Mechanism of interferon action: Identification of a RNA binding domain within the N-terminal region of the human RNA-dependent P1/eIF-2α protein kinase

Virology ◽  
1992 ◽  
Vol 188 (1) ◽  
pp. 47-56 ◽  
Author(s):  
Stephen J. McCormack ◽  
Daniel C. Thomis ◽  
Charles E. Samuel
Keyword(s):  
Protein Kinase ◽  
Rna Binding ◽  
Binding Domain ◽  
Terminal Region ◽  
Action Identification ◽  
Rna Binding Domain

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

scholarly journals Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins

2021 ◽  
Author(s):  
Thomas Hollin ◽  
Lukasz Jaroszewski ◽  
Jason E. Stajich ◽  
Adam Godzik ◽  
Karine G. Le Roch
Keyword(s):  
Potential Function ◽  
Phylogenetic Trees ◽  
Rna Binding ◽  
Binding Domain ◽  
Terminal Region ◽  
Protein Domain ◽  
Phylogenetic Groups ◽  
Apicomplexan Parasites ◽  
History Of ◽  
Rna Binding Domain

The RNA binding domain abundant in apicomplexans (RAP) is a protein domain identified in a diverse group of proteins, called RAP proteins, many of which have been shown to be involved in RNA binding. To understand the expansion and potential function of the RAP proteins, we conducted a hidden Markov model based screen among the proteomes of 54 eukaryotes, 17 bacteria and 12 archaea. We demonstrated that the domain is present in closely and distantly related organisms with particular expansions in Alveolata and Chlorophyta, and are not unique to Apicomplexa as previously believed. All RAP proteins identified can be decomposed into two parts. In the N-terminal region, the presence of variable helical repeats seems to participate in the specific targeting of diverse RNAs, while the RAP domain is mostly identified in the C-terminal region and is highly conserved across the different phylogenetic groups studied. Several conserved residues defining the signature motif could be crucial to ensure the function(s) of the RAP proteins. Modelling of RAP domains in apicomplexan parasites confirmed an ⍺/β structure of a restriction endonuclease-like fold. The phylogenetic trees generated from multiple alignment of RAP domains and full-length proteins from various distantly related eukaryotes indicated a complex evolutionary history of this family. We further discuss these results to assess the potential function of this protein family in apicomplexan parasites.

scholarly journals Characterization of Functional Domains of Equine Infectious Anemia Virus Rev Suggests a Bipartite RNA-Binding Domain

2006 ◽  
Vol 80 (8) ◽  
pp. 3844-3852 ◽  
Author(s):  
Jae-Hyung Lee ◽  
Sean C. Murphy ◽  
Michael Belshan ◽  
Wendy O. Sparks ◽  
Yvonne Wannemuehler ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Region ◽  
Equine Infectious Anemia Virus ◽  
Rna Binding ◽  
Binding Domain ◽  
Terminal Region ◽  
Functional Domains ◽  
Equine Infectious Anemia ◽  
Rna Binding Domain ◽  
Anemia Virus

ABSTRACT Equine infectious anemia virus (EIAV) Rev is an essential regulatory protein that facilitates expression of viral mRNAs encoding structural proteins and genomic RNA and regulates alternative splicing of the bicistronic tat/rev mRNA. EIAV Rev is characterized by a high rate of genetic variation in vivo, and changes in Rev genotype and phenotype have been shown to coincide with changes in clinical disease. To better understand how genetic variation alters Rev phenotype, we undertook deletion and mutational analyses to map functional domains and to identify specific motifs that are essential for EIAV Rev activity. All functional domains are contained within the second exon of EIAV Rev. The overall organization of domains within Rev exon 2 includes a nuclear export signal, a large central region required for RNA binding, a nonessential region, and a C-terminal region required for both nuclear localization and RNA binding. Subcellular localization of green fluorescent protein-Rev mutants indicated that basic residues within the KRRRK motif in the C-terminal region of Rev are necessary for targeting of Rev to the nucleus. Two separate regions of Rev were necessary for RNA binding: a central region encompassing residues 57 to 130 and a C-terminal region spanning residues 144 to 165. Within these regions were two distinct, short arginine-rich motifs essential for RNA binding, including an RRDRW motif in the central region and the KRRRK motif near the C terminus. These findings suggest that EIAV Rev utilizes a bipartite 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
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