Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:2.7.7.48 (transcriptase)
 9,479 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.
 ...
PMID:Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. 770 18

A conserved architectural feature of ribosomes is a protuberance (the stalk) in the large subunit, essential for ribosomal interactions with translational factors and GTP hydrolysis and generated by two dimers of L12, the only multicopy protein in ribosomes. In higher plants, the rpl12 gene for chloroplast L12 is located in the nucleus. We report here the cloning and sequencing of this nuclear gene from Arabidopsis thaliana, revealing the first gene family for a chloroplast ribosomal protein (RP). A single cluster/haploid genome of three rpl12 genes is located in the sequenced 9.1-kilobase region of the Arabidopsis genome. Two of the rpl12 genes encode identical mature proteins, and the third encodes a 25% divergent RP, although the chloroplast-targeting transit peptide in each is distinct. The rpl12 genes encoding identical RPs are closely linked at their 5' ends to identical cytosolic tRNA(Pro) genes with a < 250-base pair spacer. Reverse transcriptase polymerase chain reaction experiments with total RNA isolated from Arabidopsis (and characterization of several L12 cDNA clones) show that only the tRNA-linked rpl12 genes are expressed. We also show (by polymerase chain reaction experiments with isolated total DNA) that this tRNA(Pro)-rpl12 gene linkage is conserved in spinach (inferred to contain a single gene copy) indicating its importance. The previously described enhanced translation of spinach L12 mRNA from its two tandem AUG codons and the two functional rpl12 genes in Arabidopsis probably provide two mechanisms for generating the four copies of L12/chloroplast ribosome, qualitatively different from those attempted in eubacteria.
 ...
PMID:Multicopy GTPase center protein L12 of Arabidopsis chloroplast ribosome is encoded by a clustered nuclear gene family with the expressed members closely linked to tRNA(Pro) genes. 812 49

An in vitro RNA bandshift assay has been developed to demonstrate the binding of purified recombinant encephalomyocarditis (EMC) virus RNA-dependent RNA polymerase (3Dpol) to the 3'-noncoding region (NCR) and 30 nucleotides of the adjacent 3'-terminal poly(A) tail (3'-NCR(A)) of EMC virus RNA. The binding of 3Dpol to the 3'-NCR(A) fragment was specific since four other unrelated proteins including an RNA polymerase did not bind, and unlabeled 3'-NCR(A), but not alpha-globin mRNA, tRNA, or pure poly(A), competed with radiolabeled 3'-NCR(A) for binding. Surprisingly, 3Dpol failed to bind to the 3'-NCR of EMC virus RNA lacking the poly(A) tail. The results together show that EMC virus RNA template specificity depends only on 3Dpol, the 3'-NCR, and the poly(A) tail. This suggests that 3'-poly(A) is essential for viral RNA template selection by the EMC virus RNA polymerase.
 ...
PMID:Binding of encephalomyocarditis virus RNA polymerase to the 3'-noncoding region of the viral RNA is specific and requires the 3'-poly(A) tail. 825 25

The complete nucleotide sequences of RNAs 1 and 2 of soil-borne wheat mosaic virus (SBWMV), type member of the furovirus group, were determined. RNA 1 is 7099 nucleotides (nt) and encodes a 150-kDa protein from the 5' end region, the UGA termination codon of which can be partially read through to produce a 209-kDa protein, and a 37-kDa protein in the 3' end region. The C-terminal region of the 150-kDa protein contains an NTP-binding helicase motif and the readthrough region, an RNA polymerase motif, indicating that these two overlapping proteins may form an RNA replication complex similar to those of tobamo- and tobraviruses. The 37-kDa protein has sequence similarity with the cell-to-cell transport protein of dianthoviruses. RNA 2 is 3593 nt and, from the 5' end region, encodes the 19-kDa capsid protein, whose UGA termination codon can be partially suppressed to produce an 84-kDa readthrough protein and, at the 3' proximity, a 19-kDa protein which is rich in cysteine residues. The 28K (kilodaltons, as estimated by SDS-PAGE) protein, previously considered as another capsid readthrough product, is apparently initiated at an in-frame non-AUG codon upstream from the capsid protein gene. In both RNAs 1 and 2, the 5' terminus is capped, and the 3' untranslated region possibly forms internal consecutive pseudoknots as found in tobamovirus RNA as well as a terminal tRNA-like structure similar to tymovirus RNA. An amino acid sequence comparison of RNA replicase genes indicates that, phylogenetically, SBWMV belongs to a cluster formed by tobamo-, tobra-, and hordeiviruses. Differences in the 3' end structure and in the cell-to-cell movement protein, and the distant phylogeny of the RNA replicase genes of SBWMV and beet necrotic yellow vein virus, suggest that the furoviruses should be divided into at least two groups.
 ...
PMID:Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus. 831 92

A host cell-derived tRNA3Lys molecule is utilized by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) to prime DNA synthesis from the viral RNA genome. We performed fluorescence titration experiments to characterize the interaction between RT and its natural primer, tRNA3Lys, and to address RT's putative role in the required and specific packaging of tRNA3Lys into the budding virus. Titration of RT with tRNA3Lys resulted in a 30% maximal quenching of RT tryptophan fluorescence, from which a dissociation constant (Kd) of 57.6 +/- 7.5 nM was derived. Titration of RT with Escherichia coli tRNA2Glu, E. coli tRNA2Tyr, E. coli tRNALys, yeast tRNAPhe, or in vitro-synthesized human tRNA3Lys (no base modifications) resulted in similar fluorescence changes and Kd values as obtained for the natural tRNA3Lys. The specific interaction between RT and tRNA3Lys during viral assembly suggested by previous in vivo studies is therefore not present in the fully processed, in vitro form of RT. Other factors during viral assembly must therefore cooperate in the packaging of tRNA3Lys. The nonspecific and ionic strength dependent RT-tRNA interaction detected in the present studies suggests that the overall shape and charges of tRNA constitute recognition features for RT binding. The fluorescence of the wyebutine base contained on the anticodon loop of yeast tRNAPhe was found to increase upon RT binding, supporting speculation that RT interacts with the anticodon loop of tRNA. The individual tRNAs also displaced a fluorescent DNA primer/template (p/t) substrate from RT, indicating overlapping tRNA and p/t binding sites. Cubic fit evaluation of the displacement titrations allowed further assessment of the affinities of the two competing ligands. The presence of both overlapping and separate p/t and tRNA binding regions on RT was tested by examination of the affinity of a possible RT bisubstrate type inhibitor, containing motifs proposed to be essential for both tRNA and p/t binding. Reverse transcriptase was found to bind to the mutant tRNA 10-fold more tightly than to the unaltered tRNA (Kd = 4.5 +/- 1.0 and 44.6 +/- 6.6 nM, respectively). Further analyses revealed that the tighter affinity is probably due to a preferred p/t binding mode and not to one expected if separate tRNA and p/t binding regions are accessed simultaneously by the same molecule.
 ...
PMID:Evaluation of human immunodeficiency virus type 1 reverse transcriptase primer tRNA binding by fluorescence spectroscopy: specificity and comparison to primer/template binding. 860 12

The complete sequence of a Singapore isolate of odontoglossum ringspot virus (ORSV-S1) comprises 6609 nucleotides (nt) and four open reading frames (ORFs 1 to 4). The 126/183-kDa RNA-dependent RNA polymerase (RdRp), 33-kDa movement protein (MP) and 18-kDa coat protein (CP) cistrons are located at nt 63-3401/4901, 4807-5718, and 5721-6197 on the genome, respectively. The 5' UTR contains three copies of an 8-base direct repeat and (CAA)n motifs. Characteristic tRNA-like structure and three consecutive homologous regions were present in the 3' UTR. The genomic RNA and MP of ORSV-S1 are one of the longest among all members of the TOV group. Phylogenetic analysis of all four genes indicates evolutionary divergence, but within each gene there are some degrees of evolutionary convergence. The conserved amino acid sequences in the MP can be used for the classification of tobamoviruses.
 ...
PMID:The complete sequence of a Singapore isolate of odontoglossum ringspot virus and comparison with other tobamoviruses. 866 66

Seryl t-RNA synthetase of the bacterium Thermus thermophilus contains a long arm, consisting of an antiparallel coiled coil, that is involved in binding of tRNA. Two crystallographic structures exist for this protein, in which the arm is in different conformations. Here, we use computational methods employing an empirical potential energy function to investigate the flexibility of the long arm. A conformational pathway is calculated between the 2 crystallographic structures using a method based on molecular dynamics simulation. The pathway is analyzed in terms of sequential phi and psi backbone angle changes. Several transient phi and psi displacements are present along the pathway that are not visible in the end states and may be required for transition between them. Energy maps are constructed by rotating the arm around its principal axes of inertia and energy minimizing. The map identifies 2 regions of relatively low energy which might be accessible to the arm.
 ...
PMID:Pathways for conformational change in seryl-tRNA synthetase from Thermus thermophilus. 876 61

Glycyl-tRNA synthetase, a class II aminoacyl-tRNA synthetase, catalyzes the synthesis of glycyl-tRNA, which is required to insert glycine into proteins. In a side reaction the enzyme also synthesizes dinuceloside polyphosphates, which probably participate in regulation of cell functions. Glycine is the smallest amino acid occurring in natural proteins, probably established as a protein component very early in evolution. Besides the amino and the carboxyl groups there is no functional group in the molecule. Alanine, the amino acid which is structurally most similar to glycine, possesses an additional methyl group as 'side chain'. Glycyl-tRNA synthetase is one of the few synthetases which exhibit different oligomeric structures in different organisms (alpha 2 beta 2 and alpha 2). The alpha 2 beta 2 enzymes exhibit similarities to PheRS (also an alpha 2 beta 2 enzyme). The alpha 2 forms belong to the subclass IIa enzymes with regard to sequence homologies. In eukaryotes the polypeptide is weakly associated with multienzyme complexes consisting of aminoacyl-tRNA synthetases. In the aminoacylation reaction a 'half-of-the-sites' mechanism as found for GlyRS from Bombyx mori is probably used by all glycyl-tRNA synthetases under in vivo conditions. Essentially, tRNAGly is recognized by GlyRS through standard identity elements in the anticodon region and in the acceptor stem. The last three facts may indicate that GlyRS is an enzyme which still possesses properties of a primordial aminoacyl-tRNA synthetase. Nine genes of glycyl-tRNA synthetases from six organisms have been sequenced. They encode synthetase subunits of chain lengths ranging from 300-700 amino acids. One crystal structure, that of the alpha 2 enzyme from Thermus thermophilus, has also been determined. The two subunits each possess three domains: the active site resembling that of aspartyl and seryl enzymes, a C-terminal anticodon recognition domain, and one domain which almost certainly interacts with the acceptor stem of tRNAGly. Antibodies against glycyl-RNA synthetase occur in the sera of patients suffering from polymyositis and interstitial lung disease.
 ...
PMID:Glycyl-tRNA synthetase. 883 80

During reverse transcription of retroviral RNA, synthesis of (-) strand DNA is primed by a cellular tRNA that anneals to an 18-nt primer binding site within the 5' long terminal repeat. For (+) strand synthesis using a (-) strand DNA template linked to the tRNA primer, only the first 18 nt of tRNA are replicated to regenerate the primer binding site, creating the (+) strand strong stop DNA intermediate and providing a 3' terminus capable of strand transfer and further elongation. On model HIV templates that approximate the (-) strand linked to natural modified or synthetic unmodified tRNA3Lys, we find that a (+) strand strong stop intermediate of the proper length is generated only on templates containing the natural, modified tRNA3Lys, suggesting that a posttranscriptional modification provides the termination signal. In the presence of a recipient template, synthesis after strand transfer occurs only from intermediates generated from templates containing modified tRNA3Lys. Reverse transcriptase from Moloney murine leukemia virus and avian myoblastosis virus shows the same requirement for a modified tRNA3Lys template. Because all retroviral tRNA primers contain the same 1-methyl-A58 modification, our results suggest that 1-methyl-A58 is generally required for termination of replication 18 nt into the tRNA sequence, generating the (+) strand intermediate, strand transfer, and subsequent synthesis of the entire (+) strand. The possibility that the host methyl transferase responsible for methylating A58 may provide a target for HIV chemotherapy is discussed.
 ...
PMID:Posttranscriptional modification of retroviral primers is required for late stages of DNA replication. 920 70

An RNA-dependent RNA polymerase (RdRp) activity was detergent-solubilized from the chloroplast membranes of Chinese cabbage leaves infected with turnip yellow mosaic virus (TYMV). The template-dependent, micrococcal nuclease-treated activity synthesized full-length minus strands from TYMV RNA and 3'-fragments as short as a 28-nucleotide-long RNA comprising the amino acid acceptor stem of the 3'-tRNA-like structure (TLS). Minus strands were shown to arise by de novo initiation with the insertion of GTP opposite the penultimate (C) residue of the 3'-terminal -CCA. The TYMV RdRp activity was template specific in that poly(A) RNA was not copied, and alfalfa mosaic virus (AIMV) RNA, which does not contain a 3'-TLS, was a very poor template. However, other viral RNAs with a 3'-TLS and in vitro transcripts of tRNAs were copied to varying degrees. Fully modified tRNAs were either inactive or poorly active templates, and AIMV 3'-RNA, even when provided with a 3'-terminal -ACCA, was not copied detectably. A potential role of the acceptor stem pseudoknot as a promoter element was assessed with mutations that drastically altered the structure and sequence of the pseudoknot, revealing only a twofold effect in decreasing template activity. The data show that RNAs with both a tRNA-like conformation and a -CCA 3'-terminus are potential templates for TYMV RdRp and suggest that promoter elements are not limited to the acceptor stem pseudoknot.
 ...
PMID:Turnip yellow mosaic virus RNA-dependent RNA polymerase: initiation of minus strand synthesis in vitro. 921 66


<< Previous 1 2 3 4 5 6 7 8 9 Next >>