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Functional characterization of the RNA-binding domain and motif of the double-stranded RNA-dependent protein kinase DAI (PKR). 1995

C Schmedt, and S R Green, and L Manche, and D R Taylor, and Y Ma, and M B Mathews
Cold Spring Harbor Laboratory, NY 11724, USA.

The double-stranded (ds) RNA-activated protein kinase, DAI (also known as PKR), contains an RNA-binding domain comprising two tandem repeats of a motif, the dsRBM, which is shared with a number of other proteins that interact with structured RNAs. We have expressed the entire domain and the first copy of the motif in Escherichia coli and purified the two proteins, p20 and p10, to apparent homogeneity in order to study their interactions with RNA and with the intact kinase enzyme. Both p20 and p10 bound preferentially to structured RNA molecules. Competition assays showed that in both cases the order of affinity is dsRNA > VA RNA > tRNA, but the isolated motif bound much less tightly than the entire domain. Measurement of the dissociation constants for dsRNA by quantitative gel mobility shift analysis gave apparent Kd values of 4 x 10(-9) M and 3.8 x 10(-7) M for p20 and p10, respectively. The binding of p20 molecules to dsRNA appeared to be cooperative. Multiple complexes were formed between the intact domain and dsRNA, saturating at a density of about one p20 molecule/11.25 base-pairs (or one turn) of duplex, whereas p10 achieved only about half of this packing density. The apparent Kd for the p20-VA RNA interaction was estimated as 3.5 x 10(-7) M and at least three complexes were detected, but no distinct complexes were visualized for the interaction between p10 and VA RNA. Both p20 and p10 inhibited autophosphorylation of intact DAI, probably by binding the dsRNA activator. Once activated, DAI could phosphorylate both p10 and p20, suggesting that intermolecular phosphorylation can occur.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010766 Phosphorylation The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety. Phosphorylations
D004926 Escherichia coli A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc. Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012330 RNA, Double-Stranded RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms. Double-Stranded RNA,Double Stranded RNA,RNA, Double Stranded
D017346 Protein Serine-Threonine Kinases A group of enzymes that catalyzes the phosphorylation of serine or threonine residues in proteins, with ATP or other nucleotides as phosphate donors. Protein-Serine-Threonine Kinases,Serine-Threonine Protein Kinase,Serine-Threonine Protein Kinases,Protein-Serine Kinase,Protein-Serine-Threonine Kinase,Protein-Threonine Kinase,Serine Kinase,Serine-Threonine Kinase,Serine-Threonine Kinases,Threonine Kinase,Kinase, Protein-Serine,Kinase, Protein-Serine-Threonine,Kinase, Protein-Threonine,Kinase, Serine-Threonine,Kinases, Protein Serine-Threonine,Kinases, Protein-Serine-Threonine,Kinases, Serine-Threonine,Protein Kinase, Serine-Threonine,Protein Kinases, Serine-Threonine,Protein Serine Kinase,Protein Serine Threonine Kinase,Protein Serine Threonine Kinases,Protein Threonine Kinase,Serine Threonine Kinase,Serine Threonine Kinases,Serine Threonine Protein Kinase,Serine Threonine Protein Kinases
D019892 eIF-2 Kinase A dsRNA-activated cAMP-independent protein serine/threonine kinase that is induced by interferon. In the presence of dsRNA and ATP, the kinase autophosphorylates on several serine and threonine residues. The phosphorylated enzyme catalyzes the phosphorylation of the alpha subunit of EUKARYOTIC INITIATION FACTOR-2, leading to the inhibition of protein synthesis. Protein Kinase PKR,Protein Kinase, RNA Activated,RNA-Dependent Protein Kinase,p68 Kinase,DAI Protein Kinase,DSRNA-Dep Protein Kinase,Double Stranded RNA-Dependent Kinase (dsl),Double Stranded RNA-Dependent eIF-2 alpha Protein Kinase,Eukaryotic Initiation Factor 2alpha Kinase,Heme Controlled Repressor,Heme-Controlled Inhibitor,Heme-Controlled Translational Repressor,Heme-Regulated eIF-2alpha Kinase,Hemin Controlled Repressor,Hemin-Controlled Translational Repressor,P68 Protein Kinase,Self-Phosphorylating Protein Kinase,TIK Kinase,dsRNA-Activated Inhibitor,eIF-2alpha Kinase,eRF, eIF-2 Recycling Factor,p65 Kinase,Controlled Repressor, Heme,Controlled Repressor, Hemin,DSRNA Dep Protein Kinase,Double Stranded RNA Dependent eIF 2 alpha Protein Kinase,Heme Controlled Inhibitor,Heme Controlled Translational Repressor,Heme Regulated eIF 2alpha Kinase,Hemin Controlled Translational Repressor,Inhibitor, Heme-Controlled,Inhibitor, dsRNA-Activated,Kinase PKR, Protein,Kinase, DAI Protein,Kinase, DSRNA-Dep Protein,Kinase, Heme-Regulated eIF-2alpha,Kinase, P68 Protein,Kinase, RNA-Dependent Protein,Kinase, Self-Phosphorylating Protein,Kinase, TIK,Kinase, eIF-2,Kinase, eIF-2alpha,Kinase, p65,Kinase, p68,PKR, Protein Kinase,Protein Kinase, DAI,Protein Kinase, DSRNA-Dep,Protein Kinase, P68,Protein Kinase, RNA-Dependent,Protein Kinase, Self-Phosphorylating,RNA Dependent Protein Kinase,Repressor, Heme Controlled,Repressor, Heme-Controlled Translational,Repressor, Hemin Controlled,Repressor, Hemin-Controlled Translational,Self Phosphorylating Protein Kinase,Translational Repressor, Heme-Controlled,Translational Repressor, Hemin-Controlled,dsRNA Activated Inhibitor,eIF 2 Kinase,eIF 2alpha Kinase,eIF-2alpha Kinase, Heme-Regulated,eRF, eIF 2 Recycling Factor

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