RNA Nucleotidyltransferases
Polynucleotide Adenylyltransferase
Molecular Sequence Data
Amino Acid Sequence
A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. (1/2047)
In Acanthamoeba castellanii, most of the mtDNA-encoded tRNAs are edited by a process that replaces one or more of the first three nucleotides at their 5' ends. As a result, base pairing potential is restored at acceptor stem positions (1:72, 2:71, and/or 3:70, in standard tRNA nomenclature) that are mismatched according to the corresponding tRNA gene sequence. Here we describe a novel nucleotide incorporation activity, partially purified from A. castellanii mitochondria, that has properties implicating it in mitochondrial tRNA editing in this organism. This activity is able to replace nucleotides at the first three positions of a tRNA (positions 1, 2, and 3), matching the newly incorporated residues through canonical base pairing to the respective partner nucleotide in the 3' half of the acceptor stem. Labeling experiments with natural (Escherichia coli tRNATyr) and synthetic (run-off transcripts corresponding to A. castellanii mitochondrial tRNALeu1) substrates suggest that the nucleotide incorporation activity consists of at least two components, a 5' exonuclease or endonuclease and a template-directed 3'-to-5' nucleotidyltransferase. The nucleotidyltransferase component displays an ATP requirement and generates 5' pppN... termini in vitro. The development of an accurate and efficient in vitro system opens the way for detailed studies of the biochemical properties of this novel activity and its relationship to mitochondrial tRNA editing in A. castellanii. In addition, the system will allow delineation of the structural features in a tRNA that identify it as a substrate for the labeling activity. (+info)mRNA guanylyltransferase and mRNA (guanine-7-)-methyltransferase from vaccinia virions. Donor and acceptor substrate specificites. (2/2047)
Characterization of the donor and acceptor specificities of mRNA guanylyltransferase and mRNA (guanine-7-)-methyltransferase isolated from vaccinia virus cores has enabled us to discriminate between alternative reaction sequences leading to the formation of the 5'-terminal m7G(5')pppN-structure. The mRNA guanylyltransferase catalyzes the transfer of a residue of GMP from GTP to acceptors which possess a 5'-terminal diphosphate. A diphosphate-terminated polyribonucleotide is preferred to a mononucleoside diphosphate as an acceptor suggesting that the guanylyltransferase reaction occurs after initiation of RNA synthesis. Although all of the homopolyribonucleotides tested (pp(A)n, pp(G)n, pp(I)n, pp(U)n, and pp(C)n) are acceptors for the mRNA guanylyltransferase indicating lack of strict sequence specificity, those containing purines are preferred. Only GTP and dGTP are donors in the reaction; 7-methylguanosine (m7G) triphosphate specifically is not a donor indicating that guanylylation must precede guanine-7-methylation. The preferred acceptor of the mRNA (guanine-7-)-methyltransferase is the product of the guanylyltransferase reaction, a polyribonucleotide with the 5'-terminal sequence G(5')pppN-. The enzyme can also catalyze, but less efficiently methylation of the following: dinucleoside triphosphates with the structure G(5')pppN, GTP, dGTP, ITP, GDP, GMP, and guanosine. The enzyme will not catalyze the transfer of methyl groups to ATP, XTP, CTP, UTP, or to guanosine-containing compounds with phosphate groups in either positions 2' or 3' or in 3'-5' phosphodiester linkages. The latter specificity provides an explanation for the absence of internal 7-methylguanosine in mRNA. In the presence of PPi, the mRNA guanylyltransferase catalyzes the pyrophosphorolysis of the dinucleoside triphosphate G(5')pppA, but not of m7G(5')pppA. Since PPi is generated in the process of RNA chain elongation, stabilization of the 5'-terminal sequences of mRNA is afforded by guanine-7-methylation. (+info)Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. (3/2047)
In order to search for a common structural motif in the phosphate-binding sites of protein-mononucleotide complexes, we investigated the structural variety of phosphate-binding schemes by an all-against-all comparison of 491 binding sites found in the Protein Data Bank. We found four frequently occurring structural motifs composed of protein atoms interacting with phosphate groups, each of which appears in different protein superfamilies with different folds. The most frequently occurring motif, which we call the structural P-loop, is shared by 13 superfamilies and is characterized by a four-residue fragment, GXXX, interacting with a phosphate group through the backbone atoms. Various sequence motifs, including Walker's A motif or the P-loop, turn out to be a structural P-loop found in a few specific superfamilies. The other three motifs are found in pairs of superfamilies: protein kinase and glutathione synthetase ATPase domain like, actin-like ATPase domain and nucleotidyltransferase, and FMN-linked oxidoreductase and PRTase. (+info)acs1 of Haemophilus influenzae type a capsulation locus region II encodes a bifunctional ribulose 5-phosphate reductase- CDP-ribitol pyrophosphorylase. (4/2047)
The serotype-specific, 5.9-kb region II of the Haemophilus influenzae type a capsulation locus was sequenced and found to contain four open reading frames termed acs1 to acs4. Acs1 was 96% identical to H. influenzae type b Orf1, previously shown to have CDP-ribitol pyrophosphorylase activity (J. Van Eldere, L. Brophy, B. Loynds, P. Celis, I. Hancock, S. Carman, J. S. Kroll, and E. R. Moxon, Mol. Microbiol. 15:107-118, 1995). Low but significant homology to other pyrophosphorylases was only detected in the N-terminal part of Acs1, whereas the C-terminal part was homologous to several short-chain dehydrogenases/reductases, suggesting that Acs1 might be a bifunctional enzyme. To test this hypothesis, acs1 was cloned in an expression vector and overexpressed in Escherichia coli. Cells expressing this protein displayed both ribitol 5-phosphate dehydrogenase and CDP-ribitol pyrophosphorylase activities, whereas these activities were not detectable in control cells. Acs1 was purified to near homogeneity and found to copurify with ribitol 5-phosphate dehydrogenase and CDP-ribitol pyrophosphorylase activities. These had superimposable elution profiles from DEAE-Sepharose and Blue-Sepharose columns. The dehydrogenase activity was specific for ribulose 5-phosphate and NADPH in one direction and for ribitol 5-phosphate and NADP+ in the other direction and was markedly stimulated by CTP. The pyrophosphorylase showed activity with CTP and ribitol 5-phosphate or arabitol 5-phosphate. We conclude that acs1 encodes a bifunctional enzyme that converts ribulose 5-phosphate into ribitol 5-phosphate and further into CDP-ribitol, which is the activated precursor form for incorporation of ribitol 5-phosphate into the H. influenzae type a capsular polysaccharide. (+info)Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis. (5/2047)
Vitamin C (L-ascorbic acid; AsA) acts as a potent antioxidant and cellular reductant in plants and animals. AsA has long been known to have many critical physiological roles in plants, yet its biosynthesis is only currently being defined. A pathway for AsA biosynthesis that features GDP-mannose and L-galactose has recently been proposed for plants. We have isolated a collection of AsA-deficient mutants of Arabidopsis thaliana that are valuable tools for testing of an AsA biosynthetic pathway. The best-characterized of these mutants (vtc1) contains approximately 25% of wild-type AsA and is defective in AsA biosynthesis. By using a combination of biochemical, molecular, and genetic techniques, we have demonstrated that the VTC1 locus encodes a GDP-mannose pyrophosphorylase (mannose-1-P guanyltransferase). This enzyme provides GDP-mannose, which is used for cell wall carbohydrate biosynthesis and protein glycosylation as well as for AsA biosynthesis. In addition to genetically defining the first locus involved in AsA biosynthesis, this work highlights the power of using traditional mutagenesis techniques coupled with the Arabidopsis Genome Initiative to rapidly clone physiologically important genes. (+info)Studies on the adenine nucleotide translocase from rat liver mitochondria. Isolation, partial characterization and immunochemical properties of carboxyatractylate-binding protein. (6/2047)
1. Solubility of mitochondrial membranes in various solvent systems was determined quantitatively. The most effective agent was the anionic detergent, sodium dodecylsulphate, which solubilizes 90% of the protein at the concentration of 0.1% followed by Triton X-100 (70%), sodium deoxycholate (60%), Brij 56 (50%), and guanidine hydrochloride (40%) at a concentration of 2 M. 2. Affinity chromatography of a clear 0.1% sodium dodecylsulphate solution of digitonized mitochondria on Sepharose 4B containing carboxyatractylate always resulted in the separation of two fractions, one of which was not retained by the column and the other which could be obtained after elution with 2% sodium dodecylsulphate. 3. The retained protein showed a high binding specificity for ATP and [3H]atractylate when compared with the unretained fraction. The amount of bound [3H]atractylate or carboxyatractylate-sensitive binding of ATP was 10.5 +/- 4 nmol/mg protein, and 22 +/- 8 nmol/mg protein, respectively. 4. The major component within the retained fraction, comprising 85% of the total weight, was protein, followed by phospholipids (14%) and approximately 1% triglycerides. Sodium dodecylsulphate-polyacrylamide gel electrophoresis revealed a major (95%) and a minor (5%) component with an apparent molecular weight of 26000 +/- 1000 and 8300 +/- 400, respectively. The gels did not stain for carbohydrates. Ultracentrifugal analysis showed a single, symmetrical boundry. 5. Double immunodiffusion analysis gave a single precipitin line with the corresponding antiserum. [14C]ADP exchange of digitonin particles was completely inhibited by an antiserum to the carboxyatractylate binding protein fraction, whereas the adenine nucleotide transport of intact mitochondria remained unaffected. In the presence of specific immunoglobulins state-3 respiration rate of digitonin particles was prolonged and reduced by approximately 25%. State-4 respiration rate was unaffected. (+info)Ultrasensitive glycogen synthesis in Cyanobacteria. (7/2047)
Cyanobacter ADPglucose pyrophosphorylase exhibits a ultrasensitive response in activity towards its allosteric effector 3-phosphoglycerate, elicited by orthophosphate and polyethyleneglycol-induced molecular crowding. The ultrasensitive response was observed either when the enzyme operates in the zero or first order region for its physiological substrates. The ultrasensitivity exhibited maximal amplification factors of 15-19-fold with respect to 1% of the maximal system velocity. Only a 2.4-3.8-fold increase in 3PGA concentration was necessary to augment the flux from 10% to 90% through AGPase as compared with 200-fold required for the control. The results are discussed in terms of finely tuned regulatory mechanisms of polysaccharide synthesis in oxygenic photosynthetic organisms. (+info)A new resistance gene, linB, conferring resistance to lincosamides by nucleotidylation in Enterococcus faecium HM1025. (8/2047)
Resistance to lincomycin and clindamycin in the clinical isolate Enterococcus faecium HM1025 is due to a ribosomal methylase encoded by an ermAM-like gene and the plasmid-mediated inactivation of these antibiotics. We have cloned and determined the nucleotide sequence of the gene responsible for the inactivation of lincosamides, linB. This gene encodes a 267-amino-acid lincosamide nucleotidyltransferase. The enzyme catalyzes 3(5'-adenylation) (the adenylation of the hydroxyl group in position 3 of the molecules) of lincomycin and clindamycin. Expression of linB was observed in both Escherichia coli and Staphylococcus aureus. The deduced amino acid sequence of the enzyme did not display any significant homology with staphylococcal nucleotidyltransferases encoded by linA and linA' genes. Sequences homologous to linB were found in 14 other clinical isolates of E. faecium, indicating the spread of the resistance trait in this species. (+info)RNA nucleotidyltransferases are a class of enzymes that catalyze the template-independent addition of nucleotides to the 3' end of RNA molecules, using nucleoside triphosphates as substrates. These enzymes play crucial roles in various biological processes, including RNA maturation, quality control, and regulation.
The reaction catalyzed by RNA nucleotidyltransferases involves the formation of a phosphodiester bond between the 3'-hydroxyl group of the RNA substrate and the alpha-phosphate group of the incoming nucleoside triphosphate. This results in the elongation of the RNA molecule by one or more nucleotides, depending on the specific enzyme and context.
Examples of RNA nucleotidyltransferases include poly(A) polymerases, which add poly(A) tails to mRNAs during processing, and terminal transferases, which are involved in DNA repair and V(D)J recombination in the immune system. These enzymes have been implicated in various diseases, including cancer and neurological disorders, making them potential targets for therapeutic intervention.
Nucleotidyltransferases are a class of enzymes that catalyze the transfer of nucleotides to an acceptor molecule, such as RNA or DNA. These enzymes play crucial roles in various biological processes, including DNA replication, repair, and recombination, as well as RNA synthesis and modification.
The reaction catalyzed by nucleotidyltransferases typically involves the donation of a nucleoside triphosphate (NTP) to an acceptor molecule, resulting in the formation of a phosphodiester bond between the nucleotides. The reaction can be represented as follows:
NTP + acceptor → NMP + pyrophosphate
where NTP is the nucleoside triphosphate donor and NMP is the nucleoside monophosphate product.
There are several subclasses of nucleotidyltransferases, including polymerases, ligases, and terminases. These enzymes have distinct functions and substrate specificities, but all share the ability to transfer nucleotides to an acceptor molecule.
Examples of nucleotidyltransferases include DNA polymerase, RNA polymerase, reverse transcriptase, telomerase, and ligase. These enzymes are essential for maintaining genome stability and function, and their dysregulation has been implicated in various diseases, including cancer and neurodegenerative disorders.
Polynucleotide adenylyltransferase is not a medical term per se, but rather a biological term used to describe an enzyme that catalyzes the addition of adenine residues to the 3'-hydroxyl end of polynucleotides. In other words, these enzymes transfer AMP (adenosine monophosphate) molecules to the ends of DNA or RNA strands, creating a chain of adenine nucleotides.
One of the most well-known examples of this class of enzyme is terminal transferase, which is often used in research settings for various molecular biology techniques such as adding homopolymeric tails to DNA molecules. It's worth noting that while these enzymes have important applications in scientific research, they are not typically associated with medical diagnoses or treatments.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.
DNA nucleotidyltransferases are a class of enzymes that catalyze the addition of one or more nucleotides to the 3'-hydroxyl end of a DNA molecule. These enzymes play important roles in various biological processes, including DNA repair, recombination, and replication.
The reaction catalyzed by DNA nucleotidyltransferases involves the transfer of a nucleotide triphosphate (NTP) to the 3'-hydroxyl end of a DNA molecule, resulting in the formation of a phosphodiester bond and the release of pyrophosphate. The enzymes can add a single nucleotide or multiple nucleotides, depending on the specific enzyme and its function.
DNA nucleotidyltransferases are classified into several subfamilies based on their sequence similarity and function, including polymerases, terminal transferases, and primases. These enzymes have been extensively studied for their potential applications in biotechnology and medicine, such as in DNA sequencing, diagnostics, and gene therapy.
Nucleotidyltransferase
Kanamycin nucleotidyltransferase
TRNA nucleotidyltransferase
Gentamicin 2"-nucleotidyltransferase
CCA tRNA nucleotidyltransferase
Aldose-1-phosphate nucleotidyltransferase
Nucleoside-triphosphate-aldose-1-phosphate nucleotidyltransferase
Transferase
Guanylyltransferase
TRAMP complex
Polynucleotide adenylyltransferase
TRNT1
TENT5D
Calicheamicin
Capping enzyme
Adenylylation
Staphylococcus aureus
MB21D1
IsomiR
Transfer RNA
N-methylphosphoethanolamine cytidylyltransferase
glutamate-ammonia-ligase) adenylyltransferase
Phenylalanine adenylyltransferase
FMN adenylyltransferase
2,3-dihydroxybenzoyl)adenylate synthase
Fucose-1-phosphate guanylyltransferase
Streptomycin 3"-adenylyltransferase
D-ribitol-5-phosphate cytidylyltransferase
protein-PII) uridylyltransferase
Ribose-5-phosphate adenylyltransferase
Nucleotidyltransferase - Wikipedia
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TRNA1
- Predicted to enable nucleotidyltransferase activity and tRNA binding activity. (nih.gov)
Protein1
- PNPT1 (polyribonucleotide nucleotidyltransferase 1, mitochondirla) is a RNA-binding protein implicated in numerous RNA metabolic processes. (thermofisher.com)
Phosphorus-contai1
- Nucleotidyltransferases are transferase enzymes of phosphorus-containing groups, e.g., substituents of nucleotidylic acids or simply nucleoside monophosphates. (wikipedia.org)
Metabolic1
- They are classified under EC number 2.7.7 and they can be categorised into: Uridylyltransferases, which transfer uridylyl- groups Adenylyltransferases, which transfer adenylyl- groups Guanylyltransferases, which transfer guanylyl- groups Cytitidylyltransferases, which transfer cytidylyl- groups Thymidylyltransferases, which transfer thymidylyl- groups Many metabolic enzymes are modified by nucleotidyltransferases. (wikipedia.org)
Polyribonucleotide1
- Danio rerio polyribonucleotide nucleotidyltransferase 1 (pnpt1), mRNA. (genscript.com)
Protein1
- The MenT toxins are members of the widespread nucleotidyltransferase-like DUF1814 protein family. (dur.ac.uk)
Polymerases1
- The characterization of LinB enabled its classification as a member of a nucleotidyltransferase superfamily, along with nucleotide polymerases and aminoglycoside nucleotidyltransferases, and this relationship offers further support for the LinB mechanism. (rcsb.org)
Enzymes3
- Nucleotidyltransferases are transferase enzymes of phosphorus-containing groups, e.g., substituents of nucleotidylic acids or simply nucleoside monophosphates. (wikipedia.org)
- They are classified under EC number 2.7.7 and they can be categorised into: Uridylyltransferases, which transfer uridylyl- groups Adenylyltransferases, which transfer adenylyl- groups Guanylyltransferases, which transfer guanylyl- groups Cytitidylyltransferases, which transfer cytidylyl- groups Thymidylyltransferases, which transfer thymidylyl- groups Many metabolic enzymes are modified by nucleotidyltransferases. (wikipedia.org)
- cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are immune sensors that synthesize nucleotide second messengers and initiate antiviral responses in bacterial and animal cells. (nih.gov)
CGAS1
- cGAS (Cyclic GMP-AMP synthase) is a nucleotidyltransferase that catalyzes the formation of cyclic GMP-AMP (cGAMP) from ATP and GTP and plays a key role in innate immunity. (thermofisher.com)
Domain1
- The N-terminal nucleotidyltransferase (NiRAN) domain contained in the nsp12-encoded ribonucleic acid (RNA)-dependent RNA polymerase (RdRP) was found to be a potential target for the inhibition of viral replication. (news-medical.net)