Methyl dynamics for understanding hydrophobic core packing of dynamically different motifs of double-stranded RNA binding domain of protein kinase R

2005 ◽  
Vol 62 (2) ◽  
pp. 501-508 ◽  
Author(s):  
Ravi P. Barnwal ◽  
Tista R. Chaudhuri ◽  
S. Nanduri ◽  
J. Qin ◽  
K.V.R. Chary
Keyword(s):  
Protein Kinase ◽  
Rna Binding ◽  
Binding Domain ◽  
Hydrophobic Core ◽  
Protein Kinase R ◽  
Double Stranded Rna ◽  
Methyl Dynamics ◽  
Rna Binding Domain ◽  
Core Packing

scholarly journals Two functionally distinct RNA-binding motifs in the regulatory domain of the protein kinase DAI.

1995 ◽  
Vol 15 (1) ◽  
pp. 358-364 ◽  
Author(s):  
S R Green ◽  
L Manche ◽  
M B Mathews
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Alpha Helix ◽  
Binding Domain ◽  
Single Amino Acid ◽  
Double Stranded Rna ◽  
C Terminus ◽  
Rna Binding Domain

The RNA-binding domain of the protein kinase DAI, the double-stranded RNA inhibitor of translation, contains two repeats of a motif that is also found in a number of other RNA-binding proteins. This motif consists of 67 amino acid residues and is predicted to contain a positively charged alpha helix at its C terminus. We have analyzed the effects of equivalent single amino acid changes in three conserved residues distributed over each copy of the motif. Mutants in the C-terminal portion of either repeat were severely defective, indicating that both copies of the motif are essential for RNA binding. Changes in the N-terminal and central parts of the motif were more debilitating if they were made in the first motif than in the second, suggesting that the first motif is the more important for RNA binding and that the second motif is structurally more flexible. When the second motif was replaced by a duplicate of the first motif, the ectopic copy retained its greater sensitivity to mutation, implying that the two motifs have distinct functions with respect to the process of RNA binding. Furthermore, the mutations have the same effect on the binding of double-stranded RNA and VA RNA, consistent with the existence of a single RNA-binding domain for both activating and inhibitory RNAs.

scholarly journals Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation

1998 ◽  
Vol 17 (18) ◽  
pp. 5458-5465 ◽  
Author(s):  
Sambasivarao Nanduri ◽  
Bruce W. Carpick ◽  
Yanwu Yang ◽  
Bryan R.G. Williams ◽  
Jun Qin
Keyword(s):  
Protein Kinase ◽  
Molecular Basis ◽  
Rna Binding ◽  
Binding Domain ◽  
Double Stranded Rna ◽  
Rna Binding Domain

Functional Characterization of the RNA-binding Domain and Motif of the Double-stranded RNA-dependent Protein Kinase DAI (PKR)

1995 ◽  
Vol 249 (1) ◽  
pp. 29-44 ◽  
Author(s):  
Christian Schmedt ◽  
Simon R. Green ◽  
Lisa Manche ◽  
Deborah R. Taylor ◽  
Yuliang Ma ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Rna Binding ◽  
Functional Characterization ◽  
Binding Domain ◽  
Dependent Protein Kinase ◽  
Double Stranded Rna ◽  
Dependent Protein ◽  
Rna Binding Domain

scholarly journals Identification of the gene encoding a type 1 RNase H with an N-terminal double-stranded RNA binding domain from a psychrotrophic bacterium

FEBS Journal ◽  
2007 ◽  
Vol 274 (14) ◽  
pp. 3715-3727 ◽  
Author(s):  
Takashi Tadokoro ◽  
Hyongi Chon ◽  
Yuichi Koga ◽  
Kazufumi Takano ◽  
Shigenori Kanaya
Keyword(s):  
Rna Binding ◽  
Rnase H ◽  
Binding Domain ◽  
Gene Encoding ◽  
Double Stranded Rna ◽  
Psychrotrophic Bacterium ◽  
Rna Binding Domain

scholarly journals Binding and Nuclear Relocalization of Protein Kinase R by Human Cytomegalovirus TRS1

2006 ◽  
Vol 80 (23) ◽  
pp. 11817-11826 ◽  
Author(s):  
Morgan Hakki ◽  
Emily E. Marshall ◽  
Katherine L. De Niro ◽  
Adam P. Geballe
Keyword(s):  
Protein Kinase ◽  
Human Cytomegalovirus ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Underlying Mechanism ◽  
Cellular Protein ◽  
Initiation Factor ◽  
Protein Kinase R ◽  
Double Stranded Rna

ABSTRACT The human cytomegalovirus (HCMV) TRS1 and IRS1 genes block the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2α) and the consequent shutoff of cellular protein synthesis that occur during infection with vaccinia virus (VV) deleted of the double-stranded RNA binding protein gene E3L (VVΔE3L). To further define the underlying mechanism, we first evaluated the effect of pTRS1 on protein kinase R (PKR), the double-stranded RNA (dsRNA)-dependent eIF2α kinase. Immunoblot analyses revealed that pTRS1 expression in the context of a VVΔE3L recombinant decreased levels of PKR in the cytoplasm and increased its levels in the nucleus of infected cells, an effect not seen with wild-type VV or a VVΔE3L recombinant virus expressing E3L. This effect of pTRS1 was confirmed by visualizing the nuclear relocalization of PKR-EGFP expressed by transient transfection. PKR present in both the nuclear and cytoplasmic fractions was nonphosphorylated, indicating that it was unactivated when TRS1 was present. PKR also accumulated in the nucleus during HCMV infection as determined by indirect immunofluorescence and immunoblot analysis. Binding assays revealed that pTRS1 interacted with PKR in mammalian cells and in vitro. This interaction required the same carboxy-terminal region of pTRS1 that is necessary to rescue VVΔE3L replication in HeLa cells. The carboxy terminus of pIRS1 was also required for rescue of VVΔE3L and for mediating an interaction of pIRS1 with PKR. These results suggest that these HCMV genes directly interact with PKR and inhibit its activation by sequestering it in the nucleus, away from both its activator, cytoplasmic dsRNA, and its substrate, eIF2α.

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