursor tRNA(Glu) acting as an effective substrate for both enzymes in the presence of equal concentrations of appropriate tRNA substrates isolated from E. coli.

Adenosine Triphosphate↗

PubMed2000

The role of tightly bound ATP in Escherichia coli tRNA nucleotidyltransferase.

BACKGROUND: The CCA-adding enzyme [ATP(CTP): tRNA nucleotidyltransferase (EC. 2.7.7.25)] catalyses the addition of the conserved CCA sequence to the 3'-terminus of tRNAs. All CCA-adding enzymes are classified into the nucleotidyltransferase superfamily. In the absence of ATP, the Escherichia coli CCA-adding enzyme displays anomalous poly(C) polymerase activity. RESULTS: We show that CCA-adding enzyme over-expressed in E. coli exists in an ATP-bound form. The affinities of ATP and CTP towards the enzyme were estimated by several methods, and the dissociation constants for ATP and CTP were determined to be 6.3 and 188 microM, respectively. AMP-incorporation terminated the nucleotidyltransferase reaction, while in the absence of ATP, the enzyme continued poly(C) polymerization. In the case of a tRNA substrate with a mutation in the T-loop region, normal CC was added at a much slower rate compared with the wild-type, but anomalous poly(C) polymerization occurred at the same rate as in the wild-type. CONCLUSION: Based on the findings outlined above, we concluded that the E. coli CCA-adding enzyme possesses at least two distinct nucleotide binding sites, one responsible for ATP binding and the other(s) for CTP binding. The addition of ATP from the tight ATP binding site terminates nucleotide incorporation, thus limiting poly(C) polymerization to CCA. It is also suggested that during anomalous poly(C) polymerization, tRNA translocates from the tRNA binding site upon the third C addition.

Adenosine Triphosphate↗

PubMed1974

Isolation and partial characterization of Escherichia coli mutants with low levels of transfer ribonucleic acid nucleotidyltransferase.

To determine the function of the enzyme transfer ribonucleic acid (tRNA) nucleotidyltransferase in vivo, five mutants of Escherichia coli containing low levels of this enzyme were isolated. Since no selection procedure for such mutants existed, these strains were isolated by assay of large numbers of colonies from a heavily mutagenized stock. A procedure employing cells made permeable to tRNA and ATP was used to screen the large number of colonies required for the isolation. All the mutants contained less than 20% of the normal level of the AMP-incorporating activity of tRNA nucleotidyltransferase in extracts prepared by several methods, and the best mutant contained only about 2% of this activity. Three of the mutants also had equally low levels of the cytidine 5'-monophosphate-incorporating activity of the enzyme. Despite these low activities, the mutant strains displayed relatively normal growth characteristics at all temperatures examined. The enzyme in the mutant strains was not temperature sensitive, nor were any other abnormal biochemical properties detected. tRNA isolated from the mutant strains was missing significant amounts of its 3' terminal adenosine 5'-monophosphate residue, amounting to 10 to 15% in the best mutant. However, only small amounts of the terminal cytidine 5'-monophosphate residue were missing. The results indicate that tRNA nucleotidyltransferase is involved in some aspect of synthesis or repair of the 3' terminus of tRNA, and that the enzyme is present in large excess over its requirements for this function.

Adenosine Monophosphate↗

PubMed1975

A novel function of Escherichia coli transfer RNA nucleotidyltransferase. Biosynthesis of the C-C-A sequence in a phage T4 transfer RNA precursor.

The biosynthesis of the phage T4-coded proline and serine transfer RNA species proceeds through a precursor RNA containing both tRNA sequences. Neither tRNA sequence in the precursor RNA contains the 3'-terminal C-C-A common to all mature tRNAs. Seidman and McClain ((1975) Proc. Natl. Acad. Sci. U. S. A. 72, 1491-1495) have proposed that the C-C-A sequence is added to serine tRNA while it is still part of the large precursor RNA. In the present work, I show that, in vitro, a purified preparation of Escherichia coli tRNA nucleotidyltransferase (EC 2.7.7.25) accurately synthesized 3'-terminal C-C-A in the serine tRNA portion of the precursor RNA. This result establishes a role of tRNA nucleotidyltransferase in the biosynthesis of the phage T4 serine tRNA. The finding that tRNA nucleotidyltransferase utilizes the large precursor RNA as a substrate represents a novel function of the enzyme.

Adenine Nucleotides↗

PubMed1990

Purification and properties of yeast ATP (CTP):tRNA nucleotidyltransferase from wild type and overproducing cells.

ATP (CTP):tRNA nucleotidyltransferase (EC 2.7.7.25) has been purified from wild type cells of the yeast Saccharomyces cerevisiae, as well as from a strain that overproduces the activity. Purification from the wild type strain was accomplished with a multistep protocol including ammonium sulfate fractionation, anion exchange chromatography, gel filtration, and affinity chromatography. The purified enzyme is near homogeneity as evidenced by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and at 59,000 Da is smaller than reported previously. A similar molecular mass is obtained by gel filtration demonstrating that the enzyme is active as a monomer. The pH optimum for the enzyme is around 9.5. The apparent KM values for ATP and CTP were determined to be 5.6 x 10(-4) M and 1.8 x 10(-4) M, respectively. Purification of the enzyme from the overproducing cells was accomplished by a three step protocol with high yield. The nucleotidyltransferase activity from the overproducing cells had a KM for CTP indistinguishable from that of the wild type enzyme, and the mobility of the protein on sodium dodecyl sulfate gels was the same regardless of the source. Thus, the overproducing strain appears to be a good source for large amounts of yeast nucleotidyltransferase for further biochemical and structural studies.

Chromatography↗

PubMed1986

A mutation in Escherichia coli tRNA nucleotidyltransferase that affects only AMP incorporation is in a sequence often associated with nucleotide-binding proteins.

Escherichia coli strain 5C15 contains a mutation in the cca gene that decreases AMP incorporation by tRNA nucleotidyltransferase while leaving CMP incorporation unaffected. Earlier studies of the purified mutant enzyme suggested that the mutation was localized to the AMP-incorporating site. In order to analyze this mutation in more detail, the cca gene from strain 5C15 was cloned into plasmid pUC8. Analysis of tRNA nucleotidyltransferase activity in extracts of a strain transformed with this plasmid demonstrated an elevated level of CMP incorporation, but low AMP incorporation, as expected from the properties of the original mutant. Sequence analysis of the mutant cca gene revealed only a single G to A point mutation leading to a glycine to aspartic acid substitution at position 70 of the peptide chain. The amino acid change was localized to one of two Gly-X-Gly-X-X-Gly sequences present in the protein. This sequence has been identified previously near the nucleotide-binding domain of various proteins, but it has not been noted in enzymes that incorporate nucleotide residues. However, other sequences often associated with ATP-binding domains are not found in tRNA nucleotidyltransferase. The implications of these findings for our understanding of nucleotide-binding domains are discussed.

Adenosine Monophosphate↗

PubMed1979

Effect of nucleoside 5'-triphosphates on tRNA nucleotidyltransferase activity in cytoplasmic fractions of various types of mammalian cells.

The tRNA nucleotidyltransferase activity (3H-CMP incorporation into 3'-terminus of tRNApC) in cytoplasmic fractions of various types of cells such as Ehrlich ascites tumor cells, mouse liver and spleen cells, rat spleen, lymph node, and macrophages cells was found to be dependent on the concentrations of nucleoside 5'-triphosphates (ATP, GTP, UTP, dATP, dGTP, dCTP, and/or dTTP). The purified tRNA nucleotidyltransferase did not show such dependency. The dependency of the enzyme activity on nucleoside 5'triphosphates in the crude cytoplasmic fractions was possibly due to the presence of inhibitors which interfere with the repair system of defective 3'-termini of tRNA. Two kinds of inhibitors were distinguishable in the cytoplasmic fractions. One was unstable on heat treatment at 55 decrees C and showed ribonuclease activity for the tRNA 3'-terminus. The other which lacked ribonuclease activity was rather stable to the heat treatment and inhibited purified tRNA nucleotidyltransferase. The actions of both inhibitors were suppressed by nucleoside 5'-triphosphates.

Animals↗

PubMed1994

Interplay of heterogeneous transcriptional start sites and translational selection of AUGs dictate the production of mitochondrial and cytosolic/nuclear tRNA nucleotidyltransferase from the same gene in yeast.

ATP (CTP):tRNA nucleotidyltransferase catalyzes the addition of the CCA end to tRNAs. In yeast, nucleotidyltransferase is encoded by the CCA1 gene and is localized to three cellular compartments: mitochondria, nucleus, and cytosol. There are three in-frame ATGs near the 5' end of the CCA1 open reading frame. Primer extension experiments show multiple transcription initiation sites upstream of ATG1 and between ATG1 and ATG2. Fractionation of cells carrying a CCA1-COXIV fusion gene demonstrates that all three in-frame AUGs are used as sites of initiation of translation. Therefore, both transcription of CCA1 mRNA with heterogeneous 5' ends and translation from downstream AUGs in CCA1 mRNAs play a role in the synthesis of three nucleotidyltransferase isozymes. Protein initiating from AUG1 is required for mitochondrial protein synthesis and, like many other proteins targeted to mitochondria, it is processed at the amino terminus upon import into the organelle. The shorter proteins arising from AUG2 and AUG3 provide nuclear/cytosol activity.

Amino Acid Sequence↗

PubMed1990

Purines in tRNAs required for recognition by ATP/CTP:tRNA nucleotidyltransferase from rabbit liver.

Recognition of tRNA by the enzyme ATP/CTP:tRNA nucleotidyltransferase from rabbit liver was studied using 12 tRNAs, previously treated with the chemical modifier diethylpyrocarbonate (DEP). Such chemically modified tRNAs were labeled with 32P by nucleotidyltransferase, using alpha-[32P]ATP as a cosubstrate. A carbethoxylated purine at position 57 in the psi-loop interfered with recognition of the tRNA in all instances. DEP-modified purines at other positions (58 in the psi-loop, 52 or 53 in the psi-stem, and 71-73 in the acceptor stem), also interfered with the interaction, but in only a few tRNAs. The mammalian enzyme was more similar to the homologous enzyme from yeast than that from bacteria, in its requirements for chemically unmodified purines. The extent of exclusion of modified bases from 32P-labeled material diminished as the concentration of enzyme increased, demonstrating that interference was not due to the inability of the chemically altered tRNA to refold into a recognizable conformation. The degree of purification of the enzyme did not affect the identity of bases that inhibited the reaction when modified.

Adenosine Triphosphate↗

PubMed2003

The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies.

The crystal structure of HI0074 from Haemophilus influenzae, a protein of unknown function, has been determined at a resolution of 2.4 A. The molecules form an up-down, four-helix bundle, and associate into homodimers. The fold is most closely related to the substrate-binding domain of KNTase, yet the amino acid sequences of the two proteins exhibit no significant homology. Sequence analyses of completely and incompletely sequenced genomes reveal that the two adjacent genes, HI0074 and HI0073, and their close relatives comprise a new family of nucleotidyltransferases, with 15 members at the time of writing. The analyses also indicate that this is one of eight families of a large nucleotidyltransferase superfamily, whose members were identified based on the proximity of the nucleotide- and substrate-binding domains on the respective genomes. Both HI0073 and HI0074 were annotated "hypothetical" in the original genome sequencing publication. HI0073 was cloned, expressed, and purified, and was shown to form a complex with HI0074 by polyacrylamide gel electrophoresis under nondenaturing conditions, analytic size exclusion chromatography, and dynamic light scattering. Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer.

Amino Acid Sequence↗

PubMed2002

Characterization of a gene encoding tRNA nucleotidyltransferase from Candida glabrata.

A gene encoding ATP (CTP):tRNA nucleotidyltransferase (EC2.7.7.25) was isolated from Candida (Torulopsis) glabrata by complementation in Saccharomyces cerevisiae. The predicted amino acid sequence of the protein revealed a large region with high sequence similarity to members of the Class II group of the nucleotidyltransferase superfamily and an N-terminal region characteristic of a mitochondrial targeting sequence. The essential role of the carboxylates within the conserved DXD and RRD motifs was confirmed by mutagenesis. C. glabrata strains bearing truncated CCA1 genes that lacked sequences encoding the putative mitochondrial targeting peptide were unable to grow on non-fermentable carbon sources but were able to grow on a fermentable carbon source. These results suggest that, as in S. cerevisiae, the C. glabrata CCA-adding enzyme is a sorting isozyme that functions in multiple cellular compartments. Mapping of the 5'-ends of primary transcripts of CCA1 revealed multiple transcription start sites located both upstream of and between two in-frame start codons. When the cells were cultured on a non-fermentable carbon source the longer transcripts appeared more abundant, suggesting that the choice of transcription start sites was influenced by carbon source. The shorter transcripts, which lacked sequences encoding the mitochondrial targeting information, were more predominant in cells grown on glucose. These observations suggest that expression of CCA-adding isozymes in C. glabrata may be regulated. The DNA sequence has been assigned GenBank Accession No. AF098803.

Amino Acid Sequence↗

PubMed1997

Unidentified open reading frames in the genome of Methanococcus jannaschii are similar in sequence to an archaebacterial gene for tRNA nucleotidyltransferase.

The protein sequence of ATP/CTP:tRNA nucleotidyltransferase (cca) from Sulfolobus shibatae was used to search open reading frames in the genome of Methanococcus jannaschii. Translations of two unidentified open reading frames showed significant sequence similarity to portions of the Sulfolobus cca protein. When the two open reading frames were joined together, the expanded open reading frame was similar in sequence to the entire Sulfolobus cca protein and displayed features of the active site signature sequence proposed for members of class I enzymes within the superfamily of nucleotidyltransferases (Yue et al., 1996, RNA 2, 895-908). A possible UUG start codon was identified based on significant sequence similarity of the resulting amino-terminal region to that of Sulfolobus, and on a six-base complementarity between an adjacent upstream sequence and Methanococcus 16S rRNA.

Amino Acid Sequence↗

PubMed1992

Crystallization and preliminary crystallographic analysis of a thermostable mutant of kanamycin nucleotidyltransferase.

A thermostable mutant of kanamycin nucleotidyltransferase isolated by cloning and selection for kanamycin resistance in Bacillus stearothermophilus at 70 degrees C has been crystallized in a form suitable for high-resolution diffraction analysis. This enzyme catalyzes nucleotidyl group transfer from nucleoside triphosphates such as ATP to hydroxyl groups of various aminoglycosides, thus inactivating the antibiotic. The kanamycin nucleotidyltransferase gene, originally encoded on plasmid pUB110 from the mesophile Staphylococcus aureus, was transferred to the thermophile B. stearothermophilus via shuttle plasmids and the mutant carrying the substitutions D80Y and T130K was isolated from kanamycin-resistant colonies grown at 70 degrees C. The thermostable enzyme was crystallized in two forms from solutions of polyethylene glycol 8000 (PEG8000) using batch and vapor diffusion methods. Type I crystals grown from 19% (w/v) PEG8000 and 200 mM NaCl belong to the orthorhombic space group C222(1), have unit cell dimensions of a = 128.4, b = 156.8, c = 155.8 A, and diffract to at least 2.4-A resolution. The type II form of the crystals were grown from 10% PEG8000, 200 mM KCl, and 3 mM CoCl2, and belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 with unit cell dimensions of a = b = 78.9, and c = 220.4 A; these crystals diffract to at least 2.5-A resolution.

Crystallization↗

PubMed1976

A physiological role for tRNA nucleotidyltransferase during bacteriophage infection.

Bacteriophage infection of E. coli cells deficient in the enzyme tRNA nucleotidyltransferase (cca mutants) resulted in greatly decreased production of viable progeny phage compared to wild type cells. This decrease amounted to as much as 90% in the case of T-even bacteriophages, and 50-65% for T-odd bacteriophages. However, infection by the RNA phages, Qbeta and f2, was unaffected by the cca mutation. Examination of T4 infection of cca hosts indicated that phage development proceeded normally, that near-normal numbers of progeny particles were formed, but that most of these particles were non-viable. Possible functions for E. coli tRNA nucleotidyltransferase during bacteriophage infection are discussed.

Bacteriophage T4↗